From debc085cf692cb4f2a8a9585d0acfe4a7b06bfb9 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 22 Jun 2022 22:50:07 +0200 Subject: [PATCH 001/265] add placeholder skeleton for MCPL-input --- include/openmc/source.h | 19 +++++++++++++++++++ src/source.cpp | 21 +++++++++++++++++++++ 2 files changed, 40 insertions(+) diff --git a/include/openmc/source.h b/include/openmc/source.h index 18fddc6899..cadbfe93bb 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -100,6 +100,25 @@ private: vector sites_; //!< Source sites from a file }; +//============================================================================== +// MCPL-file input source +//============================================================================== +class MCPLFileSource : public Source { +public: + // Constructors, destructors + MCPLFileSource(std::string path); + ~MCPLFileSource(); + + // Defer implementation to custom source library + SourceSite sample(uint64_t* seed) const override + +private: + vector sites_; //! Date: Thu, 23 Jun 2022 11:34:53 +0200 Subject: [PATCH 002/265] include mcpl header --- src/source.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/source.cpp b/src/source.cpp index cd8b5e5743..5e26fa0a8d 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -31,6 +31,10 @@ #include "openmc/state_point.h" #include "openmc/xml_interface.h" +#ifdef HAS_MCPL +#include +#endif + namespace openmc { //============================================================================== From 5d74af4bf766ab732d320081be47b9c4f78303fe Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Thu, 23 Jun 2022 11:35:46 +0200 Subject: [PATCH 003/265] declarations of MCPL-internals --- include/openmc/source.h | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/include/openmc/source.h b/include/openmc/source.h index cadbfe93bb..69dd47eae9 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -109,11 +109,20 @@ public: MCPLFileSource(std::string path); ~MCPLFileSource(); - // Defer implementation to custom source library - SourceSite sample(uint64_t* seed) const override + // Properties + ParticleType particle_type() const { return particle_; } + + //! Sample from the external source distribution + //! \param[inout] seed Pseudorandom seed pointer + //! \return Site read from MCPL-file + SourceSite sample(uint64_t* seed) const override; private: + ParticleType particle_ {ParticleType::neutron}; //!< Type of particle emitted vector sites_; //! Date: Thu, 23 Jun 2022 11:37:05 +0200 Subject: [PATCH 004/265] internals of sample and constructor --- src/source.cpp | 51 ++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 47 insertions(+), 4 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 5e26fa0a8d..231f355fc2 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -337,7 +337,7 @@ CustomSourceWrapper::~CustomSourceWrapper() } //=========================================================================== -// Read an MCPL-file +// Read particles from an MCPL-file //=========================================================================== MCPLFileSource::MCPLFileSource(std::string path) { @@ -348,12 +348,55 @@ MCPLFileSource::MCPLFileSource(std::string path) // Read the source from a binary file instead of sampling from some // assumed source distribution - write_message(6, "Reading source file from {}...", path); + write_message(6, "Reading mcpl source file from {}",path); // Open the mcpl file - id_t file_id = mcpl_open(path.c_str) - + mcpl_file = mcpl_open(path.c_str); + //do checks on the mcpl_file to see if particles are many enough. + // should model this on the example source shown in the docs. + uint64_t nparticles=mcpl_hdr_nparticles(mcpl_file); + +} + +MCPLFileSource::~MCPLFilsSource(){ + mcpl_close_file(mcpl_file); +} + +SourceSite MCPLFileSource::sample(uint64_t *seed){ + SourceSite omc_particle; + mcpl_particle *mcpl_particle; + //extract particle from mcpl-file + mcpl_particle=mcpl_reazd(mcplfile); + // check if it is a neutron or a photon. otherwise skip + while ( mcpl_particle->pdgcode!=2112 && mcpl_particle->pdgcode!=22 ) + { + mcpl_particle(mcpl_read(mcplfile); + //check for file exhaustion + } + + if(mcpl_particle->pdgcode=2112) { + omc_particle_=ParticleType::neutron; + } else { + omc_particle_=Particletype::photon; + } + + //particle is good, convert to openmc-formalism + omc_particle.r.x=mcpl_particle.x; + omc_particle.r.y=mcpl_particle.y; + omc_particle.r.z=mcpl_particle.z; + + omc_particle.u.x=mcpl_particle->direction[0]; + omc_particle.u.y=mcpl_particle->direction[1]; + omc_particle.u.z=mcpl_particle->direction[2]; + + //mcpl stores particles in MeV + omc_particle.E=mcpl_particle->ekin*1e6; + + omc_particle.t=mcpl_particle->time*1e-3; + omc_particle.wgt=mcpl_particle->weight; + omc_particle.delayed_group=0; + return omc_particle; } From 909b96f31e90a8a8ce40e890b3f4e73ee516466b Mon Sep 17 00:00:00 2001 From: erkn Date: Mon, 27 Jun 2022 23:25:35 +0200 Subject: [PATCH 005/265] (wip): skeleton for input only test --- .../regression_tests/source_mcpl_file/test.py | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 tests/regression_tests/source_mcpl_file/test.py diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py new file mode 100644 index 0000000000..5a6a87d878 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -0,0 +1,52 @@ +import pathlib as pl +import os +import shutil +import subprocess +import textwrap + +import openmc +import pytest + +from tests.testing_harness import TestHarness + +def model(): + subprocess.run(['gcc','-o gen_dummt_mcpl.out','-lm','-lmcpl','gen_dummy_mcpl.c'] ) + subprocess.run(['./gen_dummy_mcpl.out']) + +class SourceMCPLFileTestHarness(TestHarness): + def execute_test(self): + """Run OpenMC with the appropriate arguments and check the outputs.""" + try: + self._create_input() + self._run_openmc() + self._test_output_created() + results = self._get_results() + self._write_results(results) + self._compare_results() + finally: + self._cleanup() + + def update_results(self): + """Update the results_true using the current version of OpenMC.""" + try: + self._create_input() + self._run_openmc() + self._test_output_created() + results = self._get_results() + self._write_results(results) + self._overwrite_results() + finally: + self._cleanup() + + def _test_output_created(self): + """Check that the output files were created""" + stat epoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) + assert len(statepoint) == 1, 'Either multiple or no statepoint files ' \ + 'exist.' + assert statepoint[0].endswith('h5'), \ + 'statepoint file does not end with h5.' + +def test_mcpl_source_file(): + harness = SourceMCPLFileTestHarness('statepoint.10.h5') + harness.main() + From 3c30dbba5b643e8464eb9b45a8667e08bf6ad44b Mon Sep 17 00:00:00 2001 From: erkn Date: Mon, 27 Jun 2022 23:26:01 +0200 Subject: [PATCH 006/265] c-prog to generate a dummy mcpl --- .../source_mcpl_file/gen_dummy_mcpl.c | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c diff --git a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c new file mode 100644 index 0000000000..7b5a933f18 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c @@ -0,0 +1,97 @@ +#include +#include +#include +#include + +const int batches=10; +const int particles=10000; + +double rand01(){ + double r=rand()/((double) RAND_MAX); + return r; +} + + +int main(int argc, char **argv){ + char outfilename[128]; + snprintf(outfilename,127,"source.%d.mcpl",batches); + + /*generate an mcpl_header_of sorts*/ + mcpl_outfile_t outfile=mcpl_create_outfile(outfilename); + mcpl_particle_t *particle, Particle; + + char line[256]; + snprintf(line,255,"gen_dummy_mcpl.c"); + mcpl_hdr_set_srcname(outfile,line); + mcpl_enable_universal_pdgcode(outfile,2112);/*all particles are neutrons*/ + snprintf(line,255,"Dummy MCPL-file for testing OpenMC mcpl input"); + mcpl_hdr_add_comment(outfile,line); + + /*also add the instrument file and the command line as blobs*/ + FILE *fp; + if( (fp=fopen("gen_dummy_mcpl.c","rb"))!=NULL){ + unsigned char *buffer; + int size,status; + /*find the file size by seeking to end, "tell" the position, and then go back again*/ + fseek(fp, 0L, SEEK_END); + size = ftell(fp); // get current file pointer + fseek(fp, 0L, SEEK_SET); // seek back to beginning of file + if ( size && (buffer=malloc(size))!=NULL){ + if (size!=(fread(buffer,1,size,fp))){ + fprintf(stderr,"Warning: c source generator file not read cleanly\n"); + } + mcpl_hdr_add_data(outfile, "mcpl_point_source_file_generator", size, buffer); + free(buffer); + } + fclose(fp); + } else { + fprintf(stderr,"Warning: could not open c source generator file, hence not embedded.\n"); + } + + + /*the main particle loop*/ + particle=&Particle; + int i; + for (i=0;iposition[0]=0; + particle->position[1]=0; + particle->position[2]=0; + + /*generate a random direction on unit sphere*/ + double nrm=2.0; + double vx,vy,vz; + int iter=0; + do { + if(iter>100){ + printf("warning: exceeed max random vector attempts: at loop %d -> %g %d\n",i,nrm,iter); + } + vx=rand01()*2.0-1.0; + vy=rand01()*2.0-1.0; + vz=rand01()*2.0-1.0; + nrm=(vx*vx + vy*vy + vz*vz); + iter++; + } while (nrm>1.0); + vx/=sqrt(nrm); + vy/=sqrt(nrm); + vz/=sqrt(nrm); + particle->direction[0]=vx; + particle->direction[1]=vy; + particle->direction[2]=vz; + + /*generate the kinetic energy (in MeV) of the particle*/ + particle->ekin=1e-3; + + /*set time=0*/ + particle->time=0; + /*set weight*/ + particle->weight=1; + + particle->userflags=0; + mcpl_add_particle(outfile,particle); + } + mcpl_closeandgzip_outfile(outfile); +} From bc797c4df83b906bebe454cd1c9d7a17bd52c49c Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 5 Jul 2022 01:30:07 +0200 Subject: [PATCH 007/265] don't zip the output-file --- .../source_mcpl_file/gen_dummy_mcpl.c | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c index 7b5a933f18..f35a07fc44 100644 --- a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c +++ b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c @@ -54,20 +54,20 @@ int main(int argc, char **argv){ int i; for (i=0;iposition[0]=0; particle->position[1]=0; particle->position[2]=0; - + /*generate a random direction on unit sphere*/ double nrm=2.0; double vx,vy,vz; int iter=0; do { if(iter>100){ - printf("warning: exceeed max random vector attempts: at loop %d -> %g %d\n",i,nrm,iter); + printf("Warning: Exceeded max random vector attempts: at loop %d -> %g %d\n",i,nrm,iter); } vx=rand01()*2.0-1.0; vy=rand01()*2.0-1.0; @@ -82,9 +82,9 @@ int main(int argc, char **argv){ particle->direction[1]=vy; particle->direction[2]=vz; - /*generate the kinetic energy (in MeV) of the particle*/ + /*generate the kinetic energy (in MeV) of the particle*/ particle->ekin=1e-3; - + /*set time=0*/ particle->time=0; /*set weight*/ @@ -93,5 +93,5 @@ int main(int argc, char **argv){ particle->userflags=0; mcpl_add_particle(outfile,particle); } - mcpl_closeandgzip_outfile(outfile); + mcpl_close_outfile(outfile); } From 80e69b2e0856d5af025087283964fd5a03e20339 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 5 Jul 2022 01:53:14 +0200 Subject: [PATCH 008/265] now compiles fine if mcpl is indeed installed --- .../regression_tests/source_mcpl_file/test.py | 21 ++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index 5a6a87d878..0adf67f1aa 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -3,16 +3,13 @@ import os import shutil import subprocess import textwrap - +import glob import openmc import pytest from tests.testing_harness import TestHarness -def model(): - subprocess.run(['gcc','-o gen_dummt_mcpl.out','-lm','-lmcpl','gen_dummy_mcpl.c'] ) - subprocess.run(['./gen_dummy_mcpl.out']) - + class SourceMCPLFileTestHarness(TestHarness): def execute_test(self): """Run OpenMC with the appropriate arguments and check the outputs.""" @@ -26,6 +23,10 @@ class SourceMCPLFileTestHarness(TestHarness): finally: self._cleanup() + def _create_input(self): + subprocess.run(['gcc','-o','gen_dummy_mcpl.out','gen_dummy_mcpl.c','-lm','-lmcpl']) + subprocess.run(['./gen_dummy_mcpl.out']) + def update_results(self): """Update the results_true using the current version of OpenMC.""" try: @@ -40,13 +41,19 @@ class SourceMCPLFileTestHarness(TestHarness): def _test_output_created(self): """Check that the output files were created""" - stat epoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) + statepoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) assert len(statepoint) == 1, 'Either multiple or no statepoint files ' \ 'exist.' assert statepoint[0].endswith('h5'), \ 'statepoint file does not end with h5.' + def _cleanup(self): + super()._cleanup() + source_mcpl=glob.glob(os.path.join(os.getcwd(),'source*.mcpl')) + for f in source_mcpl: + if (os.path.exists(f)): + os.remove(f) + def test_mcpl_source_file(): harness = SourceMCPLFileTestHarness('statepoint.10.h5') harness.main() - From 6d352aa55c8fab8bf427bceeb165c6b870d94e53 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 22 Jun 2022 22:50:07 +0200 Subject: [PATCH 009/265] add placeholder skeleton for MCPL-input --- include/openmc/source.h | 19 +++++++++++++++++++ src/source.cpp | 21 +++++++++++++++++++++ 2 files changed, 40 insertions(+) diff --git a/include/openmc/source.h b/include/openmc/source.h index 18fddc6899..cadbfe93bb 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -100,6 +100,25 @@ private: vector sites_; //!< Source sites from a file }; +//============================================================================== +// MCPL-file input source +//============================================================================== +class MCPLFileSource : public Source { +public: + // Constructors, destructors + MCPLFileSource(std::string path); + ~MCPLFileSource(); + + // Defer implementation to custom source library + SourceSite sample(uint64_t* seed) const override + +private: + vector sites_; //! Date: Thu, 23 Jun 2022 11:34:53 +0200 Subject: [PATCH 010/265] include mcpl header --- src/source.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/source.cpp b/src/source.cpp index cd8b5e5743..5e26fa0a8d 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -31,6 +31,10 @@ #include "openmc/state_point.h" #include "openmc/xml_interface.h" +#ifdef HAS_MCPL +#include +#endif + namespace openmc { //============================================================================== From c43989af9c222b20413ee3b892feaf20919b8707 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Thu, 23 Jun 2022 11:35:46 +0200 Subject: [PATCH 011/265] declarations of MCPL-internals --- include/openmc/source.h | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/include/openmc/source.h b/include/openmc/source.h index cadbfe93bb..69dd47eae9 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -109,11 +109,20 @@ public: MCPLFileSource(std::string path); ~MCPLFileSource(); - // Defer implementation to custom source library - SourceSite sample(uint64_t* seed) const override + // Properties + ParticleType particle_type() const { return particle_; } + + //! Sample from the external source distribution + //! \param[inout] seed Pseudorandom seed pointer + //! \return Site read from MCPL-file + SourceSite sample(uint64_t* seed) const override; private: + ParticleType particle_ {ParticleType::neutron}; //!< Type of particle emitted vector sites_; //! Date: Thu, 23 Jun 2022 11:37:05 +0200 Subject: [PATCH 012/265] internals of sample and constructor --- src/source.cpp | 51 ++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 47 insertions(+), 4 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 5e26fa0a8d..231f355fc2 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -337,7 +337,7 @@ CustomSourceWrapper::~CustomSourceWrapper() } //=========================================================================== -// Read an MCPL-file +// Read particles from an MCPL-file //=========================================================================== MCPLFileSource::MCPLFileSource(std::string path) { @@ -348,12 +348,55 @@ MCPLFileSource::MCPLFileSource(std::string path) // Read the source from a binary file instead of sampling from some // assumed source distribution - write_message(6, "Reading source file from {}...", path); + write_message(6, "Reading mcpl source file from {}",path); // Open the mcpl file - id_t file_id = mcpl_open(path.c_str) - + mcpl_file = mcpl_open(path.c_str); + //do checks on the mcpl_file to see if particles are many enough. + // should model this on the example source shown in the docs. + uint64_t nparticles=mcpl_hdr_nparticles(mcpl_file); + +} + +MCPLFileSource::~MCPLFilsSource(){ + mcpl_close_file(mcpl_file); +} + +SourceSite MCPLFileSource::sample(uint64_t *seed){ + SourceSite omc_particle; + mcpl_particle *mcpl_particle; + //extract particle from mcpl-file + mcpl_particle=mcpl_reazd(mcplfile); + // check if it is a neutron or a photon. otherwise skip + while ( mcpl_particle->pdgcode!=2112 && mcpl_particle->pdgcode!=22 ) + { + mcpl_particle(mcpl_read(mcplfile); + //check for file exhaustion + } + + if(mcpl_particle->pdgcode=2112) { + omc_particle_=ParticleType::neutron; + } else { + omc_particle_=Particletype::photon; + } + + //particle is good, convert to openmc-formalism + omc_particle.r.x=mcpl_particle.x; + omc_particle.r.y=mcpl_particle.y; + omc_particle.r.z=mcpl_particle.z; + + omc_particle.u.x=mcpl_particle->direction[0]; + omc_particle.u.y=mcpl_particle->direction[1]; + omc_particle.u.z=mcpl_particle->direction[2]; + + //mcpl stores particles in MeV + omc_particle.E=mcpl_particle->ekin*1e6; + + omc_particle.t=mcpl_particle->time*1e-3; + omc_particle.wgt=mcpl_particle->weight; + omc_particle.delayed_group=0; + return omc_particle; } From 103c6ffa0330ab1313489a27b2d9504cfb30f7ba Mon Sep 17 00:00:00 2001 From: erkn Date: Mon, 27 Jun 2022 23:25:35 +0200 Subject: [PATCH 013/265] (wip): skeleton for input only test --- .../regression_tests/source_mcpl_file/test.py | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 tests/regression_tests/source_mcpl_file/test.py diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py new file mode 100644 index 0000000000..5a6a87d878 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -0,0 +1,52 @@ +import pathlib as pl +import os +import shutil +import subprocess +import textwrap + +import openmc +import pytest + +from tests.testing_harness import TestHarness + +def model(): + subprocess.run(['gcc','-o gen_dummt_mcpl.out','-lm','-lmcpl','gen_dummy_mcpl.c'] ) + subprocess.run(['./gen_dummy_mcpl.out']) + +class SourceMCPLFileTestHarness(TestHarness): + def execute_test(self): + """Run OpenMC with the appropriate arguments and check the outputs.""" + try: + self._create_input() + self._run_openmc() + self._test_output_created() + results = self._get_results() + self._write_results(results) + self._compare_results() + finally: + self._cleanup() + + def update_results(self): + """Update the results_true using the current version of OpenMC.""" + try: + self._create_input() + self._run_openmc() + self._test_output_created() + results = self._get_results() + self._write_results(results) + self._overwrite_results() + finally: + self._cleanup() + + def _test_output_created(self): + """Check that the output files were created""" + stat epoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) + assert len(statepoint) == 1, 'Either multiple or no statepoint files ' \ + 'exist.' + assert statepoint[0].endswith('h5'), \ + 'statepoint file does not end with h5.' + +def test_mcpl_source_file(): + harness = SourceMCPLFileTestHarness('statepoint.10.h5') + harness.main() + From 73fb335350bb3b6ed0199e9c3cc4ee19d73b163e Mon Sep 17 00:00:00 2001 From: erkn Date: Mon, 27 Jun 2022 23:26:01 +0200 Subject: [PATCH 014/265] c-prog to generate a dummy mcpl --- .../source_mcpl_file/gen_dummy_mcpl.c | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c diff --git a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c new file mode 100644 index 0000000000..7b5a933f18 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c @@ -0,0 +1,97 @@ +#include +#include +#include +#include + +const int batches=10; +const int particles=10000; + +double rand01(){ + double r=rand()/((double) RAND_MAX); + return r; +} + + +int main(int argc, char **argv){ + char outfilename[128]; + snprintf(outfilename,127,"source.%d.mcpl",batches); + + /*generate an mcpl_header_of sorts*/ + mcpl_outfile_t outfile=mcpl_create_outfile(outfilename); + mcpl_particle_t *particle, Particle; + + char line[256]; + snprintf(line,255,"gen_dummy_mcpl.c"); + mcpl_hdr_set_srcname(outfile,line); + mcpl_enable_universal_pdgcode(outfile,2112);/*all particles are neutrons*/ + snprintf(line,255,"Dummy MCPL-file for testing OpenMC mcpl input"); + mcpl_hdr_add_comment(outfile,line); + + /*also add the instrument file and the command line as blobs*/ + FILE *fp; + if( (fp=fopen("gen_dummy_mcpl.c","rb"))!=NULL){ + unsigned char *buffer; + int size,status; + /*find the file size by seeking to end, "tell" the position, and then go back again*/ + fseek(fp, 0L, SEEK_END); + size = ftell(fp); // get current file pointer + fseek(fp, 0L, SEEK_SET); // seek back to beginning of file + if ( size && (buffer=malloc(size))!=NULL){ + if (size!=(fread(buffer,1,size,fp))){ + fprintf(stderr,"Warning: c source generator file not read cleanly\n"); + } + mcpl_hdr_add_data(outfile, "mcpl_point_source_file_generator", size, buffer); + free(buffer); + } + fclose(fp); + } else { + fprintf(stderr,"Warning: could not open c source generator file, hence not embedded.\n"); + } + + + /*the main particle loop*/ + particle=&Particle; + int i; + for (i=0;iposition[0]=0; + particle->position[1]=0; + particle->position[2]=0; + + /*generate a random direction on unit sphere*/ + double nrm=2.0; + double vx,vy,vz; + int iter=0; + do { + if(iter>100){ + printf("warning: exceeed max random vector attempts: at loop %d -> %g %d\n",i,nrm,iter); + } + vx=rand01()*2.0-1.0; + vy=rand01()*2.0-1.0; + vz=rand01()*2.0-1.0; + nrm=(vx*vx + vy*vy + vz*vz); + iter++; + } while (nrm>1.0); + vx/=sqrt(nrm); + vy/=sqrt(nrm); + vz/=sqrt(nrm); + particle->direction[0]=vx; + particle->direction[1]=vy; + particle->direction[2]=vz; + + /*generate the kinetic energy (in MeV) of the particle*/ + particle->ekin=1e-3; + + /*set time=0*/ + particle->time=0; + /*set weight*/ + particle->weight=1; + + particle->userflags=0; + mcpl_add_particle(outfile,particle); + } + mcpl_closeandgzip_outfile(outfile); +} From c6c876d835fe2177426ee64f4ae8dc15d5e616f2 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 5 Jul 2022 01:30:07 +0200 Subject: [PATCH 015/265] don't zip the output-file --- .../source_mcpl_file/gen_dummy_mcpl.c | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c index 7b5a933f18..f35a07fc44 100644 --- a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c +++ b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c @@ -54,20 +54,20 @@ int main(int argc, char **argv){ int i; for (i=0;iposition[0]=0; particle->position[1]=0; particle->position[2]=0; - + /*generate a random direction on unit sphere*/ double nrm=2.0; double vx,vy,vz; int iter=0; do { if(iter>100){ - printf("warning: exceeed max random vector attempts: at loop %d -> %g %d\n",i,nrm,iter); + printf("Warning: Exceeded max random vector attempts: at loop %d -> %g %d\n",i,nrm,iter); } vx=rand01()*2.0-1.0; vy=rand01()*2.0-1.0; @@ -82,9 +82,9 @@ int main(int argc, char **argv){ particle->direction[1]=vy; particle->direction[2]=vz; - /*generate the kinetic energy (in MeV) of the particle*/ + /*generate the kinetic energy (in MeV) of the particle*/ particle->ekin=1e-3; - + /*set time=0*/ particle->time=0; /*set weight*/ @@ -93,5 +93,5 @@ int main(int argc, char **argv){ particle->userflags=0; mcpl_add_particle(outfile,particle); } - mcpl_closeandgzip_outfile(outfile); + mcpl_close_outfile(outfile); } From 8719a539f9f8c9134ded079b2eec64c6cdf3aa82 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 5 Jul 2022 01:53:14 +0200 Subject: [PATCH 016/265] now compiles fine if mcpl is indeed installed --- .../regression_tests/source_mcpl_file/test.py | 21 ++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index 5a6a87d878..0adf67f1aa 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -3,16 +3,13 @@ import os import shutil import subprocess import textwrap - +import glob import openmc import pytest from tests.testing_harness import TestHarness -def model(): - subprocess.run(['gcc','-o gen_dummt_mcpl.out','-lm','-lmcpl','gen_dummy_mcpl.c'] ) - subprocess.run(['./gen_dummy_mcpl.out']) - + class SourceMCPLFileTestHarness(TestHarness): def execute_test(self): """Run OpenMC with the appropriate arguments and check the outputs.""" @@ -26,6 +23,10 @@ class SourceMCPLFileTestHarness(TestHarness): finally: self._cleanup() + def _create_input(self): + subprocess.run(['gcc','-o','gen_dummy_mcpl.out','gen_dummy_mcpl.c','-lm','-lmcpl']) + subprocess.run(['./gen_dummy_mcpl.out']) + def update_results(self): """Update the results_true using the current version of OpenMC.""" try: @@ -40,13 +41,19 @@ class SourceMCPLFileTestHarness(TestHarness): def _test_output_created(self): """Check that the output files were created""" - stat epoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) + statepoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) assert len(statepoint) == 1, 'Either multiple or no statepoint files ' \ 'exist.' assert statepoint[0].endswith('h5'), \ 'statepoint file does not end with h5.' + def _cleanup(self): + super()._cleanup() + source_mcpl=glob.glob(os.path.join(os.getcwd(),'source*.mcpl')) + for f in source_mcpl: + if (os.path.exists(f)): + os.remove(f) + def test_mcpl_source_file(): harness = SourceMCPLFileTestHarness('statepoint.10.h5') harness.main() - From 0d1c346b5a12d2a452450b435a80cf4a2fbbe608 Mon Sep 17 00:00:00 2001 From: erkn Date: Sat, 9 Jul 2022 16:31:00 +0200 Subject: [PATCH 017/265] fix misprints --- src/source.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 231f355fc2..37e580b18d 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -345,7 +345,7 @@ MCPLFileSource::MCPLFileSource(std::string path) if (!file_exists(path)) { fatal_error(fmt::format("Source file '{}' does not exist.", path)); } - + // Read the source from a binary file instead of sampling from some // assumed source distribution write_message(6, "Reading mcpl source file from {}",path); @@ -367,7 +367,7 @@ SourceSite MCPLFileSource::sample(uint64_t *seed){ SourceSite omc_particle; mcpl_particle *mcpl_particle; //extract particle from mcpl-file - mcpl_particle=mcpl_reazd(mcplfile); + mcpl_particle=mcpl_read(mcplfile); // check if it is a neutron or a photon. otherwise skip while ( mcpl_particle->pdgcode!=2112 && mcpl_particle->pdgcode!=22 ) { @@ -375,9 +375,9 @@ SourceSite MCPLFileSource::sample(uint64_t *seed){ //check for file exhaustion } - if(mcpl_particle->pdgcode=2112) { + if(mcpl_particle->pdgcode==2112) { omc_particle_=ParticleType::neutron; - } else { + } else if (mcpl_particle->pdgcode==22){ omc_particle_=Particletype::photon; } From 7a6c69fbd5daefcca4b612affdbac6ecd46e9d32 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Mon, 11 Jul 2022 09:49:29 +0200 Subject: [PATCH 018/265] fix misprints --- src/source.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 231f355fc2..9ec1ff798c 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -367,7 +367,7 @@ SourceSite MCPLFileSource::sample(uint64_t *seed){ SourceSite omc_particle; mcpl_particle *mcpl_particle; //extract particle from mcpl-file - mcpl_particle=mcpl_reazd(mcplfile); + mcpl_particle=mcpl_read(mcplfile); // check if it is a neutron or a photon. otherwise skip while ( mcpl_particle->pdgcode!=2112 && mcpl_particle->pdgcode!=22 ) { @@ -375,9 +375,9 @@ SourceSite MCPLFileSource::sample(uint64_t *seed){ //check for file exhaustion } - if(mcpl_particle->pdgcode=2112) { + if(mcpl_particle->pdgcode==2112) { omc_particle_=ParticleType::neutron; - } else { + } else if (mcpl_particle->pdgcode==22){ omc_particle_=Particletype::photon; } @@ -390,9 +390,9 @@ SourceSite MCPLFileSource::sample(uint64_t *seed){ omc_particle.u.y=mcpl_particle->direction[1]; omc_particle.u.z=mcpl_particle->direction[2]; - //mcpl stores particles in MeV + //mcpl stores kinetic energy in MeV omc_particle.E=mcpl_particle->ekin*1e6; - + //mcpl stores time in ms omc_particle.t=mcpl_particle->time*1e-3; omc_particle.wgt=mcpl_particle->weight; omc_particle.delayed_group=0; From 34746926d349d0e04134893aa987c49d9508e121 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 12 Jul 2022 13:48:55 +0200 Subject: [PATCH 019/265] add necessary xmls --- tests/regression_tests/source_mcpl_file/geometry.xml | 8 ++++++++ tests/regression_tests/source_mcpl_file/materials.xml | 9 +++++++++ 2 files changed, 17 insertions(+) create mode 100644 tests/regression_tests/source_mcpl_file/geometry.xml create mode 100644 tests/regression_tests/source_mcpl_file/materials.xml diff --git a/tests/regression_tests/source_mcpl_file/geometry.xml b/tests/regression_tests/source_mcpl_file/geometry.xml new file mode 100644 index 0000000000..bc56030e18 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/geometry.xml @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/tests/regression_tests/source_mcpl_file/materials.xml b/tests/regression_tests/source_mcpl_file/materials.xml new file mode 100644 index 0000000000..2472a74717 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/materials.xml @@ -0,0 +1,9 @@ + + + + + + + + + From 25cfc328d04c930a8d75ba41eb46ed7e26c64cae Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 12 Jul 2022 13:49:56 +0200 Subject: [PATCH 020/265] set seed to make test deteministic --- tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c index f35a07fc44..61eea95c6f 100644 --- a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c +++ b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c @@ -52,6 +52,7 @@ int main(int argc, char **argv){ /*the main particle loop*/ particle=&Particle; int i; + srand(1234); for (i=0;i Date: Tue, 12 Jul 2022 13:50:35 +0200 Subject: [PATCH 021/265] test target result --- tests/regression_tests/source_mcpl_file/results_true.dat | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 tests/regression_tests/source_mcpl_file/results_true.dat diff --git a/tests/regression_tests/source_mcpl_file/results_true.dat b/tests/regression_tests/source_mcpl_file/results_true.dat new file mode 100644 index 0000000000..f2209006a1 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/results_true.dat @@ -0,0 +1,2 @@ +k-combined: +3.017557E-01 3.398770E-03 From b0bb63cb3508d0dff59fd950a60dc35db2188b19 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 12 Jul 2022 13:50:53 +0200 Subject: [PATCH 022/265] yet another necessary file --- tests/regression_tests/source_mcpl_file/settings.xml | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 tests/regression_tests/source_mcpl_file/settings.xml diff --git a/tests/regression_tests/source_mcpl_file/settings.xml b/tests/regression_tests/source_mcpl_file/settings.xml new file mode 100644 index 0000000000..8b1510e0ce --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/settings.xml @@ -0,0 +1,11 @@ + + + + 10 + 5 + 1000 + + + source.10.mcpl + + From e480b5c851c542e53ff6e83236994f23c2bfdba3 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 12 Jul 2022 14:40:01 +0200 Subject: [PATCH 023/265] add a check that the test input got created as intended --- tests/regression_tests/source_mcpl_file/test.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index 0adf67f1aa..922ddddd31 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -15,6 +15,7 @@ class SourceMCPLFileTestHarness(TestHarness): """Run OpenMC with the appropriate arguments and check the outputs.""" try: self._create_input() + self._test_input_created() self._run_openmc() self._test_output_created() results = self._get_results() @@ -31,6 +32,7 @@ class SourceMCPLFileTestHarness(TestHarness): """Update the results_true using the current version of OpenMC.""" try: self._create_input() + self._test_input_created() self._run_openmc() self._test_output_created() results = self._get_results() @@ -39,6 +41,14 @@ class SourceMCPLFileTestHarness(TestHarness): finally: self._cleanup() + def _test_input_created(self): + """Check that the input mcpl.file was generated as it should""" + mcplfile=glob.glob(os.path.join(os.getcwd(),'source.10.mcpl')) + assert len(mcplfile) == 1, 'Either multiple or no mcpl files ' \ + 'exist.' + assert mcplfile[0].endswith('mcpl'), \ + 'output file does not end with mcpl.' + def _test_output_created(self): """Check that the output files were created""" statepoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) @@ -55,5 +65,5 @@ class SourceMCPLFileTestHarness(TestHarness): os.remove(f) def test_mcpl_source_file(): - harness = SourceMCPLFileTestHarness('statepoint.10.h5') + harness = SourceMCPLFileTestHarness('source.10.mcpl') harness.main() From 8c9bb761e5d3838a33822f7fa283acab106cc736 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 13 Jul 2022 10:25:55 +0200 Subject: [PATCH 024/265] fix bugs and finalize interface to MCPL --- include/openmc/source.h | 22 +++++++------ src/source.cpp | 73 +++++++++++++++++++++++++---------------- 2 files changed, 57 insertions(+), 38 deletions(-) diff --git a/include/openmc/source.h b/include/openmc/source.h index 69dd47eae9..4d7ec104aa 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -12,6 +12,10 @@ #include "openmc/particle.h" #include "openmc/vector.h" +#ifdef OPENMC_MCPL +#include +#endif + namespace openmc { //============================================================================== @@ -100,6 +104,7 @@ private: vector sites_; //!< Source sites from a file }; +#ifdef OPENMC_MCPL //============================================================================== // MCPL-file input source //============================================================================== @@ -109,24 +114,21 @@ public: MCPLFileSource(std::string path); ~MCPLFileSource(); - // Properties - ParticleType particle_type() const { return particle_; } - + // Methods //! Sample from the external source distribution //! \param[inout] seed Pseudorandom seed pointer //! \return Site read from MCPL-file - SourceSite sample(uint64_t* seed) const override; + SourceSite sample(uint64_t* seed) const; private: - ParticleType particle_ {ParticleType::neutron}; //!< Type of particle emitted + SourceSite read_single_particle() const; + void read_source_bank(vector &sites_); + vector sites_; //! #endif @@ -336,6 +336,7 @@ CustomSourceWrapper::~CustomSourceWrapper() #endif } +#ifdef OPENMC_MCPL //=========================================================================== // Read particles from an MCPL-file //=========================================================================== @@ -351,54 +352,70 @@ MCPLFileSource::MCPLFileSource(std::string path) write_message(6, "Reading mcpl source file from {}",path); // Open the mcpl file - mcpl_file = mcpl_open(path.c_str); + mcpl_file = mcpl_open_file(path.c_str()); //do checks on the mcpl_file to see if particles are many enough. // should model this on the example source shown in the docs. - uint64_t nparticles=mcpl_hdr_nparticles(mcpl_file); + n_sites=mcpl_hdr_nparticles(mcpl_file); + read_source_bank(sites_); } -MCPLFileSource::~MCPLFilsSource(){ +MCPLFileSource::~MCPLFileSource(){ mcpl_close_file(mcpl_file); } -SourceSite MCPLFileSource::sample(uint64_t *seed){ - SourceSite omc_particle; - mcpl_particle *mcpl_particle; +SourceSite MCPLFileSource::sample(uint64_t* seed) const +{ + size_t i_site = sites_.size() * prn(seed); + return sites_[i_site]; +} + +void MCPLFileSource::read_source_bank(vector &sites_) +{ + sites_.resize(n_sites); + for (int i=0;ipdgcode!=2112 && mcpl_particle->pdgcode!=22 ) - { - mcpl_particle(mcpl_read(mcplfile); - //check for file exhaustion + mcpl_particle=mcpl_read(mcpl_file); + // check if it is a neutron or a photon. otherwise skip + while ( mcpl_particle->pdgcode!=2112 && mcpl_particle->pdgcode!=22 ) { + mcpl_particle=mcpl_read(mcpl_file); + //should check for file exhaustion This could happen if particles are other than + //neutrons or photons } if(mcpl_particle->pdgcode==2112) { - omc_particle_=ParticleType::neutron; - } else if (mcpl_particle->pdgcode==22){ - omc_particle_=Particletype::photon; + omc_particle_.particle=ParticleType::neutron; + } else if (mcpl_particle->pdgcode==22) { + omc_particle_.particle=ParticleType::photon; } //particle is good, convert to openmc-formalism - omc_particle.r.x=mcpl_particle.x; - omc_particle.r.y=mcpl_particle.y; - omc_particle.r.z=mcpl_particle.z; + omc_particle_.r.x=mcpl_particle->position[0]; + omc_particle_.r.y=mcpl_particle->position[1]; + omc_particle_.r.z=mcpl_particle->position[2]; - omc_particle.u.x=mcpl_particle->direction[0]; - omc_particle.u.y=mcpl_particle->direction[1]; - omc_particle.u.z=mcpl_particle->direction[2]; + omc_particle_.u.x=mcpl_particle->direction[0]; + omc_particle_.u.y=mcpl_particle->direction[1]; + omc_particle_.u.z=mcpl_particle->direction[2]; //mcpl stores kinetic energy in MeV - omc_particle.E=mcpl_particle->ekin*1e6; + omc_particle_.E=mcpl_particle->ekin*1e6; //mcpl stores time in ms - omc_particle.t=mcpl_particle->time*1e-3; - omc_particle.wgt=mcpl_particle->weight; - omc_particle.delayed_group=0; - return omc_particle; + omc_particle_.time=mcpl_particle->time*1e-3; + omc_particle_.wgt=mcpl_particle->weight; + omc_particle_.delayed_group=0; + return omc_particle_; } - +#endif //OPENMC_MCPL //============================================================================== // Non-member functions From 915d69fb3d217cf705158dba680b8f02a99208c7 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 13 Jul 2022 10:26:24 +0200 Subject: [PATCH 025/265] add an option to turn on mcpl-support --- CMakeLists.txt | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/CMakeLists.txt b/CMakeLists.txt index 85dcd7084d..6af9643cdb 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -36,6 +36,7 @@ option(OPENMC_ENABLE_COVERAGE "Compile with coverage analysis flags" option(OPENMC_USE_DAGMC "Enable support for DAGMC (CAD) geometry" OFF) option(OPENMC_USE_LIBMESH "Enable support for libMesh unstructured mesh tallies" OFF) option(OPENMC_USE_MPI "Enable MPI" OFF) +option(OPENMC_USE_MCPL "Enable MPCPL" OFF) #=============================================================================== # Set a default build configuration if not explicitly specified @@ -154,6 +155,10 @@ if(OPENMC_ENABLE_COVERAGE) list(APPEND ldflags --coverage) endif() +if(OPENMC_USE_MCPL) + list(APPEND ldflags -lmcpl) +endif() + # Show flags being used message(STATUS "OpenMC C++ flags: ${cxxflags}") message(STATUS "OpenMC Linker flags: ${ldflags}") @@ -408,6 +413,10 @@ endif() if (OPENMC_USE_MPI) target_compile_definitions(libopenmc PUBLIC -DOPENMC_MPI) endif() +if(OPENMC_USE_MCPL) + target_compile_definitions(libopenmc PUBLIC -DOPENMC_MCPL) +endif() + # Set git SHA1 hash as a compile definition if(GIT_FOUND) From b140eeb7cb4c7a1ee76172cd21c32c2e9951a24b Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 13 Jul 2022 10:27:18 +0200 Subject: [PATCH 026/265] add a source type to the settings interface --- src/settings.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/settings.cpp b/src/settings.cpp index eb0d4936c7..12e0a80509 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -430,6 +430,9 @@ void read_settings_xml() if (check_for_node(node, "file")) { auto path = get_node_value(node, "file", false, true); model::external_sources.push_back(make_unique(path)); + } else if (check_for_node(node, "mcpl")) { + auto path = get_node_value(node, "mcpl", false, true); + model::external_sources.push_back(make_unique(path)); } else if (check_for_node(node, "library")) { // Get shared library path and parameters auto path = get_node_value(node, "library", false, true); From cd163ef0b91fb4acc30630528b0728d8bab3098e Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 13 Jul 2022 12:13:10 +0200 Subject: [PATCH 027/265] only add mcpl-support if OPENMC_MCPL is defined --- src/settings.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/settings.cpp b/src/settings.cpp index 12e0a80509..d419cab06f 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -430,9 +430,11 @@ void read_settings_xml() if (check_for_node(node, "file")) { auto path = get_node_value(node, "file", false, true); model::external_sources.push_back(make_unique(path)); +#ifdef OPENMC_MCPL } else if (check_for_node(node, "mcpl")) { auto path = get_node_value(node, "mcpl", false, true); model::external_sources.push_back(make_unique(path)); +#endif } else if (check_for_node(node, "library")) { // Get shared library path and parameters auto path = get_node_value(node, "library", false, true); From a79233b3ec85f59647fb800da7db0973ce9365e8 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 13 Jul 2022 14:13:33 +0200 Subject: [PATCH 028/265] needed to avoid name clashes with other tests --- tests/regression_tests/source_mcpl_file/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 tests/regression_tests/source_mcpl_file/__init__.py diff --git a/tests/regression_tests/source_mcpl_file/__init__.py b/tests/regression_tests/source_mcpl_file/__init__.py new file mode 100644 index 0000000000..e69de29bb2 From eff690fd90032abd0d4a5e68f5babcc38c476de1 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 13 Jul 2022 20:55:53 +0200 Subject: [PATCH 029/265] fail without tripping the entire test-process --- tests/regression_tests/source_mcpl_file/test.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index 922ddddd31..f55a769047 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -1,11 +1,6 @@ -import pathlib as pl import os -import shutil import subprocess -import textwrap import glob -import openmc -import pytest from tests.testing_harness import TestHarness @@ -25,7 +20,8 @@ class SourceMCPLFileTestHarness(TestHarness): self._cleanup() def _create_input(self): - subprocess.run(['gcc','-o','gen_dummy_mcpl.out','gen_dummy_mcpl.c','-lm','-lmcpl']) + compiled=subprocess.run(['gcc','-o','gen_dummy_mcpl.out','gen_dummy_mcpl.c','-lm','-lmcpl']) + assert compiled==0, 'Could not compile mcpl-file generator code' subprocess.run(['./gen_dummy_mcpl.out']) def update_results(self): From 1ba696741412b17ac676cc2a0b4a78c606906d35 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Fri, 15 Jul 2022 21:35:59 +0200 Subject: [PATCH 030/265] fix typo Co-authored-by: Paul Romano --- CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 6af9643cdb..be56f1c12f 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -36,7 +36,7 @@ option(OPENMC_ENABLE_COVERAGE "Compile with coverage analysis flags" option(OPENMC_USE_DAGMC "Enable support for DAGMC (CAD) geometry" OFF) option(OPENMC_USE_LIBMESH "Enable support for libMesh unstructured mesh tallies" OFF) option(OPENMC_USE_MPI "Enable MPI" OFF) -option(OPENMC_USE_MCPL "Enable MPCPL" OFF) +option(OPENMC_USE_MCPL "Enable MCPL" OFF) #=============================================================================== # Set a default build configuration if not explicitly specified From 380cfc150b449ef56debb5261caa010a52c42bdd Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 9 Aug 2022 08:12:19 +0200 Subject: [PATCH 031/265] refactor MCPL file read part of FileSource A new constructor is added to FileSource that reads from a given MCPL-file. --- include/openmc/source.h | 30 +--------- src/settings.cpp | 2 +- src/source.cpp | 128 +++++++++++++++------------------------- 3 files changed, 52 insertions(+), 108 deletions(-) diff --git a/include/openmc/source.h b/include/openmc/source.h index 4d7ec104aa..5c2dae9311 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -96,7 +96,9 @@ class FileSource : public Source { public: // Constructors explicit FileSource(std::string path); - +#ifdef OPENMC_MCPL + explicit FileSource(mcpl_file_t mcpl_file); +#endif // Methods SourceSite sample(uint64_t* seed) const override; @@ -104,32 +106,6 @@ private: vector sites_; //!< Source sites from a file }; -#ifdef OPENMC_MCPL -//============================================================================== -// MCPL-file input source -//============================================================================== -class MCPLFileSource : public Source { -public: - // Constructors, destructors - MCPLFileSource(std::string path); - ~MCPLFileSource(); - - // Methods - //! Sample from the external source distribution - //! \param[inout] seed Pseudorandom seed pointer - //! \return Site read from MCPL-file - SourceSite sample(uint64_t* seed) const; - -private: - SourceSite read_single_particle() const; - void read_source_bank(vector &sites_); - - vector sites_; //!(path)); + model::external_sources.push_back(make_unique(mcpl_open_file(path.c_str()))); #endif } else if (check_for_node(node, "library")) { // Get shared library path and parameters diff --git a/src/source.cpp b/src/source.cpp index 82978f1030..49e51c4b16 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -277,6 +277,54 @@ FileSource::FileSource(std::string path) file_close(file_id); } +#ifdef OPENMC_MCPL +FileSource::FileSource(mcpl_file_t mcpl_file) +{ + //do checks on the mcpl_file to see if particles are many enough. + // should model this on the example source shown in the docs. + size_t n_sites=mcpl_hdr_nparticles(mcpl_file); + + sites_.resize(n_sites); + for (int i=0;ipdgcode!=2112 && mcpl_particle->pdgcode!=22 ) { + mcpl_particle=mcpl_read(mcpl_file); + //should check for file exhaustion This could happen if particles are other than + //neutrons or photons + } + + if(mcpl_particle->pdgcode==2112) { + site_.particle=ParticleType::neutron; + } else if (mcpl_particle->pdgcode==22) { + site_.particle=ParticleType::photon; + } + + //particle is good, convert to openmc-formalism + site_.r.x=mcpl_particle->position[0]; + site_.r.y=mcpl_particle->position[1]; + site_.r.z=mcpl_particle->position[2]; + + site_.u.x=mcpl_particle->direction[0]; + site_.u.y=mcpl_particle->direction[1]; + site_.u.z=mcpl_particle->direction[2]; + + //mcpl stores kinetic energy in MeV + site_.E=mcpl_particle->ekin*1e6; + //mcpl stores time in ms + site_.time=mcpl_particle->time*1e-3; + site_.wgt=mcpl_particle->weight; + site_.delayed_group=0; + sites_[i]=site_; + } + mcpl_close_file(mcpl_file); +} +#endif //OPENMC_MCPL + SourceSite FileSource::sample(uint64_t* seed) const { size_t i_site = sites_.size() * prn(seed); @@ -336,86 +384,6 @@ CustomSourceWrapper::~CustomSourceWrapper() #endif } -#ifdef OPENMC_MCPL -//=========================================================================== -// Read particles from an MCPL-file -//=========================================================================== -MCPLFileSource::MCPLFileSource(std::string path) -{ - // Check if source file exists - if (!file_exists(path)) { - fatal_error(fmt::format("Source file '{}' does not exist.", path)); - } - - // Read the source from a binary file instead of sampling from some - // assumed source distribution - write_message(6, "Reading mcpl source file from {}",path); - - // Open the mcpl file - mcpl_file = mcpl_open_file(path.c_str()); - - //do checks on the mcpl_file to see if particles are many enough. - // should model this on the example source shown in the docs. - n_sites=mcpl_hdr_nparticles(mcpl_file); - - read_source_bank(sites_); -} - -MCPLFileSource::~MCPLFileSource(){ - mcpl_close_file(mcpl_file); -} - -SourceSite MCPLFileSource::sample(uint64_t* seed) const -{ - size_t i_site = sites_.size() * prn(seed); - return sites_[i_site]; -} - -void MCPLFileSource::read_source_bank(vector &sites_) -{ - sites_.resize(n_sites); - for (int i=0;ipdgcode!=2112 && mcpl_particle->pdgcode!=22 ) { - mcpl_particle=mcpl_read(mcpl_file); - //should check for file exhaustion This could happen if particles are other than - //neutrons or photons - } - - if(mcpl_particle->pdgcode==2112) { - omc_particle_.particle=ParticleType::neutron; - } else if (mcpl_particle->pdgcode==22) { - omc_particle_.particle=ParticleType::photon; - } - - //particle is good, convert to openmc-formalism - omc_particle_.r.x=mcpl_particle->position[0]; - omc_particle_.r.y=mcpl_particle->position[1]; - omc_particle_.r.z=mcpl_particle->position[2]; - - omc_particle_.u.x=mcpl_particle->direction[0]; - omc_particle_.u.y=mcpl_particle->direction[1]; - omc_particle_.u.z=mcpl_particle->direction[2]; - - //mcpl stores kinetic energy in MeV - omc_particle_.E=mcpl_particle->ekin*1e6; - //mcpl stores time in ms - omc_particle_.time=mcpl_particle->time*1e-3; - omc_particle_.wgt=mcpl_particle->weight; - omc_particle_.delayed_group=0; - return omc_particle_; -} -#endif //OPENMC_MCPL //============================================================================== // Non-member functions From aa571c2c33b421e2524e249ca00f9584e891dd0a Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 6 Sep 2022 02:22:21 +0200 Subject: [PATCH 032/265] wip add MCPL-out to openmc code for writing a source_bank/point compiles but is untested --- include/openmc/state_point.h | 9 +++ src/state_point.cpp | 125 +++++++++++++++++++++++++++++++++++ 2 files changed, 134 insertions(+) diff --git a/include/openmc/state_point.h b/include/openmc/state_point.h index 5ada2bf88d..2d92c935a6 100644 --- a/include/openmc/state_point.h +++ b/include/openmc/state_point.h @@ -9,6 +9,10 @@ #include "openmc/particle.h" #include "openmc/vector.h" +#ifdef OPENMC_MCPL +#include +#endif + namespace openmc { void load_state_point(); @@ -21,5 +25,10 @@ void write_tally_results_nr(hid_t file_id); void restart_set_keff(); void write_unstructured_mesh_results(); +#ifdef OPENMC_MCPL +void write_mcpl_source_point(const char *filename_, bool surf_source_bank = false); +void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank); +#endif + } // namespace openmc #endif // OPENMC_STATE_POINT_H diff --git a/src/state_point.cpp b/src/state_point.cpp index 9ea0459153..babd670a2d 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -28,6 +28,10 @@ #include "openmc/timer.h" #include "openmc/vector.h" +#ifdef OPENMC_MCPL +#include +#endif + namespace openmc { extern "C" int openmc_statepoint_write(const char* filename, bool* write_source) @@ -598,6 +602,45 @@ void write_source_point(const char* filename, bool surf_source_bank) file_close(file_id); } +void write_mcpl_point(const char *filename, bool surf_source_bank) +{ + std::string filename_; + if (filename) { + filename_ = filename; + } else { + // Determine width for zero padding + int w = std::to_string(settings::n_max_batches).size(); + + filename_ = fmt::format("{0}source.{1:0{2}}.mcpl", settings::path_output, + simulation::current_batch, w); + } + + mcpl_outfile_t file_id; + + std::string line; + if (mpi::master) { + // this must be rewritten: file_open is h5-specific + file_id = mcpl_create_outfile(filename_.c_str()); + //write_attribute(file_id, "filetype", "source"); + //write header stuff (oopy in xml-files as binary blobs for instance)) + if (VERSION_DEV){ + line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}-development"); + } else { + line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}"); + } + mcpl_hdr_set_srcname(file_id,line.c_str()); + } + + write_mcpl_source_bank(file_id, surf_source_bank); + + if (mpi::master) { + //change this - this is h5 specific + mcpl_closeandgzip_outfile(file_id); + } + +} + + void write_source_bank(hid_t group_id, bool surf_source_bank) { hid_t banktype = h5banktype(); @@ -714,6 +757,88 @@ void write_source_bank(hid_t group_id, bool surf_source_bank) H5Tclose(banktype); } +void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) +{ + int64_t dims_size = settings::n_particles; + int64_t count_size = simulation::work_per_rank; + + // Set vectors for source bank and starting bank index of each process + vector* bank_index = &simulation::work_index; + vector* source_bank = &simulation::source_bank; + vector surf_source_index_vector; + vector surf_source_bank_vector; + + if(surf_source_bank) { + surf_source_index_vector = calculate_surf_source_size(); + dims_size = surf_source_index_vector[mpi::n_procs]; + count_size = simulation::surf_source_bank.size(); + + bank_index = &surf_source_index_vector; + + // Copy data in a SharedArray into a vector. + surf_source_bank_vector.resize(count_size); + surf_source_bank_vector.assign(simulation::surf_source_bank.data(), + simulation::surf_source_bank.data() + count_size); + source_bank = &surf_source_bank_vector; + } + + if (mpi::master) { + //write particles from the master node + //loop over the other nodes and receive data - then write those. + for (int i = 0; i < mpi::n_procs; ++i) { +#ifdef OPENMC_MPI + if (i>0) + MPI_Recv(source_bank->data(), count[0], mpi::source_site, i, i, + mpi::intracomm, MPI_STATUS_IGNORE); +#endif + //now write the source_banke data again. + for (vector::iterator _site=source_bank->begin(); _site!=source_bank->end();_site++){ + //particle is now at the iterator + //write it to the mcpl-file + mcpl_particle_t p; + p.position[0]=_site->r.x; + p.position[1]=_site->r.y; + p.position[2]=_site->r.z; + + p.direction[0]=_site->u.x; + p.direction[1]=_site->u.y; + p.direction[2]=_site->u.x; + + //mcpl stores kinetic energy in MeV + p.ekin=_site->E*1e-6; + + p.time=_site->time*1e3; + + p.weight=_site->wgt; + + switch(_site->particle){ + case ParticleType::neutron: + p.pdgcode=2112; + break; + case ParticleType::photon: + p.pdgcode=22; + break; + case ParticleType::electron: + p.pdgcode=11; + break; + case ParticleType::positron: + p.pdgcode=-11; + break; + } + + mcpl_add_particle(file_id,&p); + } + } + } else { +#ifdef OPENMC_MPI + MPI_Send(source_bank->data(), count_size, mpi::source_site, 0, mpi::rank, + mpi::intracomm); +#endif + } + +} + + // Determine member names of a compound HDF5 datatype std::string dtype_member_names(hid_t dtype_id) { From be09b442fbfc41d029ed0eccef87ea25477f40aa Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 6 Sep 2022 09:11:41 +0200 Subject: [PATCH 033/265] allow electrons and positrons as well --- src/source.cpp | 29 ++++++++++++++++++++--------- 1 file changed, 20 insertions(+), 9 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 82978f1030..e7c944cb58 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -383,19 +383,30 @@ SourceSite MCPLFileSource::read_single_particle() const { SourceSite omc_particle_; const mcpl_particle_t *mcpl_particle; - //extract particle from mcpl-file + // extract particle from mcpl-file mcpl_particle=mcpl_read(mcpl_file); - // check if it is a neutron or a photon. otherwise skip - while ( mcpl_particle->pdgcode!=2112 && mcpl_particle->pdgcode!=22 ) { + // check if it is a neutron, photon, electron, or positron. Otherwise skip. + int pdg=mcpl_particle->pdgcode; + while ( pdg!=2112 && pdg!=22 && pdg!=11 && pdg!=-11) { mcpl_particle=mcpl_read(mcpl_file); - //should check for file exhaustion This could happen if particles are other than - //neutrons or photons + pdg=mcpl_particle->pdgcode; + //should check for file exhaustion. This could happen if particles are other than + //neutrons, photons, electrons, or positrons. } - if(mcpl_particle->pdgcode==2112) { - omc_particle_.particle=ParticleType::neutron; - } else if (mcpl_particle->pdgcode==22) { - omc_particle_.particle=ParticleType::photon; + switch(pdg){ + case 2112: + omc_particle_.particle=ParticleType::neutron; + break; + case 22: + omc_particle_.particle=ParticleType::photon; + break; + case 11: + omc_particle_.particle=ParticleType::electron; + break; + case -11: + omc_particle_.particle=ParticleType::positron; + break; } //particle is good, convert to openmc-formalism From 4e5ba4b4601209f389c394cd3747891e76b43f1c Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 6 Sep 2022 09:12:01 +0200 Subject: [PATCH 034/265] expose a python function to check for mcpl --- openmc/lib/__init__.py | 3 +++ src/source.cpp | 6 ++++++ 2 files changed, 9 insertions(+) diff --git a/openmc/lib/__init__.py b/openmc/lib/__init__.py index c14b0d9c28..1e337fc073 100644 --- a/openmc/lib/__init__.py +++ b/openmc/lib/__init__.py @@ -48,6 +48,9 @@ def _coord_levels(): def _libmesh_enabled(): return c_bool.in_dll(_dll, "LIBMESH_ENABLED").value +def _mcpl_enabled(): + return c_bool.in_dll(_dll, "MCPL_ENABLED").value + from .error import * from .core import * from .nuclide import * diff --git a/src/source.cpp b/src/source.cpp index e7c944cb58..9b426c3cfa 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -41,6 +41,12 @@ namespace openmc { // Global variables //============================================================================== +#ifdef OPENMC_MCPL +const bool MCPL_ENABLED = true; +#else +const bool MCPL_ENABLED = false; +#endif + namespace model { vector> external_sources; From 32e71395b3ad44ecc7080ba39d4b920adfb88702 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 6 Sep 2022 23:06:19 +0200 Subject: [PATCH 035/265] add a trigger to simulation control --- src/simulation.cpp | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/simulation.cpp b/src/simulation.cpp index b70535c330..05c8c04508 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -406,6 +406,13 @@ void finalize_batch() auto filename = settings::path_output + "surface_source.h5"; write_source_point(filename.c_str(), true); } + + if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ + auto filename = settings::path_output + ".mcpl"; + write_mcplt_source_point(filename.c_str(), true); + } + + } void initialize_generation() From ab665fb4563be28b6cfd365634049c90f133f485 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Fri, 15 Jul 2022 21:35:59 +0200 Subject: [PATCH 036/265] fix typo Co-authored-by: Paul Romano --- CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 6af9643cdb..be56f1c12f 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -36,7 +36,7 @@ option(OPENMC_ENABLE_COVERAGE "Compile with coverage analysis flags" option(OPENMC_USE_DAGMC "Enable support for DAGMC (CAD) geometry" OFF) option(OPENMC_USE_LIBMESH "Enable support for libMesh unstructured mesh tallies" OFF) option(OPENMC_USE_MPI "Enable MPI" OFF) -option(OPENMC_USE_MCPL "Enable MPCPL" OFF) +option(OPENMC_USE_MCPL "Enable MCPL" OFF) #=============================================================================== # Set a default build configuration if not explicitly specified From 71568d4f4bffa21a2a9c26725619cd180a9a59ff Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 9 Aug 2022 08:12:19 +0200 Subject: [PATCH 037/265] refactor MCPL file read part of FileSource A new constructor is added to FileSource that reads from a given MCPL-file. --- include/openmc/source.h | 30 ++--------- src/settings.cpp | 2 +- src/source.cpp | 116 +++++++++++++++++----------------------- 3 files changed, 53 insertions(+), 95 deletions(-) diff --git a/include/openmc/source.h b/include/openmc/source.h index 4d7ec104aa..5c2dae9311 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -96,7 +96,9 @@ class FileSource : public Source { public: // Constructors explicit FileSource(std::string path); - +#ifdef OPENMC_MCPL + explicit FileSource(mcpl_file_t mcpl_file); +#endif // Methods SourceSite sample(uint64_t* seed) const override; @@ -104,32 +106,6 @@ private: vector sites_; //!< Source sites from a file }; -#ifdef OPENMC_MCPL -//============================================================================== -// MCPL-file input source -//============================================================================== -class MCPLFileSource : public Source { -public: - // Constructors, destructors - MCPLFileSource(std::string path); - ~MCPLFileSource(); - - // Methods - //! Sample from the external source distribution - //! \param[inout] seed Pseudorandom seed pointer - //! \return Site read from MCPL-file - SourceSite sample(uint64_t* seed) const; - -private: - SourceSite read_single_particle() const; - void read_source_bank(vector &sites_); - - vector sites_; //!(path)); + model::external_sources.push_back(make_unique(mcpl_open_file(path.c_str()))); #endif } else if (check_for_node(node, "library")) { // Get shared library path and parameters diff --git a/src/source.cpp b/src/source.cpp index 9b426c3cfa..9cdf1632bf 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -283,6 +283,54 @@ FileSource::FileSource(std::string path) file_close(file_id); } +#ifdef OPENMC_MCPL +FileSource::FileSource(mcpl_file_t mcpl_file) +{ + //do checks on the mcpl_file to see if particles are many enough. + // should model this on the example source shown in the docs. + size_t n_sites=mcpl_hdr_nparticles(mcpl_file); + + sites_.resize(n_sites); + for (int i=0;ipdgcode!=2112 && mcpl_particle->pdgcode!=22 ) { + mcpl_particle=mcpl_read(mcpl_file); + //should check for file exhaustion This could happen if particles are other than + //neutrons or photons + } + + if(mcpl_particle->pdgcode==2112) { + site_.particle=ParticleType::neutron; + } else if (mcpl_particle->pdgcode==22) { + site_.particle=ParticleType::photon; + } + + //particle is good, convert to openmc-formalism + site_.r.x=mcpl_particle->position[0]; + site_.r.y=mcpl_particle->position[1]; + site_.r.z=mcpl_particle->position[2]; + + site_.u.x=mcpl_particle->direction[0]; + site_.u.y=mcpl_particle->direction[1]; + site_.u.z=mcpl_particle->direction[2]; + + //mcpl stores kinetic energy in MeV + site_.E=mcpl_particle->ekin*1e6; + //mcpl stores time in ms + site_.time=mcpl_particle->time*1e-3; + site_.wgt=mcpl_particle->weight; + site_.delayed_group=0; + sites_[i]=site_; + } + mcpl_close_file(mcpl_file); +} +#endif //OPENMC_MCPL + SourceSite FileSource::sample(uint64_t* seed) const { size_t i_site = sites_.size() * prn(seed); @@ -366,73 +414,7 @@ MCPLFileSource::MCPLFileSource(std::string path) read_source_bank(sites_); } - -MCPLFileSource::~MCPLFileSource(){ - mcpl_close_file(mcpl_file); -} - -SourceSite MCPLFileSource::sample(uint64_t* seed) const -{ - size_t i_site = sites_.size() * prn(seed); - return sites_[i_site]; -} - -void MCPLFileSource::read_source_bank(vector &sites_) -{ - sites_.resize(n_sites); - for (int i=0;ipdgcode; - while ( pdg!=2112 && pdg!=22 && pdg!=11 && pdg!=-11) { - mcpl_particle=mcpl_read(mcpl_file); - pdg=mcpl_particle->pdgcode; - //should check for file exhaustion. This could happen if particles are other than - //neutrons, photons, electrons, or positrons. - } - - switch(pdg){ - case 2112: - omc_particle_.particle=ParticleType::neutron; - break; - case 22: - omc_particle_.particle=ParticleType::photon; - break; - case 11: - omc_particle_.particle=ParticleType::electron; - break; - case -11: - omc_particle_.particle=ParticleType::positron; - break; - } - - //particle is good, convert to openmc-formalism - omc_particle_.r.x=mcpl_particle->position[0]; - omc_particle_.r.y=mcpl_particle->position[1]; - omc_particle_.r.z=mcpl_particle->position[2]; - - omc_particle_.u.x=mcpl_particle->direction[0]; - omc_particle_.u.y=mcpl_particle->direction[1]; - omc_particle_.u.z=mcpl_particle->direction[2]; - - //mcpl stores kinetic energy in MeV - omc_particle_.E=mcpl_particle->ekin*1e6; - //mcpl stores time in ms - omc_particle_.time=mcpl_particle->time*1e-3; - omc_particle_.wgt=mcpl_particle->weight; - omc_particle_.delayed_group=0; - return omc_particle_; -} -#endif //OPENMC_MCPL +#endif //============================================================================== // Non-member functions From 73a391daef86e3a93c0c7180d9ff7f670afff240 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 6 Sep 2022 02:22:21 +0200 Subject: [PATCH 038/265] wip add MCPL-out to openmc code for writing a source_bank/point compiles but is untested --- include/openmc/state_point.h | 9 +++ src/state_point.cpp | 125 +++++++++++++++++++++++++++++++++++ 2 files changed, 134 insertions(+) diff --git a/include/openmc/state_point.h b/include/openmc/state_point.h index 5ada2bf88d..2d92c935a6 100644 --- a/include/openmc/state_point.h +++ b/include/openmc/state_point.h @@ -9,6 +9,10 @@ #include "openmc/particle.h" #include "openmc/vector.h" +#ifdef OPENMC_MCPL +#include +#endif + namespace openmc { void load_state_point(); @@ -21,5 +25,10 @@ void write_tally_results_nr(hid_t file_id); void restart_set_keff(); void write_unstructured_mesh_results(); +#ifdef OPENMC_MCPL +void write_mcpl_source_point(const char *filename_, bool surf_source_bank = false); +void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank); +#endif + } // namespace openmc #endif // OPENMC_STATE_POINT_H diff --git a/src/state_point.cpp b/src/state_point.cpp index 9ea0459153..babd670a2d 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -28,6 +28,10 @@ #include "openmc/timer.h" #include "openmc/vector.h" +#ifdef OPENMC_MCPL +#include +#endif + namespace openmc { extern "C" int openmc_statepoint_write(const char* filename, bool* write_source) @@ -598,6 +602,45 @@ void write_source_point(const char* filename, bool surf_source_bank) file_close(file_id); } +void write_mcpl_point(const char *filename, bool surf_source_bank) +{ + std::string filename_; + if (filename) { + filename_ = filename; + } else { + // Determine width for zero padding + int w = std::to_string(settings::n_max_batches).size(); + + filename_ = fmt::format("{0}source.{1:0{2}}.mcpl", settings::path_output, + simulation::current_batch, w); + } + + mcpl_outfile_t file_id; + + std::string line; + if (mpi::master) { + // this must be rewritten: file_open is h5-specific + file_id = mcpl_create_outfile(filename_.c_str()); + //write_attribute(file_id, "filetype", "source"); + //write header stuff (oopy in xml-files as binary blobs for instance)) + if (VERSION_DEV){ + line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}-development"); + } else { + line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}"); + } + mcpl_hdr_set_srcname(file_id,line.c_str()); + } + + write_mcpl_source_bank(file_id, surf_source_bank); + + if (mpi::master) { + //change this - this is h5 specific + mcpl_closeandgzip_outfile(file_id); + } + +} + + void write_source_bank(hid_t group_id, bool surf_source_bank) { hid_t banktype = h5banktype(); @@ -714,6 +757,88 @@ void write_source_bank(hid_t group_id, bool surf_source_bank) H5Tclose(banktype); } +void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) +{ + int64_t dims_size = settings::n_particles; + int64_t count_size = simulation::work_per_rank; + + // Set vectors for source bank and starting bank index of each process + vector* bank_index = &simulation::work_index; + vector* source_bank = &simulation::source_bank; + vector surf_source_index_vector; + vector surf_source_bank_vector; + + if(surf_source_bank) { + surf_source_index_vector = calculate_surf_source_size(); + dims_size = surf_source_index_vector[mpi::n_procs]; + count_size = simulation::surf_source_bank.size(); + + bank_index = &surf_source_index_vector; + + // Copy data in a SharedArray into a vector. + surf_source_bank_vector.resize(count_size); + surf_source_bank_vector.assign(simulation::surf_source_bank.data(), + simulation::surf_source_bank.data() + count_size); + source_bank = &surf_source_bank_vector; + } + + if (mpi::master) { + //write particles from the master node + //loop over the other nodes and receive data - then write those. + for (int i = 0; i < mpi::n_procs; ++i) { +#ifdef OPENMC_MPI + if (i>0) + MPI_Recv(source_bank->data(), count[0], mpi::source_site, i, i, + mpi::intracomm, MPI_STATUS_IGNORE); +#endif + //now write the source_banke data again. + for (vector::iterator _site=source_bank->begin(); _site!=source_bank->end();_site++){ + //particle is now at the iterator + //write it to the mcpl-file + mcpl_particle_t p; + p.position[0]=_site->r.x; + p.position[1]=_site->r.y; + p.position[2]=_site->r.z; + + p.direction[0]=_site->u.x; + p.direction[1]=_site->u.y; + p.direction[2]=_site->u.x; + + //mcpl stores kinetic energy in MeV + p.ekin=_site->E*1e-6; + + p.time=_site->time*1e3; + + p.weight=_site->wgt; + + switch(_site->particle){ + case ParticleType::neutron: + p.pdgcode=2112; + break; + case ParticleType::photon: + p.pdgcode=22; + break; + case ParticleType::electron: + p.pdgcode=11; + break; + case ParticleType::positron: + p.pdgcode=-11; + break; + } + + mcpl_add_particle(file_id,&p); + } + } + } else { +#ifdef OPENMC_MPI + MPI_Send(source_bank->data(), count_size, mpi::source_site, 0, mpi::rank, + mpi::intracomm); +#endif + } + +} + + // Determine member names of a compound HDF5 datatype std::string dtype_member_names(hid_t dtype_id) { From d07223bf681e5d6e1d7cbde0dac6f97059a12767 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 6 Sep 2022 23:06:19 +0200 Subject: [PATCH 039/265] add a trigger to simulation control --- src/simulation.cpp | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/simulation.cpp b/src/simulation.cpp index b70535c330..05c8c04508 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -406,6 +406,13 @@ void finalize_batch() auto filename = settings::path_output + "surface_source.h5"; write_source_point(filename.c_str(), true); } + + if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ + auto filename = settings::path_output + ".mcpl"; + write_mcplt_source_point(filename.c_str(), true); + } + + } void initialize_generation() From 55f2be19e6c0ef51d7a7946ac15a9f2df51da6da Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Fri, 16 Sep 2022 16:07:22 +0200 Subject: [PATCH 040/265] refactor MCPL file read part of FileSource A new constructor is added to FileSource that reads from a given MCPL-file. --- src/source.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/source.cpp b/src/source.cpp index 626d02f9d7..21522438cf 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -426,6 +426,7 @@ MCPLFileSource::MCPLFileSource(std::string path) read_source_bank(sites_); } +<<<<<<< HEAD MCPLFileSource::~MCPLFileSource(){ mcpl_close_file(mcpl_file); @@ -495,6 +496,9 @@ SourceSite MCPLFileSource::read_single_particle() const #endif //OPENMC_MCPL ======= >>>>>>> 380cfc150b449ef56debb5261caa010a52c42bdd +======= +#endif +>>>>>>> 71568d4f4 (refactor MCPL file read part of FileSource) //============================================================================== // Non-member functions From f0af56b181555f52d05f245240846f4ce8eadcaa Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 6 Sep 2022 02:22:21 +0200 Subject: [PATCH 041/265] wip add MCPL-out to openmc code for writing a source_bank/point compiles but is untested --- include/openmc/state_point.h | 9 +++ src/state_point.cpp | 125 +++++++++++++++++++++++++++++++++++ 2 files changed, 134 insertions(+) diff --git a/include/openmc/state_point.h b/include/openmc/state_point.h index 5ada2bf88d..2d92c935a6 100644 --- a/include/openmc/state_point.h +++ b/include/openmc/state_point.h @@ -9,6 +9,10 @@ #include "openmc/particle.h" #include "openmc/vector.h" +#ifdef OPENMC_MCPL +#include +#endif + namespace openmc { void load_state_point(); @@ -21,5 +25,10 @@ void write_tally_results_nr(hid_t file_id); void restart_set_keff(); void write_unstructured_mesh_results(); +#ifdef OPENMC_MCPL +void write_mcpl_source_point(const char *filename_, bool surf_source_bank = false); +void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank); +#endif + } // namespace openmc #endif // OPENMC_STATE_POINT_H diff --git a/src/state_point.cpp b/src/state_point.cpp index 9ea0459153..babd670a2d 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -28,6 +28,10 @@ #include "openmc/timer.h" #include "openmc/vector.h" +#ifdef OPENMC_MCPL +#include +#endif + namespace openmc { extern "C" int openmc_statepoint_write(const char* filename, bool* write_source) @@ -598,6 +602,45 @@ void write_source_point(const char* filename, bool surf_source_bank) file_close(file_id); } +void write_mcpl_point(const char *filename, bool surf_source_bank) +{ + std::string filename_; + if (filename) { + filename_ = filename; + } else { + // Determine width for zero padding + int w = std::to_string(settings::n_max_batches).size(); + + filename_ = fmt::format("{0}source.{1:0{2}}.mcpl", settings::path_output, + simulation::current_batch, w); + } + + mcpl_outfile_t file_id; + + std::string line; + if (mpi::master) { + // this must be rewritten: file_open is h5-specific + file_id = mcpl_create_outfile(filename_.c_str()); + //write_attribute(file_id, "filetype", "source"); + //write header stuff (oopy in xml-files as binary blobs for instance)) + if (VERSION_DEV){ + line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}-development"); + } else { + line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}"); + } + mcpl_hdr_set_srcname(file_id,line.c_str()); + } + + write_mcpl_source_bank(file_id, surf_source_bank); + + if (mpi::master) { + //change this - this is h5 specific + mcpl_closeandgzip_outfile(file_id); + } + +} + + void write_source_bank(hid_t group_id, bool surf_source_bank) { hid_t banktype = h5banktype(); @@ -714,6 +757,88 @@ void write_source_bank(hid_t group_id, bool surf_source_bank) H5Tclose(banktype); } +void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) +{ + int64_t dims_size = settings::n_particles; + int64_t count_size = simulation::work_per_rank; + + // Set vectors for source bank and starting bank index of each process + vector* bank_index = &simulation::work_index; + vector* source_bank = &simulation::source_bank; + vector surf_source_index_vector; + vector surf_source_bank_vector; + + if(surf_source_bank) { + surf_source_index_vector = calculate_surf_source_size(); + dims_size = surf_source_index_vector[mpi::n_procs]; + count_size = simulation::surf_source_bank.size(); + + bank_index = &surf_source_index_vector; + + // Copy data in a SharedArray into a vector. + surf_source_bank_vector.resize(count_size); + surf_source_bank_vector.assign(simulation::surf_source_bank.data(), + simulation::surf_source_bank.data() + count_size); + source_bank = &surf_source_bank_vector; + } + + if (mpi::master) { + //write particles from the master node + //loop over the other nodes and receive data - then write those. + for (int i = 0; i < mpi::n_procs; ++i) { +#ifdef OPENMC_MPI + if (i>0) + MPI_Recv(source_bank->data(), count[0], mpi::source_site, i, i, + mpi::intracomm, MPI_STATUS_IGNORE); +#endif + //now write the source_banke data again. + for (vector::iterator _site=source_bank->begin(); _site!=source_bank->end();_site++){ + //particle is now at the iterator + //write it to the mcpl-file + mcpl_particle_t p; + p.position[0]=_site->r.x; + p.position[1]=_site->r.y; + p.position[2]=_site->r.z; + + p.direction[0]=_site->u.x; + p.direction[1]=_site->u.y; + p.direction[2]=_site->u.x; + + //mcpl stores kinetic energy in MeV + p.ekin=_site->E*1e-6; + + p.time=_site->time*1e3; + + p.weight=_site->wgt; + + switch(_site->particle){ + case ParticleType::neutron: + p.pdgcode=2112; + break; + case ParticleType::photon: + p.pdgcode=22; + break; + case ParticleType::electron: + p.pdgcode=11; + break; + case ParticleType::positron: + p.pdgcode=-11; + break; + } + + mcpl_add_particle(file_id,&p); + } + } + } else { +#ifdef OPENMC_MPI + MPI_Send(source_bank->data(), count_size, mpi::source_site, 0, mpi::rank, + mpi::intracomm); +#endif + } + +} + + // Determine member names of a compound HDF5 datatype std::string dtype_member_names(hid_t dtype_id) { From 04c8ffc81c7ed7ced0c3525b5ec13f15f8fc079c Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 6 Sep 2022 23:06:19 +0200 Subject: [PATCH 042/265] add a trigger to simulation control --- src/simulation.cpp | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/simulation.cpp b/src/simulation.cpp index b70535c330..05c8c04508 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -406,6 +406,13 @@ void finalize_batch() auto filename = settings::path_output + "surface_source.h5"; write_source_point(filename.c_str(), true); } + + if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ + auto filename = settings::path_output + ".mcpl"; + write_mcplt_source_point(filename.c_str(), true); + } + + } void initialize_generation() From 314f3dbbab75104f217d1e20e2146ced28108707 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 4 Oct 2022 10:11:06 +0200 Subject: [PATCH 043/265] do not define these functions if no MCPL present --- src/state_point.cpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index babd670a2d..5b00f302dc 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -602,6 +602,7 @@ void write_source_point(const char* filename, bool surf_source_bank) file_close(file_id); } +#ifdef OPENMC_MCPL void write_mcpl_point(const char *filename, bool surf_source_bank) { std::string filename_; @@ -639,7 +640,7 @@ void write_mcpl_point(const char *filename, bool surf_source_bank) } } - +#endif void write_source_bank(hid_t group_id, bool surf_source_bank) { @@ -757,6 +758,7 @@ void write_source_bank(hid_t group_id, bool surf_source_bank) H5Tclose(banktype); } +#ifdef OPENMC_MCPL void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) { int64_t dims_size = settings::n_particles; @@ -837,7 +839,7 @@ void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) } } - +#endif // Determine member names of a compound HDF5 datatype std::string dtype_member_names(hid_t dtype_id) From 2de20231ad584fa7a77a5b135c82f6e995671bcc Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 10:56:36 +0200 Subject: [PATCH 044/265] use find_package instead - MCPL now supports this --- CMakeLists.txt | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index be56f1c12f..98dc4fcaf0 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -128,6 +128,13 @@ if(${HDF5_VERSION} VERSION_GREATER_EQUAL 1.12.0) list(APPEND cxxflags -DH5Oget_info_by_idx_vers=1 -DH5O_info_t_vers=1) endif() +#=============================================================================== +# MCPL +#=============================================================================== +if (OPENMC_USE_MCPL) + find_package(MCPL REQUIRED) +endif() + #=============================================================================== # Set compile/link flags based on which compiler is being used #=============================================================================== @@ -155,10 +162,6 @@ if(OPENMC_ENABLE_COVERAGE) list(APPEND ldflags --coverage) endif() -if(OPENMC_USE_MCPL) - list(APPEND ldflags -lmcpl) -endif() - # Show flags being used message(STATUS "OpenMC C++ flags: ${cxxflags}") message(STATUS "OpenMC Linker flags: ${ldflags}") @@ -413,10 +416,6 @@ endif() if (OPENMC_USE_MPI) target_compile_definitions(libopenmc PUBLIC -DOPENMC_MPI) endif() -if(OPENMC_USE_MCPL) - target_compile_definitions(libopenmc PUBLIC -DOPENMC_MCPL) -endif() - # Set git SHA1 hash as a compile definition if(GIT_FOUND) @@ -460,6 +459,11 @@ if (OPENMC_USE_MPI) target_link_libraries(libopenmc MPI::MPI_CXX) endif() +if (OPENMC_USE_MCPL) + target_compile_definitions(libopenmc PUBLIC OPENMC_MCPL) + target_link_libraries(libopenmc MCPL::mcpl) +endif() + #=============================================================================== # openmc executable #=============================================================================== From 7418cb99dd7c22e80532dcc46a9d2c4c04ceb63d Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 10:59:02 +0200 Subject: [PATCH 045/265] add mcpl-output settings --- include/openmc/settings.h | 1 + src/settings.cpp | 8 +++++++- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/include/openmc/settings.h b/include/openmc/settings.h index 1e061b235b..66825867d8 100644 --- a/include/openmc/settings.h +++ b/include/openmc/settings.h @@ -48,6 +48,7 @@ extern bool source_latest; //!< write latest source at each batch? extern bool source_separate; //!< write source to separate file? extern bool source_write; //!< write source in HDF5 files? extern bool surf_source_write; //!< write surface source file? +extern bool surf_mcpl_write; //!< write surface mcpl file? extern bool surf_source_read; //!< read surface source file? extern bool survival_biasing; //!< use survival biasing? extern bool temperature_multipole; //!< use multipole data? diff --git a/src/settings.cpp b/src/settings.cpp index 11dd96e025..d1762596c6 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -61,6 +61,7 @@ bool source_latest {false}; bool source_separate {false}; bool source_write {true}; bool surf_source_write {false}; +bool surf_mcpl_write {false}; bool surf_source_read {false}; bool survival_biasing {false}; bool temperature_multipole {false}; @@ -682,9 +683,14 @@ void read_settings_xml() max_surface_particles = std::stoll(get_node_value(node_ssw, "max_particles")); } +#ifdef OPENMC_MCPL + if(check_for_node(node_ssw, "mcpl")){ + surf_mcpl_write=true; + } +#endif } - // If source is not seperate and is to be written out in the statepoint file, + // If source is not separate and is to be written out in the statepoint file, // make sure that the sourcepoint batch numbers are contained in the // statepoint list if (!source_separate) { From 172c518f0e161d0176385c67d3717ad9fb229038 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 10:59:28 +0200 Subject: [PATCH 046/265] fix typo --- src/simulation.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/simulation.cpp b/src/simulation.cpp index 05c8c04508..353ef99265 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -409,7 +409,7 @@ void finalize_batch() if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ auto filename = settings::path_output + ".mcpl"; - write_mcplt_source_point(filename.c_str(), true); + write_mcpl_source_point(filename.c_str(), true); } From 83e2921034f5c448d500b93634999cdb3f350e0b Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 11:00:39 +0200 Subject: [PATCH 047/265] add cond. compilation guards for MCPL functions --- src/state_point.cpp | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index babd670a2d..7c1a454476 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -602,7 +602,8 @@ void write_source_point(const char* filename, bool surf_source_bank) file_close(file_id); } -void write_mcpl_point(const char *filename, bool surf_source_bank) +#ifdef OPENMC_MCPL +void write_mcpl_source_point(const char *filename, bool surf_source_bank) { std::string filename_; if (filename) { @@ -639,7 +640,7 @@ void write_mcpl_point(const char *filename, bool surf_source_bank) } } - +#endif void write_source_bank(hid_t group_id, bool surf_source_bank) { @@ -757,6 +758,7 @@ void write_source_bank(hid_t group_id, bool surf_source_bank) H5Tclose(banktype); } +#ifdef OPENMC_MCPL void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) { int64_t dims_size = settings::n_particles; @@ -837,7 +839,7 @@ void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) } } - +#endif // Determine member names of a compound HDF5 datatype std::string dtype_member_names(hid_t dtype_id) From 5e82bb2e1f1b2857375566f98669be6c93b22638 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 6 Sep 2022 09:12:01 +0200 Subject: [PATCH 048/265] expose a python function to check for mcpl --- openmc/lib/__init__.py | 3 +++ src/source.cpp | 6 ++++++ 2 files changed, 9 insertions(+) diff --git a/openmc/lib/__init__.py b/openmc/lib/__init__.py index c14b0d9c28..1e337fc073 100644 --- a/openmc/lib/__init__.py +++ b/openmc/lib/__init__.py @@ -48,6 +48,9 @@ def _coord_levels(): def _libmesh_enabled(): return c_bool.in_dll(_dll, "LIBMESH_ENABLED").value +def _mcpl_enabled(): + return c_bool.in_dll(_dll, "MCPL_ENABLED").value + from .error import * from .core import * from .nuclide import * diff --git a/src/source.cpp b/src/source.cpp index 49e51c4b16..eace931d63 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -41,6 +41,12 @@ namespace openmc { // Global variables //============================================================================== +#ifdef OPENMC_MCPL +const bool MCPL_ENABLED = true; +#else +const bool MCPL_ENABLED = false; +#endif + namespace model { vector> external_sources; From 6038555def28547a0f392f0eeded8d8d49269d51 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 6 Sep 2022 02:22:21 +0200 Subject: [PATCH 049/265] wip add MCPL-out to openmc code for writing a source_bank/point compiles but is untested --- include/openmc/state_point.h | 9 +++ src/state_point.cpp | 125 +++++++++++++++++++++++++++++++++++ 2 files changed, 134 insertions(+) diff --git a/include/openmc/state_point.h b/include/openmc/state_point.h index 5ada2bf88d..2d92c935a6 100644 --- a/include/openmc/state_point.h +++ b/include/openmc/state_point.h @@ -9,6 +9,10 @@ #include "openmc/particle.h" #include "openmc/vector.h" +#ifdef OPENMC_MCPL +#include +#endif + namespace openmc { void load_state_point(); @@ -21,5 +25,10 @@ void write_tally_results_nr(hid_t file_id); void restart_set_keff(); void write_unstructured_mesh_results(); +#ifdef OPENMC_MCPL +void write_mcpl_source_point(const char *filename_, bool surf_source_bank = false); +void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank); +#endif + } // namespace openmc #endif // OPENMC_STATE_POINT_H diff --git a/src/state_point.cpp b/src/state_point.cpp index 9ea0459153..babd670a2d 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -28,6 +28,10 @@ #include "openmc/timer.h" #include "openmc/vector.h" +#ifdef OPENMC_MCPL +#include +#endif + namespace openmc { extern "C" int openmc_statepoint_write(const char* filename, bool* write_source) @@ -598,6 +602,45 @@ void write_source_point(const char* filename, bool surf_source_bank) file_close(file_id); } +void write_mcpl_point(const char *filename, bool surf_source_bank) +{ + std::string filename_; + if (filename) { + filename_ = filename; + } else { + // Determine width for zero padding + int w = std::to_string(settings::n_max_batches).size(); + + filename_ = fmt::format("{0}source.{1:0{2}}.mcpl", settings::path_output, + simulation::current_batch, w); + } + + mcpl_outfile_t file_id; + + std::string line; + if (mpi::master) { + // this must be rewritten: file_open is h5-specific + file_id = mcpl_create_outfile(filename_.c_str()); + //write_attribute(file_id, "filetype", "source"); + //write header stuff (oopy in xml-files as binary blobs for instance)) + if (VERSION_DEV){ + line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}-development"); + } else { + line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}"); + } + mcpl_hdr_set_srcname(file_id,line.c_str()); + } + + write_mcpl_source_bank(file_id, surf_source_bank); + + if (mpi::master) { + //change this - this is h5 specific + mcpl_closeandgzip_outfile(file_id); + } + +} + + void write_source_bank(hid_t group_id, bool surf_source_bank) { hid_t banktype = h5banktype(); @@ -714,6 +757,88 @@ void write_source_bank(hid_t group_id, bool surf_source_bank) H5Tclose(banktype); } +void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) +{ + int64_t dims_size = settings::n_particles; + int64_t count_size = simulation::work_per_rank; + + // Set vectors for source bank and starting bank index of each process + vector* bank_index = &simulation::work_index; + vector* source_bank = &simulation::source_bank; + vector surf_source_index_vector; + vector surf_source_bank_vector; + + if(surf_source_bank) { + surf_source_index_vector = calculate_surf_source_size(); + dims_size = surf_source_index_vector[mpi::n_procs]; + count_size = simulation::surf_source_bank.size(); + + bank_index = &surf_source_index_vector; + + // Copy data in a SharedArray into a vector. + surf_source_bank_vector.resize(count_size); + surf_source_bank_vector.assign(simulation::surf_source_bank.data(), + simulation::surf_source_bank.data() + count_size); + source_bank = &surf_source_bank_vector; + } + + if (mpi::master) { + //write particles from the master node + //loop over the other nodes and receive data - then write those. + for (int i = 0; i < mpi::n_procs; ++i) { +#ifdef OPENMC_MPI + if (i>0) + MPI_Recv(source_bank->data(), count[0], mpi::source_site, i, i, + mpi::intracomm, MPI_STATUS_IGNORE); +#endif + //now write the source_banke data again. + for (vector::iterator _site=source_bank->begin(); _site!=source_bank->end();_site++){ + //particle is now at the iterator + //write it to the mcpl-file + mcpl_particle_t p; + p.position[0]=_site->r.x; + p.position[1]=_site->r.y; + p.position[2]=_site->r.z; + + p.direction[0]=_site->u.x; + p.direction[1]=_site->u.y; + p.direction[2]=_site->u.x; + + //mcpl stores kinetic energy in MeV + p.ekin=_site->E*1e-6; + + p.time=_site->time*1e3; + + p.weight=_site->wgt; + + switch(_site->particle){ + case ParticleType::neutron: + p.pdgcode=2112; + break; + case ParticleType::photon: + p.pdgcode=22; + break; + case ParticleType::electron: + p.pdgcode=11; + break; + case ParticleType::positron: + p.pdgcode=-11; + break; + } + + mcpl_add_particle(file_id,&p); + } + } + } else { +#ifdef OPENMC_MPI + MPI_Send(source_bank->data(), count_size, mpi::source_site, 0, mpi::rank, + mpi::intracomm); +#endif + } + +} + + // Determine member names of a compound HDF5 datatype std::string dtype_member_names(hid_t dtype_id) { From 2ba7f8d1882cf5e2562b473e233b4ca84ab81080 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 6 Sep 2022 23:06:19 +0200 Subject: [PATCH 050/265] add a trigger to simulation control --- src/simulation.cpp | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/simulation.cpp b/src/simulation.cpp index b70535c330..05c8c04508 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -406,6 +406,13 @@ void finalize_batch() auto filename = settings::path_output + "surface_source.h5"; write_source_point(filename.c_str(), true); } + + if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ + auto filename = settings::path_output + ".mcpl"; + write_mcplt_source_point(filename.c_str(), true); + } + + } void initialize_generation() From 91cd304f0e4fd32eb6df0bdb75dd3f7d169013ce Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 10:56:36 +0200 Subject: [PATCH 051/265] use find_package instead - MCPL now supports this --- CMakeLists.txt | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index be56f1c12f..98dc4fcaf0 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -128,6 +128,13 @@ if(${HDF5_VERSION} VERSION_GREATER_EQUAL 1.12.0) list(APPEND cxxflags -DH5Oget_info_by_idx_vers=1 -DH5O_info_t_vers=1) endif() +#=============================================================================== +# MCPL +#=============================================================================== +if (OPENMC_USE_MCPL) + find_package(MCPL REQUIRED) +endif() + #=============================================================================== # Set compile/link flags based on which compiler is being used #=============================================================================== @@ -155,10 +162,6 @@ if(OPENMC_ENABLE_COVERAGE) list(APPEND ldflags --coverage) endif() -if(OPENMC_USE_MCPL) - list(APPEND ldflags -lmcpl) -endif() - # Show flags being used message(STATUS "OpenMC C++ flags: ${cxxflags}") message(STATUS "OpenMC Linker flags: ${ldflags}") @@ -413,10 +416,6 @@ endif() if (OPENMC_USE_MPI) target_compile_definitions(libopenmc PUBLIC -DOPENMC_MPI) endif() -if(OPENMC_USE_MCPL) - target_compile_definitions(libopenmc PUBLIC -DOPENMC_MCPL) -endif() - # Set git SHA1 hash as a compile definition if(GIT_FOUND) @@ -460,6 +459,11 @@ if (OPENMC_USE_MPI) target_link_libraries(libopenmc MPI::MPI_CXX) endif() +if (OPENMC_USE_MCPL) + target_compile_definitions(libopenmc PUBLIC OPENMC_MCPL) + target_link_libraries(libopenmc MCPL::mcpl) +endif() + #=============================================================================== # openmc executable #=============================================================================== From 9b58c2f6dc93c4c51ce6ee7a26e7ffc645434020 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 10:59:02 +0200 Subject: [PATCH 052/265] add mcpl-output settings --- include/openmc/settings.h | 1 + src/settings.cpp | 8 +++++++- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/include/openmc/settings.h b/include/openmc/settings.h index 1e061b235b..66825867d8 100644 --- a/include/openmc/settings.h +++ b/include/openmc/settings.h @@ -48,6 +48,7 @@ extern bool source_latest; //!< write latest source at each batch? extern bool source_separate; //!< write source to separate file? extern bool source_write; //!< write source in HDF5 files? extern bool surf_source_write; //!< write surface source file? +extern bool surf_mcpl_write; //!< write surface mcpl file? extern bool surf_source_read; //!< read surface source file? extern bool survival_biasing; //!< use survival biasing? extern bool temperature_multipole; //!< use multipole data? diff --git a/src/settings.cpp b/src/settings.cpp index 11dd96e025..d1762596c6 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -61,6 +61,7 @@ bool source_latest {false}; bool source_separate {false}; bool source_write {true}; bool surf_source_write {false}; +bool surf_mcpl_write {false}; bool surf_source_read {false}; bool survival_biasing {false}; bool temperature_multipole {false}; @@ -682,9 +683,14 @@ void read_settings_xml() max_surface_particles = std::stoll(get_node_value(node_ssw, "max_particles")); } +#ifdef OPENMC_MCPL + if(check_for_node(node_ssw, "mcpl")){ + surf_mcpl_write=true; + } +#endif } - // If source is not seperate and is to be written out in the statepoint file, + // If source is not separate and is to be written out in the statepoint file, // make sure that the sourcepoint batch numbers are contained in the // statepoint list if (!source_separate) { From 43538ac2021f36caf0d72e002a119a806aa14b71 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 10:59:28 +0200 Subject: [PATCH 053/265] fix typo --- src/simulation.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/simulation.cpp b/src/simulation.cpp index 05c8c04508..353ef99265 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -409,7 +409,7 @@ void finalize_batch() if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ auto filename = settings::path_output + ".mcpl"; - write_mcplt_source_point(filename.c_str(), true); + write_mcpl_source_point(filename.c_str(), true); } From cba745b28b6e384311393c177456b518b60b4f55 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 11:00:39 +0200 Subject: [PATCH 054/265] add cond. compilation guards for MCPL functions --- src/state_point.cpp | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index babd670a2d..7c1a454476 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -602,7 +602,8 @@ void write_source_point(const char* filename, bool surf_source_bank) file_close(file_id); } -void write_mcpl_point(const char *filename, bool surf_source_bank) +#ifdef OPENMC_MCPL +void write_mcpl_source_point(const char *filename, bool surf_source_bank) { std::string filename_; if (filename) { @@ -639,7 +640,7 @@ void write_mcpl_point(const char *filename, bool surf_source_bank) } } - +#endif void write_source_bank(hid_t group_id, bool surf_source_bank) { @@ -757,6 +758,7 @@ void write_source_bank(hid_t group_id, bool surf_source_bank) H5Tclose(banktype); } +#ifdef OPENMC_MCPL void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) { int64_t dims_size = settings::n_particles; @@ -837,7 +839,7 @@ void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) } } - +#endif // Determine member names of a compound HDF5 datatype std::string dtype_member_names(hid_t dtype_id) From 179df586853b65600518a0ea62526cc2193e0206 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Fri, 16 Sep 2022 16:07:22 +0200 Subject: [PATCH 055/265] refactor MCPL file read part of FileSource A new constructor is added to FileSource that reads from a given MCPL-file. --- src/source.cpp | 73 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) diff --git a/src/source.cpp b/src/source.cpp index eace931d63..bd76969d17 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -391,6 +391,79 @@ CustomSourceWrapper::~CustomSourceWrapper() } +MCPLFileSource::~MCPLFileSource(){ + mcpl_close_file(mcpl_file); +} + +SourceSite MCPLFileSource::sample(uint64_t* seed) const +{ + size_t i_site = sites_.size() * prn(seed); + return sites_[i_site]; +} + +void MCPLFileSource::read_source_bank(vector &sites_) +{ + sites_.resize(n_sites); + for (int i=0;ipdgcode; + while ( pdg!=2112 && pdg!=22 && pdg!=11 && pdg!=-11) { + mcpl_particle=mcpl_read(mcpl_file); + pdg=mcpl_particle->pdgcode; + //should check for file exhaustion. This could happen if particles are other than + //neutrons, photons, electrons, or positrons. + } + + switch(pdg){ + case 2112: + omc_particle_.particle=ParticleType::neutron; + break; + case 22: + omc_particle_.particle=ParticleType::photon; + break; + case 11: + omc_particle_.particle=ParticleType::electron; + break; + case -11: + omc_particle_.particle=ParticleType::positron; + break; + } + + //particle is good, convert to openmc-formalism + omc_particle_.r.x=mcpl_particle->position[0]; + omc_particle_.r.y=mcpl_particle->position[1]; + omc_particle_.r.z=mcpl_particle->position[2]; + + omc_particle_.u.x=mcpl_particle->direction[0]; + omc_particle_.u.y=mcpl_particle->direction[1]; + omc_particle_.u.z=mcpl_particle->direction[2]; + + //mcpl stores kinetic energy in MeV + omc_particle_.E=mcpl_particle->ekin*1e6; + //mcpl stores time in ms + omc_particle_.time=mcpl_particle->time*1e-3; + omc_particle_.wgt=mcpl_particle->weight; + omc_particle_.delayed_group=0; + return omc_particle_; +} +#endif //OPENMC_MCPL +======= +>>>>>>> 380cfc150b449ef56debb5261caa010a52c42bdd +======= +#endif +>>>>>>> 71568d4f4 (refactor MCPL file read part of FileSource) +>>>>>>> 55f2be19e (refactor MCPL file read part of FileSource) + //============================================================================== // Non-member functions //============================================================================== From e3fbeac636c2e9a47599c60e04b2a1ba4d9ba46d Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 6 Sep 2022 02:22:21 +0200 Subject: [PATCH 056/265] wip add MCPL-out to openmc code for writing a source_bank/point compiles but is untested --- src/source.cpp | 6 ------ src/state_point.cpp | 1 + 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index bd76969d17..f205a0a256 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -457,12 +457,6 @@ SourceSite MCPLFileSource::read_single_particle() const return omc_particle_; } #endif //OPENMC_MCPL -======= ->>>>>>> 380cfc150b449ef56debb5261caa010a52c42bdd -======= -#endif ->>>>>>> 71568d4f4 (refactor MCPL file read part of FileSource) ->>>>>>> 55f2be19e (refactor MCPL file read part of FileSource) //============================================================================== // Non-member functions diff --git a/src/state_point.cpp b/src/state_point.cpp index 7c1a454476..31979c0c56 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -642,6 +642,7 @@ void write_mcpl_source_point(const char *filename, bool surf_source_bank) } #endif + void write_source_bank(hid_t group_id, bool surf_source_bank) { hid_t banktype = h5banktype(); From 3b7c4f6d2f141311cba5ad9e5f773b3bc3381852 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 4 Oct 2022 10:11:06 +0200 Subject: [PATCH 057/265] do not define these functions if no MCPL present --- src/state_point.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index 31979c0c56..7c1a454476 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -642,7 +642,6 @@ void write_mcpl_source_point(const char *filename, bool surf_source_bank) } #endif - void write_source_bank(hid_t group_id, bool surf_source_bank) { hid_t banktype = h5banktype(); From 982377b0cdfc573469aad799852a0f2dd50b2e68 Mon Sep 17 00:00:00 2001 From: erkn Date: Wed, 5 Oct 2022 14:31:05 +0200 Subject: [PATCH 058/265] fix misnamed variable and remove accientally committed code --- src/source.cpp | 169 ++----------------------------------------------- 1 file changed, 4 insertions(+), 165 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index e1891c5e94..e35734747f 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -308,16 +308,16 @@ FileSource::FileSource(mcpl_file_t mcpl_file) switch(pdg){ case 2112: - omc_particle_.particle=ParticleType::neutron; + site_.particle=ParticleType::neutron; break; case 22: - omc_particle_.particle=ParticleType::photon; + site_.particle=ParticleType::photon; break; case 11: - omc_particle_.particle=ParticleType::electron; + site_.particle=ParticleType::electron; break; case -11: - omc_particle_.particle=ParticleType::positron; + site_.particle=ParticleType::positron; break; } @@ -401,167 +401,6 @@ CustomSourceWrapper::~CustomSourceWrapper() #endif } -<<<<<<< HEAD -<<<<<<< HEAD -#ifdef OPENMC_MCPL -//=========================================================================== -// Read particles from an MCPL-file -//=========================================================================== -MCPLFileSource::MCPLFileSource(std::string path) -{ - // Check if source file exists - if (!file_exists(path)) { - fatal_error(fmt::format("Source file '{}' does not exist.", path)); - } - - // Read the source from a binary file instead of sampling from some - // assumed source distribution - write_message(6, "Reading mcpl source file from {}",path); - - // Open the mcpl file - mcpl_file = mcpl_open_file(path.c_str()); - - //do checks on the mcpl_file to see if particles are many enough. - // should model this on the example source shown in the docs. - n_sites=mcpl_hdr_nparticles(mcpl_file); - - read_source_bank(sites_); -} -<<<<<<< HEAD - -MCPLFileSource::~MCPLFileSource(){ - mcpl_close_file(mcpl_file); -} - -SourceSite MCPLFileSource::sample(uint64_t* seed) const -{ - size_t i_site = sites_.size() * prn(seed); - return sites_[i_site]; -} - -void MCPLFileSource::read_source_bank(vector &sites_) -{ - sites_.resize(n_sites); - for (int i=0;ipdgcode; - while ( pdg!=2112 && pdg!=22 && pdg!=11 && pdg!=-11) { - mcpl_particle=mcpl_read(mcpl_file); - pdg=mcpl_particle->pdgcode; - //should check for file exhaustion. This could happen if particles are other than - //neutrons, photons, electrons, or positrons. - } - - switch(pdg){ - case 2112: - omc_particle_.particle=ParticleType::neutron; - break; - case 22: - omc_particle_.particle=ParticleType::photon; - break; - case 11: - omc_particle_.particle=ParticleType::electron; - break; - case -11: - omc_particle_.particle=ParticleType::positron; - break; - } - - //particle is good, convert to openmc-formalism - omc_particle_.r.x=mcpl_particle->position[0]; - omc_particle_.r.y=mcpl_particle->position[1]; - omc_particle_.r.z=mcpl_particle->position[2]; - - omc_particle_.u.x=mcpl_particle->direction[0]; - omc_particle_.u.y=mcpl_particle->direction[1]; - omc_particle_.u.z=mcpl_particle->direction[2]; - - //mcpl stores kinetic energy in MeV - omc_particle_.E=mcpl_particle->ekin*1e6; - //mcpl stores time in ms - omc_particle_.time=mcpl_particle->time*1e-3; - omc_particle_.wgt=mcpl_particle->weight; - omc_particle_.delayed_group=0; - return omc_particle_; -} -#endif //OPENMC_MCPL - -MCPLFileSource::~MCPLFileSource(){ - mcpl_close_file(mcpl_file); -} - -SourceSite MCPLFileSource::sample(uint64_t* seed) const -{ - size_t i_site = sites_.size() * prn(seed); - return sites_[i_site]; -} - -void MCPLFileSource::read_source_bank(vector &sites_) -{ - sites_.resize(n_sites); - for (int i=0;ipdgcode; - while ( pdg!=2112 && pdg!=22 && pdg!=11 && pdg!=-11) { - mcpl_particle=mcpl_read(mcpl_file); - pdg=mcpl_particle->pdgcode; - //should check for file exhaustion. This could happen if particles are other than - //neutrons, photons, electrons, or positrons. - } - - switch(pdg){ - case 2112: - omc_particle_.particle=ParticleType::neutron; - break; - case 22: - omc_particle_.particle=ParticleType::photon; - break; - case 11: - omc_particle_.particle=ParticleType::electron; - break; - case -11: - omc_particle_.particle=ParticleType::positron; - break; - } - - //particle is good, convert to openmc-formalism - omc_particle_.r.x=mcpl_particle->position[0]; - omc_particle_.r.y=mcpl_particle->position[1]; - omc_particle_.r.z=mcpl_particle->position[2]; - - omc_particle_.u.x=mcpl_particle->direction[0]; - omc_particle_.u.y=mcpl_particle->direction[1]; - omc_particle_.u.z=mcpl_particle->direction[2]; - - //mcpl stores kinetic energy in MeV - omc_particle_.E=mcpl_particle->ekin*1e6; - //mcpl stores time in ms - omc_particle_.time=mcpl_particle->time*1e-3; - omc_particle_.wgt=mcpl_particle->weight; - omc_particle_.delayed_group=0; - return omc_particle_; -} -#endif //OPENMC_MCPL //============================================================================== // Non-member functions From 12f088a5ce68c639c9772574eb69c4be5de452fe Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Thu, 6 Oct 2022 01:33:21 +0200 Subject: [PATCH 059/265] must have a full filename --- src/simulation.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/simulation.cpp b/src/simulation.cpp index 353ef99265..2c9e7e8566 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -408,7 +408,7 @@ void finalize_batch() } if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ - auto filename = settings::path_output + ".mcpl"; + auto filename = settings::path_output + "surface_source.mcpl"; write_mcpl_source_point(filename.c_str(), true); } From 0706a0eca305c8fc4a0a5cbfb0c5b6e46099753e Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 11 Oct 2022 00:46:32 +0200 Subject: [PATCH 060/265] fix malformed format string --- src/state_point.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index 7c1a454476..e197ee162a 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -625,9 +625,9 @@ void write_mcpl_source_point(const char *filename, bool surf_source_bank) //write_attribute(file_id, "filetype", "source"); //write header stuff (oopy in xml-files as binary blobs for instance)) if (VERSION_DEV){ - line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}-development"); + line=fmt::format("OpenMC {0}.{1}.{2}-development",VERSION_MAJOR,VERSION_MINOR,VERSION_RELEASE); } else { - line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}"); + line=fmt::format("OpenMC {0}.{1}.{2}",VERSION_MAJOR,VERSION_MINOR,VERSION_RELEASE); } mcpl_hdr_set_srcname(file_id,line.c_str()); } From aeadaf0b2f1a59fcd2c3f8cb3ad8fa7dab36e342 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 11 Oct 2022 00:48:44 +0200 Subject: [PATCH 061/265] fix typo causing unit length errors --- src/state_point.cpp | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index e197ee162a..a8a4be034e 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -802,9 +802,11 @@ void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) p.position[1]=_site->r.y; p.position[2]=_site->r.z; + //mcpl requires that the direction vector is unit length + //which is also the case in openmc p.direction[0]=_site->u.x; p.direction[1]=_site->u.y; - p.direction[2]=_site->u.x; + p.direction[2]=_site->u.z; //mcpl stores kinetic energy in MeV p.ekin=_site->E*1e-6; From 72251eb30a996e6aaa9672292a1483c69d53a652 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 11 Oct 2022 02:00:33 +0200 Subject: [PATCH 062/265] enable mcpl surf_source_write in the python layer --- openmc/settings.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/openmc/settings.py b/openmc/settings.py index 2d81216599..45ff0edc68 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -165,6 +165,7 @@ class Settings: banked (int) :max_particles: Maximum number of particles to be banked on surfaces per process (int) + :mcpl: Output in the form of an MCPL-file (bool) survival_biasing : bool Indicate whether survival biasing is to be used tabular_legendre : dict @@ -643,7 +644,7 @@ class Settings: cv.check_type('surface source writing options', surf_source_write, Mapping) for key, value in surf_source_write.items(): cv.check_value('surface source writing key', key, - ('surface_ids', 'max_particles')) + ('surface_ids', 'max_particles', 'mcpl')) if key == 'surface_ids': cv.check_type('surface ids for source banking', value, Iterable, Integral) @@ -655,6 +656,9 @@ class Settings: value, Integral) cv.check_greater_than('maximum particle banks on surfaces per process', value, 0) + elif key == 'mcpl': + cv.check_type('write to an MCPL-format file', value, bool) + self._surf_source_write = surf_source_write @confidence_intervals.setter @@ -1023,6 +1027,9 @@ class Settings: if 'max_particles' in self._surf_source_write: subelement = ET.SubElement(element, "max_particles") subelement.text = str(self._surf_source_write['max_particles']) + if 'mcpl' in self._surf_source_write: + subelement = ET.SubElement(element, "mcpl") + subelement.text = str(self._surf_source_write['mcpl']).lower() def _create_confidence_intervals(self, root): if self._confidence_intervals is not None: From bf0c5d7f9a8d118e4770d4ed4ca184c93aa30896 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 22 Jun 2022 22:50:07 +0200 Subject: [PATCH 063/265] add placeholder skeleton for MCPL-input --- include/openmc/source.h | 19 +++++++++++++++++++ src/source.cpp | 21 +++++++++++++++++++++ 2 files changed, 40 insertions(+) diff --git a/include/openmc/source.h b/include/openmc/source.h index 04b9ff8563..0f1965cb8d 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -110,6 +110,25 @@ private: vector sites_; //!< Source sites from a file }; +//============================================================================== +// MCPL-file input source +//============================================================================== +class MCPLFileSource : public Source { +public: + // Constructors, destructors + MCPLFileSource(std::string path); + ~MCPLFileSource(); + + // Defer implementation to custom source library + SourceSite sample(uint64_t* seed) const override + +private: + vector sites_; //! Date: Thu, 23 Jun 2022 11:34:53 +0200 Subject: [PATCH 064/265] include mcpl header --- src/source.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/source.cpp b/src/source.cpp index 1e84f8334c..7c1184602a 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -33,6 +33,10 @@ #include "openmc/state_point.h" #include "openmc/xml_interface.h" +#ifdef HAS_MCPL +#include +#endif + namespace openmc { //============================================================================== From 249a554980801a3c2cc3be336369c95c0e447436 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Thu, 23 Jun 2022 11:35:46 +0200 Subject: [PATCH 065/265] declarations of MCPL-internals --- include/openmc/source.h | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/include/openmc/source.h b/include/openmc/source.h index 0f1965cb8d..24a3d10aed 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -119,11 +119,20 @@ public: MCPLFileSource(std::string path); ~MCPLFileSource(); - // Defer implementation to custom source library - SourceSite sample(uint64_t* seed) const override + // Properties + ParticleType particle_type() const { return particle_; } + + //! Sample from the external source distribution + //! \param[inout] seed Pseudorandom seed pointer + //! \return Site read from MCPL-file + SourceSite sample(uint64_t* seed) const override; private: + ParticleType particle_ {ParticleType::neutron}; //!< Type of particle emitted vector sites_; //! Date: Thu, 23 Jun 2022 11:37:05 +0200 Subject: [PATCH 066/265] internals of sample and constructor --- src/source.cpp | 51 ++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 47 insertions(+), 4 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 7c1184602a..3dfd007078 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -383,7 +383,7 @@ CustomSourceWrapper::~CustomSourceWrapper() } //=========================================================================== -// Read an MCPL-file +// Read particles from an MCPL-file //=========================================================================== MCPLFileSource::MCPLFileSource(std::string path) { @@ -394,12 +394,55 @@ MCPLFileSource::MCPLFileSource(std::string path) // Read the source from a binary file instead of sampling from some // assumed source distribution - write_message(6, "Reading source file from {}...", path); + write_message(6, "Reading mcpl source file from {}",path); // Open the mcpl file - id_t file_id = mcpl_open(path.c_str) - + mcpl_file = mcpl_open(path.c_str); + //do checks on the mcpl_file to see if particles are many enough. + // should model this on the example source shown in the docs. + uint64_t nparticles=mcpl_hdr_nparticles(mcpl_file); + +} + +MCPLFileSource::~MCPLFilsSource(){ + mcpl_close_file(mcpl_file); +} + +SourceSite MCPLFileSource::sample(uint64_t *seed){ + SourceSite omc_particle; + mcpl_particle *mcpl_particle; + //extract particle from mcpl-file + mcpl_particle=mcpl_reazd(mcplfile); + // check if it is a neutron or a photon. otherwise skip + while ( mcpl_particle->pdgcode!=2112 && mcpl_particle->pdgcode!=22 ) + { + mcpl_particle(mcpl_read(mcplfile); + //check for file exhaustion + } + + if(mcpl_particle->pdgcode=2112) { + omc_particle_=ParticleType::neutron; + } else { + omc_particle_=Particletype::photon; + } + + //particle is good, convert to openmc-formalism + omc_particle.r.x=mcpl_particle.x; + omc_particle.r.y=mcpl_particle.y; + omc_particle.r.z=mcpl_particle.z; + + omc_particle.u.x=mcpl_particle->direction[0]; + omc_particle.u.y=mcpl_particle->direction[1]; + omc_particle.u.z=mcpl_particle->direction[2]; + + //mcpl stores particles in MeV + omc_particle.E=mcpl_particle->ekin*1e6; + + omc_particle.t=mcpl_particle->time*1e-3; + omc_particle.wgt=mcpl_particle->weight; + omc_particle.delayed_group=0; + return omc_particle; } From 999acbba9a9f69648e9b91198fe4ff0792838b1d Mon Sep 17 00:00:00 2001 From: erkn Date: Mon, 27 Jun 2022 23:25:35 +0200 Subject: [PATCH 067/265] (wip): skeleton for input only test --- .../regression_tests/source_mcpl_file/test.py | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 tests/regression_tests/source_mcpl_file/test.py diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py new file mode 100644 index 0000000000..5a6a87d878 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -0,0 +1,52 @@ +import pathlib as pl +import os +import shutil +import subprocess +import textwrap + +import openmc +import pytest + +from tests.testing_harness import TestHarness + +def model(): + subprocess.run(['gcc','-o gen_dummt_mcpl.out','-lm','-lmcpl','gen_dummy_mcpl.c'] ) + subprocess.run(['./gen_dummy_mcpl.out']) + +class SourceMCPLFileTestHarness(TestHarness): + def execute_test(self): + """Run OpenMC with the appropriate arguments and check the outputs.""" + try: + self._create_input() + self._run_openmc() + self._test_output_created() + results = self._get_results() + self._write_results(results) + self._compare_results() + finally: + self._cleanup() + + def update_results(self): + """Update the results_true using the current version of OpenMC.""" + try: + self._create_input() + self._run_openmc() + self._test_output_created() + results = self._get_results() + self._write_results(results) + self._overwrite_results() + finally: + self._cleanup() + + def _test_output_created(self): + """Check that the output files were created""" + stat epoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) + assert len(statepoint) == 1, 'Either multiple or no statepoint files ' \ + 'exist.' + assert statepoint[0].endswith('h5'), \ + 'statepoint file does not end with h5.' + +def test_mcpl_source_file(): + harness = SourceMCPLFileTestHarness('statepoint.10.h5') + harness.main() + From 3e805cce158630e70df95abb5d20368983339031 Mon Sep 17 00:00:00 2001 From: erkn Date: Mon, 27 Jun 2022 23:26:01 +0200 Subject: [PATCH 068/265] c-prog to generate a dummy mcpl --- .../source_mcpl_file/gen_dummy_mcpl.c | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c diff --git a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c new file mode 100644 index 0000000000..7b5a933f18 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c @@ -0,0 +1,97 @@ +#include +#include +#include +#include + +const int batches=10; +const int particles=10000; + +double rand01(){ + double r=rand()/((double) RAND_MAX); + return r; +} + + +int main(int argc, char **argv){ + char outfilename[128]; + snprintf(outfilename,127,"source.%d.mcpl",batches); + + /*generate an mcpl_header_of sorts*/ + mcpl_outfile_t outfile=mcpl_create_outfile(outfilename); + mcpl_particle_t *particle, Particle; + + char line[256]; + snprintf(line,255,"gen_dummy_mcpl.c"); + mcpl_hdr_set_srcname(outfile,line); + mcpl_enable_universal_pdgcode(outfile,2112);/*all particles are neutrons*/ + snprintf(line,255,"Dummy MCPL-file for testing OpenMC mcpl input"); + mcpl_hdr_add_comment(outfile,line); + + /*also add the instrument file and the command line as blobs*/ + FILE *fp; + if( (fp=fopen("gen_dummy_mcpl.c","rb"))!=NULL){ + unsigned char *buffer; + int size,status; + /*find the file size by seeking to end, "tell" the position, and then go back again*/ + fseek(fp, 0L, SEEK_END); + size = ftell(fp); // get current file pointer + fseek(fp, 0L, SEEK_SET); // seek back to beginning of file + if ( size && (buffer=malloc(size))!=NULL){ + if (size!=(fread(buffer,1,size,fp))){ + fprintf(stderr,"Warning: c source generator file not read cleanly\n"); + } + mcpl_hdr_add_data(outfile, "mcpl_point_source_file_generator", size, buffer); + free(buffer); + } + fclose(fp); + } else { + fprintf(stderr,"Warning: could not open c source generator file, hence not embedded.\n"); + } + + + /*the main particle loop*/ + particle=&Particle; + int i; + for (i=0;iposition[0]=0; + particle->position[1]=0; + particle->position[2]=0; + + /*generate a random direction on unit sphere*/ + double nrm=2.0; + double vx,vy,vz; + int iter=0; + do { + if(iter>100){ + printf("warning: exceeed max random vector attempts: at loop %d -> %g %d\n",i,nrm,iter); + } + vx=rand01()*2.0-1.0; + vy=rand01()*2.0-1.0; + vz=rand01()*2.0-1.0; + nrm=(vx*vx + vy*vy + vz*vz); + iter++; + } while (nrm>1.0); + vx/=sqrt(nrm); + vy/=sqrt(nrm); + vz/=sqrt(nrm); + particle->direction[0]=vx; + particle->direction[1]=vy; + particle->direction[2]=vz; + + /*generate the kinetic energy (in MeV) of the particle*/ + particle->ekin=1e-3; + + /*set time=0*/ + particle->time=0; + /*set weight*/ + particle->weight=1; + + particle->userflags=0; + mcpl_add_particle(outfile,particle); + } + mcpl_closeandgzip_outfile(outfile); +} From c6b42e828cf8bf9bccf77d296976ff83902fb346 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 5 Jul 2022 01:30:07 +0200 Subject: [PATCH 069/265] don't zip the output-file --- .../source_mcpl_file/gen_dummy_mcpl.c | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c index 7b5a933f18..f35a07fc44 100644 --- a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c +++ b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c @@ -54,20 +54,20 @@ int main(int argc, char **argv){ int i; for (i=0;iposition[0]=0; particle->position[1]=0; particle->position[2]=0; - + /*generate a random direction on unit sphere*/ double nrm=2.0; double vx,vy,vz; int iter=0; do { if(iter>100){ - printf("warning: exceeed max random vector attempts: at loop %d -> %g %d\n",i,nrm,iter); + printf("Warning: Exceeded max random vector attempts: at loop %d -> %g %d\n",i,nrm,iter); } vx=rand01()*2.0-1.0; vy=rand01()*2.0-1.0; @@ -82,9 +82,9 @@ int main(int argc, char **argv){ particle->direction[1]=vy; particle->direction[2]=vz; - /*generate the kinetic energy (in MeV) of the particle*/ + /*generate the kinetic energy (in MeV) of the particle*/ particle->ekin=1e-3; - + /*set time=0*/ particle->time=0; /*set weight*/ @@ -93,5 +93,5 @@ int main(int argc, char **argv){ particle->userflags=0; mcpl_add_particle(outfile,particle); } - mcpl_closeandgzip_outfile(outfile); + mcpl_close_outfile(outfile); } From b2f83857e4af32848570abc33985a40587e77489 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 5 Jul 2022 01:53:14 +0200 Subject: [PATCH 070/265] now compiles fine if mcpl is indeed installed --- .../regression_tests/source_mcpl_file/test.py | 21 ++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index 5a6a87d878..0adf67f1aa 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -3,16 +3,13 @@ import os import shutil import subprocess import textwrap - +import glob import openmc import pytest from tests.testing_harness import TestHarness -def model(): - subprocess.run(['gcc','-o gen_dummt_mcpl.out','-lm','-lmcpl','gen_dummy_mcpl.c'] ) - subprocess.run(['./gen_dummy_mcpl.out']) - + class SourceMCPLFileTestHarness(TestHarness): def execute_test(self): """Run OpenMC with the appropriate arguments and check the outputs.""" @@ -26,6 +23,10 @@ class SourceMCPLFileTestHarness(TestHarness): finally: self._cleanup() + def _create_input(self): + subprocess.run(['gcc','-o','gen_dummy_mcpl.out','gen_dummy_mcpl.c','-lm','-lmcpl']) + subprocess.run(['./gen_dummy_mcpl.out']) + def update_results(self): """Update the results_true using the current version of OpenMC.""" try: @@ -40,13 +41,19 @@ class SourceMCPLFileTestHarness(TestHarness): def _test_output_created(self): """Check that the output files were created""" - stat epoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) + statepoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) assert len(statepoint) == 1, 'Either multiple or no statepoint files ' \ 'exist.' assert statepoint[0].endswith('h5'), \ 'statepoint file does not end with h5.' + def _cleanup(self): + super()._cleanup() + source_mcpl=glob.glob(os.path.join(os.getcwd(),'source*.mcpl')) + for f in source_mcpl: + if (os.path.exists(f)): + os.remove(f) + def test_mcpl_source_file(): harness = SourceMCPLFileTestHarness('statepoint.10.h5') harness.main() - From 005189bfdfa9f956139af45c6504e22d2eb8659c Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Mon, 11 Jul 2022 09:49:29 +0200 Subject: [PATCH 071/265] fix misprints --- src/source.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 3dfd007078..3ef5ae16f0 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -413,7 +413,7 @@ SourceSite MCPLFileSource::sample(uint64_t *seed){ SourceSite omc_particle; mcpl_particle *mcpl_particle; //extract particle from mcpl-file - mcpl_particle=mcpl_reazd(mcplfile); + mcpl_particle=mcpl_read(mcplfile); // check if it is a neutron or a photon. otherwise skip while ( mcpl_particle->pdgcode!=2112 && mcpl_particle->pdgcode!=22 ) { @@ -421,9 +421,9 @@ SourceSite MCPLFileSource::sample(uint64_t *seed){ //check for file exhaustion } - if(mcpl_particle->pdgcode=2112) { + if(mcpl_particle->pdgcode==2112) { omc_particle_=ParticleType::neutron; - } else { + } else if (mcpl_particle->pdgcode==22){ omc_particle_=Particletype::photon; } @@ -436,9 +436,9 @@ SourceSite MCPLFileSource::sample(uint64_t *seed){ omc_particle.u.y=mcpl_particle->direction[1]; omc_particle.u.z=mcpl_particle->direction[2]; - //mcpl stores particles in MeV + //mcpl stores kinetic energy in MeV omc_particle.E=mcpl_particle->ekin*1e6; - + //mcpl stores time in ms omc_particle.t=mcpl_particle->time*1e-3; omc_particle.wgt=mcpl_particle->weight; omc_particle.delayed_group=0; From 935396e40bf97a6ba4a9dcf2dcac30b5a80056ba Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 12 Jul 2022 13:48:55 +0200 Subject: [PATCH 072/265] add necessary xmls --- tests/regression_tests/source_mcpl_file/geometry.xml | 8 ++++++++ tests/regression_tests/source_mcpl_file/materials.xml | 9 +++++++++ 2 files changed, 17 insertions(+) create mode 100644 tests/regression_tests/source_mcpl_file/geometry.xml create mode 100644 tests/regression_tests/source_mcpl_file/materials.xml diff --git a/tests/regression_tests/source_mcpl_file/geometry.xml b/tests/regression_tests/source_mcpl_file/geometry.xml new file mode 100644 index 0000000000..bc56030e18 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/geometry.xml @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/tests/regression_tests/source_mcpl_file/materials.xml b/tests/regression_tests/source_mcpl_file/materials.xml new file mode 100644 index 0000000000..2472a74717 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/materials.xml @@ -0,0 +1,9 @@ + + + + + + + + + From e87ebfebc29b07f9ca575629364165fc129ed512 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 12 Jul 2022 13:49:56 +0200 Subject: [PATCH 073/265] set seed to make test deteministic --- tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c index f35a07fc44..61eea95c6f 100644 --- a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c +++ b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c @@ -52,6 +52,7 @@ int main(int argc, char **argv){ /*the main particle loop*/ particle=&Particle; int i; + srand(1234); for (i=0;i Date: Tue, 12 Jul 2022 13:50:35 +0200 Subject: [PATCH 074/265] test target result --- tests/regression_tests/source_mcpl_file/results_true.dat | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 tests/regression_tests/source_mcpl_file/results_true.dat diff --git a/tests/regression_tests/source_mcpl_file/results_true.dat b/tests/regression_tests/source_mcpl_file/results_true.dat new file mode 100644 index 0000000000..f2209006a1 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/results_true.dat @@ -0,0 +1,2 @@ +k-combined: +3.017557E-01 3.398770E-03 From c21ff938c79bd905bb0f6e60c7abbf960b3d87f3 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 12 Jul 2022 13:50:53 +0200 Subject: [PATCH 075/265] yet another necessary file --- tests/regression_tests/source_mcpl_file/settings.xml | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 tests/regression_tests/source_mcpl_file/settings.xml diff --git a/tests/regression_tests/source_mcpl_file/settings.xml b/tests/regression_tests/source_mcpl_file/settings.xml new file mode 100644 index 0000000000..8b1510e0ce --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/settings.xml @@ -0,0 +1,11 @@ + + + + 10 + 5 + 1000 + + + source.10.mcpl + + From a123d239ddf016167cef9c99add91c5f665ac19c Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 12 Jul 2022 14:40:01 +0200 Subject: [PATCH 076/265] add a check that the test input got created as intended --- tests/regression_tests/source_mcpl_file/test.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index 0adf67f1aa..922ddddd31 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -15,6 +15,7 @@ class SourceMCPLFileTestHarness(TestHarness): """Run OpenMC with the appropriate arguments and check the outputs.""" try: self._create_input() + self._test_input_created() self._run_openmc() self._test_output_created() results = self._get_results() @@ -31,6 +32,7 @@ class SourceMCPLFileTestHarness(TestHarness): """Update the results_true using the current version of OpenMC.""" try: self._create_input() + self._test_input_created() self._run_openmc() self._test_output_created() results = self._get_results() @@ -39,6 +41,14 @@ class SourceMCPLFileTestHarness(TestHarness): finally: self._cleanup() + def _test_input_created(self): + """Check that the input mcpl.file was generated as it should""" + mcplfile=glob.glob(os.path.join(os.getcwd(),'source.10.mcpl')) + assert len(mcplfile) == 1, 'Either multiple or no mcpl files ' \ + 'exist.' + assert mcplfile[0].endswith('mcpl'), \ + 'output file does not end with mcpl.' + def _test_output_created(self): """Check that the output files were created""" statepoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) @@ -55,5 +65,5 @@ class SourceMCPLFileTestHarness(TestHarness): os.remove(f) def test_mcpl_source_file(): - harness = SourceMCPLFileTestHarness('statepoint.10.h5') + harness = SourceMCPLFileTestHarness('source.10.mcpl') harness.main() From 1509420c214275d2c27b458caefdfc943cd413de Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 13 Jul 2022 10:25:55 +0200 Subject: [PATCH 077/265] fix bugs and finalize interface to MCPL --- include/openmc/source.h | 22 +++++++------ src/source.cpp | 73 +++++++++++++++++++++++++---------------- 2 files changed, 57 insertions(+), 38 deletions(-) diff --git a/include/openmc/source.h b/include/openmc/source.h index 24a3d10aed..0c944aef93 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -14,6 +14,10 @@ #include "openmc/particle.h" #include "openmc/vector.h" +#ifdef OPENMC_MCPL +#include +#endif + namespace openmc { //============================================================================== @@ -110,6 +114,7 @@ private: vector sites_; //!< Source sites from a file }; +#ifdef OPENMC_MCPL //============================================================================== // MCPL-file input source //============================================================================== @@ -119,24 +124,21 @@ public: MCPLFileSource(std::string path); ~MCPLFileSource(); - // Properties - ParticleType particle_type() const { return particle_; } - + // Methods //! Sample from the external source distribution //! \param[inout] seed Pseudorandom seed pointer //! \return Site read from MCPL-file - SourceSite sample(uint64_t* seed) const override; + SourceSite sample(uint64_t* seed) const; private: - ParticleType particle_ {ParticleType::neutron}; //!< Type of particle emitted + SourceSite read_single_particle() const; + void read_source_bank(vector &sites_); + vector sites_; //! #endif @@ -382,6 +382,7 @@ CustomSourceWrapper::~CustomSourceWrapper() #endif } +#ifdef OPENMC_MCPL //=========================================================================== // Read particles from an MCPL-file //=========================================================================== @@ -397,54 +398,70 @@ MCPLFileSource::MCPLFileSource(std::string path) write_message(6, "Reading mcpl source file from {}",path); // Open the mcpl file - mcpl_file = mcpl_open(path.c_str); + mcpl_file = mcpl_open_file(path.c_str()); //do checks on the mcpl_file to see if particles are many enough. // should model this on the example source shown in the docs. - uint64_t nparticles=mcpl_hdr_nparticles(mcpl_file); + n_sites=mcpl_hdr_nparticles(mcpl_file); + read_source_bank(sites_); } -MCPLFileSource::~MCPLFilsSource(){ +MCPLFileSource::~MCPLFileSource(){ mcpl_close_file(mcpl_file); } -SourceSite MCPLFileSource::sample(uint64_t *seed){ - SourceSite omc_particle; - mcpl_particle *mcpl_particle; +SourceSite MCPLFileSource::sample(uint64_t* seed) const +{ + size_t i_site = sites_.size() * prn(seed); + return sites_[i_site]; +} + +void MCPLFileSource::read_source_bank(vector &sites_) +{ + sites_.resize(n_sites); + for (int i=0;ipdgcode!=2112 && mcpl_particle->pdgcode!=22 ) - { - mcpl_particle(mcpl_read(mcplfile); - //check for file exhaustion + mcpl_particle=mcpl_read(mcpl_file); + // check if it is a neutron or a photon. otherwise skip + while ( mcpl_particle->pdgcode!=2112 && mcpl_particle->pdgcode!=22 ) { + mcpl_particle=mcpl_read(mcpl_file); + //should check for file exhaustion This could happen if particles are other than + //neutrons or photons } if(mcpl_particle->pdgcode==2112) { - omc_particle_=ParticleType::neutron; - } else if (mcpl_particle->pdgcode==22){ - omc_particle_=Particletype::photon; + omc_particle_.particle=ParticleType::neutron; + } else if (mcpl_particle->pdgcode==22) { + omc_particle_.particle=ParticleType::photon; } //particle is good, convert to openmc-formalism - omc_particle.r.x=mcpl_particle.x; - omc_particle.r.y=mcpl_particle.y; - omc_particle.r.z=mcpl_particle.z; + omc_particle_.r.x=mcpl_particle->position[0]; + omc_particle_.r.y=mcpl_particle->position[1]; + omc_particle_.r.z=mcpl_particle->position[2]; - omc_particle.u.x=mcpl_particle->direction[0]; - omc_particle.u.y=mcpl_particle->direction[1]; - omc_particle.u.z=mcpl_particle->direction[2]; + omc_particle_.u.x=mcpl_particle->direction[0]; + omc_particle_.u.y=mcpl_particle->direction[1]; + omc_particle_.u.z=mcpl_particle->direction[2]; //mcpl stores kinetic energy in MeV - omc_particle.E=mcpl_particle->ekin*1e6; + omc_particle_.E=mcpl_particle->ekin*1e6; //mcpl stores time in ms - omc_particle.t=mcpl_particle->time*1e-3; - omc_particle.wgt=mcpl_particle->weight; - omc_particle.delayed_group=0; - return omc_particle; + omc_particle_.time=mcpl_particle->time*1e-3; + omc_particle_.wgt=mcpl_particle->weight; + omc_particle_.delayed_group=0; + return omc_particle_; } - +#endif //OPENMC_MCPL //============================================================================== // Non-member functions From 2cbcd53f077b3afc7d01e0ebfe70ba1e0790fe39 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 13 Jul 2022 10:26:24 +0200 Subject: [PATCH 078/265] add an option to turn on mcpl-support --- CMakeLists.txt | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/CMakeLists.txt b/CMakeLists.txt index 521b46cfc6..1408e85afc 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -36,6 +36,7 @@ option(OPENMC_ENABLE_COVERAGE "Compile with coverage analysis flags" option(OPENMC_USE_DAGMC "Enable support for DAGMC (CAD) geometry" OFF) option(OPENMC_USE_LIBMESH "Enable support for libMesh unstructured mesh tallies" OFF) option(OPENMC_USE_MPI "Enable MPI" OFF) +option(OPENMC_USE_MCPL "Enable MPCPL" OFF) # Warnings for deprecated options foreach(OLD_OPT IN ITEMS "openmp" "profile" "coverage" "dagmc" "libmesh") @@ -185,6 +186,10 @@ if(OPENMC_ENABLE_COVERAGE) list(APPEND ldflags --coverage) endif() +if(OPENMC_USE_MCPL) + list(APPEND ldflags -lmcpl) +endif() + # Show flags being used message(STATUS "OpenMC C++ flags: ${cxxflags}") message(STATUS "OpenMC Linker flags: ${ldflags}") @@ -439,6 +444,10 @@ endif() if (OPENMC_USE_MPI) target_compile_definitions(libopenmc PUBLIC -DOPENMC_MPI) endif() +if(OPENMC_USE_MCPL) + target_compile_definitions(libopenmc PUBLIC -DOPENMC_MCPL) +endif() + # Set git SHA1 hash as a compile definition if(GIT_FOUND) From 46e648cf383df7b7b72b4f1f5c389f3c191c69a1 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 13 Jul 2022 10:27:18 +0200 Subject: [PATCH 079/265] add a source type to the settings interface --- src/settings.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/settings.cpp b/src/settings.cpp index eb0d4936c7..12e0a80509 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -430,6 +430,9 @@ void read_settings_xml() if (check_for_node(node, "file")) { auto path = get_node_value(node, "file", false, true); model::external_sources.push_back(make_unique(path)); + } else if (check_for_node(node, "mcpl")) { + auto path = get_node_value(node, "mcpl", false, true); + model::external_sources.push_back(make_unique(path)); } else if (check_for_node(node, "library")) { // Get shared library path and parameters auto path = get_node_value(node, "library", false, true); From 96ae7b4228798549d1bb969777a73f926ba19465 Mon Sep 17 00:00:00 2001 From: erkn Date: Sat, 9 Jul 2022 16:31:00 +0200 Subject: [PATCH 080/265] fix misprints --- src/source.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/source.cpp b/src/source.cpp index bdfe5349c8..4b27bdc7eb 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -392,7 +392,7 @@ MCPLFileSource::MCPLFileSource(std::string path) if (!file_exists(path)) { fatal_error(fmt::format("Source file '{}' does not exist.", path)); } - + // Read the source from a binary file instead of sampling from some // assumed source distribution write_message(6, "Reading mcpl source file from {}",path); From 2fa445193870a1bd6818fd82d1ea755e890c2309 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 13 Jul 2022 12:13:10 +0200 Subject: [PATCH 081/265] only add mcpl-support if OPENMC_MCPL is defined --- src/settings.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/settings.cpp b/src/settings.cpp index 12e0a80509..d419cab06f 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -430,9 +430,11 @@ void read_settings_xml() if (check_for_node(node, "file")) { auto path = get_node_value(node, "file", false, true); model::external_sources.push_back(make_unique(path)); +#ifdef OPENMC_MCPL } else if (check_for_node(node, "mcpl")) { auto path = get_node_value(node, "mcpl", false, true); model::external_sources.push_back(make_unique(path)); +#endif } else if (check_for_node(node, "library")) { // Get shared library path and parameters auto path = get_node_value(node, "library", false, true); From 2773add0473f28d225c1ad9efbc6fcc9e97230ed Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 13 Jul 2022 14:13:33 +0200 Subject: [PATCH 082/265] needed to avoid name clashes with other tests --- tests/regression_tests/source_mcpl_file/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 tests/regression_tests/source_mcpl_file/__init__.py diff --git a/tests/regression_tests/source_mcpl_file/__init__.py b/tests/regression_tests/source_mcpl_file/__init__.py new file mode 100644 index 0000000000..e69de29bb2 From bb8c022d77f8e22ad3d856edeb2b1a16a6311067 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 13 Jul 2022 20:55:53 +0200 Subject: [PATCH 083/265] fail without tripping the entire test-process --- tests/regression_tests/source_mcpl_file/test.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index 922ddddd31..f55a769047 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -1,11 +1,6 @@ -import pathlib as pl import os -import shutil import subprocess -import textwrap import glob -import openmc -import pytest from tests.testing_harness import TestHarness @@ -25,7 +20,8 @@ class SourceMCPLFileTestHarness(TestHarness): self._cleanup() def _create_input(self): - subprocess.run(['gcc','-o','gen_dummy_mcpl.out','gen_dummy_mcpl.c','-lm','-lmcpl']) + compiled=subprocess.run(['gcc','-o','gen_dummy_mcpl.out','gen_dummy_mcpl.c','-lm','-lmcpl']) + assert compiled==0, 'Could not compile mcpl-file generator code' subprocess.run(['./gen_dummy_mcpl.out']) def update_results(self): From 2730f1954f154df24ed7171e9dda39e4325c1b2c Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 6 Sep 2022 09:11:41 +0200 Subject: [PATCH 084/265] allow electrons and positrons as well --- src/source.cpp | 29 ++++++++++++++++++++--------- 1 file changed, 20 insertions(+), 9 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 4b27bdc7eb..cfcd79e0a6 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -429,19 +429,30 @@ SourceSite MCPLFileSource::read_single_particle() const { SourceSite omc_particle_; const mcpl_particle_t *mcpl_particle; - //extract particle from mcpl-file + // extract particle from mcpl-file mcpl_particle=mcpl_read(mcpl_file); - // check if it is a neutron or a photon. otherwise skip - while ( mcpl_particle->pdgcode!=2112 && mcpl_particle->pdgcode!=22 ) { + // check if it is a neutron, photon, electron, or positron. Otherwise skip. + int pdg=mcpl_particle->pdgcode; + while ( pdg!=2112 && pdg!=22 && pdg!=11 && pdg!=-11) { mcpl_particle=mcpl_read(mcpl_file); - //should check for file exhaustion This could happen if particles are other than - //neutrons or photons + pdg=mcpl_particle->pdgcode; + //should check for file exhaustion. This could happen if particles are other than + //neutrons, photons, electrons, or positrons. } - if(mcpl_particle->pdgcode==2112) { - omc_particle_.particle=ParticleType::neutron; - } else if (mcpl_particle->pdgcode==22) { - omc_particle_.particle=ParticleType::photon; + switch(pdg){ + case 2112: + omc_particle_.particle=ParticleType::neutron; + break; + case 22: + omc_particle_.particle=ParticleType::photon; + break; + case 11: + omc_particle_.particle=ParticleType::electron; + break; + case -11: + omc_particle_.particle=ParticleType::positron; + break; } //particle is good, convert to openmc-formalism From 3b052f03cfce7605bf96641346800022e462a02a Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 6 Sep 2022 09:12:01 +0200 Subject: [PATCH 085/265] expose a python function to check for mcpl --- openmc/lib/__init__.py | 3 +++ src/source.cpp | 6 ++++++ 2 files changed, 9 insertions(+) diff --git a/openmc/lib/__init__.py b/openmc/lib/__init__.py index c14b0d9c28..1e337fc073 100644 --- a/openmc/lib/__init__.py +++ b/openmc/lib/__init__.py @@ -48,6 +48,9 @@ def _coord_levels(): def _libmesh_enabled(): return c_bool.in_dll(_dll, "LIBMESH_ENABLED").value +def _mcpl_enabled(): + return c_bool.in_dll(_dll, "MCPL_ENABLED").value + from .error import * from .core import * from .nuclide import * diff --git a/src/source.cpp b/src/source.cpp index cfcd79e0a6..dbfcd1ceba 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -43,6 +43,12 @@ namespace openmc { // Global variables //============================================================================== +#ifdef OPENMC_MCPL +const bool MCPL_ENABLED = true; +#else +const bool MCPL_ENABLED = false; +#endif + namespace model { vector> external_sources; From 5640bdb9eb25bc5675928490ef4bf925e9155ae1 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Fri, 15 Jul 2022 21:35:59 +0200 Subject: [PATCH 086/265] fix typo Co-authored-by: Paul Romano --- CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 1408e85afc..32beb41ecd 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -36,7 +36,7 @@ option(OPENMC_ENABLE_COVERAGE "Compile with coverage analysis flags" option(OPENMC_USE_DAGMC "Enable support for DAGMC (CAD) geometry" OFF) option(OPENMC_USE_LIBMESH "Enable support for libMesh unstructured mesh tallies" OFF) option(OPENMC_USE_MPI "Enable MPI" OFF) -option(OPENMC_USE_MCPL "Enable MPCPL" OFF) +option(OPENMC_USE_MCPL "Enable MCPL" OFF) # Warnings for deprecated options foreach(OLD_OPT IN ITEMS "openmp" "profile" "coverage" "dagmc" "libmesh") From 95338eada002270c437906cb55607945dabe39b0 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 9 Aug 2022 08:12:19 +0200 Subject: [PATCH 087/265] refactor MCPL file read part of FileSource A new constructor is added to FileSource that reads from a given MCPL-file. --- include/openmc/source.h | 30 +-------- src/settings.cpp | 2 +- src/source.cpp | 139 ++++++++++++++-------------------------- 3 files changed, 52 insertions(+), 119 deletions(-) diff --git a/include/openmc/source.h b/include/openmc/source.h index 0c944aef93..bb7e2d55f7 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -106,7 +106,9 @@ class FileSource : public Source { public: // Constructors explicit FileSource(std::string path); - +#ifdef OPENMC_MCPL + explicit FileSource(mcpl_file_t mcpl_file); +#endif // Methods SourceSite sample(uint64_t* seed) const override; @@ -114,32 +116,6 @@ private: vector sites_; //!< Source sites from a file }; -#ifdef OPENMC_MCPL -//============================================================================== -// MCPL-file input source -//============================================================================== -class MCPLFileSource : public Source { -public: - // Constructors, destructors - MCPLFileSource(std::string path); - ~MCPLFileSource(); - - // Methods - //! Sample from the external source distribution - //! \param[inout] seed Pseudorandom seed pointer - //! \return Site read from MCPL-file - SourceSite sample(uint64_t* seed) const; - -private: - SourceSite read_single_particle() const; - void read_source_bank(vector &sites_); - - vector sites_; //!(path)); + model::external_sources.push_back(make_unique(mcpl_open_file(path.c_str()))); #endif } else if (check_for_node(node, "library")) { // Get shared library path and parameters diff --git a/src/source.cpp b/src/source.cpp index dbfcd1ceba..e43f03929b 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -329,6 +329,54 @@ FileSource::FileSource(std::string path) file_close(file_id); } +#ifdef OPENMC_MCPL +FileSource::FileSource(mcpl_file_t mcpl_file) +{ + //do checks on the mcpl_file to see if particles are many enough. + // should model this on the example source shown in the docs. + size_t n_sites=mcpl_hdr_nparticles(mcpl_file); + + sites_.resize(n_sites); + for (int i=0;ipdgcode!=2112 && mcpl_particle->pdgcode!=22 ) { + mcpl_particle=mcpl_read(mcpl_file); + //should check for file exhaustion This could happen if particles are other than + //neutrons or photons + } + + if(mcpl_particle->pdgcode==2112) { + site_.particle=ParticleType::neutron; + } else if (mcpl_particle->pdgcode==22) { + site_.particle=ParticleType::photon; + } + + //particle is good, convert to openmc-formalism + site_.r.x=mcpl_particle->position[0]; + site_.r.y=mcpl_particle->position[1]; + site_.r.z=mcpl_particle->position[2]; + + site_.u.x=mcpl_particle->direction[0]; + site_.u.y=mcpl_particle->direction[1]; + site_.u.z=mcpl_particle->direction[2]; + + //mcpl stores kinetic energy in MeV + site_.E=mcpl_particle->ekin*1e6; + //mcpl stores time in ms + site_.time=mcpl_particle->time*1e-3; + site_.wgt=mcpl_particle->weight; + site_.delayed_group=0; + sites_[i]=site_; + } + mcpl_close_file(mcpl_file); +} +#endif //OPENMC_MCPL + SourceSite FileSource::sample(uint64_t* seed) const { size_t i_site = sites_.size() * prn(seed); @@ -388,97 +436,6 @@ CustomSourceWrapper::~CustomSourceWrapper() #endif } -#ifdef OPENMC_MCPL -//=========================================================================== -// Read particles from an MCPL-file -//=========================================================================== -MCPLFileSource::MCPLFileSource(std::string path) -{ - // Check if source file exists - if (!file_exists(path)) { - fatal_error(fmt::format("Source file '{}' does not exist.", path)); - } - - // Read the source from a binary file instead of sampling from some - // assumed source distribution - write_message(6, "Reading mcpl source file from {}",path); - - // Open the mcpl file - mcpl_file = mcpl_open_file(path.c_str()); - - //do checks on the mcpl_file to see if particles are many enough. - // should model this on the example source shown in the docs. - n_sites=mcpl_hdr_nparticles(mcpl_file); - - read_source_bank(sites_); -} - -MCPLFileSource::~MCPLFileSource(){ - mcpl_close_file(mcpl_file); -} - -SourceSite MCPLFileSource::sample(uint64_t* seed) const -{ - size_t i_site = sites_.size() * prn(seed); - return sites_[i_site]; -} - -void MCPLFileSource::read_source_bank(vector &sites_) -{ - sites_.resize(n_sites); - for (int i=0;ipdgcode; - while ( pdg!=2112 && pdg!=22 && pdg!=11 && pdg!=-11) { - mcpl_particle=mcpl_read(mcpl_file); - pdg=mcpl_particle->pdgcode; - //should check for file exhaustion. This could happen if particles are other than - //neutrons, photons, electrons, or positrons. - } - - switch(pdg){ - case 2112: - omc_particle_.particle=ParticleType::neutron; - break; - case 22: - omc_particle_.particle=ParticleType::photon; - break; - case 11: - omc_particle_.particle=ParticleType::electron; - break; - case -11: - omc_particle_.particle=ParticleType::positron; - break; - } - - //particle is good, convert to openmc-formalism - omc_particle_.r.x=mcpl_particle->position[0]; - omc_particle_.r.y=mcpl_particle->position[1]; - omc_particle_.r.z=mcpl_particle->position[2]; - - omc_particle_.u.x=mcpl_particle->direction[0]; - omc_particle_.u.y=mcpl_particle->direction[1]; - omc_particle_.u.z=mcpl_particle->direction[2]; - - //mcpl stores kinetic energy in MeV - omc_particle_.E=mcpl_particle->ekin*1e6; - //mcpl stores time in ms - omc_particle_.time=mcpl_particle->time*1e-3; - omc_particle_.wgt=mcpl_particle->weight; - omc_particle_.delayed_group=0; - return omc_particle_; -} -#endif //OPENMC_MCPL //============================================================================== // Non-member functions From 5462216deba46d017db7905a312f0ed458cde6a7 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 6 Sep 2022 02:22:21 +0200 Subject: [PATCH 088/265] wip add MCPL-out to openmc code for writing a source_bank/point compiles but is untested --- include/openmc/state_point.h | 9 +++ src/state_point.cpp | 125 +++++++++++++++++++++++++++++++++++ 2 files changed, 134 insertions(+) diff --git a/include/openmc/state_point.h b/include/openmc/state_point.h index 5ada2bf88d..2d92c935a6 100644 --- a/include/openmc/state_point.h +++ b/include/openmc/state_point.h @@ -9,6 +9,10 @@ #include "openmc/particle.h" #include "openmc/vector.h" +#ifdef OPENMC_MCPL +#include +#endif + namespace openmc { void load_state_point(); @@ -21,5 +25,10 @@ void write_tally_results_nr(hid_t file_id); void restart_set_keff(); void write_unstructured_mesh_results(); +#ifdef OPENMC_MCPL +void write_mcpl_source_point(const char *filename_, bool surf_source_bank = false); +void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank); +#endif + } // namespace openmc #endif // OPENMC_STATE_POINT_H diff --git a/src/state_point.cpp b/src/state_point.cpp index 470dd77182..dfbd7f65c5 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -28,6 +28,10 @@ #include "openmc/timer.h" #include "openmc/vector.h" +#ifdef OPENMC_MCPL +#include +#endif + namespace openmc { extern "C" int openmc_statepoint_write(const char* filename, bool* write_source) @@ -599,6 +603,45 @@ void write_source_point(const char* filename, bool surf_source_bank) file_close(file_id); } +void write_mcpl_point(const char *filename, bool surf_source_bank) +{ + std::string filename_; + if (filename) { + filename_ = filename; + } else { + // Determine width for zero padding + int w = std::to_string(settings::n_max_batches).size(); + + filename_ = fmt::format("{0}source.{1:0{2}}.mcpl", settings::path_output, + simulation::current_batch, w); + } + + mcpl_outfile_t file_id; + + std::string line; + if (mpi::master) { + // this must be rewritten: file_open is h5-specific + file_id = mcpl_create_outfile(filename_.c_str()); + //write_attribute(file_id, "filetype", "source"); + //write header stuff (oopy in xml-files as binary blobs for instance)) + if (VERSION_DEV){ + line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}-development"); + } else { + line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}"); + } + mcpl_hdr_set_srcname(file_id,line.c_str()); + } + + write_mcpl_source_bank(file_id, surf_source_bank); + + if (mpi::master) { + //change this - this is h5 specific + mcpl_closeandgzip_outfile(file_id); + } + +} + + void write_source_bank(hid_t group_id, bool surf_source_bank) { hid_t banktype = h5banktype(); @@ -715,6 +758,88 @@ void write_source_bank(hid_t group_id, bool surf_source_bank) H5Tclose(banktype); } +void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) +{ + int64_t dims_size = settings::n_particles; + int64_t count_size = simulation::work_per_rank; + + // Set vectors for source bank and starting bank index of each process + vector* bank_index = &simulation::work_index; + vector* source_bank = &simulation::source_bank; + vector surf_source_index_vector; + vector surf_source_bank_vector; + + if(surf_source_bank) { + surf_source_index_vector = calculate_surf_source_size(); + dims_size = surf_source_index_vector[mpi::n_procs]; + count_size = simulation::surf_source_bank.size(); + + bank_index = &surf_source_index_vector; + + // Copy data in a SharedArray into a vector. + surf_source_bank_vector.resize(count_size); + surf_source_bank_vector.assign(simulation::surf_source_bank.data(), + simulation::surf_source_bank.data() + count_size); + source_bank = &surf_source_bank_vector; + } + + if (mpi::master) { + //write particles from the master node + //loop over the other nodes and receive data - then write those. + for (int i = 0; i < mpi::n_procs; ++i) { +#ifdef OPENMC_MPI + if (i>0) + MPI_Recv(source_bank->data(), count[0], mpi::source_site, i, i, + mpi::intracomm, MPI_STATUS_IGNORE); +#endif + //now write the source_banke data again. + for (vector::iterator _site=source_bank->begin(); _site!=source_bank->end();_site++){ + //particle is now at the iterator + //write it to the mcpl-file + mcpl_particle_t p; + p.position[0]=_site->r.x; + p.position[1]=_site->r.y; + p.position[2]=_site->r.z; + + p.direction[0]=_site->u.x; + p.direction[1]=_site->u.y; + p.direction[2]=_site->u.x; + + //mcpl stores kinetic energy in MeV + p.ekin=_site->E*1e-6; + + p.time=_site->time*1e3; + + p.weight=_site->wgt; + + switch(_site->particle){ + case ParticleType::neutron: + p.pdgcode=2112; + break; + case ParticleType::photon: + p.pdgcode=22; + break; + case ParticleType::electron: + p.pdgcode=11; + break; + case ParticleType::positron: + p.pdgcode=-11; + break; + } + + mcpl_add_particle(file_id,&p); + } + } + } else { +#ifdef OPENMC_MPI + MPI_Send(source_bank->data(), count_size, mpi::source_site, 0, mpi::rank, + mpi::intracomm); +#endif + } + +} + + // Determine member names of a compound HDF5 datatype std::string dtype_member_names(hid_t dtype_id) { From 1519f4f3e6acc5d91dbbb7c952589a2fe39e5537 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 6 Sep 2022 23:06:19 +0200 Subject: [PATCH 089/265] add a trigger to simulation control --- src/simulation.cpp | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/simulation.cpp b/src/simulation.cpp index d7292cb9d9..9c19c2106d 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -407,6 +407,13 @@ void finalize_batch() auto filename = settings::path_output + "surface_source.h5"; write_source_point(filename.c_str(), true); } + + if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ + auto filename = settings::path_output + ".mcpl"; + write_mcplt_source_point(filename.c_str(), true); + } + + } void initialize_generation() From f76e416ee64524ef06705db4f2fa306e4be472f1 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 10:56:36 +0200 Subject: [PATCH 090/265] use find_package instead - MCPL now supports this --- CMakeLists.txt | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 32beb41ecd..24018eb0f1 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -159,6 +159,13 @@ if(${HDF5_VERSION} VERSION_GREATER_EQUAL 1.12.0) list(APPEND cxxflags -DH5Oget_info_by_idx_vers=1 -DH5O_info_t_vers=1) endif() +#=============================================================================== +# MCPL +#=============================================================================== +if (OPENMC_USE_MCPL) + find_package(MCPL REQUIRED) +endif() + #=============================================================================== # Set compile/link flags based on which compiler is being used #=============================================================================== @@ -186,10 +193,6 @@ if(OPENMC_ENABLE_COVERAGE) list(APPEND ldflags --coverage) endif() -if(OPENMC_USE_MCPL) - list(APPEND ldflags -lmcpl) -endif() - # Show flags being used message(STATUS "OpenMC C++ flags: ${cxxflags}") message(STATUS "OpenMC Linker flags: ${ldflags}") @@ -444,10 +447,6 @@ endif() if (OPENMC_USE_MPI) target_compile_definitions(libopenmc PUBLIC -DOPENMC_MPI) endif() -if(OPENMC_USE_MCPL) - target_compile_definitions(libopenmc PUBLIC -DOPENMC_MCPL) -endif() - # Set git SHA1 hash as a compile definition if(GIT_FOUND) @@ -491,6 +490,11 @@ if (OPENMC_USE_MPI) target_link_libraries(libopenmc MPI::MPI_CXX) endif() +if (OPENMC_USE_MCPL) + target_compile_definitions(libopenmc PUBLIC OPENMC_MCPL) + target_link_libraries(libopenmc MCPL::mcpl) +endif() + #=============================================================================== # openmc executable #=============================================================================== From b6aa2dc429bf7545826991c426bf0843624c7377 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 10:59:02 +0200 Subject: [PATCH 091/265] add mcpl-output settings --- include/openmc/settings.h | 1 + src/settings.cpp | 8 +++++++- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/include/openmc/settings.h b/include/openmc/settings.h index 1e061b235b..66825867d8 100644 --- a/include/openmc/settings.h +++ b/include/openmc/settings.h @@ -48,6 +48,7 @@ extern bool source_latest; //!< write latest source at each batch? extern bool source_separate; //!< write source to separate file? extern bool source_write; //!< write source in HDF5 files? extern bool surf_source_write; //!< write surface source file? +extern bool surf_mcpl_write; //!< write surface mcpl file? extern bool surf_source_read; //!< read surface source file? extern bool survival_biasing; //!< use survival biasing? extern bool temperature_multipole; //!< use multipole data? diff --git a/src/settings.cpp b/src/settings.cpp index 11dd96e025..d1762596c6 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -61,6 +61,7 @@ bool source_latest {false}; bool source_separate {false}; bool source_write {true}; bool surf_source_write {false}; +bool surf_mcpl_write {false}; bool surf_source_read {false}; bool survival_biasing {false}; bool temperature_multipole {false}; @@ -682,9 +683,14 @@ void read_settings_xml() max_surface_particles = std::stoll(get_node_value(node_ssw, "max_particles")); } +#ifdef OPENMC_MCPL + if(check_for_node(node_ssw, "mcpl")){ + surf_mcpl_write=true; + } +#endif } - // If source is not seperate and is to be written out in the statepoint file, + // If source is not separate and is to be written out in the statepoint file, // make sure that the sourcepoint batch numbers are contained in the // statepoint list if (!source_separate) { From 22ce618601c8dbefd4759c51d50b7a17ba09dbba Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 10:59:28 +0200 Subject: [PATCH 092/265] fix typo --- src/simulation.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/simulation.cpp b/src/simulation.cpp index 9c19c2106d..fcb115849d 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -410,7 +410,7 @@ void finalize_batch() if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ auto filename = settings::path_output + ".mcpl"; - write_mcplt_source_point(filename.c_str(), true); + write_mcpl_source_point(filename.c_str(), true); } From 76e726b527c1b738b8b5842999e69ec4d6c4c57d Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 11:00:39 +0200 Subject: [PATCH 093/265] add cond. compilation guards for MCPL functions --- src/state_point.cpp | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index dfbd7f65c5..14a5411283 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -603,7 +603,8 @@ void write_source_point(const char* filename, bool surf_source_bank) file_close(file_id); } -void write_mcpl_point(const char *filename, bool surf_source_bank) +#ifdef OPENMC_MCPL +void write_mcpl_source_point(const char *filename, bool surf_source_bank) { std::string filename_; if (filename) { @@ -640,7 +641,7 @@ void write_mcpl_point(const char *filename, bool surf_source_bank) } } - +#endif void write_source_bank(hid_t group_id, bool surf_source_bank) { @@ -758,6 +759,7 @@ void write_source_bank(hid_t group_id, bool surf_source_bank) H5Tclose(banktype); } +#ifdef OPENMC_MCPL void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) { int64_t dims_size = settings::n_particles; @@ -838,7 +840,7 @@ void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) } } - +#endif // Determine member names of a compound HDF5 datatype std::string dtype_member_names(hid_t dtype_id) From bdc76d95fce06f3e94dea3afa9b8305309958179 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Fri, 16 Sep 2022 16:07:22 +0200 Subject: [PATCH 094/265] refactor MCPL file read part of FileSource A new constructor is added to FileSource that reads from a given MCPL-file. --- src/source.cpp | 73 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) diff --git a/src/source.cpp b/src/source.cpp index e43f03929b..cf584e12ea 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -437,6 +437,79 @@ CustomSourceWrapper::~CustomSourceWrapper() } +MCPLFileSource::~MCPLFileSource(){ + mcpl_close_file(mcpl_file); +} + +SourceSite MCPLFileSource::sample(uint64_t* seed) const +{ + size_t i_site = sites_.size() * prn(seed); + return sites_[i_site]; +} + +void MCPLFileSource::read_source_bank(vector &sites_) +{ + sites_.resize(n_sites); + for (int i=0;ipdgcode; + while ( pdg!=2112 && pdg!=22 && pdg!=11 && pdg!=-11) { + mcpl_particle=mcpl_read(mcpl_file); + pdg=mcpl_particle->pdgcode; + //should check for file exhaustion. This could happen if particles are other than + //neutrons, photons, electrons, or positrons. + } + + switch(pdg){ + case 2112: + omc_particle_.particle=ParticleType::neutron; + break; + case 22: + omc_particle_.particle=ParticleType::photon; + break; + case 11: + omc_particle_.particle=ParticleType::electron; + break; + case -11: + omc_particle_.particle=ParticleType::positron; + break; + } + + //particle is good, convert to openmc-formalism + omc_particle_.r.x=mcpl_particle->position[0]; + omc_particle_.r.y=mcpl_particle->position[1]; + omc_particle_.r.z=mcpl_particle->position[2]; + + omc_particle_.u.x=mcpl_particle->direction[0]; + omc_particle_.u.y=mcpl_particle->direction[1]; + omc_particle_.u.z=mcpl_particle->direction[2]; + + //mcpl stores kinetic energy in MeV + omc_particle_.E=mcpl_particle->ekin*1e6; + //mcpl stores time in ms + omc_particle_.time=mcpl_particle->time*1e-3; + omc_particle_.wgt=mcpl_particle->weight; + omc_particle_.delayed_group=0; + return omc_particle_; +} +#endif //OPENMC_MCPL +======= +>>>>>>> 380cfc150b449ef56debb5261caa010a52c42bdd +======= +#endif +>>>>>>> 71568d4f4 (refactor MCPL file read part of FileSource) +>>>>>>> 55f2be19e (refactor MCPL file read part of FileSource) + //============================================================================== // Non-member functions //============================================================================== From 6bceb7c30c05509823a7b0a6cb2e518d3a7ff5e4 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 6 Sep 2022 02:22:21 +0200 Subject: [PATCH 095/265] wip add MCPL-out to openmc code for writing a source_bank/point compiles but is untested --- src/source.cpp | 6 ------ src/state_point.cpp | 1 + 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index cf584e12ea..99ec3a74d1 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -503,12 +503,6 @@ SourceSite MCPLFileSource::read_single_particle() const return omc_particle_; } #endif //OPENMC_MCPL -======= ->>>>>>> 380cfc150b449ef56debb5261caa010a52c42bdd -======= -#endif ->>>>>>> 71568d4f4 (refactor MCPL file read part of FileSource) ->>>>>>> 55f2be19e (refactor MCPL file read part of FileSource) //============================================================================== // Non-member functions diff --git a/src/state_point.cpp b/src/state_point.cpp index 14a5411283..1b133a1215 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -643,6 +643,7 @@ void write_mcpl_source_point(const char *filename, bool surf_source_bank) } #endif + void write_source_bank(hid_t group_id, bool surf_source_bank) { hid_t banktype = h5banktype(); From 56cddd25e2d8540da5356fbbe8f3bbde13ce11b5 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 4 Oct 2022 10:11:06 +0200 Subject: [PATCH 096/265] do not define these functions if no MCPL present --- src/state_point.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index 1b133a1215..14a5411283 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -643,7 +643,6 @@ void write_mcpl_source_point(const char *filename, bool surf_source_bank) } #endif - void write_source_bank(hid_t group_id, bool surf_source_bank) { hid_t banktype = h5banktype(); From 3c33ec3b9fc513794e7e683620fbce99aedb9bcb Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 9 Aug 2022 08:12:19 +0200 Subject: [PATCH 097/265] refactor MCPL file read part of FileSource A new constructor is added to FileSource that reads from a given MCPL-file. --- src/source.cpp | 67 -------------------------------------------------- 1 file changed, 67 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 99ec3a74d1..e43f03929b 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -437,73 +437,6 @@ CustomSourceWrapper::~CustomSourceWrapper() } -MCPLFileSource::~MCPLFileSource(){ - mcpl_close_file(mcpl_file); -} - -SourceSite MCPLFileSource::sample(uint64_t* seed) const -{ - size_t i_site = sites_.size() * prn(seed); - return sites_[i_site]; -} - -void MCPLFileSource::read_source_bank(vector &sites_) -{ - sites_.resize(n_sites); - for (int i=0;ipdgcode; - while ( pdg!=2112 && pdg!=22 && pdg!=11 && pdg!=-11) { - mcpl_particle=mcpl_read(mcpl_file); - pdg=mcpl_particle->pdgcode; - //should check for file exhaustion. This could happen if particles are other than - //neutrons, photons, electrons, or positrons. - } - - switch(pdg){ - case 2112: - omc_particle_.particle=ParticleType::neutron; - break; - case 22: - omc_particle_.particle=ParticleType::photon; - break; - case 11: - omc_particle_.particle=ParticleType::electron; - break; - case -11: - omc_particle_.particle=ParticleType::positron; - break; - } - - //particle is good, convert to openmc-formalism - omc_particle_.r.x=mcpl_particle->position[0]; - omc_particle_.r.y=mcpl_particle->position[1]; - omc_particle_.r.z=mcpl_particle->position[2]; - - omc_particle_.u.x=mcpl_particle->direction[0]; - omc_particle_.u.y=mcpl_particle->direction[1]; - omc_particle_.u.z=mcpl_particle->direction[2]; - - //mcpl stores kinetic energy in MeV - omc_particle_.E=mcpl_particle->ekin*1e6; - //mcpl stores time in ms - omc_particle_.time=mcpl_particle->time*1e-3; - omc_particle_.wgt=mcpl_particle->weight; - omc_particle_.delayed_group=0; - return omc_particle_; -} -#endif //OPENMC_MCPL - //============================================================================== // Non-member functions //============================================================================== From 52cf6823e6c1df7dbcc30b0c860412dc124a18a3 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 6 Sep 2022 02:22:21 +0200 Subject: [PATCH 098/265] wip add MCPL-out to openmc code for writing a source_bank/point compiles but is untested --- src/state_point.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/state_point.cpp b/src/state_point.cpp index 14a5411283..1b133a1215 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -643,6 +643,7 @@ void write_mcpl_source_point(const char *filename, bool surf_source_bank) } #endif + void write_source_bank(hid_t group_id, bool surf_source_bank) { hid_t banktype = h5banktype(); From 9d7105ebc7ff43d973f55d59a815d62be0a8ba5b Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 6 Sep 2022 02:22:21 +0200 Subject: [PATCH 099/265] wip add MCPL-out to openmc code for writing a source_bank/point compiles but is untested --- src/state_point.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index 1b133a1215..c41c3dd53d 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -603,6 +603,7 @@ void write_source_point(const char* filename, bool surf_source_bank) file_close(file_id); } + #ifdef OPENMC_MCPL void write_mcpl_source_point(const char *filename, bool surf_source_bank) { @@ -641,8 +642,8 @@ void write_mcpl_source_point(const char *filename, bool surf_source_bank) } } -#endif +#endif void write_source_bank(hid_t group_id, bool surf_source_bank) { From cd9eb5b1b237bbd420b7c2eef93023d3e1f1e20b Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Tue, 6 Sep 2022 23:06:19 +0200 Subject: [PATCH 100/265] add a trigger to simulation control --- src/simulation.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/simulation.cpp b/src/simulation.cpp index fcb115849d..7fda9d5239 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -408,10 +408,10 @@ void finalize_batch() write_source_point(filename.c_str(), true); } - if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ - auto filename = settings::path_output + ".mcpl"; - write_mcpl_source_point(filename.c_str(), true); - } +if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ + auto filename = settings::path_output + ".mcpl"; + write_mcpl_source_point(filename.c_str(), true); +} } From 8b783749341798cc9c8bc71d0ab374297824f1fc Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 10:59:28 +0200 Subject: [PATCH 101/265] fix typo --- src/simulation.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/simulation.cpp b/src/simulation.cpp index 7fda9d5239..fcb115849d 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -408,10 +408,10 @@ void finalize_batch() write_source_point(filename.c_str(), true); } -if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ - auto filename = settings::path_output + ".mcpl"; - write_mcpl_source_point(filename.c_str(), true); -} + if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ + auto filename = settings::path_output + ".mcpl"; + write_mcpl_source_point(filename.c_str(), true); + } } From 172fec23568ae6793c2b23c1b54e02c6b01483d7 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 5 Oct 2022 11:00:39 +0200 Subject: [PATCH 102/265] add cond. compilation guards for MCPL functions --- src/state_point.cpp | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index c41c3dd53d..14a5411283 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -603,7 +603,6 @@ void write_source_point(const char* filename, bool surf_source_bank) file_close(file_id); } - #ifdef OPENMC_MCPL void write_mcpl_source_point(const char *filename, bool surf_source_bank) { @@ -642,7 +641,6 @@ void write_mcpl_source_point(const char *filename, bool surf_source_bank) } } - #endif void write_source_bank(hid_t group_id, bool surf_source_bank) From 9065bdac3aeafe0d411c2d4a26ef873e39cb4c40 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Fri, 16 Sep 2022 16:07:22 +0200 Subject: [PATCH 103/265] refactor MCPL file read part of FileSource A new constructor is added to FileSource that reads from a given MCPL-file. --- src/source.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/source.cpp b/src/source.cpp index e43f03929b..3e1ddb3f38 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -436,7 +436,6 @@ CustomSourceWrapper::~CustomSourceWrapper() #endif } - //============================================================================== // Non-member functions //============================================================================== From 28cd0c5d3ae44a1ab3fe11f3ced08d6589530aa6 Mon Sep 17 00:00:00 2001 From: erkn Date: Wed, 5 Oct 2022 14:31:05 +0200 Subject: [PATCH 104/265] fix misnamed variable and remove accientally committed code --- src/source.cpp | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 3e1ddb3f38..d3037386b2 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -350,10 +350,19 @@ FileSource::FileSource(mcpl_file_t mcpl_file) //neutrons or photons } - if(mcpl_particle->pdgcode==2112) { - site_.particle=ParticleType::neutron; - } else if (mcpl_particle->pdgcode==22) { - site_.particle=ParticleType::photon; + switch(pdg){ + case 2112: + site_.particle=ParticleType::neutron; + break; + case 22: + site_.particle=ParticleType::photon; + break; + case 11: + site_.particle=ParticleType::electron; + break; + case -11: + site_.particle=ParticleType::positron; + break; } //particle is good, convert to openmc-formalism From 6e523fa1f8ca0b6eef6a5e110fc7ceb86446d8f6 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Thu, 6 Oct 2022 01:33:21 +0200 Subject: [PATCH 105/265] must have a full filename --- src/simulation.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/simulation.cpp b/src/simulation.cpp index fcb115849d..82fce7c221 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -409,7 +409,7 @@ void finalize_batch() } if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ - auto filename = settings::path_output + ".mcpl"; + auto filename = settings::path_output + "surface_source.mcpl"; write_mcpl_source_point(filename.c_str(), true); } From 93a9270efcf0697db410c21d184b4e0d933da875 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 11 Oct 2022 00:46:32 +0200 Subject: [PATCH 106/265] fix malformed format string --- src/state_point.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index 14a5411283..acae2e8d01 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -626,9 +626,9 @@ void write_mcpl_source_point(const char *filename, bool surf_source_bank) //write_attribute(file_id, "filetype", "source"); //write header stuff (oopy in xml-files as binary blobs for instance)) if (VERSION_DEV){ - line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}-development"); + line=fmt::format("OpenMC {0}.{1}.{2}-development",VERSION_MAJOR,VERSION_MINOR,VERSION_RELEASE); } else { - line=fmt::format("OpenMC {VERSION_MAJOR}.{VERSION_MINOR}.{VERSION_RELEASE}"); + line=fmt::format("OpenMC {0}.{1}.{2}",VERSION_MAJOR,VERSION_MINOR,VERSION_RELEASE); } mcpl_hdr_set_srcname(file_id,line.c_str()); } From 59a949de362f5133c43971636bcb71a557ae03e0 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 11 Oct 2022 00:48:44 +0200 Subject: [PATCH 107/265] fix typo causing unit length errors --- src/state_point.cpp | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index acae2e8d01..fb915484b3 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -803,9 +803,11 @@ void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) p.position[1]=_site->r.y; p.position[2]=_site->r.z; + //mcpl requires that the direction vector is unit length + //which is also the case in openmc p.direction[0]=_site->u.x; p.direction[1]=_site->u.y; - p.direction[2]=_site->u.x; + p.direction[2]=_site->u.z; //mcpl stores kinetic energy in MeV p.ekin=_site->E*1e-6; From 7759028d803d052f220abbc00a876a1c33b00949 Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 11 Oct 2022 02:00:33 +0200 Subject: [PATCH 108/265] enable mcpl surf_source_write in the python layer --- openmc/settings.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/openmc/settings.py b/openmc/settings.py index ad5a9b28ae..0937a3e480 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -171,6 +171,7 @@ class Settings: banked (int) :max_particles: Maximum number of particles to be banked on surfaces per process (int) + :mcpl: Output in the form of an MCPL-file (bool) survival_biasing : bool Indicate whether survival biasing is to be used tabular_legendre : dict @@ -652,7 +653,7 @@ class Settings: cv.check_type('surface source writing options', surf_source_write, Mapping) for key, value in surf_source_write.items(): cv.check_value('surface source writing key', key, - ('surface_ids', 'max_particles')) + ('surface_ids', 'max_particles', 'mcpl')) if key == 'surface_ids': cv.check_type('surface ids for source banking', value, Iterable, Integral) @@ -664,6 +665,9 @@ class Settings: value, Integral) cv.check_greater_than('maximum particle banks on surfaces per process', value, 0) + elif key == 'mcpl': + cv.check_type('write to an MCPL-format file', value, bool) + self._surf_source_write = surf_source_write @confidence_intervals.setter @@ -1032,6 +1036,9 @@ class Settings: if 'max_particles' in self._surf_source_write: subelement = ET.SubElement(element, "max_particles") subelement.text = str(self._surf_source_write['max_particles']) + if 'mcpl' in self._surf_source_write: + subelement = ET.SubElement(element, "mcpl") + subelement.text = str(self._surf_source_write['mcpl']).lower() def _create_confidence_intervals(self, root): if self._confidence_intervals is not None: From e3f1bdaca1f5144563c4ceac45f10e4b0b5b7963 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 12 Oct 2022 19:30:38 +0200 Subject: [PATCH 109/265] enable mcpl from the python layer if the source filename ends with mcpl use that --- openmc/source.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/openmc/source.py b/openmc/source.py index 48e14f6f71..fdb2d5bc25 100644 --- a/openmc/source.py +++ b/openmc/source.py @@ -223,7 +223,10 @@ class Source: if self.particle != 'neutron': element.set("particle", self.particle) if self.file is not None: - element.set("file", self.file) + if (self.file.endswith('.mcpl')): + element.set("mcpl", self.file) + else: + element.set("file", self.file) if self.library is not None: element.set("library", self.library) if self.parameters is not None: From ca396268b586719df5638057b9161dbb2cdb048a Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 12 Oct 2022 19:32:09 +0200 Subject: [PATCH 110/265] protect against compilation wo mcpl --- src/simulation.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/simulation.cpp b/src/simulation.cpp index 82fce7c221..d90c33ffd6 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -407,12 +407,12 @@ void finalize_batch() auto filename = settings::path_output + "surface_source.h5"; write_source_point(filename.c_str(), true); } - +#ifdef OPENMC_MCPL if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ auto filename = settings::path_output + "surface_source.mcpl"; write_mcpl_source_point(filename.c_str(), true); } - +#endif } From 94fb5f8fa6818f88c9fcf9007535a80846cb6c2d Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 12 Oct 2022 19:32:40 +0200 Subject: [PATCH 111/265] enable MPI mpi-nodes are gathered sequentially (as for h5) --- src/state_point.cpp | 28 +++++++++++++++++++++------- 1 file changed, 21 insertions(+), 7 deletions(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index fb915484b3..983147c62e 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -786,30 +786,40 @@ void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) } if (mpi::master) { - //write particles from the master node + // Particles are writeen to disk from the master node only + + // Save source bank sites since the array is overwritten below +#ifdef OPENMC_MPI + vector temp_source {source_bank->begin(), source_bank->end()}; +#endif + //loop over the other nodes and receive data - then write those. for (int i = 0; i < mpi::n_procs; ++i) { + // number of particles for node node i + size_t count[] { + static_cast((*bank_index)[i + 1] - (*bank_index)[i])}; + #ifdef OPENMC_MPI if (i>0) MPI_Recv(source_bank->data(), count[0], mpi::source_site, i, i, mpi::intracomm, MPI_STATUS_IGNORE); #endif - //now write the source_banke data again. + // now write the source_bank data again. for (vector::iterator _site=source_bank->begin(); _site!=source_bank->end();_site++){ - //particle is now at the iterator - //write it to the mcpl-file + // particle is now at the iterator + // write it to the mcpl-file mcpl_particle_t p; p.position[0]=_site->r.x; p.position[1]=_site->r.y; p.position[2]=_site->r.z; - //mcpl requires that the direction vector is unit length - //which is also the case in openmc + // mcpl requires that the direction vector is unit length + // which is also the case in openmc p.direction[0]=_site->u.x; p.direction[1]=_site->u.y; p.direction[2]=_site->u.z; - //mcpl stores kinetic energy in MeV + // mcpl stores kinetic energy in MeV p.ekin=_site->E*1e-6; p.time=_site->time*1e3; @@ -834,6 +844,10 @@ void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) mcpl_add_particle(file_id,&p); } } +#ifdef OPENMC_MPI + // Restore state of source bank + std::copy(temp_source.begin(), temp_source.end(), source_bank->begin()); +#endif } else { #ifdef OPENMC_MPI MPI_Send(source_bank->data(), count_size, mpi::source_site, 0, mpi::rank, From 81fa3b45a35595f4913845d5cc1a4580e173d0d7 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Thu, 13 Oct 2022 23:09:12 +0200 Subject: [PATCH 112/265] mcpl-file output simimlar to regular source output file --- include/openmc/settings.h | 1 + src/settings.cpp | 1 + src/simulation.cpp | 14 ++++++++++++++ 3 files changed, 16 insertions(+) diff --git a/include/openmc/settings.h b/include/openmc/settings.h index 66825867d8..5b755784e4 100644 --- a/include/openmc/settings.h +++ b/include/openmc/settings.h @@ -47,6 +47,7 @@ extern "C" bool run_CE; //!< run with continuous-energy data? extern bool source_latest; //!< write latest source at each batch? extern bool source_separate; //!< write source to separate file? extern bool source_write; //!< write source in HDF5 files? +extern bool source_mcpl_write; //!< write source in mcpl files? extern bool surf_source_write; //!< write surface source file? extern bool surf_mcpl_write; //!< write surface mcpl file? extern bool surf_source_read; //!< read surface source file? diff --git a/src/settings.cpp b/src/settings.cpp index d1762596c6..7aed383da1 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -60,6 +60,7 @@ bool run_CE {true}; bool source_latest {false}; bool source_separate {false}; bool source_write {true}; +bool source_mcpl_write {true}; bool surf_source_write {false}; bool surf_mcpl_write {false}; bool surf_source_read {false}; diff --git a/src/simulation.cpp b/src/simulation.cpp index d90c33ffd6..70053a9a89 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -399,6 +399,20 @@ void finalize_batch() auto filename = settings::path_output + "source.h5"; write_source_point(filename.c_str()); } + +#ifdef OPENMC_MCPL + if (contains(settings::sourcepoint_batch, simulation::current_batch) && + settings::source_mcpl_write && settings::source_separate) { + write_mcpl_source_point(nullptr); + } + + // Write a continously-overwritten source point if requested. + if (settings::source_latest && setting::source_mcpl_write) { + auto filename = settings::path_output + "source.mcpl"; + write_mcpl_source_point(filename.c_str()); + } +#endif + } // Write out surface source if requested. From 5da08f6b0e1aa687b242bab32facdd5f29cf0d9d Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Fri, 14 Oct 2022 01:40:52 +0200 Subject: [PATCH 113/265] fix logic to avoid writing both kinds of source file --- src/settings.cpp | 3 +++ src/simulation.cpp | 43 +++++++++++++++++++++++-------------------- 2 files changed, 26 insertions(+), 20 deletions(-) diff --git a/src/settings.cpp b/src/settings.cpp index 7aed383da1..9098eb6205 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -654,6 +654,9 @@ void read_settings_xml() if (check_for_node(node_sp, "write")) { source_write = get_node_value_bool(node_sp, "write"); } + if (check_for_node(node_sp, "mcpl")) { + source_write = get_node_value_bool(node_sp, "mcpl"); + } if (check_for_node(node_sp, "overwrite_latest")) { source_latest = get_node_value_bool(node_sp, "overwrite_latest"); source_separate = source_latest; diff --git a/src/simulation.cpp b/src/simulation.cpp index 70053a9a89..d7cc2237d5 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -389,30 +389,33 @@ void finalize_batch() if (settings::run_mode == RunMode::EIGENVALUE) { // Write out a separate source point if it's been specified for this batch - if (contains(settings::sourcepoint_batch, simulation::current_batch) && - settings::source_write && settings::source_separate) { - write_source_point(nullptr); - } - - // Write a continously-overwritten source point if requested. - if (settings::source_latest) { - auto filename = settings::path_output + "source.h5"; - write_source_point(filename.c_str()); - } - #ifdef OPENMC_MCPL - if (contains(settings::sourcepoint_batch, simulation::current_batch) && - settings::source_mcpl_write && settings::source_separate) { - write_mcpl_source_point(nullptr); - } + if(! settings::source_mcpl_write) { +#endif + if (contains(settings::sourcepoint_batch, simulation::current_batch) && + settings::source_write && settings::source_separate) { + write_source_point(nullptr); + } - // Write a continously-overwritten source point if requested. - if (settings::source_latest && setting::source_mcpl_write) { - auto filename = settings::path_output + "source.mcpl"; - write_mcpl_source_point(filename.c_str()); + // Write a continously-overwritten source point if requested. + if (settings::source_latest) { + auto filename = settings::path_output + "source.h5"; + write_source_point(filename.c_str()); + } +#ifdef OPENMC_MCPL + } else { + if (contains(settings::sourcepoint_batch, simulation::current_batch) && + settings::source_mcpl_write && settings::source_separate) { + write_mcpl_source_point(nullptr); + } + + // Write a continously-overwritten source point if requested. + if (settings::source_latest && settings::source_mcpl_write) { + auto filename = settings::path_output + "source.mcpl"; + write_mcpl_source_point(filename.c_str()); + } } #endif - } // Write out surface source if requested. From 344efa8de6454998dd55d00d6f213946d266cadf Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Fri, 14 Oct 2022 01:41:21 +0200 Subject: [PATCH 114/265] don't compress by default --- src/state_point.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index 983147c62e..d0fe92bdf5 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -637,7 +637,7 @@ void write_mcpl_source_point(const char *filename, bool surf_source_bank) if (mpi::master) { //change this - this is h5 specific - mcpl_closeandgzip_outfile(file_id); + mcpl_close_outfile(file_id); } } From 04edce7dc29543fe4e8f730f9ee516ae87c61195 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Fri, 14 Oct 2022 01:41:44 +0200 Subject: [PATCH 115/265] do read and write regression test almost dientical to source_file reg. test --- .../source_mcpl_file/results_true.dat | 2 +- .../source_mcpl_file/settings.xml | 6 +- .../regression_tests/source_mcpl_file/test.py | 146 +++++++++++------- 3 files changed, 97 insertions(+), 57 deletions(-) diff --git a/tests/regression_tests/source_mcpl_file/results_true.dat b/tests/regression_tests/source_mcpl_file/results_true.dat index f2209006a1..19460623f5 100644 --- a/tests/regression_tests/source_mcpl_file/results_true.dat +++ b/tests/regression_tests/source_mcpl_file/results_true.dat @@ -1,2 +1,2 @@ k-combined: -3.017557E-01 3.398770E-03 +3.039964E-01 3.654869E-04 diff --git a/tests/regression_tests/source_mcpl_file/settings.xml b/tests/regression_tests/source_mcpl_file/settings.xml index 8b1510e0ce..47b010bffe 100644 --- a/tests/regression_tests/source_mcpl_file/settings.xml +++ b/tests/regression_tests/source_mcpl_file/settings.xml @@ -1,11 +1,15 @@ + + 10 5 1000 - source.10.mcpl + + -4 -4 -4 4 4 4 + diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index f55a769047..a005fc2d83 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -1,65 +1,101 @@ -import os -import subprocess +#!/usr/bin/env python + import glob +import os -from tests.testing_harness import TestHarness +from tests.testing_harness import * -class SourceMCPLFileTestHarness(TestHarness): - def execute_test(self): - """Run OpenMC with the appropriate arguments and check the outputs.""" - try: - self._create_input() - self._test_input_created() - self._run_openmc() - self._test_output_created() - results = self._get_results() - self._write_results(results) - self._compare_results() - finally: - self._cleanup() +settings1=""" + + + + + 10 + 5 + 1000 + + + + -4 -4 -4 4 4 4 + + + +""" - def _create_input(self): - compiled=subprocess.run(['gcc','-o','gen_dummy_mcpl.out','gen_dummy_mcpl.c','-lm','-lmcpl']) - assert compiled==0, 'Could not compile mcpl-file generator code' - subprocess.run(['./gen_dummy_mcpl.out']) +settings2 = """ + + + 10 + 5 + 1000 + + + source.10.{0} + + +""" - def update_results(self): - """Update the results_true using the current version of OpenMC.""" - try: - self._create_input() - self._test_input_created() - self._run_openmc() - self._test_output_created() - results = self._get_results() - self._write_results(results) - self._overwrite_results() - finally: - self._cleanup() - def _test_input_created(self): - """Check that the input mcpl.file was generated as it should""" - mcplfile=glob.glob(os.path.join(os.getcwd(),'source.10.mcpl')) - assert len(mcplfile) == 1, 'Either multiple or no mcpl files ' \ - 'exist.' - assert mcplfile[0].endswith('mcpl'), \ - 'output file does not end with mcpl.' +class SourceFileTestHarness(TestHarness): + def execute_test(self): + """Run OpenMC with the appropriate arguments and check the outputs.""" + try: + self._run_openmc() + self._test_output_created() + self._run_openmc_restart() + results = self._get_results() + self._write_results(results) + self._compare_results() + finally: + self._cleanup() - def _test_output_created(self): - """Check that the output files were created""" - statepoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) - assert len(statepoint) == 1, 'Either multiple or no statepoint files ' \ - 'exist.' - assert statepoint[0].endswith('h5'), \ - 'statepoint file does not end with h5.' + def update_results(self): + """Update the results_true using the current version of OpenMC.""" + try: + self._run_openmc() + self._test_output_created() + self._run_openmc_restart() + results = self._get_results() + self._write_results(results) + self._overwrite_results() + finally: + self._cleanup() - def _cleanup(self): - super()._cleanup() - source_mcpl=glob.glob(os.path.join(os.getcwd(),'source*.mcpl')) - for f in source_mcpl: - if (os.path.exists(f)): - os.remove(f) + def _test_output_created(self): + """Make sure statepoint and source files have been created.""" + statepoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) + assert len(statepoint) == 1, 'Either multiple or no statepoint files ' \ + 'exist.' + assert statepoint[0].endswith('h5'), \ + 'Statepoint file is not a HDF5 file.' -def test_mcpl_source_file(): - harness = SourceMCPLFileTestHarness('source.10.mcpl') - harness.main() + source = glob.glob(os.path.join(os.getcwd(), 'source.10.mcpl*')) + assert len(source) == 1, 'Either multiple or no source files exist.' + assert source[0].endswith('mcpl') or source[0].endswith('mcpl.gz'), \ + 'Source file is not a MCPL file.' + + def _run_openmc_restart(self): + # Get the name of the source file. + source = glob.glob(os.path.join(os.getcwd(), 'source.10.*')) + + # Write the new settings.xml file. + with open('settings.xml','w') as fh: + fh.write(settings2.format(source[0].split('.')[-1])) + + # Run OpenMC. + self._run_openmc() + + def _cleanup(self): + TestHarness._cleanup(self) + output = glob.glob(os.path.join(os.getcwd(), 'source.*')) + #for f in output: + # if os.path.exists(f): + # os.remove(f) + with open('settings.xml','w') as fh: + fh.write(settings1) + + +def test_source_file(): + harness = SourceFileTestHarness('statepoint.10.h5') + harness.main() From 0e0cd0a22d059159a8799906f57d12cec99c1a89 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian Date: Mon, 13 Sep 2021 01:25:36 -0300 Subject: [PATCH 116/265] Added hooks for NCrystal --- CMakeLists.txt | 16 +++++++++ include/openmc/material.h | 8 +++++ include/openmc/particle_data.h | 3 ++ include/openmc/physics.h | 27 ++++++++++++++++ include/openmc/settings.h | 3 ++ openmc/material.py | 59 ++++++++++++++++++++++++++++++++++ src/material.cpp | 36 ++++++++++++++++++++- src/physics.cpp | 21 +++++++++++- src/settings.cpp | 4 +++ 9 files changed, 175 insertions(+), 2 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 521b46cfc6..7be54dc3e4 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -36,6 +36,7 @@ option(OPENMC_ENABLE_COVERAGE "Compile with coverage analysis flags" option(OPENMC_USE_DAGMC "Enable support for DAGMC (CAD) geometry" OFF) option(OPENMC_USE_LIBMESH "Enable support for libMesh unstructured mesh tallies" OFF) option(OPENMC_USE_MPI "Enable MPI" OFF) +option(OPENMC_USE_NCRYSTAL "Enable support for NCrystal scattering" OFF) # Warnings for deprecated options foreach(OLD_OPT IN ITEMS "openmp" "profile" "coverage" "dagmc" "libmesh") @@ -98,6 +99,14 @@ macro(find_package_write_status pkg) endif() endmacro() +#=============================================================================== +# NCrystal Scattering Support +#=============================================================================== + +if(OPENMC_USE_NCRYSTAL) + find_package(NCrystal REQUIRED PATH_SUFFIXES ./)#fixme +endif() + #=============================================================================== # DAGMC Geometry Support - need DAGMC/MOAB #=============================================================================== @@ -482,6 +491,13 @@ if (OPENMC_USE_MPI) target_link_libraries(libopenmc MPI::MPI_CXX) endif() +if(OPENMC_USE_NCRYSTAL) + target_compile_definitions(libopenmc PRIVATE NCRYSTAL) + target_link_libraries(libopenmc NCrystal::NCrystal) +endif() + + + #=============================================================================== # openmc executable #=============================================================================== diff --git a/include/openmc/material.h b/include/openmc/material.h index b251a3ca85..55f8ae20d1 100644 --- a/include/openmc/material.h +++ b/include/openmc/material.h @@ -15,6 +15,10 @@ #include "openmc/particle.h" #include "openmc/vector.h" +#ifdef NCRYSTAL +#include "NCrystal/NCrystal.hh" +#endif + namespace openmc { //============================================================================== @@ -157,6 +161,10 @@ public: std::string name_; //!< Name of material vector nuclide_; //!< Indices in nuclides vector vector element_; //!< Indices in elements vector +#ifdef NCRYSTAL + std::string cfg_; //!< NCrystal configuration string + std::shared_ptr m_NCrystal_mat_; +#endif xt::xtensor atom_density_; //!< Nuclide atom density in [atom/b-cm] double density_; //!< Total atom density in [atom/b-cm] double density_gpcc_; //!< Total atom density in [g/cm^3] diff --git a/include/openmc/particle_data.h b/include/openmc/particle_data.h index d3d00571a8..06ca5990a5 100644 --- a/include/openmc/particle_data.h +++ b/include/openmc/particle_data.h @@ -162,6 +162,9 @@ struct MacroXS { double fission; //!< macroscopic fission xs double nu_fission; //!< macroscopic production xs double photon_prod; //!< macroscopic photon production xs +#ifdef NCRYSTAL + double NCrystal_XS; //!< macroscopic cross section of processes handled by NCrystal +#endif // Photon cross sections double coherent; //!< macroscopic coherent xs diff --git a/include/openmc/physics.h b/include/openmc/physics.h index 262b3a8841..a1db072914 100644 --- a/include/openmc/physics.h +++ b/include/openmc/physics.h @@ -8,6 +8,10 @@ #include "openmc/reaction.h" #include "openmc/vector.h" +#ifdef NCRYSTAL +#include "NCrystal/NCRNG.hh" +#endif + namespace openmc { //============================================================================== @@ -101,6 +105,29 @@ void sample_secondary_photons(Particle& p, int i_nuclide); //! \param[in] p, particle to be split or rouletted with the weight window. void split_particle(Particle& p); +#ifdef NCRYSTAL +//============================================================================== +// NCrystal wrapper class for the OpenMC random number generator +//============================================================================== + +class NcrystalRNG_Wrapper : public NCrystal::RNGStream { + uint64_t* openmc_seed_; +public: + constexpr NcrystalRNG_Wrapper(uint64_t* s) noexcept : openmc_seed_(s) {} + //Can be cheaply created on the stack just before being used in calls to + //ProcImpl::Scatter objects, like: + // + // RNG_Wrapper rng(seed); + // +protected: + //double actualGenerate() override { return prn(openmc_seed_); } + double actualGenerate() override { + return std::max( std::numeric_limits::min(), prn(openmc_seed_) ); + } + +}; +#endif + } // namespace openmc #endif // OPENMC_PHYSICS_H diff --git a/include/openmc/settings.h b/include/openmc/settings.h index 1e061b235b..ba1a30e307 100644 --- a/include/openmc/settings.h +++ b/include/openmc/settings.h @@ -120,6 +120,9 @@ extern int trigger_batch_interval; //!< Batch interval for triggers extern "C" int verbosity; //!< How verbose to make output extern double weight_cutoff; //!< Weight cutoff for Russian roulette extern double weight_survive; //!< Survival weight after Russian roulette +#ifdef NCRYSTAL +extern double ncrystal_max_energy; // Energy in eV to switch between NCrystal and ENDF +#endif } // namespace settings //============================================================================== diff --git a/openmc/material.py b/openmc/material.py index e99eec52c4..1fe62961d9 100644 --- a/openmc/material.py +++ b/openmc/material.py @@ -118,6 +118,7 @@ class Material(IDManagerMixin): self._volume = None self._atoms = {} self._isotropic = [] + self._NCrystal_cfg = None # A list of tuples (nuclide, percent, percent type) self._nuclides = [] @@ -140,6 +141,8 @@ class Material(IDManagerMixin): string += '{: <16}\n'.format('\tS(a,b) Tables') + string += '{: <16}=\t{}\n'.format('\tNCrystal conf', self._NCrystal_cfg) + for sab in self._sab: string += '{: <16}=\t{}\n'.format('\tS(a,b)', sab) @@ -331,6 +334,48 @@ class Material(IDManagerMixin): return material + @classmethod + def from_NCrystal(cls, cfg): + """Create material from NCrystal configuration string + Density is set from the NCrystal value, + and material temperature from the configuration string. + + Parameters + ---------- + cfg : str + NCrystal configuration string + + Returns + ------- + openmc.Material + Material instance + + """ + + try: + import NCrystal + except ImportError: + raise SystemExit("ERROR: NCrystal Python module is required.") + + NC_mat = NCrystal.createInfo(cfg) + NC_comp = NC_mat.getComposition() + + # Create the Material + material = cls() + + for frac, atom in NC_comp: + if (atom.A() == 0): + material.add_element(atom.displayLabel(), frac, 'ao') + else: + material.add_nuclide(atom.displayLabel(), frac, 'ao') + + material._NCrystal_cfg = cfg + material._density_units = "g/cm3" + material._density = NC_mat.getDensity() + material.temperature = NC_mat.getTemperature() + + return material + def add_volume_information(self, volume_calc): """Add volume information to a material. @@ -405,6 +450,9 @@ class Material(IDManagerMixin): 'macroscopic data-set has already been added'.format(self._id) raise ValueError(msg) + if self._NCrystal_cfg is not None: + raise ValueError("Cannot add nuclides to NCrystal material") + # If nuclide name doesn't look valid, give a warning try: Z, _, _ = openmc.data.zam(nuclide) @@ -609,6 +657,9 @@ class Material(IDManagerMixin): raise ValueError("Element name should be given by the " "element's symbol or name, e.g., 'Zr', 'zirconium'") + if self._NCrystal_cfg is not None: + raise ValueError("Cannot add elements to NCrystal material") + # Allow for element identifier to be given as a symbol or name if len(element) > 2: el = element.lower() @@ -1135,6 +1186,14 @@ class Material(IDManagerMixin): if self._volume: element.set("volume", str(self._volume)) + if self._NCrystal_cfg: + if self._sab: + raise ValueError("NCrystal materials are not compatible with S(a,b).") + if self._macroscopic is not None: + raise ValueError("NCrystal materials are not compatible macroscopic cross sections.") + + element.set("cfg", str(self._NCrystal_cfg)) + # Create temperature XML subelement if self.temperature is not None: element.set("temperature", str(self.temperature)) diff --git a/src/material.cpp b/src/material.cpp index 30dfa5ed50..d7fae83617 100644 --- a/src/material.cpp +++ b/src/material.cpp @@ -60,6 +60,14 @@ Material::Material(pugi::xml_node node) name_ = get_node_value(node, "name"); } +#ifdef NCRYSTAL + if (check_for_node(node, "cfg")) { + cfg_ = get_node_value(node, "cfg"); + write_message(5, "NCrystal config string: >>{}<< ", cfg_); + m_NCrystal_mat_ = NCrystal::FactImpl::createScatter(cfg_); + } +#endif + if (check_for_node(node, "depletable")) { depletable_ = get_node_value_bool(node, "depletable"); } @@ -792,6 +800,17 @@ void Material::calculate_neutron_xs(Particle& p) const // Initialize position in i_sab_nuclides int j = 0; +#ifdef NCRYSTAL + double ncrystal_xs = -1; + + if (m_NCrystal_mat_ != nullptr && p.E() < settings::ncrystal_max_energy){ + // Calculate scattering XS per atom with NCrystal, only once per material + NCrystal::CachePtr dummyCache; + auto nc_energy = NCrystal::NeutronEnergy{p.E()}; + ncrystal_xs = m_NCrystal_mat_->crossSection( dummyCache, nc_energy, {p.u().x, p.u().y, p.u().z}).get(); + } +#endif + // Add contribution from each nuclide in material for (int i = 0; i < nuclide_.size(); ++i) { // ====================================================================== @@ -830,10 +849,25 @@ void Material::calculate_neutron_xs(Particle& p) const int i_nuclide = nuclide_[i]; // Calculate microscopic cross section for this nuclide - const auto& micro {p.neutron_xs(i_nuclide)}; +#ifndef NCRYSTAL + const +#endif + auto& micro {p.neutron_xs(i_nuclide)}; if (p.E() != micro.last_E || p.sqrtkT() != micro.last_sqrtkT || i_sab != micro.index_sab || sab_frac != micro.sab_frac) { data::nuclides[i_nuclide]->calculate_xs(i_sab, i_grid, sab_frac, p); +#ifdef NCRYSTAL + if (ncrystal_xs >= 0.0){ + if ( micro.thermal > 0 || micro.thermal_elastic > 0) { + fatal_error("S(a,b) treatment and NCrystal are not compatible."); + } + data::nuclides[i_nuclide]->calculate_elastic_xs(p); + // remove free atom cross section + // and replace it by scattering cross section per atom from NCrystal + micro.total = micro.total - micro.elastic + ncrystal_xs; + micro.elastic = ncrystal_xs; + } +#endif } // ====================================================================== diff --git a/src/physics.cpp b/src/physics.cpp index bcdcf7ecf9..9eff4aed7e 100644 --- a/src/physics.cpp +++ b/src/physics.cpp @@ -140,8 +140,27 @@ void sample_neutron_reaction(Particle& p) // Sample a scattering reaction and determine the secondary energy of the // exiting neutron - scatter(p, i_nuclide); +#ifdef NCRYSTAL + if (model::materials[p.material_]->m_NCrystal_mat_ != nullptr && p.E() < settings::ncrystal_max_energy){ + + NcrystalRNG_Wrapper rng(p.current_seed()); // Initialize RNG + //create a cache pointer for multi thread physics + NCrystal::CachePtr dummyCache;//fixme: avoid recreating here (triggers malloc) + auto nc_energy = NCrystal::NeutronEnergy{p.E()}; + auto outcome = model::materials[p.material_]->m_NCrystal_mat_->sampleScatter( dummyCache, rng , nc_energy, {p.u().x, p.u().y, p.u().z}); + p.E_last() = p.E(); + p.E() = outcome.ekin.get(); + Direction u_old {p.u()}; + p.u() = Direction(outcome.direction[0], outcome.direction[1], outcome.direction[2]); + p.mu_ = u_old.dot(p.u()); + p.event_mt_ = ELASTIC;//fixme: define a new label for NCrystal? + } else { + scatter(p, i_nuclide); + } +#else + scatter(p, i_nuclide); +#endif // Advance URR seed stream 'N' times after energy changes if (p.E() != p.E_last()) { p.stream() = STREAM_URR_PTABLE; diff --git a/src/settings.cpp b/src/settings.cpp index eb0d4936c7..3f3e970541 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -118,6 +118,10 @@ int verbosity {7}; double weight_cutoff {0.25}; double weight_survive {1.0}; +#ifdef NCRYSTAL +double ncrystal_max_energy{5.0}; +#endif + } // namespace settings //============================================================================== From 0f33e0b11c6add029f354eb3e5c89b002eec7500 Mon Sep 17 00:00:00 2001 From: Thomas Kittelmann Date: Tue, 13 Sep 2022 14:22:04 +0200 Subject: [PATCH 117/265] Add temporary requirement of natural elements in NCrystal materials --- openmc/material.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/openmc/material.py b/openmc/material.py index 1fe62961d9..0a293eb0f8 100644 --- a/openmc/material.py +++ b/openmc/material.py @@ -364,10 +364,9 @@ class Material(IDManagerMixin): material = cls() for frac, atom in NC_comp: - if (atom.A() == 0): - material.add_element(atom.displayLabel(), frac, 'ao') - else: - material.add_nuclide(atom.displayLabel(), frac, 'ao') + if not atom.isNaturalElement(): + raise ValueError('NCrystal-OpenMC interface only works with natural elements for now.') + material.add_element(atom.elementName(), frac, 'ao') material._NCrystal_cfg = cfg material._density_units = "g/cm3" From 9c54ac0b6b53336f834b5f868aa85e3e140239f8 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian Date: Tue, 13 Sep 2022 16:07:50 +0200 Subject: [PATCH 118/265] Fix access to private attributes --- include/openmc/material.h | 6 ++++++ src/physics.cpp | 9 ++++----- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/include/openmc/material.h b/include/openmc/material.h index 55f8ae20d1..eef557088c 100644 --- a/include/openmc/material.h +++ b/include/openmc/material.h @@ -155,6 +155,12 @@ public: //! \return Temperature in [K] double temperature() const; +#ifdef NCRYSTAL + //! Gwet pointer to NCrystal material object + //! \return Pointer to NCrystal material object + std::shared_ptr m_NCrystal_mat() const {return m_NCrystal_mat_}; +#endif + //---------------------------------------------------------------------------- // Data int32_t id_ {C_NONE}; //!< Unique ID diff --git a/src/physics.cpp b/src/physics.cpp index 9eff4aed7e..948307521e 100644 --- a/src/physics.cpp +++ b/src/physics.cpp @@ -142,19 +142,18 @@ void sample_neutron_reaction(Particle& p) // exiting neutron #ifdef NCRYSTAL - if (model::materials[p.material_]->m_NCrystal_mat_ != nullptr && p.E() < settings::ncrystal_max_energy){ - + if (model::materials[p.material()]->m_NCrystal_mat() != nullptr && p.E() < settings::ncrystal_max_energy){ NcrystalRNG_Wrapper rng(p.current_seed()); // Initialize RNG //create a cache pointer for multi thread physics NCrystal::CachePtr dummyCache;//fixme: avoid recreating here (triggers malloc) auto nc_energy = NCrystal::NeutronEnergy{p.E()}; - auto outcome = model::materials[p.material_]->m_NCrystal_mat_->sampleScatter( dummyCache, rng , nc_energy, {p.u().x, p.u().y, p.u().z}); + auto outcome = model::materials[p.material()]->m_NCrystal_mat()->sampleScatter( dummyCache, rng , nc_energy, {p.u().x, p.u().y, p.u().z}); p.E_last() = p.E(); p.E() = outcome.ekin.get(); Direction u_old {p.u()}; p.u() = Direction(outcome.direction[0], outcome.direction[1], outcome.direction[2]); - p.mu_ = u_old.dot(p.u()); - p.event_mt_ = ELASTIC;//fixme: define a new label for NCrystal? + p.mu() = u_old.dot(p.u()); + p.event_mt() = ELASTIC;//fixme: define a new label for NCrystal? } else { scatter(p, i_nuclide); } From 70d5c76ebd70cf43349423f17028c3cb1dfe1daa Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian Date: Tue, 13 Sep 2022 16:10:05 +0200 Subject: [PATCH 119/265] Fixed material.h --- include/openmc/material.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/openmc/material.h b/include/openmc/material.h index eef557088c..10e64773e3 100644 --- a/include/openmc/material.h +++ b/include/openmc/material.h @@ -158,7 +158,7 @@ public: #ifdef NCRYSTAL //! Gwet pointer to NCrystal material object //! \return Pointer to NCrystal material object - std::shared_ptr m_NCrystal_mat() const {return m_NCrystal_mat_}; + std::shared_ptr m_NCrystal_mat() const {return m_NCrystal_mat_; }; #endif //---------------------------------------------------------------------------- From 29a10eafd3db601ffa9a7e7bf882431c150ee1b2 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian Date: Fri, 16 Sep 2022 09:03:09 -0300 Subject: [PATCH 120/265] Removed MacroNCrystalXS This was left from a previous implementation. Now it is not needed because NCrystal just takes over all neutron scattering events below a given energy threshold. --- include/openmc/particle_data.h | 3 --- 1 file changed, 3 deletions(-) diff --git a/include/openmc/particle_data.h b/include/openmc/particle_data.h index 06ca5990a5..d3d00571a8 100644 --- a/include/openmc/particle_data.h +++ b/include/openmc/particle_data.h @@ -162,9 +162,6 @@ struct MacroXS { double fission; //!< macroscopic fission xs double nu_fission; //!< macroscopic production xs double photon_prod; //!< macroscopic photon production xs -#ifdef NCRYSTAL - double NCrystal_XS; //!< macroscopic cross section of processes handled by NCrystal -#endif // Photon cross sections double coherent; //!< macroscopic coherent xs From 2e19260dea9176f03f2d5d80be19c8c819d339d3 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian Date: Mon, 26 Sep 2022 11:19:54 +0200 Subject: [PATCH 121/265] Implement recommended changes --- CMakeLists.txt | 2 +- include/openmc/material.h | 8 ++++---- include/openmc/physics.h | 10 ++-------- openmc/material.py | 31 ++++++++++++++----------------- src/material.cpp | 16 +++++++++------- src/physics.cpp | 10 +++++----- 6 files changed, 35 insertions(+), 42 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 7be54dc3e4..7080accfd0 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -104,7 +104,7 @@ endmacro() #=============================================================================== if(OPENMC_USE_NCRYSTAL) - find_package(NCrystal REQUIRED PATH_SUFFIXES ./)#fixme + find_package(NCrystal REQUIRED) endif() #=============================================================================== diff --git a/include/openmc/material.h b/include/openmc/material.h index 10e64773e3..30d8ffb7d0 100644 --- a/include/openmc/material.h +++ b/include/openmc/material.h @@ -156,9 +156,9 @@ public: double temperature() const; #ifdef NCRYSTAL - //! Gwet pointer to NCrystal material object + //! Get pointer to NCrystal material object //! \return Pointer to NCrystal material object - std::shared_ptr m_NCrystal_mat() const {return m_NCrystal_mat_; }; + std::shared_ptr ncrystal_mat() const {return ncrystal_mat_; }; #endif //---------------------------------------------------------------------------- @@ -168,8 +168,8 @@ public: vector nuclide_; //!< Indices in nuclides vector vector element_; //!< Indices in elements vector #ifdef NCRYSTAL - std::string cfg_; //!< NCrystal configuration string - std::shared_ptr m_NCrystal_mat_; + std::string ncrystal_cfg_; //!< NCrystal configuration string + std::shared_ptr ncrystal_mat_; #endif xt::xtensor atom_density_; //!< Nuclide atom density in [atom/b-cm] double density_; //!< Total atom density in [atom/b-cm] diff --git a/include/openmc/physics.h b/include/openmc/physics.h index a1db072914..109f7caffb 100644 --- a/include/openmc/physics.h +++ b/include/openmc/physics.h @@ -110,17 +110,11 @@ void split_particle(Particle& p); // NCrystal wrapper class for the OpenMC random number generator //============================================================================== -class NcrystalRNG_Wrapper : public NCrystal::RNGStream { +class NCrystalRNGWrapper : public NCrystal::RNGStream { uint64_t* openmc_seed_; public: - constexpr NcrystalRNG_Wrapper(uint64_t* s) noexcept : openmc_seed_(s) {} - //Can be cheaply created on the stack just before being used in calls to - //ProcImpl::Scatter objects, like: - // - // RNG_Wrapper rng(seed); - // + constexpr NCrystalRNGWrapper(uint64_t* seed) noexcept : openmc_seed_(seed) {} protected: - //double actualGenerate() override { return prn(openmc_seed_); } double actualGenerate() override { return std::max( std::numeric_limits::min(), prn(openmc_seed_) ); } diff --git a/openmc/material.py b/openmc/material.py index 0a293eb0f8..15d1f8ac9a 100644 --- a/openmc/material.py +++ b/openmc/material.py @@ -118,7 +118,7 @@ class Material(IDManagerMixin): self._volume = None self._atoms = {} self._isotropic = [] - self._NCrystal_cfg = None + self._ncrystal_cfg = None # A list of tuples (nuclide, percent, percent type) self._nuclides = [] @@ -141,7 +141,7 @@ class Material(IDManagerMixin): string += '{: <16}\n'.format('\tS(a,b) Tables') - string += '{: <16}=\t{}\n'.format('\tNCrystal conf', self._NCrystal_cfg) + string += '{: <16}=\t{}\n'.format('\tNCrystal conf', self._ncrystal_cfg) for sab in self._sab: string += '{: <16}=\t{}\n'.format('\tS(a,b)', sab) @@ -335,7 +335,7 @@ class Material(IDManagerMixin): return material @classmethod - def from_NCrystal(cls, cfg): + def from_ncrystal(cls, cfg): """Create material from NCrystal configuration string Density is set from the NCrystal value, and material temperature from the configuration string. @@ -352,26 +352,23 @@ class Material(IDManagerMixin): """ - try: - import NCrystal - except ImportError: - raise SystemExit("ERROR: NCrystal Python module is required.") + import NCrystal - NC_mat = NCrystal.createInfo(cfg) - NC_comp = NC_mat.getComposition() + nc_mat = NCrystal.createInfo(cfg) + nc_comp = nc_mat.getComposition() # Create the Material material = cls() - for frac, atom in NC_comp: + for frac, atom in nc_comp: if not atom.isNaturalElement(): raise ValueError('NCrystal-OpenMC interface only works with natural elements for now.') material.add_element(atom.elementName(), frac, 'ao') - material._NCrystal_cfg = cfg + material._ncrystal_cfg = cfg material._density_units = "g/cm3" - material._density = NC_mat.getDensity() - material.temperature = NC_mat.getTemperature() + material._density = nc_mat.getDensity() + material.temperature = nc_mat.getTemperature() return material @@ -449,7 +446,7 @@ class Material(IDManagerMixin): 'macroscopic data-set has already been added'.format(self._id) raise ValueError(msg) - if self._NCrystal_cfg is not None: + if self._ncrystal_cfg is not None: raise ValueError("Cannot add nuclides to NCrystal material") # If nuclide name doesn't look valid, give a warning @@ -656,7 +653,7 @@ class Material(IDManagerMixin): raise ValueError("Element name should be given by the " "element's symbol or name, e.g., 'Zr', 'zirconium'") - if self._NCrystal_cfg is not None: + if self._ncrystal_cfg is not None: raise ValueError("Cannot add elements to NCrystal material") # Allow for element identifier to be given as a symbol or name @@ -1185,13 +1182,13 @@ class Material(IDManagerMixin): if self._volume: element.set("volume", str(self._volume)) - if self._NCrystal_cfg: + if self._ncrystal_cfg: if self._sab: raise ValueError("NCrystal materials are not compatible with S(a,b).") if self._macroscopic is not None: raise ValueError("NCrystal materials are not compatible macroscopic cross sections.") - element.set("cfg", str(self._NCrystal_cfg)) + element.set("cfg", str(self._ncrystal_cfg)) # Create temperature XML subelement if self.temperature is not None: diff --git a/src/material.cpp b/src/material.cpp index d7fae83617..13acbba1f1 100644 --- a/src/material.cpp +++ b/src/material.cpp @@ -63,8 +63,8 @@ Material::Material(pugi::xml_node node) #ifdef NCRYSTAL if (check_for_node(node, "cfg")) { cfg_ = get_node_value(node, "cfg"); - write_message(5, "NCrystal config string: >>{}<< ", cfg_); - m_NCrystal_mat_ = NCrystal::FactImpl::createScatter(cfg_); + write_message(5, "NCrystal config string: '{}'", ncrystal_cfg_); + ncrystal_mat_ = NCrystal::FactImpl::createScatter(ncrystal_cfg_); } #endif @@ -803,11 +803,11 @@ void Material::calculate_neutron_xs(Particle& p) const #ifdef NCRYSTAL double ncrystal_xs = -1; - if (m_NCrystal_mat_ != nullptr && p.E() < settings::ncrystal_max_energy){ + if (ncrystal_mat_ && p.E() < settings::ncrystal_max_energy){ // Calculate scattering XS per atom with NCrystal, only once per material - NCrystal::CachePtr dummyCache; + NCrystal::CachePtr dummy_cache; auto nc_energy = NCrystal::NeutronEnergy{p.E()}; - ncrystal_xs = m_NCrystal_mat_->crossSection( dummyCache, nc_energy, {p.u().x, p.u().y, p.u().z}).get(); + ncrystal_xs = ncrystal_mat_->crossSection( dummy_cache, nc_energy, {p.u().x, p.u().y, p.u().z}).get(); } #endif @@ -849,8 +849,10 @@ void Material::calculate_neutron_xs(Particle& p) const int i_nuclide = nuclide_[i]; // Calculate microscopic cross section for this nuclide -#ifndef NCRYSTAL - const +#ifdef NCRYSTAL + auto& micro {p.neutron_xs(i_nuclide)}; +#else + const auto& micro {p.neutron_xs(i_nuclide)}; #endif auto& micro {p.neutron_xs(i_nuclide)}; if (p.E() != micro.last_E || p.sqrtkT() != micro.last_sqrtkT || diff --git a/src/physics.cpp b/src/physics.cpp index 948307521e..bad4997727 100644 --- a/src/physics.cpp +++ b/src/physics.cpp @@ -142,18 +142,18 @@ void sample_neutron_reaction(Particle& p) // exiting neutron #ifdef NCRYSTAL - if (model::materials[p.material()]->m_NCrystal_mat() != nullptr && p.E() < settings::ncrystal_max_energy){ - NcrystalRNG_Wrapper rng(p.current_seed()); // Initialize RNG + if (model::materials[p.material()]->ncrystal_mat() && p.E() < settings::ncrystal_max_energy){ + NCrystalRNGWrapper rng(p.current_seed()); // Initialize RNG //create a cache pointer for multi thread physics - NCrystal::CachePtr dummyCache;//fixme: avoid recreating here (triggers malloc) + NCrystal::CachePtr dummy_cache; auto nc_energy = NCrystal::NeutronEnergy{p.E()}; - auto outcome = model::materials[p.material()]->m_NCrystal_mat()->sampleScatter( dummyCache, rng , nc_energy, {p.u().x, p.u().y, p.u().z}); + auto outcome = model::materials[p.material()]->ncrystal_mat()->sampleScatter( dummy_cache, rng , nc_energy, {p.u().x, p.u().y, p.u().z}); p.E_last() = p.E(); p.E() = outcome.ekin.get(); Direction u_old {p.u()}; p.u() = Direction(outcome.direction[0], outcome.direction[1], outcome.direction[2]); p.mu() = u_old.dot(p.u()); - p.event_mt() = ELASTIC;//fixme: define a new label for NCrystal? + p.event_mt() = ELASTIC; } else { scatter(p, i_nuclide); } From 5afcc9e49b60ec1c5e2290d4725bac7a96e1692e Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian Date: Mon, 26 Sep 2022 11:30:39 +0200 Subject: [PATCH 122/265] Apply clang-format --- include/openmc/material.h | 13 ++++++++----- include/openmc/physics.h | 17 ++++++++++------- include/openmc/settings.h | 3 ++- src/material.cpp | 33 ++++++++++++++++++--------------- src/physics.cpp | 18 +++++++++++------- src/settings.cpp | 2 +- 6 files changed, 50 insertions(+), 36 deletions(-) diff --git a/include/openmc/material.h b/include/openmc/material.h index 30d8ffb7d0..47e3e6a167 100644 --- a/include/openmc/material.h +++ b/include/openmc/material.h @@ -158,15 +158,18 @@ public: #ifdef NCRYSTAL //! Get pointer to NCrystal material object //! \return Pointer to NCrystal material object - std::shared_ptr ncrystal_mat() const {return ncrystal_mat_; }; + std::shared_ptr ncrystal_mat() const + { + return ncrystal_mat_; + }; #endif //---------------------------------------------------------------------------- // Data - int32_t id_ {C_NONE}; //!< Unique ID - std::string name_; //!< Name of material - vector nuclide_; //!< Indices in nuclides vector - vector element_; //!< Indices in elements vector + int32_t id_ {C_NONE}; //!< Unique ID + std::string name_; //!< Name of material + vector nuclide_; //!< Indices in nuclides vector + vector element_; //!< Indices in elements vector #ifdef NCRYSTAL std::string ncrystal_cfg_; //!< NCrystal configuration string std::shared_ptr ncrystal_mat_; diff --git a/include/openmc/physics.h b/include/openmc/physics.h index 109f7caffb..23995e7af9 100644 --- a/include/openmc/physics.h +++ b/include/openmc/physics.h @@ -111,14 +111,17 @@ void split_particle(Particle& p); //============================================================================== class NCrystalRNGWrapper : public NCrystal::RNGStream { - uint64_t* openmc_seed_; -public: - constexpr NCrystalRNGWrapper(uint64_t* seed) noexcept : openmc_seed_(seed) {} -protected: - double actualGenerate() override { - return std::max( std::numeric_limits::min(), prn(openmc_seed_) ); - } + uint64_t* openmc_seed_; +public: + constexpr NCrystalRNGWrapper(uint64_t* seed) noexcept : openmc_seed_(seed) {} + +protected: + double actualGenerate() override + { + return std::max( + std::numeric_limits::min(), prn(openmc_seed_)); + } }; #endif diff --git a/include/openmc/settings.h b/include/openmc/settings.h index ba1a30e307..9bb447005c 100644 --- a/include/openmc/settings.h +++ b/include/openmc/settings.h @@ -121,7 +121,8 @@ extern "C" int verbosity; //!< How verbose to make output extern double weight_cutoff; //!< Weight cutoff for Russian roulette extern double weight_survive; //!< Survival weight after Russian roulette #ifdef NCRYSTAL -extern double ncrystal_max_energy; // Energy in eV to switch between NCrystal and ENDF +extern double + ncrystal_max_energy; //!< Energy in eV to switch between NCrystal and ENDF #endif } // namespace settings diff --git a/src/material.cpp b/src/material.cpp index 13acbba1f1..e894084e29 100644 --- a/src/material.cpp +++ b/src/material.cpp @@ -64,7 +64,7 @@ Material::Material(pugi::xml_node node) if (check_for_node(node, "cfg")) { cfg_ = get_node_value(node, "cfg"); write_message(5, "NCrystal config string: '{}'", ncrystal_cfg_); - ncrystal_mat_ = NCrystal::FactImpl::createScatter(ncrystal_cfg_); + ncrystal_mat_ = NCrystal::FactImpl::createScatter(ncrystal_cfg_); } #endif @@ -375,8 +375,8 @@ void Material::finalize() this->init_thermal(); } -// Normalize density -this->normalize_density(); + // Normalize density + this->normalize_density(); } void Material::normalize_density() @@ -803,11 +803,14 @@ void Material::calculate_neutron_xs(Particle& p) const #ifdef NCRYSTAL double ncrystal_xs = -1; - if (ncrystal_mat_ && p.E() < settings::ncrystal_max_energy){ + if (ncrystal_mat_ && p.E() < settings::ncrystal_max_energy) { // Calculate scattering XS per atom with NCrystal, only once per material NCrystal::CachePtr dummy_cache; - auto nc_energy = NCrystal::NeutronEnergy{p.E()}; - ncrystal_xs = ncrystal_mat_->crossSection( dummy_cache, nc_energy, {p.u().x, p.u().y, p.u().z}).get(); + auto nc_energy = NCrystal::NeutronEnergy {p.E()}; + ncrystal_xs = + ncrystal_mat_ + ->crossSection(dummy_cache, nc_energy, {p.u().x, p.u().y, p.u().z}) + .get(); } #endif @@ -859,15 +862,15 @@ void Material::calculate_neutron_xs(Particle& p) const i_sab != micro.index_sab || sab_frac != micro.sab_frac) { data::nuclides[i_nuclide]->calculate_xs(i_sab, i_grid, sab_frac, p); #ifdef NCRYSTAL - if (ncrystal_xs >= 0.0){ - if ( micro.thermal > 0 || micro.thermal_elastic > 0) { - fatal_error("S(a,b) treatment and NCrystal are not compatible."); - } - data::nuclides[i_nuclide]->calculate_elastic_xs(p); - // remove free atom cross section - // and replace it by scattering cross section per atom from NCrystal - micro.total = micro.total - micro.elastic + ncrystal_xs; - micro.elastic = ncrystal_xs; + if (ncrystal_xs >= 0.0) { + if (micro.thermal > 0 || micro.thermal_elastic > 0) { + fatal_error("S(a,b) treatment and NCrystal are not compatible."); + } + data::nuclides[i_nuclide]->calculate_elastic_xs(p); + // remove free atom cross section + // and replace it by scattering cross section per atom from NCrystal + micro.total = micro.total - micro.elastic + ncrystal_xs; + micro.elastic = ncrystal_xs; } #endif } diff --git a/src/physics.cpp b/src/physics.cpp index bad4997727..e19640314e 100644 --- a/src/physics.cpp +++ b/src/physics.cpp @@ -138,20 +138,24 @@ void sample_neutron_reaction(Particle& p) if (!p.alive()) return; - // Sample a scattering reaction and determine the secondary energy of the - // exiting neutron + // Sample a scattering reaction and determine the secondary energy of the + // exiting neutron #ifdef NCRYSTAL - if (model::materials[p.material()]->ncrystal_mat() && p.E() < settings::ncrystal_max_energy){ + if (model::materials[p.material()]->ncrystal_mat() && + p.E() < settings::ncrystal_max_energy) { NCrystalRNGWrapper rng(p.current_seed()); // Initialize RNG - //create a cache pointer for multi thread physics + // create a cache pointer for multi thread physics NCrystal::CachePtr dummy_cache; - auto nc_energy = NCrystal::NeutronEnergy{p.E()}; - auto outcome = model::materials[p.material()]->ncrystal_mat()->sampleScatter( dummy_cache, rng , nc_energy, {p.u().x, p.u().y, p.u().z}); + auto nc_energy = NCrystal::NeutronEnergy {p.E()}; + auto outcome = + model::materials[p.material()]->ncrystal_mat()->sampleScatter( + dummy_cache, rng, nc_energy, {p.u().x, p.u().y, p.u().z}); p.E_last() = p.E(); p.E() = outcome.ekin.get(); Direction u_old {p.u()}; - p.u() = Direction(outcome.direction[0], outcome.direction[1], outcome.direction[2]); + p.u() = Direction( + outcome.direction[0], outcome.direction[1], outcome.direction[2]); p.mu() = u_old.dot(p.u()); p.event_mt() = ELASTIC; } else { diff --git a/src/settings.cpp b/src/settings.cpp index 3f3e970541..87c24eedd3 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -119,7 +119,7 @@ double weight_cutoff {0.25}; double weight_survive {1.0}; #ifdef NCRYSTAL -double ncrystal_max_energy{5.0}; +double ncrystal_max_energy {5.0}; #endif } // namespace settings From fdf763e801b1439da96009fd5dadeadeb93e36f7 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian Date: Mon, 26 Sep 2022 12:35:12 +0200 Subject: [PATCH 123/265] Couple of fixes --- src/material.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/material.cpp b/src/material.cpp index e894084e29..9531e9f43a 100644 --- a/src/material.cpp +++ b/src/material.cpp @@ -62,7 +62,7 @@ Material::Material(pugi::xml_node node) #ifdef NCRYSTAL if (check_for_node(node, "cfg")) { - cfg_ = get_node_value(node, "cfg"); + ncrystal_cfg_ = get_node_value(node, "cfg"); write_message(5, "NCrystal config string: '{}'", ncrystal_cfg_); ncrystal_mat_ = NCrystal::FactImpl::createScatter(ncrystal_cfg_); } @@ -857,7 +857,6 @@ void Material::calculate_neutron_xs(Particle& p) const #else const auto& micro {p.neutron_xs(i_nuclide)}; #endif - auto& micro {p.neutron_xs(i_nuclide)}; if (p.E() != micro.last_E || p.sqrtkT() != micro.last_sqrtkT || i_sab != micro.index_sab || sab_frac != micro.sab_frac) { data::nuclides[i_nuclide]->calculate_xs(i_sab, i_grid, sab_frac, p); From 52ee2c37ced8fce859d2ec6a06c6909dd0d04b44 Mon Sep 17 00:00:00 2001 From: Thomas Kittelmann Date: Thu, 20 Oct 2022 11:36:22 +0200 Subject: [PATCH 124/265] Print where NCrystal was found as suggested by @paulromano Co-authored-by: Paul Romano --- CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/CMakeLists.txt b/CMakeLists.txt index 7080accfd0..2815230d43 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -105,6 +105,7 @@ endmacro() if(OPENMC_USE_NCRYSTAL) find_package(NCrystal REQUIRED) + message(STATUS "Found NCrystal: ${NCrystal_DIR} (version ${NCrystal_VERSION})") endif() #=============================================================================== From a5b811ec899470f9b0bb3e387f0f672ae8490321 Mon Sep 17 00:00:00 2001 From: Thomas Kittelmann Date: Thu, 20 Oct 2022 13:25:05 +0200 Subject: [PATCH 125/265] Use new NCrystal getFlattenedComposition method to better support more complicated materials --- openmc/material.py | 63 +++++++++++++++++++++++++++++++++------------- 1 file changed, 46 insertions(+), 17 deletions(-) diff --git a/openmc/material.py b/openmc/material.py index 15d1f8ac9a..de4a22cb8e 100644 --- a/openmc/material.py +++ b/openmc/material.py @@ -335,15 +335,23 @@ class Material(IDManagerMixin): return material @classmethod - def from_ncrystal(cls, cfg): - """Create material from NCrystal configuration string - Density is set from the NCrystal value, - and material temperature from the configuration string. - + def from_ncrystal(cls, cfg, material_id=None, name=''): + """Create material from NCrystal configuration string. Density, + temperature, and material composition, and (ultimately) thermal neutron + scattering, will be automatically be provided by NCrystal based on this + string. The name and material_id parameters are simply passed on to the + Material constructor. + Parameters ---------- cfg : str NCrystal configuration string + material_id : int, optional + Unique identifier for the material. If not specified, an identifier will + automatically be assigned. + name : str, optional + Name of the material. If not specified, the name will be the empty + string. Returns ------- @@ -353,22 +361,43 @@ class Material(IDManagerMixin): """ import NCrystal - nc_mat = NCrystal.createInfo(cfg) - nc_comp = nc_mat.getComposition() + + def openmc_natabund( Z ): + #nc_mat.getFlattenedComposition might need natural abundancies. + #This call-back function is used so NCrystal can flatten composition + #using OpenMC's natural abundancies. In practice this function will + #only get invoked in the unlikely case where a material is specified + #by referring both to natural elements and specific isotopes of the + #same element. + elem_name = openmc.data.ATOMIC_SYMBOL.get( Z, None ) + if not elem_name: + raise ValueError( f'Element with Z={Z} is not known' ) + l = [] + for iso_name,abund in openmc.data.isotopes( elem_name ): + l.append( ( int(iso_name[ len(elem_name) : ]), abund ) ) + return l + + flat_compos = nc_mat.getFlattenedComposition( preferNaturalElements = True, + naturalAbundProvider = openmc_natabund ) # Create the Material - material = cls() + material = cls( material_id = material_id, + name = name, + temperature = nc_mat.getTemperature() ) - for frac, atom in nc_comp: - if not atom.isNaturalElement(): - raise ValueError('NCrystal-OpenMC interface only works with natural elements for now.') - material.add_element(atom.elementName(), frac, 'ao') + for Z, A_vals in flat_compos: + elemname = openmc.data.ATOMIC_SYMBOL.get(Z,None) + if not elemname: + raise ValueError(f'Element with Z={Z} is not known') + for A, frac in A_vals: + if A: + material.add_nuclide( elemname + str(A), frac, 'ao' ) + else: + material.add_element( elemname, frac, 'ao' ) - material._ncrystal_cfg = cfg - material._density_units = "g/cm3" - material._density = nc_mat.getDensity() - material.temperature = nc_mat.getTemperature() + material.set_density( 'g/cm3', nc_mat.getDensity() ) + material._ncrystal_cfg = NCrystal.normaliseCfg( cfg ) return material @@ -1186,7 +1215,7 @@ class Material(IDManagerMixin): if self._sab: raise ValueError("NCrystal materials are not compatible with S(a,b).") if self._macroscopic is not None: - raise ValueError("NCrystal materials are not compatible macroscopic cross sections.") + raise ValueError("NCrystal materials are not compatible with macroscopic cross sections.") element.set("cfg", str(self._ncrystal_cfg)) From f2e807e942ed421cd03fc87823c579e47dfcce3c Mon Sep 17 00:00:00 2001 From: Thomas Kittelmann Date: Thu, 20 Oct 2022 13:26:45 +0200 Subject: [PATCH 126/265] Move NCrystalRNGWrapper data member into explicit private section as requested --- include/openmc/physics.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/openmc/physics.h b/include/openmc/physics.h index 23995e7af9..806297c4ea 100644 --- a/include/openmc/physics.h +++ b/include/openmc/physics.h @@ -111,8 +111,6 @@ void split_particle(Particle& p); //============================================================================== class NCrystalRNGWrapper : public NCrystal::RNGStream { - uint64_t* openmc_seed_; - public: constexpr NCrystalRNGWrapper(uint64_t* seed) noexcept : openmc_seed_(seed) {} @@ -122,6 +120,8 @@ protected: return std::max( std::numeric_limits::min(), prn(openmc_seed_)); } +private: + uint64_t* openmc_seed_; }; #endif From aca4fcb42bbfb45bd3ded0f9f1bbf8b7107aa632 Mon Sep 17 00:00:00 2001 From: Thomas Kittelmann Date: Fri, 21 Oct 2022 10:30:05 +0200 Subject: [PATCH 127/265] NCrystal cfgstr printout now mentions material ID --- src/material.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/material.cpp b/src/material.cpp index 9531e9f43a..32f5f2e865 100644 --- a/src/material.cpp +++ b/src/material.cpp @@ -63,7 +63,7 @@ Material::Material(pugi::xml_node node) #ifdef NCRYSTAL if (check_for_node(node, "cfg")) { ncrystal_cfg_ = get_node_value(node, "cfg"); - write_message(5, "NCrystal config string: '{}'", ncrystal_cfg_); + write_message(5, "NCrystal config string for material #{}: '{}'", this->id(), ncrystal_cfg_); ncrystal_mat_ = NCrystal::FactImpl::createScatter(ncrystal_cfg_); } #endif From a3dd55d8bc4b28323b73e9a36c52f950db6ea1fb Mon Sep 17 00:00:00 2001 From: Thomas Kittelmann Date: Fri, 21 Oct 2022 15:04:57 +0200 Subject: [PATCH 128/265] first stab at gha-install-ncrystal.sh --- tools/ci/gha-install-ncrystal.sh | 62 ++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100755 tools/ci/gha-install-ncrystal.sh diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh new file mode 100755 index 0000000000..c18087f235 --- /dev/null +++ b/tools/ci/gha-install-ncrystal.sh @@ -0,0 +1,62 @@ +#!/bin/bash +set -ex +cd $HOME + +#Use the NCrystal develop branch (in the near future we can move this to master): +git clone https://github.com/mctools/ncrystal --branch develop --single-branch --depth 1 ncrystal_src + +SRC_DIR="$PWD/ncrystal_src" +BLD_DIR="$PWD/ncrystal_bld" +INST_DIR="$PWD/ncrystal_inst" +PYTHON=$(which python3) + +CPU_COUNT=1 + +mkdir "$BLD_DIR" +cd ncrystal_bld + +#cmake -Dstatic=on .. && make 2>/dev/null && sudo make install + +cmake \ + "${SRC_DIR}" \ + -DBUILD_SHARED_LIBS=ON \ + -DNCRYSTAL_NOTOUCH_CMAKE_BUILD_TYPE=ON \ + -DMODIFY_RPATH=OFF \ + -DCMAKE_BUILD_TYPE=Release \ + -DBUILD_EXAMPLES=OFF \ + -DINSTALL_SETUPSH=OFF \ + -DEMBED_DATA=ON \ + -DINSTALL_DATA=OFF \ + -DNO_DIRECT_PYMODINST=ON \ + -DPython3_EXECUTABLE="$PYTHON" + +make -j${CPU_COUNT:-1} +make install + +#Note: There is no "make test" or "make ctest" functionality for NCrystal +# yet. If it appears in the future, we should add it here. + + +#The next stuff is not pretty, but it is needed as a temporary +#workaround until NCrystal add better support for system-wide +#installations in CMake: + +cat < ./findncrystallib.py +import pathlib +libname = pathlib.Path('./cfg_ncrystal_libname.txt').read_text().strip() +libs = list(pathlib.Path("/usr").glob("**/lib*/**/%s"%libname)) +assert len(libs)==1 +pathlib.Path('ncrystal_liblocation.txt').write_text(str(libs[0])) +EOF + +python3 ./findncrystallib.py + +TMPNCRYSTALLIBLOCATION=$(cat ./ncrystal_liblocation.txt) + +cat < ./ncrystal_pypkg/NCrystal/_nclibpath.py +#File autogenerated for working with systemwide install of NCrystal: +import pathlib +liblocation = pathlib.Path('${TMPNCRYSTALLIBLOCATION}'.strip()) +EOF + +$PYTHON -m pip install ./ncrystal_pypkg/ -vv From e64bf6a7ffb1b33f732e804bf10ff376d2cba700 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Thu, 10 Nov 2022 12:31:45 -0300 Subject: [PATCH 129/265] Add installation instructions for NCrystal --- docs/source/usersguide/install.rst | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/docs/source/usersguide/install.rst b/docs/source/usersguide/install.rst index 74be9ba0bc..9e5ba1ffd9 100644 --- a/docs/source/usersguide/install.rst +++ b/docs/source/usersguide/install.rst @@ -271,6 +271,16 @@ Prerequisites cmake -DOPENMC_USE_DAGMC=on -DCMAKE_PREFIX_PATH=/path/to/dagmc/installation .. + * NCrystal_ library for defining materials with enhanced thermal neutron transport + + Adding this option allows the creation of materials from NCrystal, which + replaces the scattering kernel treatment of ACE files with a modular, on-the-fly approach. + To use it `install `_ and + `initialize `_ + NCrystal and turn on the option in the CMake configuration step: + + cmake -DOPENMC_USE_NCRYSTAL=on .. + * libMesh_ mesh library framework for numerical simulations of partial differential equations This optional dependency enables support for unstructured mesh tally @@ -294,6 +304,7 @@ Prerequisites .. _MOAB: https://bitbucket.org/fathomteam/moab .. _libMesh: https://libmesh.github.io/ .. _libpng: http://www.libpng.org/pub/png/libpng.html +.. _NCrystal: https://github.com/mctools/ncrystal Obtaining the Source -------------------- @@ -362,6 +373,12 @@ OPENMC_USE_DAGMC should also be defined as `DAGMC_ROOT` in the CMake configuration command. (Default: off) +OPENMC_USE_NCRYSTAL + Turns on support for NCrystal materials. NCrystal must be + `installed `_ and + `initialized `_. + (Default: off) + OPENMC_USE_LIBMESH Enables the use of unstructured mesh tallies with libMesh_. (Default: off) From 1f3c5ed6bc4b29259d300a0d9b0fac0decf0eff6 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Thu, 10 Nov 2022 13:04:47 -0300 Subject: [PATCH 130/265] Add use instructions and examples for NCrystal --- docs/source/usersguide/materials.rst | 37 ++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/docs/source/usersguide/materials.rst b/docs/source/usersguide/materials.rst index 8b43f1a2ac..ab5a8c5afa 100644 --- a/docs/source/usersguide/materials.rst +++ b/docs/source/usersguide/materials.rst @@ -101,6 +101,42 @@ you would need to add hydrogen and oxygen to a material and then assign the .. _usersguide_naming: +------------------ +Adding NCrystal materials +------------------ + +Additional support for thermal scattering can be added by using NCrystal_. +The :meth:`Material.from_ncrystal` class method generates a material object from +an `NCrystal configuration string `_. +Temperature, material composition and density are passed from the configuration string +and the `NCMAT file `_ +that define the material, e.g: + +:: + + mat = openmc.Material.from_ncrystal('Al_sg225.ncmat') + +defines a material containing polycrystalline alumnium, + +:: + + mat = openmc.Material.from_ncrystal(""""Ge_sg227.ncmat;dcutoff=0.5;mos=40arcsec; + dir1=@crys_hkl:5,1,1@lab:0,0,1; + dir2=@crys_hkl:0,-1,1@lab:0,1,0""") + +defines an oriented germanium single crystal with 40 arcsec mosaicity. + +NCrystal only handles low energy neutron interactions. Other interaction are +provided by standard ACE files. NCrystal_ comes with a `predefined library +https://github.com/mctools/ncrystal/wiki/Data-library`_ but more materials can +be added by creating NCMAT files or on-the-fly in the configuration string. + +.. warning:: Currently, NCrystal_ materials cannot be modified after created. + Density, temperature and composition should be defined in the + configuration string or the NCMAT file. + +.. _NCrystal: https://github.com/mctools/ncrystal + ------------------ Naming Conventions ------------------ @@ -222,3 +258,4 @@ been generated, you can tell OpenMC to use this file either by setting materials.cross_sections = '/path/to/cross_sections.xml' .. _MCNP: https://mcnp.lanl.gov/ + From e224adf4313056e8dfb8700126d7329511de0721 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 16 Nov 2022 10:31:15 +0100 Subject: [PATCH 131/265] follow source code conventions Co-authored-by: Paul Romano --- include/openmc/state_point.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/openmc/state_point.h b/include/openmc/state_point.h index 2d92c935a6..698ed2c93a 100644 --- a/include/openmc/state_point.h +++ b/include/openmc/state_point.h @@ -26,7 +26,7 @@ void restart_set_keff(); void write_unstructured_mesh_results(); #ifdef OPENMC_MCPL -void write_mcpl_source_point(const char *filename_, bool surf_source_bank = false); +void write_mcpl_source_point(const char* filename, bool surf_source_bank = false); void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank); #endif From b2320ae1d477d7f3d932a406eb2989eee5cf37e3 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 16 Nov 2022 13:42:25 +0100 Subject: [PATCH 132/265] not needed since mcpl-file is created by openmc --- .../source_mcpl_file/gen_dummy_mcpl.c | 98 ------------------- 1 file changed, 98 deletions(-) delete mode 100644 tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c diff --git a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c b/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c deleted file mode 100644 index 61eea95c6f..0000000000 --- a/tests/regression_tests/source_mcpl_file/gen_dummy_mcpl.c +++ /dev/null @@ -1,98 +0,0 @@ -#include -#include -#include -#include - -const int batches=10; -const int particles=10000; - -double rand01(){ - double r=rand()/((double) RAND_MAX); - return r; -} - - -int main(int argc, char **argv){ - char outfilename[128]; - snprintf(outfilename,127,"source.%d.mcpl",batches); - - /*generate an mcpl_header_of sorts*/ - mcpl_outfile_t outfile=mcpl_create_outfile(outfilename); - mcpl_particle_t *particle, Particle; - - char line[256]; - snprintf(line,255,"gen_dummy_mcpl.c"); - mcpl_hdr_set_srcname(outfile,line); - mcpl_enable_universal_pdgcode(outfile,2112);/*all particles are neutrons*/ - snprintf(line,255,"Dummy MCPL-file for testing OpenMC mcpl input"); - mcpl_hdr_add_comment(outfile,line); - - /*also add the instrument file and the command line as blobs*/ - FILE *fp; - if( (fp=fopen("gen_dummy_mcpl.c","rb"))!=NULL){ - unsigned char *buffer; - int size,status; - /*find the file size by seeking to end, "tell" the position, and then go back again*/ - fseek(fp, 0L, SEEK_END); - size = ftell(fp); // get current file pointer - fseek(fp, 0L, SEEK_SET); // seek back to beginning of file - if ( size && (buffer=malloc(size))!=NULL){ - if (size!=(fread(buffer,1,size,fp))){ - fprintf(stderr,"Warning: c source generator file not read cleanly\n"); - } - mcpl_hdr_add_data(outfile, "mcpl_point_source_file_generator", size, buffer); - free(buffer); - } - fclose(fp); - } else { - fprintf(stderr,"Warning: could not open c source generator file, hence not embedded.\n"); - } - - - /*the main particle loop*/ - particle=&Particle; - int i; - srand(1234); - for (i=0;iposition[0]=0; - particle->position[1]=0; - particle->position[2]=0; - - /*generate a random direction on unit sphere*/ - double nrm=2.0; - double vx,vy,vz; - int iter=0; - do { - if(iter>100){ - printf("Warning: Exceeded max random vector attempts: at loop %d -> %g %d\n",i,nrm,iter); - } - vx=rand01()*2.0-1.0; - vy=rand01()*2.0-1.0; - vz=rand01()*2.0-1.0; - nrm=(vx*vx + vy*vy + vz*vz); - iter++; - } while (nrm>1.0); - vx/=sqrt(nrm); - vy/=sqrt(nrm); - vz/=sqrt(nrm); - particle->direction[0]=vx; - particle->direction[1]=vy; - particle->direction[2]=vz; - - /*generate the kinetic energy (in MeV) of the particle*/ - particle->ekin=1e-3; - - /*set time=0*/ - particle->time=0; - /*set weight*/ - particle->weight=1; - - particle->userflags=0; - mcpl_add_particle(outfile,particle); - } - mcpl_close_outfile(outfile); -} From 3e60d51f904ca413030716aa1882866bebab8c23 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 16 Nov 2022 13:54:08 +0100 Subject: [PATCH 133/265] from_xml mcpl-settings functionality --- openmc/settings.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/openmc/settings.py b/openmc/settings.py index 0937a3e480..b2c184f780 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1341,13 +1341,15 @@ class Settings: def _surf_source_write_from_xml_element(self, root): elem = root.find('surf_source_write') if elem is not None: - for key in ('surface_ids', 'max_particles'): + for key in ('surface_ids', 'max_particles','mcpl'): value = get_text(elem, key) if value is not None: if key == 'surface_ids': value = [int(x) for x in value.split()] elif key in ('max_particles'): value = int(value) + elif key == 'mcpl': + value = True self.surf_source_write[key] = value def _confidence_intervals_from_xml_element(self, root): From cf96ddf8bbedac4d72e1730e313d5b7a9cd94284 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Thu, 17 Nov 2022 13:47:03 +0100 Subject: [PATCH 134/265] Basic introduction to NCrystal Included references to the main papers and documentation --- docs/source/methods/cross_sections.rst | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/docs/source/methods/cross_sections.rst b/docs/source/methods/cross_sections.rst index 3396d7f251..c700b3f2d3 100644 --- a/docs/source/methods/cross_sections.rst +++ b/docs/source/methods/cross_sections.rst @@ -178,6 +178,24 @@ been selected. There are three methods available: section data is loaded for a single temperature and is used in the unresolved resonance and fast energy ranges. +------------------ +NCrystal materials +------------------ + +As an alternative of the standard thermal scattering treatment using :math:`S(\alpha,\beta)` +tables, OpenMC allows to create materials using NCrystal_. In addition to the regular thermal elastic, +and thermal inelastic processes, NCrystal allows the generation of models for materials that +cannot currently included in ACE files such as oriented single crystals (see the `NCrystal paper`_), +and further extend the physics `using plugins`_. Thermal scattering kernels are generated on +the fly from dynamic and structural data, or loaded from :math:`S(\alpha,\beta)` tables converted +from ENDF6 evaluations. These kernels are sampled in a direct way using a fast `rejection algorithm`_ +that does not require previous processing. A `large library` of materials is already included in +the NCrystal distribution, and new materials can be easily defined from scratch in the `NCMAT format` +or `combining existing files`. + +The compositions of the materials defined in NCrystal are passed on to OpenMC all other reactions +except for thermal neutron scattering are handled by continuous energy ACE libraries. + ---------------- Multi-Group Data ---------------- @@ -279,3 +297,10 @@ or even isotropic scattering. .. _ENDF/B data: https://www.nndc.bnl.gov/endf-b8.0/ .. _Leppanen: https://doi.org/10.1016/j.anucene.2009.03.019 .. _algorithms: http://ab-initio.mit.edu/wiki/index.php/Faddeeva_Package +.. _NCrystal: https://github.com/mctools/ncrystal +.. _NCrystal paper: https://doi.org/10.1016/j.cpc.2019.07.015 +.. _using plugins: https://doi.org/10.1016/j.cpc.2021.108082 +.. _rejection algorithm: https://doi.org/10.1016/j.jcp.2018.11.043 +.. _large library: https://github.com/mctools/ncrystal/wiki/Data-library +.. _NCMAT format: https://github.com/mctools/ncrystal/wiki/NCMAT-format +.. _combining existing files: https://github.com/mctools/ncrystal/wiki/Announcement-Release3.0.0#2-multiphase-materials From 24572a71f22b588eb628e855618a4a4a27a63e4c Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian Date: Thu, 17 Nov 2022 16:33:48 +0100 Subject: [PATCH 135/265] Added simple NCrystal test --- tests/regression_tests/ncrystal/__init__.py | 0 .../regression_tests/ncrystal/inputs_true.dat | 45 +++++ .../ncrystal/results_true.dat | 181 ++++++++++++++++++ tests/regression_tests/ncrystal/test.py | 70 +++++++ 4 files changed, 296 insertions(+) create mode 100644 tests/regression_tests/ncrystal/__init__.py create mode 100644 tests/regression_tests/ncrystal/inputs_true.dat create mode 100644 tests/regression_tests/ncrystal/results_true.dat create mode 100644 tests/regression_tests/ncrystal/test.py diff --git a/tests/regression_tests/ncrystal/__init__.py b/tests/regression_tests/ncrystal/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/regression_tests/ncrystal/inputs_true.dat b/tests/regression_tests/ncrystal/inputs_true.dat new file mode 100644 index 0000000000..7a3f20eb3f --- /dev/null +++ b/tests/regression_tests/ncrystal/inputs_true.dat @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + fixed source + 100000 + 10 + + + 0 0 -20 + + + + 0.012 1.0 + + + + + + + 1 + + + 0.0 0.017453292519943295 0.03490658503988659 0.05235987755982989 0.06981317007977318 0.08726646259971647 0.10471975511965978 0.12217304763960307 0.13962634015954636 0.15707963267948966 0.17453292519943295 0.19198621771937624 0.20943951023931956 0.22689280275926285 0.24434609527920614 0.2617993877991494 0.2792526803190927 0.29670597283903605 0.3141592653589793 0.33161255787892263 0.3490658503988659 0.3665191429188092 0.3839724354387525 0.4014257279586958 0.4188790204786391 0.4363323129985824 0.4537856055185257 0.47123889803846897 0.4886921905584123 0.5061454830783556 0.5235987755982988 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0000000000..3ef0306fdf --- /dev/null +++ b/tests/regression_tests/ncrystal/results_true.dat @@ -0,0 +1,181 @@ + surface polar low [rad] polar high [rad] cellfrom nuclide score mean std. dev. +0 1 0.00e+00 1.75e-02 1 total current 9.82e-01 1.43e-04 +1 1 1.75e-02 3.49e-02 1 total current 0.00e+00 0.00e+00 +2 1 3.49e-02 5.24e-02 1 total current 1.00e-06 1.00e-06 +3 1 5.24e-02 6.98e-02 1 total current 0.00e+00 0.00e+00 +4 1 6.98e-02 8.73e-02 1 total current 0.00e+00 0.00e+00 +5 1 8.73e-02 1.05e-01 1 total current 1.00e-06 1.00e-06 +6 1 1.05e-01 1.22e-01 1 total current 0.00e+00 0.00e+00 +7 1 1.22e-01 1.40e-01 1 total current 1.00e-06 1.00e-06 +8 1 1.40e-01 1.57e-01 1 total current 1.00e-06 1.00e-06 +9 1 1.57e-01 1.75e-01 1 total current 1.00e-06 1.00e-06 +10 1 1.75e-01 1.92e-01 1 total current 0.00e+00 0.00e+00 +11 1 1.92e-01 2.09e-01 1 total current 2.00e-06 1.33e-06 +12 1 2.09e-01 2.27e-01 1 total current 0.00e+00 0.00e+00 +13 1 2.27e-01 2.44e-01 1 total current 1.00e-06 1.00e-06 +14 1 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total current 3.00e-06 1.53e-06 +49 1 8.55e-01 8.73e-01 1 total current 8.00e-06 3.27e-06 +50 1 8.73e-01 8.90e-01 1 total current 7.00e-06 2.13e-06 +51 1 8.90e-01 9.08e-01 1 total current 6.00e-06 2.21e-06 +52 1 9.08e-01 9.25e-01 1 total current 4.00e-06 2.21e-06 +53 1 9.25e-01 9.42e-01 1 total current 1.20e-05 3.27e-06 +54 1 9.42e-01 9.60e-01 1 total current 8.00e-06 3.89e-06 +55 1 9.60e-01 9.77e-01 1 total current 1.20e-05 4.42e-06 +56 1 9.77e-01 9.95e-01 1 total current 7.00e-06 3.67e-06 +57 1 9.95e-01 1.01e+00 1 total current 1.20e-05 3.89e-06 +58 1 1.01e+00 1.03e+00 1 total current 9.00e-06 2.33e-06 +59 1 1.03e+00 1.05e+00 1 total current 6.00e-06 2.67e-06 +60 1 1.05e+00 1.06e+00 1 total current 7.00e-06 2.13e-06 +61 1 1.06e+00 1.08e+00 1 total current 5.00e-06 2.24e-06 +62 1 1.08e+00 1.10e+00 1 total current 1.20e-05 2.91e-06 +63 1 1.10e+00 1.12e+00 1 total current 1.30e-05 3.35e-06 +64 1 1.12e+00 1.13e+00 1 total current 9.00e-06 3.14e-06 +65 1 1.13e+00 1.15e+00 1 total current 1.20e-05 3.89e-06 +66 1 1.15e+00 1.17e+00 1 total current 6.00e-06 2.21e-06 +67 1 1.17e+00 1.19e+00 1 total current 5.11e-03 4.20e-05 +68 1 1.19e+00 1.20e+00 1 total current 8.00e-06 3.27e-06 +69 1 1.20e+00 1.22e+00 1 total current 1.30e-05 4.48e-06 +70 1 1.22e+00 1.24e+00 1 total current 1.20e-05 3.89e-06 +71 1 1.24e+00 1.26e+00 1 total current 1.50e-05 4.28e-06 +72 1 1.26e+00 1.27e+00 1 total current 7.00e-06 3.00e-06 +73 1 1.27e+00 1.29e+00 1 total current 1.60e-05 3.71e-06 +74 1 1.29e+00 1.31e+00 1 total current 9.00e-06 3.79e-06 +75 1 1.31e+00 1.33e+00 1 total current 1.30e-05 2.60e-06 +76 1 1.33e+00 1.34e+00 1 total current 1.60e-05 3.06e-06 +77 1 1.34e+00 1.36e+00 1 total current 1.40e-05 2.67e-06 +78 1 1.36e+00 1.38e+00 1 total current 1.40e-05 6.86e-06 +79 1 1.38e+00 1.40e+00 1 total current 1.50e-05 4.28e-06 +80 1 1.40e+00 1.41e+00 1 total current 3.26e-03 6.93e-05 +81 1 1.41e+00 1.43e+00 1 total current 1.40e-05 3.71e-06 +82 1 1.43e+00 1.45e+00 1 total current 1.30e-05 3.00e-06 +83 1 1.45e+00 1.47e+00 1 total current 1.30e-05 3.67e-06 +84 1 1.47e+00 1.48e+00 1 total current 1.70e-05 5.59e-06 +85 1 1.48e+00 1.50e+00 1 total current 1.70e-05 3.67e-06 +86 1 1.50e+00 1.52e+00 1 total current 1.40e-05 3.40e-06 +87 1 1.52e+00 1.54e+00 1 total current 2.50e-05 4.53e-06 +88 1 1.54e+00 1.55e+00 1 total current 1.30e-05 5.39e-06 +89 1 1.55e+00 1.57e+00 1 total current 1.80e-05 4.67e-06 +90 1 1.57e+00 1.59e+00 1 total current 1.40e-05 4.52e-06 +91 1 1.59e+00 1.61e+00 1 total current 1.70e-05 4.23e-06 +92 1 1.61e+00 1.62e+00 1 total current 1.40e-05 3.71e-06 +93 1 1.62e+00 1.64e+00 1 total current 1.00e-05 2.11e-06 +94 1 1.64e+00 1.66e+00 1 total current 2.00e-05 4.22e-06 +95 1 1.66e+00 1.68e+00 1 total current 2.30e-05 5.59e-06 +96 1 1.68e+00 1.69e+00 1 total current 1.70e-05 6.51e-06 +97 1 1.69e+00 1.71e+00 1 total current 1.30e-05 3.00e-06 +98 1 1.71e+00 1.73e+00 1 total current 1.50e-05 4.01e-06 +99 1 1.73e+00 1.75e+00 1 total current 1.70e-05 3.96e-06 +100 1 1.75e+00 1.76e+00 1 total current 1.80e-05 5.12e-06 +101 1 1.76e+00 1.78e+00 1 total current 2.50e-05 6.54e-06 +102 1 1.78e+00 1.80e+00 1 total current 1.80e-05 3.59e-06 +103 1 1.80e+00 1.82e+00 1 total current 1.50e-05 4.01e-06 +104 1 1.82e+00 1.83e+00 1 total current 1.10e-05 4.07e-06 +105 1 1.83e+00 1.85e+00 1 total current 1.50e-05 4.01e-06 +106 1 1.85e+00 1.87e+00 1 total current 1.90e-05 4.82e-06 +107 1 1.87e+00 1.88e+00 1 total current 2.20e-05 3.89e-06 +108 1 1.88e+00 1.90e+00 1 total current 2.10e-05 3.79e-06 +109 1 1.90e+00 1.92e+00 1 total current 1.50e-05 3.42e-06 +110 1 1.92e+00 1.94e+00 1 total current 2.20e-05 5.12e-06 +111 1 1.94e+00 1.95e+00 1 total current 2.10e-05 5.86e-06 +112 1 1.95e+00 1.97e+00 1 total current 2.60e-05 4.27e-06 +113 1 1.97e+00 1.99e+00 1 total current 2.20e-05 4.16e-06 +114 1 1.99e+00 2.01e+00 1 total current 2.40e-05 5.42e-06 +115 1 2.01e+00 2.02e+00 1 total current 1.60e-05 4.52e-06 +116 1 2.02e+00 2.04e+00 1 total current 1.30e-05 3.35e-06 +117 1 2.04e+00 2.06e+00 1 total current 1.90e-05 4.07e-06 +118 1 2.06e+00 2.08e+00 1 total current 1.30e-05 3.00e-06 +119 1 2.08e+00 2.09e+00 1 total current 1.40e-05 4.00e-06 +120 1 2.09e+00 2.11e+00 1 total current 3.10e-05 5.47e-06 +121 1 2.11e+00 2.13e+00 1 total current 2.30e-05 5.39e-06 +122 1 2.13e+00 2.15e+00 1 total current 2.20e-05 4.67e-06 +123 1 2.15e+00 2.16e+00 1 total current 1.70e-05 4.48e-06 +124 1 2.16e+00 2.18e+00 1 total current 1.60e-05 4.00e-06 +125 1 2.18e+00 2.20e+00 1 total current 1.80e-05 4.16e-06 +126 1 2.20e+00 2.22e+00 1 total current 1.80e-05 4.42e-06 +127 1 2.22e+00 2.23e+00 1 total current 1.80e-05 5.54e-06 +128 1 2.23e+00 2.25e+00 1 total current 1.90e-05 4.33e-06 +129 1 2.25e+00 2.27e+00 1 total current 1.00e-05 3.33e-06 +130 1 2.27e+00 2.29e+00 1 total current 1.80e-05 4.42e-06 +131 1 2.29e+00 2.30e+00 1 total current 4.15e-03 5.40e-05 +132 1 2.30e+00 2.32e+00 1 total current 1.90e-05 2.33e-06 +133 1 2.32e+00 2.34e+00 1 total current 2.30e-05 3.96e-06 +134 1 2.34e+00 2.36e+00 1 total current 1.90e-05 3.48e-06 +135 1 2.36e+00 2.37e+00 1 total current 1.60e-05 3.71e-06 +136 1 2.37e+00 2.39e+00 1 total current 1.60e-05 4.27e-06 +137 1 2.39e+00 2.41e+00 1 total current 2.30e-05 4.48e-06 +138 1 2.41e+00 2.43e+00 1 total current 2.10e-05 3.48e-06 +139 1 2.43e+00 2.44e+00 1 total current 1.60e-05 2.21e-06 +140 1 2.44e+00 2.46e+00 1 total current 9.00e-06 2.77e-06 +141 1 2.46e+00 2.48e+00 1 total current 1.30e-05 3.00e-06 +142 1 2.48e+00 2.50e+00 1 total current 2.70e-05 3.67e-06 +143 1 2.50e+00 2.51e+00 1 total current 1.90e-05 4.07e-06 +144 1 2.51e+00 2.53e+00 1 total current 1.20e-05 4.16e-06 +145 1 2.53e+00 2.55e+00 1 total current 1.30e-05 2.13e-06 +146 1 2.55e+00 2.57e+00 1 total current 1.10e-05 2.33e-06 +147 1 2.57e+00 2.58e+00 1 total current 1.50e-05 3.07e-06 +148 1 2.58e+00 2.60e+00 1 total current 1.20e-05 2.49e-06 +149 1 2.60e+00 2.62e+00 1 total current 1.80e-05 5.54e-06 +150 1 2.62e+00 2.64e+00 1 total current 1.30e-05 3.67e-06 +151 1 2.64e+00 2.65e+00 1 total current 1.60e-05 3.40e-06 +152 1 2.65e+00 2.67e+00 1 total current 7.00e-06 3.35e-06 +153 1 2.67e+00 2.69e+00 1 total current 1.00e-05 2.98e-06 +154 1 2.69e+00 2.71e+00 1 total current 7.00e-06 3.35e-06 +155 1 2.71e+00 2.72e+00 1 total current 1.20e-05 2.91e-06 +156 1 2.72e+00 2.74e+00 1 total current 9.00e-06 2.33e-06 +157 1 2.74e+00 2.76e+00 1 total current 1.00e-05 3.33e-06 +158 1 2.76e+00 2.78e+00 1 total current 1.10e-05 3.14e-06 +159 1 2.78e+00 2.79e+00 1 total current 1.00e-05 3.33e-06 +160 1 2.79e+00 2.81e+00 1 total current 1.40e-05 4.76e-06 +161 1 2.81e+00 2.83e+00 1 total current 8.00e-06 2.91e-06 +162 1 2.83e+00 2.84e+00 1 total current 5.00e-06 2.69e-06 +163 1 2.84e+00 2.86e+00 1 total current 6.00e-06 2.21e-06 +164 1 2.86e+00 2.88e+00 1 total current 5.00e-06 1.67e-06 +165 1 2.88e+00 2.90e+00 1 total current 4.00e-06 2.21e-06 +166 1 2.90e+00 2.91e+00 1 total current 7.00e-06 2.13e-06 +167 1 2.91e+00 2.93e+00 1 total current 6.00e-06 2.67e-06 +168 1 2.93e+00 2.95e+00 1 total current 7.00e-06 2.13e-06 +169 1 2.95e+00 2.97e+00 1 total current 5.00e-06 1.67e-06 +170 1 2.97e+00 2.98e+00 1 total current 3.00e-06 1.53e-06 +171 1 2.98e+00 3.00e+00 1 total current 6.00e-06 2.21e-06 +172 1 3.00e+00 3.02e+00 1 total current 3.00e-06 1.53e-06 +173 1 3.02e+00 3.04e+00 1 total current 1.00e-05 2.98e-06 +174 1 3.04e+00 3.05e+00 1 total current 2.00e-06 1.33e-06 +175 1 3.05e+00 3.07e+00 1 total current 1.00e-06 1.00e-06 +176 1 3.07e+00 3.09e+00 1 total current 2.00e-06 1.33e-06 +177 1 3.09e+00 3.11e+00 1 total current 0.00e+00 0.00e+00 +178 1 3.11e+00 3.12e+00 1 total current 1.00e-06 1.00e-06 +179 1 3.12e+00 3.14e+00 1 total current 0.00e+00 0.00e+00 \ No newline at end of file diff --git a/tests/regression_tests/ncrystal/test.py b/tests/regression_tests/ncrystal/test.py new file mode 100644 index 0000000000..51a0f07b72 --- /dev/null +++ b/tests/regression_tests/ncrystal/test.py @@ -0,0 +1,70 @@ +import numpy as np +import openmc +from tests.testing_harness import PyAPITestHarness + +def compute_angular_distribution(cfg, E0, N): + """Return a openmc.model.Model() object for a monoenergetic pencil + beam hitting a 1 mm sphere filled with the material defined by + the cfg string, and compute the angular distribution""" + + # Material definition + + m1 = openmc.Material.from_ncrystal(cfg) + materials = openmc.Materials([m1]) + + # Geometry definition + + sample_sphere = openmc.Sphere(r=0.1) + outer_sphere = openmc.Sphere(r=100, boundary_type="vacuum") + cell1 = openmc.Cell(region= -sample_sphere, fill=m1) + cell2_region= +sample_sphere&-outer_sphere + cell2 = openmc.Cell(region= cell2_region, fill=None) + uni1 = openmc.Universe(cells=[cell1, cell2]) + geometry = openmc.Geometry(uni1) + + # Source definition + + source = openmc.Source() + source.space = openmc.stats.Point(xyz = (0,0,-20)) + source.angle = openmc.stats.Monodirectional(reference_uvw = (0,0,1)) + source.energy = openmc.stats.Discrete([E0], [1.0]) + + # Execution settings + + settings = openmc.Settings() + settings.source = source + settings.run_mode = "fixed source" + settings.batches = 10 + settings.particles = N + + # Tally definition + + tally1 = openmc.Tally(name="angular distribution") + tally1.scores = ["current"] + filter1 = openmc.filter.SurfaceFilter(sample_sphere) + filter2 = openmc.filter.PolarFilter(np.linspace(0,np.pi,180+1)) + filter3 = openmc.filter.CellFromFilter(cell1) + tally1.filters = [filter1, filter2, filter3] + tallies = openmc.Tallies([tally1]) + + return openmc.model.Model(geometry, materials, settings, tallies) + + +class NCrystalTest(PyAPITestHarness): + def _get_results(self): + """Digest info in the statepoint and return as a string.""" + + # Read the statepoint file. + sp = openmc.StatePoint(self._sp_name) + tal = sp.get_tally(name='angular distribution') + df = tal.get_pandas_dataframe() + return df.to_string() + +def test_ncrystal(): + NParticles = 100000 + T = 293.6 # K + E0 = 0.012 # eV + cfg = 'Al_sg225.ncmat' + test = compute_angular_distribution(cfg, E0, NParticles) + harness = NCrystalTest('statepoint.10.h5', model=test) + harness.main() From 54745f507641489bc82acbfb4303a728c7bf4fca Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Fri, 18 Nov 2022 11:11:37 -0300 Subject: [PATCH 136/265] Changed example NCrystal cfg strings --- docs/source/usersguide/materials.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/usersguide/materials.rst b/docs/source/usersguide/materials.rst index ab5a8c5afa..1886a772be 100644 --- a/docs/source/usersguide/materials.rst +++ b/docs/source/usersguide/materials.rst @@ -114,13 +114,13 @@ that define the material, e.g: :: - mat = openmc.Material.from_ncrystal('Al_sg225.ncmat') + mat = openmc.Material.from_ncrystal('Al_sg225.ncmat;temp=300K') defines a material containing polycrystalline alumnium, :: - mat = openmc.Material.from_ncrystal(""""Ge_sg227.ncmat;dcutoff=0.5;mos=40arcsec; + mat = openmc.Material.from_ncrystal("""Ge_sg227.ncmat;dcutoff=0.5;mos=40arcsec; dir1=@crys_hkl:5,1,1@lab:0,0,1; dir2=@crys_hkl:0,-1,1@lab:0,1,0""") From 91f939a391032db72220e4be715b888d0f8db287 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian Date: Fri, 18 Nov 2022 18:26:31 +0100 Subject: [PATCH 137/265] Add flag for NCrystal --- include/openmc/settings.h | 2 ++ openmc/lib/__init__.py | 3 +++ src/settings.cpp | 7 +++++++ tests/regression_tests/ncrystal/test.py | 7 +++++++ 4 files changed, 19 insertions(+) diff --git a/include/openmc/settings.h b/include/openmc/settings.h index 9bb447005c..b01c75d45c 100644 --- a/include/openmc/settings.h +++ b/include/openmc/settings.h @@ -20,6 +20,8 @@ namespace openmc { // Global variable declarations //============================================================================== +extern "C" const bool NCRYSTAL_ENABLED; + namespace settings { // Boolean flags diff --git a/openmc/lib/__init__.py b/openmc/lib/__init__.py index c14b0d9c28..55e2ec11b3 100644 --- a/openmc/lib/__init__.py +++ b/openmc/lib/__init__.py @@ -42,6 +42,9 @@ else: def _dagmc_enabled(): return c_bool.in_dll(_dll, "DAGMC_ENABLED").value +def _ncrystal_enabled(): + return c_bool.in_dll(_dll, "NCRYSTAL_ENABLED").value + def _coord_levels(): return c_int.in_dll(_dll, "n_coord_levels").value diff --git a/src/settings.cpp b/src/settings.cpp index 87c24eedd3..be7228d681 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -36,6 +36,13 @@ namespace openmc { // Global variables //============================================================================== +#ifdef NCRYSTAL +const bool NCRYSTAL_ENABLED = true; +#else +const bool NCRYSTAL_ENABLED = false; +#endif + + namespace settings { // Default values for boolean flags diff --git a/tests/regression_tests/ncrystal/test.py b/tests/regression_tests/ncrystal/test.py index 51a0f07b72..0a47d634df 100644 --- a/tests/regression_tests/ncrystal/test.py +++ b/tests/regression_tests/ncrystal/test.py @@ -1,7 +1,14 @@ import numpy as np import openmc +import openmc.lib +import pytest + from tests.testing_harness import PyAPITestHarness +pytestmark = pytest.mark.skipif( + not openmc.lib._ncrystal_enabled(), + reason="NCrystal materials are not enabled.") + def compute_angular_distribution(cfg, E0, N): """Return a openmc.model.Model() object for a monoenergetic pencil beam hitting a 1 mm sphere filled with the material defined by From 5f8e64b463aa2e0509d2b9955dc7de6686d5497b Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Fri, 18 Nov 2022 17:47:21 -0300 Subject: [PATCH 138/265] Add NCrystal vairables to ci.yml --- .github/workflows/ci.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e267c0d8e1..321f188744 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -29,6 +29,7 @@ jobs: mpi: [n, y] omp: [n, y] dagmc: [n] + ncrystal: [n] libmesh: [n] event: [n] vectfit: [n] @@ -47,6 +48,10 @@ jobs: python-version: '3.10' mpi: y omp: y + - ncrystal: y + python-version: '3.10' + mpi: n + omp: n - libmesh: y python-version: '3.10' mpi: y @@ -64,7 +69,7 @@ jobs: omp: n mpi: y name: "Python ${{ matrix.python-version }} (omp=${{ matrix.omp }}, - mpi=${{ matrix.mpi }}, dagmc=${{ matrix.dagmc }}, + mpi=${{ matrix.mpi }}, dagmc=${{ matrix.dagmc }}, ncrystal=${{ matrix.ncrystal }}, libmesh=${{ matrix.libmesh }}, event=${{ matrix.event }} vectfit=${{ matrix.vectfit }})" @@ -73,6 +78,7 @@ jobs: PHDF5: ${{ matrix.mpi }} OMP: ${{ matrix.omp }} DAGMC: ${{ matrix.dagmc }} + NCRYSTAL: ${{ matrix.ncrystal }} EVENT: ${{ matrix.event }} VECTFIT: ${{ matrix.vectfit }} LIBMESH: ${{ matrix.libmesh }} From 87ed26babee2c7b69c229529e146d335a90fd952 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Fri, 18 Nov 2022 17:48:19 -0300 Subject: [PATCH 139/265] Add option to install NCrystal --- tools/ci/gha-install.sh | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh index aa40eb90b1..e5390be1e1 100755 --- a/tools/ci/gha-install.sh +++ b/tools/ci/gha-install.sh @@ -17,6 +17,11 @@ if [[ $DAGMC = 'y' ]]; then ./tools/ci/gha-install-dagmc.sh fi +# Install NCrystal if needed +if [[ $NCRYSTAL = 'y' ]]; then + ./tools/ci/gha-install-ncrystal.sh +fi + # Install vectfit for WMP generation if needed if [[ $VECTFIT = 'y' ]]; then ./tools/ci/gha-install-vectfit.sh From 8cf9dbe320baf4ff98eb57979f6e249e69ee0424 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian Date: Fri, 18 Nov 2022 22:28:04 +0100 Subject: [PATCH 140/265] Fixed in NCrystal docs --- docs/source/methods/cross_sections.rst | 4 ++-- docs/source/usersguide/materials.rst | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source/methods/cross_sections.rst b/docs/source/methods/cross_sections.rst index c700b3f2d3..64e4fac3de 100644 --- a/docs/source/methods/cross_sections.rst +++ b/docs/source/methods/cross_sections.rst @@ -190,8 +190,8 @@ and further extend the physics `using plugins`_. Thermal scattering kernels are the fly from dynamic and structural data, or loaded from :math:`S(\alpha,\beta)` tables converted from ENDF6 evaluations. These kernels are sampled in a direct way using a fast `rejection algorithm`_ that does not require previous processing. A `large library` of materials is already included in -the NCrystal distribution, and new materials can be easily defined from scratch in the `NCMAT format` -or `combining existing files`. +the NCrystal distribution, and new materials can be easily defined from scratch in the `NCMAT format`_ +or `combining existing files`_. The compositions of the materials defined in NCrystal are passed on to OpenMC all other reactions except for thermal neutron scattering are handled by continuous energy ACE libraries. diff --git a/docs/source/usersguide/materials.rst b/docs/source/usersguide/materials.rst index 1886a772be..1eaae846c3 100644 --- a/docs/source/usersguide/materials.rst +++ b/docs/source/usersguide/materials.rst @@ -127,8 +127,8 @@ defines a material containing polycrystalline alumnium, defines an oriented germanium single crystal with 40 arcsec mosaicity. NCrystal only handles low energy neutron interactions. Other interaction are -provided by standard ACE files. NCrystal_ comes with a `predefined library -https://github.com/mctools/ncrystal/wiki/Data-library`_ but more materials can +provided by standard ACE files. NCrystal_ comes with a `predefined library +`_ but more materials can be added by creating NCMAT files or on-the-fly in the configuration string. .. warning:: Currently, NCrystal_ materials cannot be modified after created. From b9e8f1324e72dc4730185b5f1f350eea62ab6757 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian Date: Fri, 18 Nov 2022 22:40:46 +0100 Subject: [PATCH 141/265] Attempt to fix NCrystal installation script --- tools/ci/gha-install-ncrystal.sh | 4 ++++ tools/ci/gha-install.py | 8 ++++++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh index c18087f235..5f577b8da9 100755 --- a/tools/ci/gha-install-ncrystal.sh +++ b/tools/ci/gha-install-ncrystal.sh @@ -28,6 +28,7 @@ cmake \ -DEMBED_DATA=ON \ -DINSTALL_DATA=OFF \ -DNO_DIRECT_PYMODINST=ON \ + -DCMAKE_INSTALL_PREFIX="${INST_DIR}" \ -DPython3_EXECUTABLE="$PYTHON" make -j${CPU_COUNT:-1} @@ -60,3 +61,6 @@ liblocation = pathlib.Path('${TMPNCRYSTALLIBLOCATION}'.strip()) EOF $PYTHON -m pip install ./ncrystal_pypkg/ -vv + +setup ${INST_DIR}/setup.sh + diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py index 4c69ba70b0..f3a29273f6 100644 --- a/tools/ci/gha-install.py +++ b/tools/ci/gha-install.py @@ -19,7 +19,7 @@ def which(program): return None -def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False): +def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrystal=False): # Create build directory and change to it shutil.rmtree('build', ignore_errors=True) os.mkdir('build') @@ -54,6 +54,9 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False): libmesh_path = os.environ.get('HOME') + '/LIBMESH' cmake_cmd.append('-DCMAKE_PREFIX_PATH=' + libmesh_path) + if ncrystal: + cmake_cmd.append('-DOPENMC_USE_NCRYSTAL=ON') + # Build in coverage mode for coverage testing cmake_cmd.append('-DOPENMC_ENABLE_COVERAGE=on') @@ -70,10 +73,11 @@ def main(): mpi = (os.environ.get('MPI') == 'y') phdf5 = (os.environ.get('PHDF5') == 'y') dagmc = (os.environ.get('DAGMC') == 'y') + ncrystal = (os.environ.get('NCRYSTAL') == 'y') libmesh = (os.environ.get('LIBMESH') == 'y') # Build and install - install(omp, mpi, phdf5, dagmc, libmesh) + install(omp, mpi, phdf5, dagmc, libmesh, ncrystal) if __name__ == '__main__': main() From 6442de68348eefe5f26ba9a0c74fd082067e95fd Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Fri, 18 Nov 2022 23:26:24 +0100 Subject: [PATCH 142/265] remove unneccessary initialization Co-authored-by: Paul Romano --- src/source.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/source.cpp b/src/source.cpp index 1c46e4939c..67a4a511da 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -381,7 +381,6 @@ FileSource::FileSource(mcpl_file_t mcpl_file) //mcpl stores time in ms site_.time=mcpl_particle->time*1e-3; site_.wgt=mcpl_particle->weight; - site_.delayed_group=0; sites_[i]=site_; } mcpl_close_file(mcpl_file); From a299dcc56b4d79e73a996ed3c47baaa2729fd795 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 16 Nov 2022 14:02:01 +0100 Subject: [PATCH 143/265] add a documentation entry to surf_source_write --- docs/source/io_formats/settings.rst | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/source/io_formats/settings.rst b/docs/source/io_formats/settings.rst index 1a8f63716f..285dfa2290 100644 --- a/docs/source/io_formats/settings.rst +++ b/docs/source/io_formats/settings.rst @@ -767,6 +767,15 @@ certain surfaces and write out the source bank in a separate file called *Default*: None + :mcpl: + An optional boolean which indicates if the banked particle should + be written to a file in the MCPL-format (documented in mcpl_). + instead of the native hdf5-based format. + + *Default*: false + + .. _mcpl: https://mctools.github.io/mcpl/mcpl.pdf + ------------------------------ ```` Element ------------------------------ From a40cc14d8ebb08da619b2d9fcaa9fc58adca1efa Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Sat, 19 Nov 2022 00:33:04 +0100 Subject: [PATCH 144/265] check in the c++-layer if it's an mcpl-file --- src/settings.cpp | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/settings.cpp b/src/settings.cpp index 9098eb6205..0ca430de62 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -431,12 +431,13 @@ void read_settings_xml() for (pugi::xml_node node : root.children("source")) { if (check_for_node(node, "file")) { auto path = get_node_value(node, "file", false, true); - model::external_sources.push_back(make_unique(path)); #ifdef OPENMC_MCPL - } else if (check_for_node(node, "mcpl")) { - auto path = get_node_value(node, "mcpl", false, true); - model::external_sources.push_back(make_unique(mcpl_open_file(path.c_str()))); + if ( (path.size() >= 5 && path.compare(path.size()-5,5,".mcpl")==0 ) || + (path.size() >= 8 && path.compare(path.size()-8,8,".mcpl.gz")==0 ) ) { + model::external_sources.push_back(make_unique(mcpl_open_file(path.c_str()))); + } else #endif + model::external_sources.push_back(make_unique(path)); } else if (check_for_node(node, "library")) { // Get shared library path and parameters auto path = get_node_value(node, "library", false, true); From 8bfb1af81e874a6e9b55c59a12e816f071592ab0 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Sat, 19 Nov 2022 01:41:02 +0100 Subject: [PATCH 145/265] remove unneccessary in-code comments --- src/state_point.cpp | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/state_point.cpp b/src/state_point.cpp index d0fe92bdf5..3ee5f13b39 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -621,10 +621,7 @@ void write_mcpl_source_point(const char *filename, bool surf_source_bank) std::string line; if (mpi::master) { - // this must be rewritten: file_open is h5-specific file_id = mcpl_create_outfile(filename_.c_str()); - //write_attribute(file_id, "filetype", "source"); - //write header stuff (oopy in xml-files as binary blobs for instance)) if (VERSION_DEV){ line=fmt::format("OpenMC {0}.{1}.{2}-development",VERSION_MAJOR,VERSION_MINOR,VERSION_RELEASE); } else { From 727161f95ab8364a04499de060e25fcdc28d474a Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Sat, 19 Nov 2022 01:44:47 +0100 Subject: [PATCH 146/265] remove some in-code comments --- src/source.cpp | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 1c46e4939c..2e6335aad2 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -332,8 +332,6 @@ FileSource::FileSource(std::string path) #ifdef OPENMC_MCPL FileSource::FileSource(mcpl_file_t mcpl_file) { - //do checks on the mcpl_file to see if particles are many enough. - // should model this on the example source shown in the docs. size_t n_sites=mcpl_hdr_nparticles(mcpl_file); sites_.resize(n_sites); @@ -348,8 +346,6 @@ FileSource::FileSource(mcpl_file_t mcpl_file) while ( pdg!=2112 && pdg!=22 && pdg!=11 && pdg!=-11) { mcpl_particle=mcpl_read(mcpl_file); pdg=mcpl_particle->pdgcode; - //should check for file exhaustion. This could happen if particles are other than - //neutrons, photons, electrons, or positrons. } switch(pdg){ From ccbef891ef7d2585b21b7bd5dd0e76d872017210 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Sat, 19 Nov 2022 01:49:31 +0100 Subject: [PATCH 147/265] update to doc-string --- docs/source/io_formats/settings.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/source/io_formats/settings.rst b/docs/source/io_formats/settings.rst index 285dfa2290..a162e8de6d 100644 --- a/docs/source/io_formats/settings.rst +++ b/docs/source/io_formats/settings.rst @@ -768,9 +768,10 @@ certain surfaces and write out the source bank in a separate file called *Default*: None :mcpl: - An optional boolean which indicates if the banked particle should + An optional boolean which indicates if the banked particles should be written to a file in the MCPL-format (documented in mcpl_). - instead of the native hdf5-based format. + instead of the native hdf5-based format.If activated the output + output file name is altered to ``surface_source.mcpl`` *Default*: false From fab1ddac003648e7954ad85b8d4718e7685df0e4 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Sat, 19 Nov 2022 02:19:41 +0100 Subject: [PATCH 148/265] prefer native as default Co-authored-by: Paul Romano --- src/settings.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/settings.cpp b/src/settings.cpp index 9098eb6205..91a13289cf 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -60,7 +60,7 @@ bool run_CE {true}; bool source_latest {false}; bool source_separate {false}; bool source_write {true}; -bool source_mcpl_write {true}; +bool source_mcpl_write {false}; bool surf_source_write {false}; bool surf_mcpl_write {false}; bool surf_source_read {false}; From d7ab491f473e87f5865e365bd5f9fbcfcd24943e Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Sat, 19 Nov 2022 08:57:00 +0100 Subject: [PATCH 149/265] Try fix of NCrystal install --- tools/ci/gha-install-ncrystal.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh index 5f577b8da9..78a1a44f21 100755 --- a/tools/ci/gha-install-ncrystal.sh +++ b/tools/ci/gha-install-ncrystal.sh @@ -45,7 +45,7 @@ make install cat < ./findncrystallib.py import pathlib libname = pathlib.Path('./cfg_ncrystal_libname.txt').read_text().strip() -libs = list(pathlib.Path("/usr").glob("**/lib*/**/%s"%libname)) +libs = list(pathlib.Path("${INST_DIR}").glob("**/lib*/**/%s"%libname)) assert len(libs)==1 pathlib.Path('ncrystal_liblocation.txt').write_text(str(libs[0])) EOF From b199db9cb9c6de05117c2749c21ce5ea3d474f7d Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Sat, 19 Nov 2022 09:06:42 +0100 Subject: [PATCH 150/265] Update gha-install-ncrystal.sh --- tools/ci/gha-install-ncrystal.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh index 78a1a44f21..715e4da94c 100755 --- a/tools/ci/gha-install-ncrystal.sh +++ b/tools/ci/gha-install-ncrystal.sh @@ -62,5 +62,5 @@ EOF $PYTHON -m pip install ./ncrystal_pypkg/ -vv -setup ${INST_DIR}/setup.sh +source ${INST_DIR}/setup.sh From 39d0c5cd61224b2a80b8c6ee75597588e132842b Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Sat, 19 Nov 2022 09:38:34 +0100 Subject: [PATCH 151/265] Try to initialize with setup.sh --- tools/ci/gha-install-ncrystal.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh index 715e4da94c..8e75cc60af 100755 --- a/tools/ci/gha-install-ncrystal.sh +++ b/tools/ci/gha-install-ncrystal.sh @@ -24,7 +24,7 @@ cmake \ -DMODIFY_RPATH=OFF \ -DCMAKE_BUILD_TYPE=Release \ -DBUILD_EXAMPLES=OFF \ - -DINSTALL_SETUPSH=OFF \ + -DINSTALL_SETUPSH=ON \ -DEMBED_DATA=ON \ -DINSTALL_DATA=OFF \ -DNO_DIRECT_PYMODINST=ON \ From 9e1abb328429072d9349fd5c01ae6249c438d187 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Sat, 19 Nov 2022 10:47:26 +0100 Subject: [PATCH 152/265] Update gha-install-ncrystal.sh --- tools/ci/gha-install-ncrystal.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh index 8e75cc60af..c080c16d8f 100755 --- a/tools/ci/gha-install-ncrystal.sh +++ b/tools/ci/gha-install-ncrystal.sh @@ -24,7 +24,7 @@ cmake \ -DMODIFY_RPATH=OFF \ -DCMAKE_BUILD_TYPE=Release \ -DBUILD_EXAMPLES=OFF \ - -DINSTALL_SETUPSH=ON \ + -DINSTALL_SETUPSH=OFF \ -DEMBED_DATA=ON \ -DINSTALL_DATA=OFF \ -DNO_DIRECT_PYMODINST=ON \ @@ -62,5 +62,5 @@ EOF $PYTHON -m pip install ./ncrystal_pypkg/ -vv -source ${INST_DIR}/setup.sh +# source ${INST_DIR}/setup.sh From c9c74f08b2cae9c57f818c4a93abf986514fd809 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Mon, 21 Nov 2022 00:34:30 +0100 Subject: [PATCH 153/265] apply clang-format --- src/source.cpp | 78 +++++++++++++++++++++++++------------------------- 1 file changed, 39 insertions(+), 39 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 2e6335aad2..af108f3fa9 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -234,7 +234,8 @@ SourceSite IndependentSource::sample(uint64_t* seed) const auto id = (domain_type_ == DomainType::CELL) ? model::cells[coord.cell]->id_ : model::universes[coord.universe]->id_; - if (found = contains(domain_ids_, id)) break; + if (found = contains(domain_ids_, id)) + break; } } } @@ -332,57 +333,57 @@ FileSource::FileSource(std::string path) #ifdef OPENMC_MCPL FileSource::FileSource(mcpl_file_t mcpl_file) { - size_t n_sites=mcpl_hdr_nparticles(mcpl_file); + size_t n_sites = mcpl_hdr_nparticles(mcpl_file); sites_.resize(n_sites); - for (int i=0;ipdgcode; - while ( pdg!=2112 && pdg!=22 && pdg!=11 && pdg!=-11) { - mcpl_particle=mcpl_read(mcpl_file); - pdg=mcpl_particle->pdgcode; + int pdg = mcpl_particle->pdgcode; + while (pdg != 2112 && pdg != 22 && pdg != 11 && pdg != -11) { + mcpl_particle = mcpl_read(mcpl_file); + pdg = mcpl_particle->pdgcode; } - switch(pdg){ - case 2112: - site_.particle=ParticleType::neutron; - break; - case 22: - site_.particle=ParticleType::photon; - break; - case 11: - site_.particle=ParticleType::electron; - break; - case -11: - site_.particle=ParticleType::positron; - break; + switch (pdg) { + case 2112: + site_.particle = ParticleType::neutron; + break; + case 22: + site_.particle = ParticleType::photon; + break; + case 11: + site_.particle = ParticleType::electron; + break; + case -11: + site_.particle = ParticleType::positron; + break; } - //particle is good, convert to openmc-formalism - site_.r.x=mcpl_particle->position[0]; - site_.r.y=mcpl_particle->position[1]; - site_.r.z=mcpl_particle->position[2]; + // particle is good, convert to openmc-formalism + site_.r.x = mcpl_particle->position[0]; + site_.r.y = mcpl_particle->position[1]; + site_.r.z = mcpl_particle->position[2]; - site_.u.x=mcpl_particle->direction[0]; - site_.u.y=mcpl_particle->direction[1]; - site_.u.z=mcpl_particle->direction[2]; + site_.u.x = mcpl_particle->direction[0]; + site_.u.y = mcpl_particle->direction[1]; + site_.u.z = mcpl_particle->direction[2]; - //mcpl stores kinetic energy in MeV - site_.E=mcpl_particle->ekin*1e6; - //mcpl stores time in ms - site_.time=mcpl_particle->time*1e-3; - site_.wgt=mcpl_particle->weight; - site_.delayed_group=0; - sites_[i]=site_; + // mcpl stores kinetic energy in MeV + site_.E = mcpl_particle->ekin * 1e6; + // mcpl stores time in ms + site_.time = mcpl_particle->time * 1e-3; + site_.wgt = mcpl_particle->weight; + site_.delayed_group = 0; + sites_[i] = site_; } mcpl_close_file(mcpl_file); } -#endif //OPENMC_MCPL +#endif // OPENMC_MCPL SourceSite FileSource::sample(uint64_t* seed) const { @@ -443,7 +444,6 @@ CustomSourceWrapper::~CustomSourceWrapper() #endif } - //============================================================================== // Non-member functions //============================================================================== From 3e6bb9d5f669d2729fa96acdb4894ed1d338f2c5 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Mon, 28 Nov 2022 08:51:23 -0300 Subject: [PATCH 154/265] Upgrade installation script to NCrystal 3.5.0 --- tools/ci/gha-install-ncrystal.sh | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh index c080c16d8f..18472dfa66 100755 --- a/tools/ci/gha-install-ncrystal.sh +++ b/tools/ci/gha-install-ncrystal.sh @@ -21,13 +21,12 @@ cmake \ "${SRC_DIR}" \ -DBUILD_SHARED_LIBS=ON \ -DNCRYSTAL_NOTOUCH_CMAKE_BUILD_TYPE=ON \ - -DMODIFY_RPATH=OFF \ + -DNCRYSTAL_MODIFY_RPATH=OFF \ -DCMAKE_BUILD_TYPE=Release \ - -DBUILD_EXAMPLES=OFF \ - -DINSTALL_SETUPSH=OFF \ - -DEMBED_DATA=ON \ - -DINSTALL_DATA=OFF \ - -DNO_DIRECT_PYMODINST=ON \ + -DNCRYSTAL_ENABLE_EXAMPLES=OFF \ + -DNCRYSTAL_ENABLE_SETUPSH=OFF \ + -DNCRYSTAL_ENABLE_DATA=OFF \ + -DNCRYSTAL_SKIP_PYMODINST=ON \ -DCMAKE_INSTALL_PREFIX="${INST_DIR}" \ -DPython3_EXECUTABLE="$PYTHON" @@ -62,5 +61,5 @@ EOF $PYTHON -m pip install ./ncrystal_pypkg/ -vv -# source ${INST_DIR}/setup.sh +eval $( "${INST_DIR}/bin/ncrystal-config --setup" ) From be330a11b6798850ddaa54635167c89030bfb511 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Mon, 28 Nov 2022 09:15:45 -0300 Subject: [PATCH 155/265] Update gha-install-ncrystal.sh --- tools/ci/gha-install-ncrystal.sh | 31 ++++--------------------------- 1 file changed, 4 insertions(+), 27 deletions(-) diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh index 18472dfa66..1bcc896275 100755 --- a/tools/ci/gha-install-ncrystal.sh +++ b/tools/ci/gha-install-ncrystal.sh @@ -25,8 +25,7 @@ cmake \ -DCMAKE_BUILD_TYPE=Release \ -DNCRYSTAL_ENABLE_EXAMPLES=OFF \ -DNCRYSTAL_ENABLE_SETUPSH=OFF \ - -DNCRYSTAL_ENABLE_DATA=OFF \ - -DNCRYSTAL_SKIP_PYMODINST=ON \ + -DNCRYSTAL_ENABLE_DATA=EMBED \ -DCMAKE_INSTALL_PREFIX="${INST_DIR}" \ -DPython3_EXECUTABLE="$PYTHON" @@ -36,30 +35,8 @@ make install #Note: There is no "make test" or "make ctest" functionality for NCrystal # yet. If it appears in the future, we should add it here. - -#The next stuff is not pretty, but it is needed as a temporary -#workaround until NCrystal add better support for system-wide -#installations in CMake: - -cat < ./findncrystallib.py -import pathlib -libname = pathlib.Path('./cfg_ncrystal_libname.txt').read_text().strip() -libs = list(pathlib.Path("${INST_DIR}").glob("**/lib*/**/%s"%libname)) -assert len(libs)==1 -pathlib.Path('ncrystal_liblocation.txt').write_text(str(libs[0])) -EOF - -python3 ./findncrystallib.py - -TMPNCRYSTALLIBLOCATION=$(cat ./ncrystal_liblocation.txt) - -cat < ./ncrystal_pypkg/NCrystal/_nclibpath.py -#File autogenerated for working with systemwide install of NCrystal: -import pathlib -liblocation = pathlib.Path('${TMPNCRYSTALLIBLOCATION}'.strip()) -EOF - -$PYTHON -m pip install ./ncrystal_pypkg/ -vv - eval $( "${INST_DIR}/bin/ncrystal-config --setup" ) +# Check installation worked + +ncrystal-config --setup From fff545ac79d39b6aad0ee4dd055ac1da38cc344a Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Mon, 28 Nov 2022 09:27:12 -0300 Subject: [PATCH 156/265] Update gha-install-ncrystal.sh --- tools/ci/gha-install-ncrystal.sh | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh index 1bcc896275..390b7dba54 100755 --- a/tools/ci/gha-install-ncrystal.sh +++ b/tools/ci/gha-install-ncrystal.sh @@ -35,8 +35,14 @@ make install #Note: There is no "make test" or "make ctest" functionality for NCrystal # yet. If it appears in the future, we should add it here. -eval $( "${INST_DIR}/bin/ncrystal-config --setup" ) +# Output the configuration to the log + +"${INST_DIR}/bin/ncrystal-config" --setup + +# Change environmental variables + +eval $( "${INST_DIR}/bin/ncrystal-config" --setup ) # Check installation worked -ncrystal-config --setup +nctool --test From 8598ff7e4311c80c3dc7993a34eb6fc40976d7ed Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Mon, 28 Nov 2022 09:45:27 -0300 Subject: [PATCH 157/265] Pass CMAKE_PREFIX_PATH from NCrystall installation --- tools/ci/gha-install.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py index f3a29273f6..95fe70abea 100644 --- a/tools/ci/gha-install.py +++ b/tools/ci/gha-install.py @@ -56,6 +56,8 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrys if ncrystal: cmake_cmd.append('-DOPENMC_USE_NCRYSTAL=ON') + ncrystal_path = os.environ.get('CMAKE_PREFIX_PATH') + cmake_cmd.append('-DCMAKE_PREFIX_PATH=' + ncrystal_path) # Build in coverage mode for coverage testing cmake_cmd.append('-DOPENMC_ENABLE_COVERAGE=on') From c98a12171010e00fb78572c72f7327b0de740718 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Mon, 28 Nov 2022 09:56:10 -0300 Subject: [PATCH 158/265] Update gha-install.py --- tools/ci/gha-install.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py index 95fe70abea..f5779c9351 100644 --- a/tools/ci/gha-install.py +++ b/tools/ci/gha-install.py @@ -56,8 +56,8 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrys if ncrystal: cmake_cmd.append('-DOPENMC_USE_NCRYSTAL=ON') - ncrystal_path = os.environ.get('CMAKE_PREFIX_PATH') - cmake_cmd.append('-DCMAKE_PREFIX_PATH=' + ncrystal_path) + ncrystal_cmake_path = os.environ.get('HOME')+'/ncrystal_inst/lib/cmake' + cmake_cmd.append('-DCMAKE_PREFIX_PATH=' + ncrystal_cmake_path) # Build in coverage mode for coverage testing cmake_cmd.append('-DOPENMC_ENABLE_COVERAGE=on') From 19bf624b34806efcffc52a8f18ad915624b8811b Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Mon, 28 Nov 2022 11:03:41 -0300 Subject: [PATCH 159/265] Add NCrystal installation test --- tools/ci/gha-script.sh | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/tools/ci/gha-script.sh b/tools/ci/gha-script.sh index c791167e99..4c125b529a 100755 --- a/tools/ci/gha-script.sh +++ b/tools/ci/gha-script.sh @@ -14,5 +14,10 @@ if [[ $EVENT == 'y' ]]; then args="${args} --event " fi +# Check NCrystal installation +if [[ $NCRYSTAL = 'y' ]]; then + nctool --test +fi + # Run regression and unit tests pytest --cov=openmc -v $args tests From 4391d601fde4f74f91d594238e98564632c695b8 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Mon, 28 Nov 2022 11:06:06 -0300 Subject: [PATCH 160/265] find NCrystal --- cmake/OpenMCConfig.cmake.in | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/cmake/OpenMCConfig.cmake.in b/cmake/OpenMCConfig.cmake.in index d0e2beb827..162e3aad79 100644 --- a/cmake/OpenMCConfig.cmake.in +++ b/cmake/OpenMCConfig.cmake.in @@ -9,6 +9,11 @@ if(@OPENMC_USE_DAGMC@) find_package(DAGMC REQUIRED HINTS @DAGMC_DIR@) endif() +if(@OPENMC_USE_NCRYSTAL@) + find_package(NCrystal REQUIRED) + message(STATUS "Found NCrystal: ${NCrystal_DIR} (version ${NCrystal_VERSION})") +endif() + if(@OPENMC_USE_LIBMESH@) include(FindPkgConfig) list(APPEND CMAKE_PREFIX_PATH @LIBMESH_PREFIX@) From e626447a4e8dbce5ff8211b0ada661c329e3cd3d Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Mon, 28 Nov 2022 11:18:32 -0300 Subject: [PATCH 161/265] Update gha-script.sh --- tools/ci/gha-script.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tools/ci/gha-script.sh b/tools/ci/gha-script.sh index 4c125b529a..85fdef49f5 100755 --- a/tools/ci/gha-script.sh +++ b/tools/ci/gha-script.sh @@ -16,6 +16,8 @@ fi # Check NCrystal installation if [[ $NCRYSTAL = 'y' ]]; then + # Change environmental variables + eval $( "${HOME}/ncrystal_inst/bin/ncrystal-config" --setup ) nctool --test fi From e7b4285bd5214d0028700c07897fe60919ef8689 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian Date: Tue, 29 Nov 2022 11:21:04 +0100 Subject: [PATCH 162/265] Cleanup --- docs/source/methods/cross_sections.rst | 2 +- docs/source/usersguide/materials.rst | 2 +- tools/ci/gha-install-ncrystal.sh | 2 -- 3 files changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/source/methods/cross_sections.rst b/docs/source/methods/cross_sections.rst index 64e4fac3de..0b87913e51 100644 --- a/docs/source/methods/cross_sections.rst +++ b/docs/source/methods/cross_sections.rst @@ -189,7 +189,7 @@ cannot currently included in ACE files such as oriented single crystals (see the and further extend the physics `using plugins`_. Thermal scattering kernels are generated on the fly from dynamic and structural data, or loaded from :math:`S(\alpha,\beta)` tables converted from ENDF6 evaluations. These kernels are sampled in a direct way using a fast `rejection algorithm`_ -that does not require previous processing. A `large library` of materials is already included in +that does not require previous processing. A `large library`_ of materials is already included in the NCrystal distribution, and new materials can be easily defined from scratch in the `NCMAT format`_ or `combining existing files`_. diff --git a/docs/source/usersguide/materials.rst b/docs/source/usersguide/materials.rst index 1eaae846c3..a3c05f4211 100644 --- a/docs/source/usersguide/materials.rst +++ b/docs/source/usersguide/materials.rst @@ -106,7 +106,7 @@ Adding NCrystal materials ------------------ Additional support for thermal scattering can be added by using NCrystal_. -The :meth:`Material.from_ncrystal` class method generates a material object from +The :meth:`Material.from_ncrystal` class method generates a :class:`openmc.Material` object from an `NCrystal configuration string `_. Temperature, material composition and density are passed from the configuration string and the `NCMAT file `_ diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh index 390b7dba54..16f77e13e2 100755 --- a/tools/ci/gha-install-ncrystal.sh +++ b/tools/ci/gha-install-ncrystal.sh @@ -15,8 +15,6 @@ CPU_COUNT=1 mkdir "$BLD_DIR" cd ncrystal_bld -#cmake -Dstatic=on .. && make 2>/dev/null && sudo make install - cmake \ "${SRC_DIR}" \ -DBUILD_SHARED_LIBS=ON \ From 2555b951a4c585ab31942d4a718c2c5354d082a8 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 3 Nov 2022 18:27:53 -0500 Subject: [PATCH 163/265] Factor out to_xml_element methods for XML classes --- openmc/geometry.py | 52 +++++++++++++-------- openmc/plots.py | 21 +++++---- openmc/settings.py | 109 ++++++++++++++++++++++++--------------------- openmc/tallies.py | 25 +++++++---- 4 files changed, 120 insertions(+), 87 deletions(-) diff --git a/openmc/geometry.py b/openmc/geometry.py index 3b69333625..889cb6b31c 100644 --- a/openmc/geometry.py +++ b/openmc/geometry.py @@ -103,6 +103,38 @@ class Geometry: if universe.id in volume_calc.volumes: universe.add_volume_information(volume_calc) + def to_xml_element(self, remove_surfs=False): + """Creates a 'geometry' element to be written to an XML file. + + Parameters + ---------- + remove_surfs : bool + Whether or not to remove redundant surfaces from the geometry when + exporting + + """ + # Find and remove redundant surfaces from the geometry + if remove_surfs: + warnings.warn("remove_surfs kwarg will be deprecated soon, please " + "set the Geometry.merge_surfaces attribute instead.") + self.merge_surfaces = True + + if self.merge_surfaces: + self.remove_redundant_surfaces() + + # Create XML representation + element = ET.Element("geometry") + self.root_universe.create_xml_subelement(element, memo=set()) + + # Sort the elements in the file + element[:] = sorted(element, key=lambda x: ( + x.tag, int(x.get('id')))) + + # Clean the indentation in the file to be user-readable + xml.clean_indentation(element) + + return element + def export_to_xml(self, path='geometry.xml', remove_surfs=False): """Export geometry to an XML file. @@ -117,25 +149,7 @@ class Geometry: .. versionadded:: 0.12 """ - # Find and remove redundant surfaces from the geometry - if remove_surfs: - warnings.warn("remove_surfs kwarg will be deprecated soon, please " - "set the Geometry.merge_surfaces attribute instead.") - self.merge_surfaces = True - - if self.merge_surfaces: - self.remove_redundant_surfaces() - - # Create XML representation - root_element = ET.Element("geometry") - self.root_universe.create_xml_subelement(root_element, memo=set()) - - # Sort the elements in the file - root_element[:] = sorted(root_element, key=lambda x: ( - x.tag, int(x.get('id')))) - - # Clean the indentation in the file to be user-readable - xml.clean_indentation(root_element) + root_element = self.to_xml_element(remove_surfs) # Check if path is a directory p = Path(path) diff --git a/openmc/plots.py b/openmc/plots.py index 2708683b1a..52dcf3fc13 100644 --- a/openmc/plots.py +++ b/openmc/plots.py @@ -909,14 +909,8 @@ class Plots(cv.CheckedList): self._plots_file.append(xml_element) - def export_to_xml(self, path='plots.xml'): - """Export plot specifications to an XML file. - - Parameters - ---------- - path : str - Path to file to write. Defaults to 'plots.xml'. - + def to_xml_element(self): + """Create a 'plots' element to be written to an XML file. """ # Reset xml element tree self._plots_file.clear() @@ -926,6 +920,17 @@ class Plots(cv.CheckedList): # Clean the indentation in the file to be user-readable clean_indentation(self._plots_file) + return self._plots_file + + def export_to_xml(self, path='plots.xml'): + """Export plot specifications to an XML file. + + Parameters + ---------- + path : str + Path to file to write. Defaults to 'plots.xml'. + + """ # Check if path is a directory p = Path(path) if p.is_dir(): diff --git a/openmc/settings.py b/openmc/settings.py index 7d327ce7cf..29e19db2e1 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1539,6 +1539,63 @@ class Settings: if text is not None: self.max_tracks = int(text) + def to_xml_element(self): + """Create a 'settings' element to be written to an XML file. + """ + + # Reset xml element tree + element = ET.Element("settings") + + self._create_run_mode_subelement(element) + self._create_particles_subelement(element) + self._create_batches_subelement(element) + self._create_inactive_subelement(element) + self._create_max_lost_particles_subelement(element) + self._create_rel_max_lost_particles_subelement(element) + self._create_generations_per_batch_subelement(element) + self._create_keff_trigger_subelement(element) + self._create_source_subelement(element) + self._create_output_subelement(element) + self._create_statepoint_subelement(element) + self._create_sourcepoint_subelement(element) + self._create_surf_source_read_subelement(element) + self._create_surf_source_write_subelement(element) + self._create_confidence_intervals(element) + self._create_electron_treatment_subelement(element) + self._create_energy_mode_subelement(element) + self._create_max_order_subelement(element) + self._create_photon_transport_subelement(element) + self._create_ptables_subelement(element) + self._create_seed_subelement(element) + self._create_survival_biasing_subelement(element) + self._create_cutoff_subelement(element) + self._create_entropy_mesh_subelement(element) + self._create_trigger_subelement(element) + self._create_no_reduce_subelement(element) + self._create_verbosity_subelement(element) + self._create_tabular_legendre_subelements(element) + self._create_temperature_subelements(element) + self._create_trace_subelement(element) + self._create_track_subelement(element) + self._create_ufs_mesh_subelement(element) + self._create_resonance_scattering_subelement(element) + self._create_volume_calcs_subelement(element) + self._create_create_fission_neutrons_subelement(element) + self._create_delayed_photon_scaling_subelement(element) + self._create_event_based_subelement(element) + self._create_max_particles_in_flight_subelement(element) + self._create_material_cell_offsets_subelement(element) + self._create_log_grid_bins_subelement(element) + self._create_write_initial_source_subelement(element) + self._create_weight_windows_subelement(element) + self._create_max_splits_subelement(element) + self._create_max_tracks_subelement(element) + + # Clean the indentation in the file to be user-readable + clean_indentation(element) + + return element + def export_to_xml(self, path: PathLike = 'settings.xml'): """Export simulation settings to an XML file. @@ -1548,57 +1605,7 @@ class Settings: Path to file to write. Defaults to 'settings.xml'. """ - - # Reset xml element tree - root_element = ET.Element("settings") - - self._create_run_mode_subelement(root_element) - self._create_particles_subelement(root_element) - self._create_batches_subelement(root_element) - self._create_inactive_subelement(root_element) - self._create_max_lost_particles_subelement(root_element) - self._create_rel_max_lost_particles_subelement(root_element) - self._create_generations_per_batch_subelement(root_element) - self._create_keff_trigger_subelement(root_element) - self._create_source_subelement(root_element) - self._create_output_subelement(root_element) - self._create_statepoint_subelement(root_element) - self._create_sourcepoint_subelement(root_element) - self._create_surf_source_read_subelement(root_element) - self._create_surf_source_write_subelement(root_element) - self._create_confidence_intervals(root_element) - self._create_electron_treatment_subelement(root_element) - self._create_energy_mode_subelement(root_element) - self._create_max_order_subelement(root_element) - self._create_photon_transport_subelement(root_element) - self._create_ptables_subelement(root_element) - self._create_seed_subelement(root_element) - self._create_survival_biasing_subelement(root_element) - self._create_cutoff_subelement(root_element) - self._create_entropy_mesh_subelement(root_element) - self._create_trigger_subelement(root_element) - self._create_no_reduce_subelement(root_element) - self._create_verbosity_subelement(root_element) - self._create_tabular_legendre_subelements(root_element) - self._create_temperature_subelements(root_element) - self._create_trace_subelement(root_element) - self._create_track_subelement(root_element) - self._create_ufs_mesh_subelement(root_element) - self._create_resonance_scattering_subelement(root_element) - self._create_volume_calcs_subelement(root_element) - self._create_create_fission_neutrons_subelement(root_element) - self._create_delayed_photon_scaling_subelement(root_element) - self._create_event_based_subelement(root_element) - self._create_max_particles_in_flight_subelement(root_element) - self._create_material_cell_offsets_subelement(root_element) - self._create_log_grid_bins_subelement(root_element) - self._create_write_initial_source_subelement(root_element) - self._create_weight_windows_subelement(root_element) - self._create_max_splits_subelement(root_element) - self._create_max_tracks_subelement(root_element) - - # Clean the indentation in the file to be user-readable - clean_indentation(root_element) + root_element = self.to_xml_element() # Check if path is a directory p = Path(path) diff --git a/openmc/tallies.py b/openmc/tallies.py index d0355f14ee..dfb0c98bfd 100644 --- a/openmc/tallies.py +++ b/openmc/tallies.py @@ -3155,6 +3155,21 @@ class Tallies(cv.CheckedList): for d in derivs: root_element.append(d.to_xml_element()) + def to_xml_element(self): + """Creates a 'tallies' element to be written to an XML file. + """ + element = ET.Element("tallies") + self._create_mesh_subelements(element) + self._create_filter_subelements(element) + self._create_tally_subelements(element) + self._create_derivative_subelements(element) + + # Clean the indentation in the file to be user-readable + clean_indentation(element) + + return element + + def export_to_xml(self, path='tallies.xml'): """Create a tallies.xml file that can be used for a simulation. @@ -3164,15 +3179,7 @@ class Tallies(cv.CheckedList): Path to file to write. Defaults to 'tallies.xml'. """ - - root_element = ET.Element("tallies") - self._create_mesh_subelements(root_element) - self._create_filter_subelements(root_element) - self._create_tally_subelements(root_element) - self._create_derivative_subelements(root_element) - - # Clean the indentation in the file to be user-readable - clean_indentation(root_element) + root_element = self.to_xml_element() # Check if path is a directory p = Path(path) From ad746cb3e1d57c2fec163fbb4b8f87286bf72852 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 3 Nov 2022 19:09:15 -0500 Subject: [PATCH 164/265] Writing all main nodes to a single XML file --- openmc/material.py | 62 +++++++++++++++++++++++++------------------ openmc/model/model.py | 34 +++++++++++++++++------- openmc/settings.py | 2 +- 3 files changed, 62 insertions(+), 36 deletions(-) diff --git a/openmc/material.py b/openmc/material.py index 420a085216..af42e2e249 100644 --- a/openmc/material.py +++ b/openmc/material.py @@ -1449,6 +1449,41 @@ class Materials(cv.CheckedList): for material in self: material.make_isotropic_in_lab() + def _write_xml(self, file): + """Writes XML content of the materials to an open file handle. + + Parameters + ---------- + file : IOTextWrapper + Open file handle to write content into. + """ + # Write the header and the opening tag for the root element. + file.write("\n") + file.write('\n') + + # Write the element. + if self.cross_sections is not None: + element = ET.Element('cross_sections') + element.text = str(self.cross_sections) + clean_indentation(element, level=1) + element.tail = element.tail.strip(' ') + file.write(' ') + reorder_attributes(element) # TODO: Remove when support is Python 3.8+ + ET.ElementTree(element).write(file, encoding='unicode') + + # Write the elements. + for material in sorted(self, key=lambda x: x.id): + element = material.to_xml_element() + clean_indentation(element, level=1) + element.tail = element.tail.strip(' ') + file.write(' ') + reorder_attributes(element) # TODO: Remove when support is Python 3.8+ + ET.ElementTree(element).write(file, encoding='unicode') + + # Write the closing tag for the root element. + file.write('\n') + + def export_to_xml(self, path: PathLike = 'materials.xml'): """Export material collection to an XML file. @@ -1468,32 +1503,7 @@ class Materials(cv.CheckedList): # one go. with open(str(p), 'w', encoding='utf-8', errors='xmlcharrefreplace') as fh: - - # Write the header and the opening tag for the root element. - fh.write("\n") - fh.write('\n') - - # Write the element. - if self.cross_sections is not None: - element = ET.Element('cross_sections') - element.text = str(self.cross_sections) - clean_indentation(element, level=1) - element.tail = element.tail.strip(' ') - fh.write(' ') - reorder_attributes(element) # TODO: Remove when support is Python 3.8+ - ET.ElementTree(element).write(fh, encoding='unicode') - - # Write the elements. - for material in sorted(self, key=lambda x: x.id): - element = material.to_xml_element() - clean_indentation(element, level=1) - element.tail = element.tail.strip(' ') - fh.write(' ') - reorder_attributes(element) # TODO: Remove when support is Python 3.8+ - ET.ElementTree(element).write(fh, encoding='unicode') - - # Write the closing tag for the root element. - fh.write('\n') + self._write_xml(fh) @classmethod def from_xml(cls, path: PathLike = 'materials.xml'): diff --git a/openmc/model/model.py b/openmc/model/model.py index 98136b2d59..5a1b86a1ff 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -5,11 +5,16 @@ import os from pathlib import Path from numbers import Integral from tempfile import NamedTemporaryFile +<<<<<<< HEAD import warnings +======= +from xml.etree import ElementTree as ET +>>>>>>> d42935a08 (Writing all main nodes to a single XML file) import h5py import openmc +import openmc._xml as xml from openmc.dummy_comm import DummyCommunicator from openmc.executor import _process_CLI_arguments from openmc.checkvalue import check_type, check_value @@ -404,7 +409,7 @@ class Model: Parameters ---------- directory : str - Directory to write XML files to. If it doesn't exist already, it + Directory to write the model.xml file to. If it doesn't exist already, it will be created. remove_surfs : bool Whether or not to remove redundant surfaces from the geometry when @@ -416,8 +421,8 @@ class Model: d = Path(directory) if not d.is_dir(): d.mkdir(parents=True) + d /= 'model.xml' - self.settings.export_to_xml(d) if remove_surfs: warnings.warn("remove_surfs kwarg will be deprecated soon, please " "set the Geometry.merge_surfaces attribute instead.") @@ -425,22 +430,33 @@ class Model: # Can be used to modify tallies in case any surfaces are redundant redundant_surfaces = self.geometry.remove_redundant_surfaces() - self.geometry.export_to_xml(d) + settings_element = self.settings.to_xml_element() + geometry_element = self.geometry.to_xml_element() # If a materials collection was specified, export it. Otherwise, look # for all materials in the geometry and use that to automatically build # a collection. if self.materials: - self.materials.export_to_xml(d) + materials = self.materials else: materials = openmc.Materials(self.geometry.get_all_materials() .values()) - materials.export_to_xml(d) - if self.tallies: - self.tallies.export_to_xml(d) - if self.plots: - self.plots.export_to_xml(d) + with open(d, 'w', encoding='utf-8', + errors='xmlcharrefreplace') as fh: + # Write the materials collection to the open XML file first. + # This will write the XML header also + materials._write_xml(fh) + # Write remaining elements as a tree + ET.ElementTree(geometry_element).write(fh, encoding='unicode') + ET.ElementTree(settings_element).write(fh, encoding='unicode') + + if self.tallies: + tallies_element = self.tallies.to_xml_element() + ET.ElementTree(tallies_element).write(fh, encoding='unicode') + if self.plots: + plots_element = self.plots.to_xml_element() + ET.ElementTree(plots_element).write(fh, encoding='unicode') def import_properties(self, filename): """Import physical properties diff --git a/openmc/settings.py b/openmc/settings.py index 29e19db2e1..dd00413516 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1595,7 +1595,7 @@ class Settings: clean_indentation(element) return element - + def export_to_xml(self, path: PathLike = 'settings.xml'): """Export simulation settings to an XML file. From a09a61e77b10416ad52613bb578e03d60af72ebf Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 3 Nov 2022 19:12:18 -0500 Subject: [PATCH 165/265] Writing all output under a single root node --- openmc/material.py | 7 +++++-- openmc/model/model.py | 6 +++++- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/openmc/material.py b/openmc/material.py index af42e2e249..9e3951ccf4 100644 --- a/openmc/material.py +++ b/openmc/material.py @@ -1449,16 +1449,19 @@ class Materials(cv.CheckedList): for material in self: material.make_isotropic_in_lab() - def _write_xml(self, file): + def _write_xml(self, file, header=True): """Writes XML content of the materials to an open file handle. Parameters ---------- file : IOTextWrapper Open file handle to write content into. + header : bool + Whether or not to write the XML header """ # Write the header and the opening tag for the root element. - file.write("\n") + if header: + file.write("\n") file.write('\n') # Write the element. diff --git a/openmc/model/model.py b/openmc/model/model.py index 5a1b86a1ff..1af3bdffc9 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -444,9 +444,12 @@ class Model: with open(d, 'w', encoding='utf-8', errors='xmlcharrefreplace') as fh: + # write the XML header + fh.write("\n") + fh.write("\n") # Write the materials collection to the open XML file first. # This will write the XML header also - materials._write_xml(fh) + materials._write_xml(fh, False) # Write remaining elements as a tree ET.ElementTree(geometry_element).write(fh, encoding='unicode') ET.ElementTree(settings_element).write(fh, encoding='unicode') @@ -457,6 +460,7 @@ class Model: if self.plots: plots_element = self.plots.to_xml_element() ET.ElementTree(plots_element).write(fh, encoding='unicode') + fh.write("\n") def import_properties(self, filename): """Import physical properties From 7a9d8c95afa53fca2a8d99cf48a6be13f1786107 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 3 Nov 2022 19:18:39 -0500 Subject: [PATCH 166/265] Keeping old option to write separate XMLs so I can still use to tests to make sure I don't break stuff. --- openmc/model/model.py | 61 ++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 60 insertions(+), 1 deletion(-) diff --git a/openmc/model/model.py b/openmc/model/model.py index 1af3bdffc9..e3c4c4ae19 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -403,7 +403,66 @@ class Model: depletion_operator.cleanup_when_done = True depletion_operator.finalize() - def export_to_xml(self, directory='.', remove_surfs=False): + def export_to_xml(self, directory='.', remove_surfs=False, separate_xmls=True): + """Export model to separate XML files. + + Parameters + ---------- + directory : str + Directory to write XML files to. If it doesn't exist already, it + will be created. + remove_surfs : bool + Whether or not to remove redundant surfaces from the geometry when + exporting. + + .. versionadded:: 0.13.1 + + separate_xmls : bool + Whether or not to write a single model.xml file or many XML files. + """ + if separate_xmls: + self.export_to_separate_xmls(directory, remove_surfs) + else: + self.export_to_single_xml(directory, remove_surfs) + + def export_to_separate_xmls(self, directory='.', remove_surfs=False): + """Export model to separate XML files. + + Parameters + ---------- + directory : str + Directory to write XML files to. If it doesn't exist already, it + will be created. + remove_surfs : bool + Whether or not to remove redundant surfaces from the geometry when + exporting. + + .. versionadded:: 0.13.1 + """ + # Create directory if required + d = Path(directory) + if not d.is_dir(): + d.mkdir(parents=True) + + self.settings.export_to_xml(d) + self.geometry.export_to_xml(d, remove_surfs=remove_surfs) + + # If a materials collection was specified, export it. Otherwise, look + # for all materials in the geometry and use that to automatically build + # a collection. + if self.materials: + self.materials.export_to_xml(d) + else: + materials = openmc.Materials(self.geometry.get_all_materials() + .values()) + materials.export_to_xml(d) + + if self.tallies: + self.tallies.export_to_xml(d) + if self.plots: + self.plots.export_to_xml(d) + + def export_to_single_xml(self, directory='.', remove_surfs=False): """Export model to XML files. Parameters From 040965245dc5a7476aa005829e7cb42f75a9233c Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 3 Nov 2022 20:10:22 -0500 Subject: [PATCH 167/265] Adding signatures for reading information from an XML node where necessary. --- include/openmc/cross_sections.h | 5 +++ include/openmc/geometry_aux.h | 6 ++++ include/openmc/material.h | 4 +++ include/openmc/plot.h | 4 +++ include/openmc/settings.h | 5 ++- include/openmc/tallies/tally.h | 8 +++-- src/cross_sections.cpp | 8 +++-- src/geometry_aux.cpp | 8 +++-- src/initialize.cpp | 63 ++++++++++++++++++++++++++++++--- src/material.cpp | 9 +++-- src/plot.cpp | 7 ++-- src/settings.cpp | 14 +++++--- src/tallies/tally.cpp | 8 +++-- 13 files changed, 127 insertions(+), 22 deletions(-) diff --git a/include/openmc/cross_sections.h b/include/openmc/cross_sections.h index 2b0473becd..06140a6a8c 100644 --- a/include/openmc/cross_sections.h +++ b/include/openmc/cross_sections.h @@ -62,6 +62,11 @@ extern vector libraries; //! libraries void read_cross_sections_xml(); +//! Read cross sections file (either XML or multigroup H5) and populate data +//! libraries +//! \param[in] root node of the cross_sections.xml +void read_cross_sections_xml(pugi::xml_node root); + //! Load nuclide and thermal scattering data from HDF5 files // //! \param[in] nuc_temps Temperatures for each nuclide in [K] diff --git a/include/openmc/geometry_aux.h b/include/openmc/geometry_aux.h index b248d491ac..a4c506c31a 100644 --- a/include/openmc/geometry_aux.h +++ b/include/openmc/geometry_aux.h @@ -10,6 +10,7 @@ #include #include "openmc/vector.h" +#include "openmc/xml_interface.h" namespace openmc { @@ -19,8 +20,13 @@ extern std::unordered_map> extern std::unordered_map universe_level_counts; } // namespace model +//! Read geometry from XML file void read_geometry_xml(); +//! Read geometry from XML node +//! \param[in] root node of geometry XML element +void read_geometry_xml(pugi::xml_node root); + //============================================================================== //! Replace Universe, Lattice, and Material IDs with indices. //============================================================================== diff --git a/include/openmc/material.h b/include/openmc/material.h index b251a3ca85..81f4e1421c 100644 --- a/include/openmc/material.h +++ b/include/openmc/material.h @@ -221,6 +221,10 @@ double density_effect(const vector& f, const vector& e_b_sq, //! Read material data from materials.xml void read_materials_xml(); +//! Read material data XML node +//! \param[in] root node of materials XML element +void read_materials_xml(pugi::xml_node root); + void free_memory_material(); } // namespace openmc diff --git a/include/openmc/plot.h b/include/openmc/plot.h index 650b7e16a1..a415b17473 100644 --- a/include/openmc/plot.h +++ b/include/openmc/plot.h @@ -279,6 +279,10 @@ void voxel_finalize(hid_t dspace, hid_t dset, hid_t memspace); //! Read plot specifications from a plots.xml file void read_plots_xml(); +//! Read plot specifications from an XML Node +//! \param[in] XML node containing plot info +void read_plots_xml(pugi::xml_node root); + //! Clear memory void free_memory_plot(); diff --git a/include/openmc/settings.h b/include/openmc/settings.h index 1e061b235b..cd0ab477c4 100644 --- a/include/openmc/settings.h +++ b/include/openmc/settings.h @@ -127,9 +127,12 @@ extern double weight_survive; //!< Survival weight after Russian roulette //============================================================================== //! Read settings from XML file -//! \param[in] root XML node for void read_settings_xml(); +//! Read settings from XML node +//! \param[in] root XML node for +void read_settings_xml(pugi::xml_node root); + void free_memory_settings(); } // namespace openmc diff --git a/include/openmc/tallies/tally.h b/include/openmc/tallies/tally.h index 3cead91dc7..56a51370a8 100644 --- a/include/openmc/tallies/tally.h +++ b/include/openmc/tallies/tally.h @@ -48,10 +48,10 @@ public: void set_nuclides(const vector& nuclides); //! returns vector of indices corresponding to the tally this is called on - const vector& filters() const { return filters_; } + const vector& filters() const { return filters_; } //! \brief Returns the tally filter at index i - int32_t filters(int i) const { return filters_[i]; } + int32_t filters(int i) const { return filters_[i]; } void set_filters(gsl::span filters); @@ -178,6 +178,10 @@ extern double global_tally_leakage; //! Read tally specification from tallies.xml void read_tallies_xml(); +//! Read tally specification from an XML node +//! \param[in] root node of tallies XML element +void read_tallies_xml(pugi::xml_node root); + //! \brief Accumulate the sum of the contributions from each history within the //! batch to a new random variable void accumulate_tallies(); diff --git a/src/cross_sections.cpp b/src/cross_sections.cpp index afb0a1f36c..2094fd551f 100644 --- a/src/cross_sections.cpp +++ b/src/cross_sections.cpp @@ -91,8 +91,7 @@ Library::Library(pugi::xml_node node, const std::string& directory) // Non-member functions //============================================================================== -void read_cross_sections_xml() -{ +void read_cross_sections_xml() { pugi::xml_document doc; std::string filename = settings::path_input + "materials.xml"; // Check if materials.xml exists @@ -104,6 +103,11 @@ void read_cross_sections_xml() auto root = doc.document_element(); + read_cross_sections_xml(root); +} + +void read_cross_sections_xml(pugi::xml_node root) +{ // Find cross_sections.xml file -- the first place to look is the // materials.xml file. If no file is found there, then we check the // OPENMC_CROSS_SECTIONS environment variable diff --git a/src/geometry_aux.cpp b/src/geometry_aux.cpp index 2614719840..83e8494de6 100644 --- a/src/geometry_aux.cpp +++ b/src/geometry_aux.cpp @@ -40,8 +40,7 @@ void update_universe_cell_count(int32_t a, int32_t b) } } -void read_geometry_xml() -{ +void read_geometry_xml() { // Display output message write_message("Reading geometry XML file...", 5); @@ -61,6 +60,11 @@ void read_geometry_xml() // Get root element pugi::xml_node root = doc.document_element(); + read_geometry_xml(root); +} + +void read_geometry_xml(pugi::xml_node root) +{ // Read surfaces, cells, lattice read_surfaces(root); read_cells(root); diff --git a/src/initialize.cpp b/src/initialize.cpp index aa353aa9cb..44f84034a7 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -14,6 +14,7 @@ #include "openmc/constants.h" #include "openmc/cross_sections.h" #include "openmc/error.h" +#include "openmc/file_utils.h" #include "openmc/geometry_aux.h" #include "openmc/hdf5_interface.h" #include "openmc/material.h" @@ -291,10 +292,53 @@ int parse_command_line(int argc, char* argv[]) void read_input_xml() { - read_settings_xml(); + + // search for a single model.xml file + // Check if settings.xml exists + std::string model_filename = settings::path_input + "model.xml"; + bool use_model_file = file_exists(model_filename); + pugi::xml_node model_root; + if (use_model_file) { + write_message("Found model.xml file."); + pugi::xml_document doc; + auto result = doc.load_file(model_filename.c_str()); + if (!result) { + fatal_error("Error processing model.xml file."); + } + auto model_root = doc.document_element(); + + auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml", "tallies.xml", "plots.xml"}; + for (const auto& input : other_inputs) { + if (file_exists(settings::path_input + input)) { + warning(fmt::format("A '{}' file is also present. This file will be ignored.", input)); + } + } + } else { + write_message("No model.xml found. Reading separate XML inputs..."); + } + if (use_model_file) { + if (!check_for_node(model_root, "settings")) { + fatal_error("No node present in the model.xml file."); + } + read_settings_xml(model_root.child("settings")); + } else { + read_settings_xml(); + } + read_cross_sections_xml(); - read_materials_xml(); - read_geometry_xml(); + if (use_model_file) { + if (!check_for_node(model_root, "materials")) { + fatal_error("No node present in the model.xml file."); + } + read_materials_xml(model_root.child("materials")); + if (!check_for_node(model_root, "geometry")) { + fatal_error("No node present in the model.xml_file."); + } + read_geometry_xml(model_root.child("geometry")); + } else { + read_materials_xml(); + read_geometry_xml(); + } // Final geometry setup and assign temperatures finalize_geometry(); @@ -302,14 +346,23 @@ void read_input_xml() // Finalize cross sections having assigned temperatures finalize_cross_sections(); - read_tallies_xml(); + if (use_model_file && check_for_node(model_root, "tallies")) { + read_tallies_xml(model_root.child("tallies")); + } else { + read_tallies_xml(); + } // Initialize distribcell_filters prepare_distribcell(); // Read the plots.xml regardless of plot mode in case plots are requested // via the API - read_plots_xml(); + if (use_model_file) { + if (check_for_node(model_root, "plots")) + read_plots_xml(model_root.child("plots")); + } else { + read_plots_xml(); + } if (settings::run_mode == RunMode::PLOTTING) { // Read plots.xml if it exists if (mpi::master && settings::verbosity >= 5) diff --git a/src/material.cpp b/src/material.cpp index 30dfa5ed50..f2e23aede2 100644 --- a/src/material.cpp +++ b/src/material.cpp @@ -1264,8 +1264,7 @@ double density_effect(const vector& f, const vector& e_b_sq, return delta - w_sq * (1.0 - beta_sq); } -void read_materials_xml() -{ +void read_materials_xml() { write_message("Reading materials XML file...", 5); pugi::xml_document doc; @@ -1281,6 +1280,12 @@ void read_materials_xml() // Loop over XML material elements and populate the array. pugi::xml_node root = doc.document_element(); + + read_materials_xml(root); +} + +void read_materials_xml(pugi::xml_node root) +{ for (pugi::xml_node material_node : root.children("material")) { model::materials.push_back(make_unique(material_node)); } diff --git a/src/plot.cpp b/src/plot.cpp index b012ed1311..e28543cdff 100644 --- a/src/plot.cpp +++ b/src/plot.cpp @@ -124,8 +124,7 @@ extern "C" int openmc_plot_geometry() return 0; } -void read_plots_xml() -{ +void read_plots_xml() { // Check if plots.xml exists; this is only necessary when the plot runmode is // initiated. Otherwise, we want to read plots.xml because it may be called // later via the API. In that case, its ok for a plots.xml to not exist @@ -141,6 +140,10 @@ void read_plots_xml() doc.load_file(filename.c_str()); pugi::xml_node root = doc.document_element(); +} + +void read_plots_xml(pugi::xml_node root) +{ for (auto node : root.children("plot")) { model::plots.emplace_back(node); model::plot_map[model::plots.back().id_] = model::plots.size() - 1; diff --git a/src/settings.cpp b/src/settings.cpp index eb0d4936c7..710fb28101 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -211,13 +211,11 @@ void get_run_parameters(pugi::xml_node node_base) } } -void read_settings_xml() -{ +void read_settings_xml() { using namespace settings; using namespace pugi; - // Check if settings.xml exists - std::string filename = path_input + "settings.xml"; + std::string filename = settings::path_input + "settings.xml"; if (!file_exists(filename)) { if (run_mode != RunMode::PLOTTING) { fatal_error( @@ -245,6 +243,14 @@ void read_settings_xml() // Get root element xml_node root = doc.document_element(); + read_settings_xml(root); +} + +void read_settings_xml(pugi::xml_node root) +{ + using namespace settings; + using namespace pugi; + // Verbosity if (check_for_node(root, "verbosity")) { verbosity = std::stoi(get_node_value(root, "verbosity")); diff --git a/src/tallies/tally.cpp b/src/tallies/tally.cpp index 51194684ae..1c1f274d79 100644 --- a/src/tallies/tally.cpp +++ b/src/tallies/tally.cpp @@ -705,8 +705,7 @@ std::string Tally::nuclide_name(int nuclide_idx) const // Non-member functions //============================================================================== -void read_tallies_xml() -{ +void read_tallies_xml() { // Check if tallies.xml exists. If not, just return since it is optional std::string filename = settings::path_input + "tallies.xml"; if (!file_exists(filename)) @@ -719,6 +718,11 @@ void read_tallies_xml() doc.load_file(filename.c_str()); pugi::xml_node root = doc.document_element(); + read_tallies_xml(root); +} + +void read_tallies_xml(pugi::xml_node root) +{ // Check for setting if (check_for_node(root, "assume_separate")) { settings::assume_separate = get_node_value_bool(root, "assume_separate"); From cdd2a6b1cacb54387de050e96c36bca74c114777 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 3 Nov 2022 20:43:29 -0500 Subject: [PATCH 168/265] Correcting doc scope and some reads --- src/initialize.cpp | 10 ++++++---- src/settings.cpp | 2 ++ 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/src/initialize.cpp b/src/initialize.cpp index 44f84034a7..cb35ebce9d 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -298,14 +298,14 @@ void read_input_xml() std::string model_filename = settings::path_input + "model.xml"; bool use_model_file = file_exists(model_filename); pugi::xml_node model_root; + pugi::xml_document doc; if (use_model_file) { - write_message("Found model.xml file."); - pugi::xml_document doc; + write_message("Reading model.xml..."); auto result = doc.load_file(model_filename.c_str()); if (!result) { fatal_error("Error processing model.xml file."); } - auto model_root = doc.document_element(); + model_root = doc.document_element(); auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml", "tallies.xml", "plots.xml"}; for (const auto& input : other_inputs) { @@ -320,12 +320,14 @@ void read_input_xml() if (!check_for_node(model_root, "settings")) { fatal_error("No node present in the model.xml file."); } - read_settings_xml(model_root.child("settings")); + auto settings_root = model_root.child("settings"); + read_settings_xml(); } else { read_settings_xml(); } read_cross_sections_xml(); + if (use_model_file) { if (!check_for_node(model_root, "materials")) { fatal_error("No node present in the model.xml file."); diff --git a/src/settings.cpp b/src/settings.cpp index 710fb28101..de24e200ac 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -266,6 +266,7 @@ void read_settings_xml(pugi::xml_node root) // Find if a multi-group or continuous-energy simulation is desired if (check_for_node(root, "energy_mode")) { + std::cout << "Here" << std::endl; std::string temp_str = get_node_value(root, "energy_mode", true, true); if (temp_str == "mg" || temp_str == "multi-group") { run_CE = false; @@ -273,6 +274,7 @@ void read_settings_xml(pugi::xml_node root) run_CE = true; } } + std::cout << "Here" << std::endl; // Look for deprecated cross_sections.xml file in settings.xml if (check_for_node(root, "cross_sections")) { From bec9bf6f20805e12134e798aca98b90dd8e71d23 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 3 Nov 2022 21:18:04 -0500 Subject: [PATCH 169/265] Refactoring model read into it's own function. --- include/openmc/initialize.h | 1 + src/initialize.cpp | 148 +++++++++++++++++++++++------------- src/settings.cpp | 19 +++-- 3 files changed, 106 insertions(+), 62 deletions(-) diff --git a/include/openmc/initialize.h b/include/openmc/initialize.h index 869be44414..47474c986b 100644 --- a/include/openmc/initialize.h +++ b/include/openmc/initialize.h @@ -11,6 +11,7 @@ int parse_command_line(int argc, char* argv[]); #ifdef OPENMC_MPI void initialize_mpi(MPI_Comm intracomm); #endif +bool read_model_xml(); void read_input_xml(); } // namespace openmc diff --git a/src/initialize.cpp b/src/initialize.cpp index cb35ebce9d..254ad88da5 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -290,81 +290,125 @@ int parse_command_line(int argc, char* argv[]) return 0; } -void read_input_xml() -{ - - // search for a single model.xml file - // Check if settings.xml exists +bool read_model_xml() { + // get verbosity from settings node std::string model_filename = settings::path_input + "model.xml"; bool use_model_file = file_exists(model_filename); - pugi::xml_node model_root; + if (!file_exists(model_filename)) return false; + + // attempt to open the document pugi::xml_document doc; - if (use_model_file) { - write_message("Reading model.xml..."); - auto result = doc.load_file(model_filename.c_str()); - if (!result) { - fatal_error("Error processing model.xml file."); - } - model_root = doc.document_element(); - - auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml", "tallies.xml", "plots.xml"}; - for (const auto& input : other_inputs) { - if (file_exists(settings::path_input + input)) { - warning(fmt::format("A '{}' file is also present. This file will be ignored.", input)); - } - } - } else { - write_message("No model.xml found. Reading separate XML inputs..."); + auto result = doc.load_file(model_filename.c_str()); + if (!result) { + fatal_error("Error processing model.xml file."); } - if (use_model_file) { - if (!check_for_node(model_root, "settings")) { + pugi::xml_node root = doc.document_element(); + + // Read settings + if (!check_for_node(root, "settings")) { fatal_error("No node present in the model.xml file."); - } - auto settings_root = model_root.child("settings"); - read_settings_xml(); - } else { - read_settings_xml(); + } + auto settings_root = root.child("settings"); + + // Verbosity + if (check_for_node(settings_root, "verbosity")) { + settings::verbosity = std::stoi(get_node_value(settings_root, "verbosity")); } - read_cross_sections_xml(); - - if (use_model_file) { - if (!check_for_node(model_root, "materials")) { - fatal_error("No node present in the model.xml file."); - } - read_materials_xml(model_root.child("materials")); - if (!check_for_node(model_root, "geometry")) { - fatal_error("No node present in the model.xml_file."); - } - read_geometry_xml(model_root.child("geometry")); - } else { - read_materials_xml(); - read_geometry_xml(); + // To this point, we haven't displayed any output since we didn't know what + // the verbosity is. Now that we checked for it, show the title if necessary + if (mpi::master) { + if (settings::verbosity >= 2) + title(); } + write_message("Reading model XML file...", 5); + + read_settings_xml(settings_root); + + // If other XML files are present, display warning + // that they will be ignored + auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml", "tallies.xml", "plots.xml"}; + for (const auto& input : other_inputs) { + if (file_exists(settings::path_input + input)) { + warning(("Other XML file input(s) are present. These file will be ignored in favor of the model.xml file.")); + break; + } + } + + // Read materials and cross sections + if (!check_for_node(root, "materials")) { + fatal_error("No node present in the model.xml file."); + } + auto materials_node = root.child("materials"); + read_cross_sections_xml(materials_node); + read_materials_xml(root.child("materials")); + + // Read geometry + if (!check_for_node(root, "geometry")) { + fatal_error("No node present in the model.xml_file."); + } + read_geometry_xml(root.child("geometry")); + // Final geometry setup and assign temperatures finalize_geometry(); // Finalize cross sections having assigned temperatures finalize_cross_sections(); - if (use_model_file && check_for_node(model_root, "tallies")) { - read_tallies_xml(model_root.child("tallies")); + if (check_for_node(root, "tallies")) + read_tallies_xml(root.child("tallies")); + + // Initialize distribcell_filters + prepare_distribcell(); + + if (check_for_node(root, "plots")) + read_plots_xml(root.child("plots")); + + if (settings::run_mode == RunMode::PLOTTING) { + // Read plots.xml if it exists + if (mpi::master && settings::verbosity >= 5) + print_plot(); + } else { - read_tallies_xml(); + // Write summary information + if (mpi::master && settings::output_summary) + write_summary(); + + // Warn if overlap checking is on + if (mpi::master && settings::check_overlaps) { + warning("Cell overlap checking is ON."); + } } + return true; +} + +void read_input_xml() +{ + // attempt to reach the model.xml file if present + if (read_model_xml()) return; + + read_settings_xml(); + read_cross_sections_xml(); + read_materials_xml(); + read_geometry_xml(); + + // Final geometry setup and assign temperatures + finalize_geometry(); + + // Finalize cross sections having assigned temperatures + finalize_cross_sections(); + + read_tallies_xml(); + // Initialize distribcell_filters prepare_distribcell(); // Read the plots.xml regardless of plot mode in case plots are requested // via the API - if (use_model_file) { - if (check_for_node(model_root, "plots")) - read_plots_xml(model_root.child("plots")); - } else { - read_plots_xml(); - } + read_plots_xml(); + if (settings::run_mode == RunMode::PLOTTING) { // Read plots.xml if it exists if (mpi::master && settings::verbosity >= 5) diff --git a/src/settings.cpp b/src/settings.cpp index de24e200ac..3048862e3f 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -243,14 +243,6 @@ void read_settings_xml() { // Get root element xml_node root = doc.document_element(); - read_settings_xml(root); -} - -void read_settings_xml(pugi::xml_node root) -{ - using namespace settings; - using namespace pugi; - // Verbosity if (check_for_node(root, "verbosity")) { verbosity = std::stoi(get_node_value(root, "verbosity")); @@ -262,11 +254,19 @@ void read_settings_xml(pugi::xml_node root) if (verbosity >= 2) title(); } + write_message("Reading settings XML file...", 5); + read_settings_xml(root); +} + +void read_settings_xml(pugi::xml_node root) +{ + using namespace settings; + using namespace pugi; + // Find if a multi-group or continuous-energy simulation is desired if (check_for_node(root, "energy_mode")) { - std::cout << "Here" << std::endl; std::string temp_str = get_node_value(root, "energy_mode", true, true); if (temp_str == "mg" || temp_str == "multi-group") { run_CE = false; @@ -274,7 +274,6 @@ void read_settings_xml(pugi::xml_node root) run_CE = true; } } - std::cout << "Here" << std::endl; // Look for deprecated cross_sections.xml file in settings.xml if (check_for_node(root, "cross_sections")) { From 81aa653d506bf3e9f9288679c8e92a6f21b6ad46 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 3 Nov 2022 21:22:41 -0500 Subject: [PATCH 170/265] Factoring out some common lines between reader functions --- include/openmc/initialize.h | 1 + src/initialize.cpp | 22 ++++++---------------- 2 files changed, 7 insertions(+), 16 deletions(-) diff --git a/include/openmc/initialize.h b/include/openmc/initialize.h index 47474c986b..d3d12d45df 100644 --- a/include/openmc/initialize.h +++ b/include/openmc/initialize.h @@ -13,6 +13,7 @@ void initialize_mpi(MPI_Comm intracomm); #endif bool read_model_xml(); void read_input_xml(); +void initial_output(); } // namespace openmc diff --git a/src/initialize.cpp b/src/initialize.cpp index 254ad88da5..aa3e15efa9 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -108,6 +108,9 @@ int openmc_init(int argc, char* argv[], const void* intracomm) // Read XML input files read_input_xml(); + // Write some initial output under the header if needed + initial_output(); + // Check for particle restart run if (settings::particle_restart_run) settings::run_mode = RunMode::PARTICLE; @@ -365,22 +368,6 @@ bool read_model_xml() { if (check_for_node(root, "plots")) read_plots_xml(root.child("plots")); - if (settings::run_mode == RunMode::PLOTTING) { - // Read plots.xml if it exists - if (mpi::master && settings::verbosity >= 5) - print_plot(); - - } else { - // Write summary information - if (mpi::master && settings::output_summary) - write_summary(); - - // Warn if overlap checking is on - if (mpi::master && settings::check_overlaps) { - warning("Cell overlap checking is ON."); - } - } - return true; } @@ -408,7 +395,10 @@ void read_input_xml() // Read the plots.xml regardless of plot mode in case plots are requested // via the API read_plots_xml(); +} +void initial_output() { + // handle some final output if (settings::run_mode == RunMode::PLOTTING) { // Read plots.xml if it exists if (mpi::master && settings::verbosity >= 5) From 9391f17cff9a798c048ec62b9eed3a9188baa534 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 3 Nov 2022 22:29:36 -0500 Subject: [PATCH 171/265] Adding import for single or multiple XMLs --- openmc/geometry.py | 46 +++++++++++----- openmc/material.py | 40 ++++++++++---- openmc/model/model.py | 37 ++++++++++++- openmc/plots.py | 28 ++++++++-- openmc/settings.py | 119 ++++++++++++++++++++++++------------------ openmc/tallies.py | 72 +++++++++++++++---------- 6 files changed, 232 insertions(+), 110 deletions(-) diff --git a/openmc/geometry.py b/openmc/geometry.py index 889cb6b31c..b4f8046bd2 100644 --- a/openmc/geometry.py +++ b/openmc/geometry.py @@ -162,13 +162,13 @@ class Geometry: tree.write(str(p), xml_declaration=True, encoding='utf-8') @classmethod - def from_xml(cls, path='geometry.xml', materials=None): - """Generate geometry from XML file + def from_xml_element(cls, elem, materials=None): + """Generate geometry from an XML element Parameters ---------- - path : str, optional - Path to geometry XML file + elem : xml.etree.ElementTree.Element + XML element materials : openmc.Materials or None Materials used to assign to cells. If None, an attempt is made to generate it from the materials.xml file. @@ -187,13 +187,10 @@ class Geometry: universes[univ_id] = univ return universes[univ_id] - tree = ET.parse(path) - root = tree.getroot() - # Get surfaces surfaces = {} periodic = {} - for surface in root.findall('surface'): + for surface in elem.findall('surface'): s = openmc.Surface.from_xml_element(surface) surfaces[s.id] = s @@ -207,15 +204,15 @@ class Geometry: surfaces[s1].periodic_surface = surfaces[s2] # Add any DAGMC universes - for elem in root.findall('dagmc_universe'): + for elem in elem.findall('dagmc_universe'): dag_univ = openmc.DAGMCUniverse.from_xml_element(elem) universes[dag_univ.id] = dag_univ # Dictionary that maps each universe to a list of cells/lattices that - # contain it (needed to determine which universe is the root) + # contain it (needed to determine which universe is the elem) child_of = defaultdict(list) - for elem in root.findall('lattice'): + for elem in elem.findall('lattice'): lat = openmc.RectLattice.from_xml_element(elem, get_universe) universes[lat.id] = lat if lat.outer is not None: @@ -223,7 +220,7 @@ class Geometry: for u in lat.universes.ravel(): child_of[u].append(lat) - for elem in root.findall('hex_lattice'): + for elem in elem.findall('hex_lattice'): lat = openmc.HexLattice.from_xml_element(elem, get_universe) universes[lat.id] = lat if lat.outer is not None: @@ -245,7 +242,7 @@ class Geometry: mats = {str(m.id): m for m in materials} mats['void'] = None - for elem in root.findall('cell'): + for elem in elem.findall('cell'): c = openmc.Cell.from_xml_element(elem, surfaces, mats, get_universe) if c.fill_type in ('universe', 'lattice'): child_of[c.fill].append(c) @@ -258,6 +255,29 @@ class Geometry: else: raise ValueError('Error determining root universe.') + @classmethod + def from_xml(cls, path='geometry.xml', materials=None): + """Generate geometry from XML file + + Parameters + ---------- + path : str, optional + Path to geometry XML file + materials : openmc.Materials or None + Materials used to assign to cells. If None, an attempt is made to + generate it from the materials.xml file. + + Returns + ------- + openmc.Geometry + Geometry object + + """ + tree = ET.parse(path) + root = tree.getroot() + + return cls.from_xml_element(root, materials) + def find(self, point): """Find cells/universes/lattices which contain a given point diff --git a/openmc/material.py b/openmc/material.py index 9e3951ccf4..c335968002 100644 --- a/openmc/material.py +++ b/openmc/material.py @@ -1508,6 +1508,34 @@ class Materials(cv.CheckedList): errors='xmlcharrefreplace') as fh: self._write_xml(fh) + @classmethod + def from_xml_element(cls, elem): + """Generate materials collection from XML file + + Parameters + ---------- + elem : xml.etree.ElementTree.Element + XML element + + Returns + ------- + openmc.Materials + Materials collection + + """ + # Generate each material + materials = cls() + for material in elem.findall('material'): + materials.append(Material.from_xml_element(material)) + + # Check for cross sections settings + xs = elem.find('cross_sections') + if xs is not None: + materials.cross_sections = xs.text + + return materials + + @classmethod def from_xml(cls, path: PathLike = 'materials.xml'): """Generate materials collection from XML file @@ -1526,14 +1554,4 @@ class Materials(cv.CheckedList): tree = ET.parse(path) root = tree.getroot() - # Generate each material - materials = cls() - for material in root.findall('material'): - materials.append(Material.from_xml_element(material)) - - # Check for cross sections settings - xs = tree.find('cross_sections') - if xs is not None: - materials.cross_sections = xs.text - - return materials + return cls.from_xml_element(root) \ No newline at end of file diff --git a/openmc/model/model.py b/openmc/model/model.py index e3c4c4ae19..2193084c36 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -208,7 +208,42 @@ class Model: self._plots.append(plot) @classmethod - def from_xml(cls, geometry='geometry.xml', materials='materials.xml', + def from_xml(cls, separate_xmls=True, **kwargs): + if separate_xmls: + return cls.from_separate_xmls(**kwargs) + else: + return cls.from_model_xml(**kwargs) + + @classmethod + def from_model_xml(cls, path='model.xml'): + """Create model from single XML file + + Parameters + ---------- + path : str or Pathlike + Path to model.xml file + """ + tree = ET.parse(path) + root = tree.getroot() + + model = cls() + + model.settings = openmc.Settings.from_xml_element(root.find('settings')) + model.materials = openmc.Materials.from_xml_element(root.find('materials')) + model.geometry = \ + openmc.Geometry.from_xml_element(root.find('geometry'), model.materials) + + if tally_node := root.find('tallies'): + print(tally_node) + model.tallies = openmc.Tallies.from_xml_element(tally_node) + + if plots_node := root.find('plots'): + model.plots = openmc.Plots.from_xml_element(plots_node) + + return model + + @classmethod + def from_separate_xmls(cls, geometry='geometry.xml', materials='materials.xml', settings='settings.xml', tallies='tallies.xml', plots='plots.xml'): """Create model from existing XML files diff --git a/openmc/plots.py b/openmc/plots.py index 52dcf3fc13..badea2e586 100644 --- a/openmc/plots.py +++ b/openmc/plots.py @@ -941,6 +941,27 @@ class Plots(cv.CheckedList): tree = ET.ElementTree(self._plots_file) tree.write(str(p), xml_declaration=True, encoding='utf-8') + @classmethod + def from_xml_element(cls, elem): + """Generate plots collection from XML file + + Parameters + ---------- + elem : xml.etree.ElementTree.Element + XML element + + Returns + ------- + openmc.Plots + Plots collection + + """ + # Generate each plot + plots = cls() + for elem in elem.findall('plot'): + plots.append(Plot.from_xml_element(elem)) + return plots + @classmethod def from_xml(cls, path='plots.xml'): """Generate plots collection from XML file @@ -958,9 +979,6 @@ class Plots(cv.CheckedList): """ tree = ET.parse(path) root = tree.getroot() + return cls.from_xml_element(root) + - # Generate each plot - plots = cls() - for elem in root.findall('plot'): - plots.append(Plot.from_xml_element(elem)) - return plots diff --git a/openmc/settings.py b/openmc/settings.py index dd00413516..c2fca98f7d 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1595,7 +1595,7 @@ class Settings: clean_indentation(element) return element - + def export_to_xml(self, path: PathLike = 'settings.xml'): """Export simulation settings to an XML file. @@ -1617,6 +1617,71 @@ class Settings: tree = ET.ElementTree(root_element) tree.write(str(p), xml_declaration=True, encoding='utf-8') + @classmethod + def from_xml_element(cls, elem): + """Generate settings from XML element + + Parameters + ---------- + elem : xml.etree.ElementTree.Element + XML element + + Returns + ------- + openmc.Settings + Settings object + + """ + settings = cls() + settings._eigenvalue_from_xml_element(elem) + settings._run_mode_from_xml_element(elem) + settings._particles_from_xml_element(elem) + settings._batches_from_xml_element(elem) + settings._inactive_from_xml_element(elem) + settings._max_lost_particles_from_xml_element(elem) + settings._rel_max_lost_particles_from_xml_element(elem) + settings._generations_per_batch_from_xml_element(elem) + settings._keff_trigger_from_xml_element(elem) + settings._source_from_xml_element(elem) + settings._volume_calcs_from_xml_element(elem) + settings._output_from_xml_element(elem) + settings._statepoint_from_xml_element(elem) + settings._sourcepoint_from_xml_element(elem) + settings._surf_source_read_from_xml_element(elem) + settings._surf_source_write_from_xml_element(elem) + settings._confidence_intervals_from_xml_element(elem) + settings._electron_treatment_from_xml_element(elem) + settings._energy_mode_from_xml_element(elem) + settings._max_order_from_xml_element(elem) + settings._photon_transport_from_xml_element(elem) + settings._ptables_from_xml_element(elem) + settings._seed_from_xml_element(elem) + settings._survival_biasing_from_xml_element(elem) + settings._cutoff_from_xml_element(elem) + settings._entropy_mesh_from_xml_element(elem) + settings._trigger_from_xml_element(elem) + settings._no_reduce_from_xml_element(elem) + settings._verbosity_from_xml_element(elem) + settings._tabular_legendre_from_xml_element(elem) + settings._temperature_from_xml_element(elem) + settings._trace_from_xml_element(elem) + settings._track_from_xml_element(elem) + settings._ufs_mesh_from_xml_element(elem) + settings._resonance_scattering_from_xml_element(elem) + settings._create_fission_neutrons_from_xml_element(elem) + settings._delayed_photon_scaling_from_xml_element(elem) + settings._event_based_from_xml_element(elem) + settings._max_particles_in_flight_from_xml_element(elem) + settings._material_cell_offsets_from_xml_element(elem) + settings._log_grid_bins_from_xml_element(elem) + settings._write_initial_source_from_xml_element(elem) + settings._weight_windows_from_xml_element(elem) + settings._max_splits_from_xml_element(elem) + settings._max_tracks_from_xml_element(elem) + + # TODO: Get volume calculations + return settings + @classmethod def from_xml(cls, path: PathLike = 'settings.xml'): """Generate settings from XML file @@ -1636,54 +1701,4 @@ class Settings: """ tree = ET.parse(path) root = tree.getroot() - - settings = cls() - settings._eigenvalue_from_xml_element(root) - settings._run_mode_from_xml_element(root) - settings._particles_from_xml_element(root) - settings._batches_from_xml_element(root) - settings._inactive_from_xml_element(root) - settings._max_lost_particles_from_xml_element(root) - settings._rel_max_lost_particles_from_xml_element(root) - settings._generations_per_batch_from_xml_element(root) - settings._keff_trigger_from_xml_element(root) - settings._source_from_xml_element(root) - settings._volume_calcs_from_xml_element(root) - settings._output_from_xml_element(root) - settings._statepoint_from_xml_element(root) - settings._sourcepoint_from_xml_element(root) - settings._surf_source_read_from_xml_element(root) - settings._surf_source_write_from_xml_element(root) - settings._confidence_intervals_from_xml_element(root) - settings._electron_treatment_from_xml_element(root) - settings._energy_mode_from_xml_element(root) - settings._max_order_from_xml_element(root) - settings._photon_transport_from_xml_element(root) - settings._ptables_from_xml_element(root) - settings._seed_from_xml_element(root) - settings._survival_biasing_from_xml_element(root) - settings._cutoff_from_xml_element(root) - settings._entropy_mesh_from_xml_element(root) - settings._trigger_from_xml_element(root) - settings._no_reduce_from_xml_element(root) - settings._verbosity_from_xml_element(root) - settings._tabular_legendre_from_xml_element(root) - settings._temperature_from_xml_element(root) - settings._trace_from_xml_element(root) - settings._track_from_xml_element(root) - settings._ufs_mesh_from_xml_element(root) - settings._resonance_scattering_from_xml_element(root) - settings._create_fission_neutrons_from_xml_element(root) - settings._delayed_photon_scaling_from_xml_element(root) - settings._event_based_from_xml_element(root) - settings._max_particles_in_flight_from_xml_element(root) - settings._material_cell_offsets_from_xml_element(root) - settings._log_grid_bins_from_xml_element(root) - settings._write_initial_source_from_xml_element(root) - settings._weight_windows_from_xml_element(root) - settings._max_splits_from_xml_element(root) - settings._max_tracks_from_xml_element(root) - - # TODO: Get volume calculations - - return settings + return cls.from_xml_element(root) diff --git a/openmc/tallies.py b/openmc/tallies.py index dfb0c98bfd..0355568ec0 100644 --- a/openmc/tallies.py +++ b/openmc/tallies.py @@ -3191,6 +3191,49 @@ class Tallies(cv.CheckedList): tree = ET.ElementTree(root_element) tree.write(str(p), xml_declaration=True, encoding='utf-8') + @classmethod + def from_xml_element(cls, elem): + """Generate tallies from an XML element + + Parameters + ---------- + elem : xml.etree.ElementTree.Element + XML element + + Returns + ------- + openmc.Tallies + Tallies object + + """ + # Read mesh elements + meshes = {} + for elem in elem.findall('mesh'): + mesh = MeshBase.from_xml_element(elem) + meshes[mesh.id] = mesh + + # Read filter elements + filters = {} + for elem in elem.findall('filter'): + filter = openmc.Filter.from_xml_element(elem, meshes=meshes) + filters[filter.id] = filter + + # Read derivative elements + derivatives = {} + for elem in elem.findall('derivative'): + deriv = openmc.TallyDerivative.from_xml_element(elem) + derivatives[deriv.id] = deriv + + # Read tally elements + tallies = [] + for elem in elem.findall('tally'): + tally = openmc.Tally.from_xml_element( + elem, filters=filters, derivatives=derivatives + ) + tallies.append(tally) + + return cls(tallies) + @classmethod def from_xml(cls, path='tallies.xml'): """Generate tallies from XML file @@ -3208,31 +3251,4 @@ class Tallies(cv.CheckedList): """ tree = ET.parse(path) root = tree.getroot() - - # Read mesh elements - meshes = {} - for elem in root.findall('mesh'): - mesh = MeshBase.from_xml_element(elem) - meshes[mesh.id] = mesh - - # Read filter elements - filters = {} - for elem in root.findall('filter'): - filter = openmc.Filter.from_xml_element(elem, meshes=meshes) - filters[filter.id] = filter - - # Read derivative elements - derivatives = {} - for elem in root.findall('derivative'): - deriv = openmc.TallyDerivative.from_xml_element(elem) - derivatives[deriv.id] = deriv - - # Read tally elements - tallies = [] - for elem in root.findall('tally'): - tally = openmc.Tally.from_xml_element( - elem, filters=filters, derivatives=derivatives - ) - tallies.append(tally) - - return cls(tallies) + return cls.from_xml_element(root) From af6b0af1e3ab2fc84224a12e55928cc0030a27d4 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 3 Nov 2022 22:41:28 -0500 Subject: [PATCH 172/265] Fix loop variable overwrite --- openmc/tallies.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/openmc/tallies.py b/openmc/tallies.py index 0355568ec0..2996f1b034 100644 --- a/openmc/tallies.py +++ b/openmc/tallies.py @@ -3208,27 +3208,27 @@ class Tallies(cv.CheckedList): """ # Read mesh elements meshes = {} - for elem in elem.findall('mesh'): - mesh = MeshBase.from_xml_element(elem) + for e in elem.findall('mesh'): + mesh = MeshBase.from_xml_element(e) meshes[mesh.id] = mesh # Read filter elements filters = {} - for elem in elem.findall('filter'): - filter = openmc.Filter.from_xml_element(elem, meshes=meshes) + for e in elem.findall('filter'): + filter = openmc.Filter.from_xml_element(e, meshes=meshes) filters[filter.id] = filter # Read derivative elements derivatives = {} - for elem in elem.findall('derivative'): - deriv = openmc.TallyDerivative.from_xml_element(elem) + for e in elem.findall('derivative'): + deriv = openmc.TallyDerivative.from_xml_element(e) derivatives[deriv.id] = deriv # Read tally elements tallies = [] - for elem in elem.findall('tally'): + for e in elem.findall('tally'): tally = openmc.Tally.from_xml_element( - elem, filters=filters, derivatives=derivatives + e, filters=filters, derivatives=derivatives ) tallies.append(tally) From 5ac6e87a68c0666ef41ef1c6d9b60aa19500b1a5 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 3 Nov 2022 23:15:14 -0500 Subject: [PATCH 173/265] Properly call read_plots_xml --- src/plot.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/plot.cpp b/src/plot.cpp index e28543cdff..1a62fe2631 100644 --- a/src/plot.cpp +++ b/src/plot.cpp @@ -140,6 +140,8 @@ void read_plots_xml() { doc.load_file(filename.c_str()); pugi::xml_node root = doc.document_element(); + + read_plots_xml(root); } void read_plots_xml(pugi::xml_node root) From 2e716589a14d2465ab4a494e12ddf86172af72e3 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 3 Nov 2022 23:57:22 -0500 Subject: [PATCH 174/265] Other bug fixes --- openmc/geometry.py | 32 ++++++++++++++++---------------- openmc/model/model.py | 6 +++--- openmc/plots.py | 7 ++++--- 3 files changed, 23 insertions(+), 22 deletions(-) diff --git a/openmc/geometry.py b/openmc/geometry.py index b4f8046bd2..d036df9c74 100644 --- a/openmc/geometry.py +++ b/openmc/geometry.py @@ -204,24 +204,24 @@ class Geometry: surfaces[s1].periodic_surface = surfaces[s2] # Add any DAGMC universes - for elem in elem.findall('dagmc_universe'): - dag_univ = openmc.DAGMCUniverse.from_xml_element(elem) + for e in elem.findall('dagmc_universe'): + dag_univ = openmc.DAGMCUniverse.from_xml_element(e) universes[dag_univ.id] = dag_univ # Dictionary that maps each universe to a list of cells/lattices that # contain it (needed to determine which universe is the elem) child_of = defaultdict(list) - for elem in elem.findall('lattice'): - lat = openmc.RectLattice.from_xml_element(elem, get_universe) + for e in elem.findall('lattice'): + lat = openmc.RectLattice.from_xml_element(e, get_universe) universes[lat.id] = lat if lat.outer is not None: child_of[lat.outer].append(lat) for u in lat.universes.ravel(): child_of[u].append(lat) - for elem in elem.findall('hex_lattice'): - lat = openmc.HexLattice.from_xml_element(elem, get_universe) + for e in elem.findall('hex_lattice'): + lat = openmc.HexLattice.from_xml_element(e, get_universe) universes[lat.id] = lat if lat.outer is not None: child_of[lat.outer].append(lat) @@ -235,15 +235,8 @@ class Geometry: for u in ring: child_of[u].append(lat) - # Create dictionary to easily look up materials - if materials is None: - filename = Path(path).parent / 'materials.xml' - materials = openmc.Materials.from_xml(str(filename)) - mats = {str(m.id): m for m in materials} - mats['void'] = None - - for elem in elem.findall('cell'): - c = openmc.Cell.from_xml_element(elem, surfaces, mats, get_universe) + for e in elem.findall('cell'): + c = openmc.Cell.from_xml_element(e, surfaces, materials, get_universe) if c.fill_type in ('universe', 'lattice'): child_of[c.fill].append(c) @@ -276,7 +269,14 @@ class Geometry: tree = ET.parse(path) root = tree.getroot() - return cls.from_xml_element(root, materials) + # Create dictionary to easily look up materials + if materials is None: + filename = Path(path).parent / 'materials.xml' + materials = openmc.Materials.from_xml(str(filename)) + mats = {str(m.id): m for m in materials} + mats['void'] = None + + return cls.from_xml_element(root, mats) def find(self, point): """Find cells/universes/lattices which contain a given point diff --git a/openmc/model/model.py b/openmc/model/model.py index 2193084c36..a839dc8f0c 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -208,11 +208,11 @@ class Model: self._plots.append(plot) @classmethod - def from_xml(cls, separate_xmls=True, **kwargs): + def from_xml(cls, *args, separate_xmls=True, **kwargs): if separate_xmls: - return cls.from_separate_xmls(**kwargs) + return cls.from_separate_xmls(*args, **kwargs) else: - return cls.from_model_xml(**kwargs) + return cls.from_model_xml(*args, **kwargs) @classmethod def from_model_xml(cls, path='model.xml'): diff --git a/openmc/plots.py b/openmc/plots.py index badea2e586..b1f1927876 100644 --- a/openmc/plots.py +++ b/openmc/plots.py @@ -919,6 +919,7 @@ class Plots(cv.CheckedList): # Clean the indentation in the file to be user-readable clean_indentation(self._plots_file) + reorder_attributes(self._plots_file) # TODO: Remove when support is Python 3.8+ return self._plots_file @@ -936,8 +937,8 @@ class Plots(cv.CheckedList): if p.is_dir(): p /= 'plots.xml' + self.to_xml_element() # Write the XML Tree to the plots.xml file - reorder_attributes(self._plots_file) # TODO: Remove when support is Python 3.8+ tree = ET.ElementTree(self._plots_file) tree.write(str(p), xml_declaration=True, encoding='utf-8') @@ -958,8 +959,8 @@ class Plots(cv.CheckedList): """ # Generate each plot plots = cls() - for elem in elem.findall('plot'): - plots.append(Plot.from_xml_element(elem)) + for e in elem.findall('plot'): + plots.append(Plot.from_xml_element(e)) return plots @classmethod From b4dcc30f92c4b8ff29b77505cdf654fa7eff7181 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Fri, 4 Nov 2022 00:58:43 -0500 Subject: [PATCH 175/265] Removing walrus operator --- openmc/model/model.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/openmc/model/model.py b/openmc/model/model.py index a839dc8f0c..bc8f0b5318 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -233,12 +233,11 @@ class Model: model.geometry = \ openmc.Geometry.from_xml_element(root.find('geometry'), model.materials) - if tally_node := root.find('tallies'): - print(tally_node) - model.tallies = openmc.Tallies.from_xml_element(tally_node) + if root.find('tallies'): + model.tallies = openmc.Tallies.from_xml_element(root.find('tallies')) - if plots_node := root.find('plots'): - model.plots = openmc.Plots.from_xml_element(plots_node) + if root.find('plots'): + model.plots = openmc.Plots.from_xml_element(root.find('plots')) return model From 611475a835be98beee0082727e94660b3fcd3000 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Fri, 4 Nov 2022 22:43:25 -0500 Subject: [PATCH 176/265] Restructureing input function calls a little --- src/initialize.cpp | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/src/initialize.cpp b/src/initialize.cpp index aa3e15efa9..3f6e69ecde 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -106,7 +106,7 @@ int openmc_init(int argc, char* argv[], const void* intracomm) openmc::openmc_set_seed(DEFAULT_SEED); // Read XML input files - read_input_xml(); + if (!read_model_xml()) read_input_xml(); // Write some initial output under the header if needed initial_output(); @@ -373,9 +373,6 @@ bool read_model_xml() { void read_input_xml() { - // attempt to reach the model.xml file if present - if (read_model_xml()) return; - read_settings_xml(); read_cross_sections_xml(); read_materials_xml(); From 021bb280c9b4cad713ecdd516c9ef8b9ee97bd2c Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Fri, 4 Nov 2022 22:45:37 -0500 Subject: [PATCH 177/265] Adding initial test for exporting model.xmls. Correcting material maps --- openmc/model/model.py | 3 ++- tests/unit_tests/test_model.py | 21 +++++++++++++++++++++ 2 files changed, 23 insertions(+), 1 deletion(-) diff --git a/openmc/model/model.py b/openmc/model/model.py index bc8f0b5318..6950642e0a 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -230,8 +230,9 @@ class Model: model.settings = openmc.Settings.from_xml_element(root.find('settings')) model.materials = openmc.Materials.from_xml_element(root.find('materials')) + materials = {str(m.id): m for m in model.materials} model.geometry = \ - openmc.Geometry.from_xml_element(root.find('geometry'), model.materials) + openmc.Geometry.from_xml_element(root.find('geometry'), materials) if root.find('tallies'): model.tallies = openmc.Tallies.from_xml_element(root.find('tallies')) diff --git a/tests/unit_tests/test_model.py b/tests/unit_tests/test_model.py index 9b05ed2a5c..ce81b00eec 100644 --- a/tests/unit_tests/test_model.py +++ b/tests/unit_tests/test_model.py @@ -7,6 +7,8 @@ import pytest import openmc import openmc.lib +from .. import cdtemp + @pytest.fixture(scope='function') def pin_model_attributes(): @@ -529,3 +531,22 @@ def test_calc_volumes(run_in_tmpdir, pin_model_attributes, mpi_intracomm): assert openmc.lib.materials[3].volume == mats[2].volume test_model.finalize_lib() + +def test_model_xml(): + + with cdtemp(): + # load a model from examples + pwr_model = openmc.examples.pwr_core() + + # export to separate XMLs manually + pwr_model.settings.export_to_xml('settings_ref.xml') + pwr_model.materials.export_to_xml('materials_ref.xml') + pwr_model.geometry.export_to_xml('geometry_ref.xml') + + # now write and read a model.xml file + pwr_model.export_to_xml(separate_xmls=False) + new_model = openmc.Model.from_xml(separate_xmls=False) + + # make sure we can also export this again to separate + # XML files + new_model.export_to_xml(separate_xmls=True) \ No newline at end of file From abd3d515b0906363ce1975ffadd983c6c5a86f2b Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Fri, 4 Nov 2022 22:46:11 -0500 Subject: [PATCH 178/265] Correcting doc strings for material mapping sent to --- openmc/cell.py | 2 +- openmc/geometry.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/openmc/cell.py b/openmc/cell.py index 0cea73b324..d03052623d 100644 --- a/openmc/cell.py +++ b/openmc/cell.py @@ -650,7 +650,7 @@ class Cell(IDManagerMixin): surfaces : dict Dictionary mapping surface IDs to :class:`openmc.Surface` instances materials : dict - Dictionary mapping material IDs to :class:`openmc.Material` + Dictionary mapping material ID strings to :class:`openmc.Material` instances (defined in :math:`openmc.Geometry.from_xml`) get_universe : function Function returning universe (defined in diff --git a/openmc/geometry.py b/openmc/geometry.py index d036df9c74..57aab18846 100644 --- a/openmc/geometry.py +++ b/openmc/geometry.py @@ -256,9 +256,9 @@ class Geometry: ---------- path : str, optional Path to geometry XML file - materials : openmc.Materials or None - Materials used to assign to cells. If None, an attempt is made to - generate it from the materials.xml file. + materials : dict + Dictionary mapping material ID strings to :class:`openmc.Material` + instances (defined in :math:`openmc.Geometry.from_xml`) Returns ------- From 662d83a7dd72240b4da8594319bab416977ec71b Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Wed, 9 Nov 2022 23:29:17 -0600 Subject: [PATCH 179/265] Running some existing regression tests using single XML file --- .../adj_cell_rotation/__init__.py | 2 + .../regression_tests/energy_laws/__init__.py | 1 + .../lattice_multiple/__init__.py | 1 + tests/regression_tests/model_xml/__init__.py | 0 .../model_xml/inputs_true.dat | 38 ++++++++++ tests/regression_tests/model_xml/test.py | 76 +++++++++++++++++++ .../photon_production/__init__.py | 1 + 7 files changed, 119 insertions(+) create mode 100644 tests/regression_tests/model_xml/__init__.py create mode 100644 tests/regression_tests/model_xml/inputs_true.dat create mode 100644 tests/regression_tests/model_xml/test.py diff --git a/tests/regression_tests/adj_cell_rotation/__init__.py b/tests/regression_tests/adj_cell_rotation/__init__.py index e69de29bb2..7efe448659 100644 --- a/tests/regression_tests/adj_cell_rotation/__init__.py +++ b/tests/regression_tests/adj_cell_rotation/__init__.py @@ -0,0 +1,2 @@ + +from .test import model \ No newline at end of file diff --git a/tests/regression_tests/energy_laws/__init__.py b/tests/regression_tests/energy_laws/__init__.py index e69de29bb2..29fbfcc0c2 100644 --- a/tests/regression_tests/energy_laws/__init__.py +++ b/tests/regression_tests/energy_laws/__init__.py @@ -0,0 +1 @@ +from .test import model \ No newline at end of file diff --git a/tests/regression_tests/lattice_multiple/__init__.py b/tests/regression_tests/lattice_multiple/__init__.py index e69de29bb2..29fbfcc0c2 100644 --- a/tests/regression_tests/lattice_multiple/__init__.py +++ b/tests/regression_tests/lattice_multiple/__init__.py @@ -0,0 +1 @@ +from .test import model \ No newline at end of file diff --git a/tests/regression_tests/model_xml/__init__.py b/tests/regression_tests/model_xml/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/regression_tests/model_xml/inputs_true.dat b/tests/regression_tests/model_xml/inputs_true.dat new file mode 100644 index 0000000000..5aedbfa143 --- /dev/null +++ b/tests/regression_tests/model_xml/inputs_true.dat @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + eigenvalue + 10000 + 10 + 5 + + + -4.0 -4.0 -4.0 4.0 4.0 4.0 + + + + diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py new file mode 100644 index 0000000000..448079b3f6 --- /dev/null +++ b/tests/regression_tests/model_xml/test.py @@ -0,0 +1,76 @@ +from difflib import unified_diff +import filecmp +import os + +import openmc +import pytest + +from tests.testing_harness import PyAPITestHarness, colorize + +# use a few models from other tests to make sure the same results are +# produced when using a single model.xml file as input +from ..adj_cell_rotation import model as adj_cell_rotation_model +from ..lattice_multiple import model as lattice_mult_model +from ..energy_laws import model as energy_laws_model +from ..photon_production import model as photon_prod_model + + +class ModelXMLTestHarness(PyAPITestHarness): + """Accept a results file to check against and assume inputs_true is the contents of a model.xml file. + """ + def __init__(self, model=None, inputs_true=None, results_true=None): + statepoint_name = f'statepoint.{model.settings.batches}.h5' + super().__init__(statepoint_name, model, inputs_true) + + self.results_true = 'results_true.dat' if results_true is None else results_true + + def _build_inputs(self): + self._model.export_to_xml(separate_xmls=False) + + def _get_inputs(self): + return open('model.xml').read() + + def _compare_inputs(self): + """Skip input comparisons for now + """ + pass + + def _compare_results(self): + """Make sure the current results agree with the reference.""" + compare = filecmp.cmp('results_test.dat', self.results_true) + if not compare: + expected = open(self.results_true).readlines() + actual = open('results_test.dat').readlines() + diff = unified_diff(expected, actual, self.results_true, + 'results_test.dat') + print('Result differences:') + print(''.join(colorize(diff))) + os.rename('results_test.dat', 'results_error.dat') + assert compare, 'Results do not agree' + + def _cleanup(self): + super()._cleanup() + if os.path.exists('model.xml'): + os.remove('model.xml') + + +models = [ +'adj_cell_rotation_model', +'lattice_mult_model', +'energy_laws_model', +'photon_prod_model' +] +paths = [ +'../adj_cell_rotation', +'../lattice_multiple', +'../energy_laws', +'../photon_production' +] + + +@pytest.mark.parametrize("model, path", zip(models, paths)) +def test_model_xml(model, path, request): + inputs = path + "/inputs_true.dat" + results = path + "/results_true.dat" + harness = ModelXMLTestHarness(request.getfixturevalue(model), inputs, results) + harness.main() \ No newline at end of file diff --git a/tests/regression_tests/photon_production/__init__.py b/tests/regression_tests/photon_production/__init__.py index e69de29bb2..29fbfcc0c2 100644 --- a/tests/regression_tests/photon_production/__init__.py +++ b/tests/regression_tests/photon_production/__init__.py @@ -0,0 +1 @@ +from .test import model \ No newline at end of file From 1e7dbe99cf7d6c262a9900930836f5786f519f9a Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 10 Nov 2022 00:01:40 -0600 Subject: [PATCH 180/265] Making sure meshes are only written once to a model.xml file --- openmc/model/model.py | 18 ++++++++++++------ openmc/settings.py | 15 ++++++++++----- openmc/tallies.py | 24 ++++++++++++------------ 3 files changed, 34 insertions(+), 23 deletions(-) diff --git a/openmc/model/model.py b/openmc/model/model.py index 6950642e0a..cb84f2c17f 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -5,11 +5,8 @@ import os from pathlib import Path from numbers import Integral from tempfile import NamedTemporaryFile -<<<<<<< HEAD import warnings -======= from xml.etree import ElementTree as ET ->>>>>>> d42935a08 (Writing all main nodes to a single XML file) import h5py @@ -234,8 +231,16 @@ class Model: model.geometry = \ openmc.Geometry.from_xml_element(root.find('geometry'), materials) + # gather meshses from other classes before reading the tally node + meshes = {} + if model.settings.entropy_mesh is not None: + meshes[model.settings.entropy_mesh.id] = model.settings.entropy_mesh + + for ww in model.settings.weight_windows: + meshes[ww.mesh.id] = ww.mesh + if root.find('tallies'): - model.tallies = openmc.Tallies.from_xml_element(root.find('tallies')) + model.tallies = openmc.Tallies.from_xml_element(root.find('tallies'), meshes) if root.find('plots'): model.plots = openmc.Plots.from_xml_element(root.find('plots')) @@ -524,7 +529,8 @@ class Model: # Can be used to modify tallies in case any surfaces are redundant redundant_surfaces = self.geometry.remove_redundant_surfaces() - settings_element = self.settings.to_xml_element() + memo = set() + settings_element = self.settings.to_xml_element(memo) geometry_element = self.geometry.to_xml_element() # If a materials collection was specified, export it. Otherwise, look @@ -549,7 +555,7 @@ class Model: ET.ElementTree(settings_element).write(fh, encoding='unicode') if self.tallies: - tallies_element = self.tallies.to_xml_element() + tallies_element = self.tallies.to_xml_element(memo) ET.ElementTree(tallies_element).write(fh, encoding='unicode') if self.plots: plots_element = self.plots.to_xml_element() diff --git a/openmc/settings.py b/openmc/settings.py index c2fca98f7d..74ec0d54a6 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1073,7 +1073,7 @@ class Settings: subelement = ET.SubElement(element, key) subelement.text = str(value) - def _create_entropy_mesh_subelement(self, root): + def _create_entropy_mesh_subelement(self, root, memo=None): if self.entropy_mesh is not None: # use default heuristic for entropy mesh if not set by user if self.entropy_mesh.dimension is None: @@ -1207,15 +1207,20 @@ class Settings: elem = ET.SubElement(root, "write_initial_source") elem.text = str(self._write_initial_source).lower() - def _create_weight_windows_subelement(self, root): + def _create_weight_windows_subelement(self, root, memo=None): for ww in self._weight_windows: # Add weight window information root.append(ww.to_xml_element()) + # check the memo for a mesh + if memo and ww.mesh.id in memo: + continue + # See if a element already exists -- if not, add it path = f"./mesh[@id='{ww.mesh.id}']" if root.find(path) is None: root.append(ww.mesh.to_xml_element()) + if memo is not None: memo.add(ww.mesh.id) if self._weight_windows_on is not None: elem = ET.SubElement(root, "weight_windows_on") @@ -1539,7 +1544,7 @@ class Settings: if text is not None: self.max_tracks = int(text) - def to_xml_element(self): + def to_xml_element(self, memo=None): """Create a 'settings' element to be written to an XML file. """ @@ -1569,7 +1574,7 @@ class Settings: self._create_seed_subelement(element) self._create_survival_biasing_subelement(element) self._create_cutoff_subelement(element) - self._create_entropy_mesh_subelement(element) + self._create_entropy_mesh_subelement(element, memo) self._create_trigger_subelement(element) self._create_no_reduce_subelement(element) self._create_verbosity_subelement(element) @@ -1587,7 +1592,7 @@ class Settings: self._create_material_cell_offsets_subelement(element) self._create_log_grid_bins_subelement(element) self._create_write_initial_source_subelement(element) - self._create_weight_windows_subelement(element) + self._create_weight_windows_subelement(element, memo) self._create_max_splits_subelement(element) self._create_max_tracks_subelement(element) diff --git a/openmc/tallies.py b/openmc/tallies.py index 2996f1b034..e37f04e252 100644 --- a/openmc/tallies.py +++ b/openmc/tallies.py @@ -3119,17 +3119,17 @@ class Tallies(cv.CheckedList): for tally in self: root_element.append(tally.to_xml_element()) - def _create_mesh_subelements(self, root_element): - already_written = set() + def _create_mesh_subelements(self, root_element, memo=None): + already_written = memo if memo else set() for tally in self: for f in tally.filters: if isinstance(f, openmc.MeshFilter): - if f.mesh.id not in already_written: - if len(f.mesh.name) > 0: - root_element.append(ET.Comment(f.mesh.name)) - - root_element.append(f.mesh.to_xml_element()) - already_written.add(f.mesh.id) + if f.mesh.id in already_written: + continue + if len(f.mesh.name) > 0: + root_element.append(ET.Comment(f.mesh.name)) + root_element.append(f.mesh.to_xml_element()) + already_written.add(f.mesh.id) def _create_filter_subelements(self, root_element): already_written = dict() @@ -3155,11 +3155,11 @@ class Tallies(cv.CheckedList): for d in derivs: root_element.append(d.to_xml_element()) - def to_xml_element(self): + def to_xml_element(self, memo=None): """Creates a 'tallies' element to be written to an XML file. """ element = ET.Element("tallies") - self._create_mesh_subelements(element) + self._create_mesh_subelements(element, memo) self._create_filter_subelements(element) self._create_tally_subelements(element) self._create_derivative_subelements(element) @@ -3192,7 +3192,7 @@ class Tallies(cv.CheckedList): tree.write(str(p), xml_declaration=True, encoding='utf-8') @classmethod - def from_xml_element(cls, elem): + def from_xml_element(cls, elem, meshes=None): """Generate tallies from an XML element Parameters @@ -3207,7 +3207,7 @@ class Tallies(cv.CheckedList): """ # Read mesh elements - meshes = {} + meshes = {} if meshes is None else meshes for e in elem.findall('mesh'): mesh = MeshBase.from_xml_element(e) meshes[mesh.id] = mesh From d034e1de9c8fe166f38624ee872b8bc46643c66a Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Wed, 23 Nov 2022 21:23:36 -0600 Subject: [PATCH 181/265] Apply suggestions from code review Incorporating suggestions from @paulromano Co-authored-by: Paul Romano --- openmc/geometry.py | 2 +- openmc/model/model.py | 6 ++---- tests/regression_tests/model_xml/test.py | 16 ++++++++-------- tests/unit_tests/test_model.py | 2 -- 4 files changed, 11 insertions(+), 15 deletions(-) diff --git a/openmc/geometry.py b/openmc/geometry.py index 57aab18846..630106628d 100644 --- a/openmc/geometry.py +++ b/openmc/geometry.py @@ -256,7 +256,7 @@ class Geometry: ---------- path : str, optional Path to geometry XML file - materials : dict + materials : dict Dictionary mapping material ID strings to :class:`openmc.Material` instances (defined in :math:`openmc.Geometry.from_xml`) diff --git a/openmc/model/model.py b/openmc/model/model.py index cb84f2c17f..559def5702 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -228,8 +228,7 @@ class Model: model.settings = openmc.Settings.from_xml_element(root.find('settings')) model.materials = openmc.Materials.from_xml_element(root.find('materials')) materials = {str(m.id): m for m in model.materials} - model.geometry = \ - openmc.Geometry.from_xml_element(root.find('geometry'), materials) + model.geometry = .Geometry.from_xml_element(root.find('geometry'), materials) # gather meshses from other classes before reading the tally node meshes = {} @@ -542,8 +541,7 @@ class Model: materials = openmc.Materials(self.geometry.get_all_materials() .values()) - with open(d, 'w', encoding='utf-8', - errors='xmlcharrefreplace') as fh: + with open(d, 'w', encoding='utf-8', errors='xmlcharrefreplace') as fh: # write the XML header fh.write("\n") fh.write("\n") diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py index 448079b3f6..289bd46552 100644 --- a/tests/regression_tests/model_xml/test.py +++ b/tests/regression_tests/model_xml/test.py @@ -55,16 +55,16 @@ class ModelXMLTestHarness(PyAPITestHarness): models = [ -'adj_cell_rotation_model', -'lattice_mult_model', -'energy_laws_model', -'photon_prod_model' + 'adj_cell_rotation_model', + 'lattice_mult_model', + 'energy_laws_model', + 'photon_prod_model' ] paths = [ -'../adj_cell_rotation', -'../lattice_multiple', -'../energy_laws', -'../photon_production' + '../adj_cell_rotation', + '../lattice_multiple', + '../energy_laws', + '../photon_production' ] diff --git a/tests/unit_tests/test_model.py b/tests/unit_tests/test_model.py index ce81b00eec..928bf0715f 100644 --- a/tests/unit_tests/test_model.py +++ b/tests/unit_tests/test_model.py @@ -7,8 +7,6 @@ import pytest import openmc import openmc.lib -from .. import cdtemp - @pytest.fixture(scope='function') def pin_model_attributes(): From b76825fa9f0598ca563d1c9d579968aa7bffa370 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Wed, 23 Nov 2022 22:16:34 -0600 Subject: [PATCH 182/265] Addressing some comments from PR --- include/openmc/initialize.h | 6 ++++- openmc/geometry.py | 6 ++--- openmc/model/model.py | 49 ++++++++++++++++++++++++---------- openmc/plots.py | 6 +++++ src/initialize.cpp | 4 +-- tests/unit_tests/test_model.py | 27 +++++++++---------- 6 files changed, 64 insertions(+), 34 deletions(-) diff --git a/include/openmc/initialize.h b/include/openmc/initialize.h index d3d12d45df..5caccceda6 100644 --- a/include/openmc/initialize.h +++ b/include/openmc/initialize.h @@ -11,8 +11,12 @@ int parse_command_line(int argc, char* argv[]); #ifdef OPENMC_MPI void initialize_mpi(MPI_Comm intracomm); #endif + +//! Read material, geometry, settings, and tallies from a single XML file bool read_model_xml(); -void read_input_xml(); +//! Read inputs from separate XML files +void read_separate_xml_files(); +//! Write some output that occurs right after initialization void initial_output(); } // namespace openmc diff --git a/openmc/geometry.py b/openmc/geometry.py index 630106628d..d036df9c74 100644 --- a/openmc/geometry.py +++ b/openmc/geometry.py @@ -256,9 +256,9 @@ class Geometry: ---------- path : str, optional Path to geometry XML file - materials : dict - Dictionary mapping material ID strings to :class:`openmc.Material` - instances (defined in :math:`openmc.Geometry.from_xml`) + materials : openmc.Materials or None + Materials used to assign to cells. If None, an attempt is made to + generate it from the materials.xml file. Returns ------- diff --git a/openmc/model/model.py b/openmc/model/model.py index 559def5702..2ed9bf668a 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -205,8 +205,24 @@ class Model: self._plots.append(plot) @classmethod - def from_xml(cls, *args, separate_xmls=True, **kwargs): - if separate_xmls: + def from_xml(cls, *args, path='model.xml', separate_xmls=True, **kwargs): + """Generate geometry from XML file + + Parameters + ---------- + path : str, optional + Path to model XML file + separate_xmls : bool + Whether or not to read from a single or separate XML files + + Returns + ------- + openmc.Geometry + Geometry object + + """ + + if separate_xmls or not Path(path).exists(): return cls.from_separate_xmls(*args, **kwargs) else: return cls.from_model_xml(*args, **kwargs) @@ -228,7 +244,7 @@ class Model: model.settings = openmc.Settings.from_xml_element(root.find('settings')) model.materials = openmc.Materials.from_xml_element(root.find('materials')) materials = {str(m.id): m for m in model.materials} - model.geometry = .Geometry.from_xml_element(root.find('geometry'), materials) + model.geometry = openmc.Geometry.from_xml_element(root.find('geometry'), materials) # gather meshses from other classes before reading the tally node meshes = {} @@ -442,8 +458,8 @@ class Model: depletion_operator.cleanup_when_done = True depletion_operator.finalize() - def export_to_xml(self, directory='.', remove_surfs=False, separate_xmls=True): - """Export model to separate XML files. + def export_to_xml(self, directory='.', remove_surfs=False, separate_xmls=True, filename='model.xml'): + """Export model to an XML file(s). Parameters ---------- @@ -453,6 +469,8 @@ class Model: remove_surfs : bool Whether or not to remove redundant surfaces from the geometry when exporting. + filename : str + Name of the single XML file to create (only used :math:`separate_xmls` if False) .. versionadded:: 0.13.1 @@ -460,11 +478,15 @@ class Model: Whether or not to write a single model.xml file or many XML files. """ if separate_xmls: - self.export_to_separate_xmls(directory, remove_surfs) + if filename != 'model.xml': + warnings.warn('Export filename parameter {filename} is ignored ' + 'because the model is being written to separate XML files.') + self._export_to_separate_xmls(directory, remove_surfs) else: - self.export_to_single_xml(directory, remove_surfs) + filename = Path(directory) / Path(filename) + self._export_to_single_xml(filename, remove_surfs) - def export_to_separate_xmls(self, directory='.', remove_surfs=False): + def _export_to_separate_xmls(self, directory='.', remove_surfs=False): """Export model to separate XML files. Parameters @@ -501,7 +523,7 @@ class Model: if self.plots: self.plots.export_to_xml(d) - def export_to_single_xml(self, directory='.', remove_surfs=False): + def _export_to_single_xml(self, path='model.xml', remove_surfs=False): """Export model to XML files. Parameters @@ -516,10 +538,9 @@ class Model: .. versionadded:: 0.13.1 """ # Create directory if required - d = Path(directory) - if not d.is_dir(): - d.mkdir(parents=True) - d /= 'model.xml' + xml_path = Path(path) + if not xml_path.parent.exists: + raise RuntimeError(f'The directory "{xml_path}" does not exist.') if remove_surfs: warnings.warn("remove_surfs kwarg will be deprecated soon, please " @@ -541,7 +562,7 @@ class Model: materials = openmc.Materials(self.geometry.get_all_materials() .values()) - with open(d, 'w', encoding='utf-8', errors='xmlcharrefreplace') as fh: + with open(xml_path, 'w', encoding='utf-8', errors='xmlcharrefreplace') as fh: # write the XML header fh.write("\n") fh.write("\n") diff --git a/openmc/plots.py b/openmc/plots.py index b1f1927876..0a04516259 100644 --- a/openmc/plots.py +++ b/openmc/plots.py @@ -911,6 +911,12 @@ class Plots(cv.CheckedList): def to_xml_element(self): """Create a 'plots' element to be written to an XML file. + + Returns + ------- + element : xml.etree.ElementTree.Element + XML element containing all plot elements + """ # Reset xml element tree self._plots_file.clear() diff --git a/src/initialize.cpp b/src/initialize.cpp index 3f6e69ecde..dc5c0c3c11 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -106,7 +106,7 @@ int openmc_init(int argc, char* argv[], const void* intracomm) openmc::openmc_set_seed(DEFAULT_SEED); // Read XML input files - if (!read_model_xml()) read_input_xml(); + if (!read_model_xml()) read_separate_xml_files(); // Write some initial output under the header if needed initial_output(); @@ -371,7 +371,7 @@ bool read_model_xml() { return true; } -void read_input_xml() +void read_separate_xml_files() { read_settings_xml(); read_cross_sections_xml(); diff --git a/tests/unit_tests/test_model.py b/tests/unit_tests/test_model.py index 928bf0715f..87557ddc53 100644 --- a/tests/unit_tests/test_model.py +++ b/tests/unit_tests/test_model.py @@ -530,21 +530,20 @@ def test_calc_volumes(run_in_tmpdir, pin_model_attributes, mpi_intracomm): test_model.finalize_lib() -def test_model_xml(): +def test_model_xml(run_in_tmpdir): - with cdtemp(): - # load a model from examples - pwr_model = openmc.examples.pwr_core() + # load a model from examples + pwr_model = openmc.examples.pwr_core() - # export to separate XMLs manually - pwr_model.settings.export_to_xml('settings_ref.xml') - pwr_model.materials.export_to_xml('materials_ref.xml') - pwr_model.geometry.export_to_xml('geometry_ref.xml') + # export to separate XMLs manually + pwr_model.settings.export_to_xml('settings_ref.xml') + pwr_model.materials.export_to_xml('materials_ref.xml') + pwr_model.geometry.export_to_xml('geometry_ref.xml') - # now write and read a model.xml file - pwr_model.export_to_xml(separate_xmls=False) - new_model = openmc.Model.from_xml(separate_xmls=False) + # now write and read a model.xml file + pwr_model.export_to_xml(separate_xmls=False) + new_model = openmc.Model.from_xml(separate_xmls=False) - # make sure we can also export this again to separate - # XML files - new_model.export_to_xml(separate_xmls=True) \ No newline at end of file + # make sure we can also export this again to separate + # XML files + new_model.export_to_xml(separate_xmls=True) \ No newline at end of file From d9847163e86a4131016a1a6a5f0cd7c0e12b34cc Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Wed, 23 Nov 2022 23:06:31 -0600 Subject: [PATCH 183/265] Adding ability to specify an input filename to the executable or to the python exec --- include/openmc/initialize.h | 4 +++ openmc/executor.py | 37 +++++++++++++++++++----- openmc/model/model.py | 1 - src/initialize.cpp | 24 +++++++++++---- tests/regression_tests/model_xml/test.py | 22 +++++++++++++- 5 files changed, 73 insertions(+), 15 deletions(-) diff --git a/include/openmc/initialize.h b/include/openmc/initialize.h index 5caccceda6..c37208e5e3 100644 --- a/include/openmc/initialize.h +++ b/include/openmc/initialize.h @@ -1,6 +1,8 @@ #ifndef OPENMC_INITIALIZE_H #define OPENMC_INITIALIZE_H +#include + #ifdef OPENMC_MPI #include "mpi.h" #endif @@ -19,6 +21,8 @@ void read_separate_xml_files(); //! Write some output that occurs right after initialization void initial_output(); + +std::string args_xml_filename {}; } // namespace openmc #endif // OPENMC_INITIALIZE_H diff --git a/openmc/executor.py b/openmc/executor.py index a73d896ffe..b143132139 100644 --- a/openmc/executor.py +++ b/openmc/executor.py @@ -9,7 +9,7 @@ from .plots import _get_plot_image def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None, plot=False, restart_file=None, threads=None, tracks=False, event_based=None, - openmc_exec='openmc', mpi_args=None): + openmc_exec='openmc', mpi_args=None, input_file=None): """Converts user-readable flags in to command-line arguments to be run with the OpenMC executable via subprocess. @@ -42,6 +42,8 @@ def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None, mpi_args : list of str, optional MPI execute command and any additional MPI arguments to pass, e.g. ['mpiexec', '-n', '8']. + input_file : str or Pathlike + Name of a single XML input file for the OpenMC executable to read. .. versionadded:: 0.13.0 @@ -82,6 +84,9 @@ def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None, if mpi_args is not None: args = mpi_args + args + if input_file is not None: + args += ['-i', input_file] + return args @@ -118,7 +123,7 @@ def _run(args, output, cwd): raise RuntimeError(error_msg) -def plot_geometry(output=True, openmc_exec='openmc', cwd='.'): +def plot_geometry(output=True, openmc_exec='openmc', cwd='.', input_file=None): """Run OpenMC in plotting mode Parameters @@ -129,6 +134,8 @@ def plot_geometry(output=True, openmc_exec='openmc', cwd='.'): Path to OpenMC executable cwd : str, optional Path to working directory to run in + input_file : str + Name of a single XML input file for the OpenMC executable to read. Raises ------ @@ -136,10 +143,13 @@ def plot_geometry(output=True, openmc_exec='openmc', cwd='.'): If the `openmc` executable returns a non-zero status """ + args = [openmc_exec, '-p'] + if input_file is not None: + args += ['-i', input_file] _run([openmc_exec, '-p'], output, cwd) -def plot_inline(plots, openmc_exec='openmc', cwd='.'): +def plot_inline(plots, openmc_exec='openmc', cwd='.', input_file=None): """Display plots inline in a Jupyter notebook. .. versionchanged:: 0.13.0 @@ -155,6 +165,8 @@ def plot_inline(plots, openmc_exec='openmc', cwd='.'): Path to OpenMC executable cwd : str, optional Path to working directory to run in + input_file : str + Name of a single XML input file for the OpenMC executable to read. Raises ------ @@ -171,7 +183,7 @@ def plot_inline(plots, openmc_exec='openmc', cwd='.'): openmc.Plots(plots).export_to_xml(cwd) # Run OpenMC in geometry plotting mode - plot_geometry(False, openmc_exec, cwd) + plot_geometry(False, openmc_exec, cwd, input_file) if plots is not None: images = [_get_plot_image(p, cwd) for p in plots] @@ -179,7 +191,8 @@ def plot_inline(plots, openmc_exec='openmc', cwd='.'): def calculate_volumes(threads=None, output=True, cwd='.', - openmc_exec='openmc', mpi_args=None): + openmc_exec='openmc', mpi_args=None, + input_file=None): """Run stochastic volume calculations in OpenMC. This function runs OpenMC in stochastic volume calculation mode. To specify @@ -210,6 +223,8 @@ def calculate_volumes(threads=None, output=True, cwd='.', cwd : str, optional Path to working directory to run in. Defaults to the current working directory. + input_file : str or Pathlike + Name of a single XML input file for the OpenMC executable to read. Raises ------ @@ -223,14 +238,16 @@ def calculate_volumes(threads=None, output=True, cwd='.', """ args = _process_CLI_arguments(volume=True, threads=threads, - openmc_exec=openmc_exec, mpi_args=mpi_args) + openmc_exec=openmc_exec, mpi_args=mpi_args, + input_file=input_file) _run(args, output, cwd) def run(particles=None, threads=None, geometry_debug=False, restart_file=None, tracks=False, output=True, cwd='.', - openmc_exec='openmc', mpi_args=None, event_based=False): + openmc_exec='openmc', mpi_args=None, event_based=False, + input_file=None): """Run an OpenMC simulation. Parameters @@ -265,6 +282,9 @@ def run(particles=None, threads=None, geometry_debug=False, .. versionadded:: 0.12 + input_file : str or Pathlike + Name of a single XML input file for the OpenMC executable to read. + Raises ------ RuntimeError @@ -275,6 +295,7 @@ def run(particles=None, threads=None, geometry_debug=False, args = _process_CLI_arguments( volume=False, geometry_debug=geometry_debug, particles=particles, restart_file=restart_file, threads=threads, tracks=tracks, - event_based=event_based, openmc_exec=openmc_exec, mpi_args=mpi_args) + event_based=event_based, openmc_exec=openmc_exec, mpi_args=mpi_args, + input_file=input_file) _run(args, output, cwd) diff --git a/openmc/model/model.py b/openmc/model/model.py index 2ed9bf668a..15effd3e4c 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -221,7 +221,6 @@ class Model: Geometry object """ - if separate_xmls or not Path(path).exists(): return cls.from_separate_xmls(*args, **kwargs) else: diff --git a/src/initialize.cpp b/src/initialize.cpp index dc5c0c3c11..02a4f9ab75 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -181,10 +181,11 @@ int parse_command_line(int argc, char* argv[]) } else if (arg == "-e" || arg == "--event") { settings::event_based = true; - + } else if (arg == "-i" || arg == "--input") { + i += 1; + args_xml_filename = std::string(argv[i]); } else if (arg == "-r" || arg == "--restart") { i += 1; - // Check what type of file this is hid_t file_id = file_open(argv[i], 'r', true); std::string filetype; @@ -295,9 +296,19 @@ int parse_command_line(int argc, char* argv[]) bool read_model_xml() { // get verbosity from settings node - std::string model_filename = settings::path_input + "model.xml"; - bool use_model_file = file_exists(model_filename); - if (!file_exists(model_filename)) return false; + + std::string xml_filename = "model.xml"; + if (!args_xml_filename.empty()) xml_filename = args_xml_filename; + std::string model_filename = settings::path_input + xml_filename; + + // check that the model file exists. If it does not and a custom filename was + // supplied by the user report an error + if (!file_exists(model_filename)) { + if (!args_xml_filename.empty()) { + fatal_error(fmt::format("The input file '{}' specified on the command line does not exist", args_xml_filename)); + } + return false; + } // attempt to open the document pugi::xml_document doc; @@ -325,6 +336,9 @@ bool read_model_xml() { title(); } + if (!args_xml_filename.empty()) + write_message(fmt::format("Reaging user-specified input '{}'...", args_xml_filename), 5); + else write_message("Reading model XML file...", 5); read_settings_xml(settings_root); diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py index 289bd46552..342d7dca90 100644 --- a/tests/regression_tests/model_xml/test.py +++ b/tests/regression_tests/model_xml/test.py @@ -73,4 +73,24 @@ def test_model_xml(model, path, request): inputs = path + "/inputs_true.dat" results = path + "/results_true.dat" harness = ModelXMLTestHarness(request.getfixturevalue(model), inputs, results) - harness.main() \ No newline at end of file + harness.main() + +def test_input_arg(run_in_tmpdir): + + pincell = openmc.examples.pwr_pin_cell() + + pincell.settings.particles = 100 + + # export to separate XML files and run + pincell.export_to_xml(separate_xmls=True) + openmc.run() + + # now export to a single XML file with a custom name + pincell.export_to_xml(filename='pincell.xml', separate_xmls=False) + + # run by specifying that single file + openmc.run(input_file='pincell.xml') + + # now ensure we get an error for an incorrect filename + with pytest.raises(RuntimeError): + openmc.run(input_file='ex-em-ell.xml') \ No newline at end of file From 366f9e905c4f049e8971f743b6cca5d210fff04e Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Wed, 23 Nov 2022 23:10:57 -0600 Subject: [PATCH 184/265] Test comment and updated error messages --- src/initialize.cpp | 8 +++++--- tests/regression_tests/model_xml/test.py | 3 ++- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/src/initialize.cpp b/src/initialize.cpp index 02a4f9ab75..68436f07e4 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -348,14 +348,15 @@ bool read_model_xml() { auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml", "tallies.xml", "plots.xml"}; for (const auto& input : other_inputs) { if (file_exists(settings::path_input + input)) { - warning(("Other XML file input(s) are present. These file will be ignored in favor of the model.xml file.")); + warning((fmt::format("Other XML file input(s) are present. These file will be ignored in favor of the {} file.", xml_filename)); break; } } // Read materials and cross sections if (!check_for_node(root, "materials")) { - fatal_error("No node present in the model.xml file."); + fatal_error( + fmt::format("No node present in the {} file.", xml_filename)); } auto materials_node = root.child("materials"); read_cross_sections_xml(materials_node); @@ -363,7 +364,8 @@ bool read_model_xml() { // Read geometry if (!check_for_node(root, "geometry")) { - fatal_error("No node present in the model.xml_file."); + fatal_error(fmt::format( + "No node present in the model.xml_file.", xml_filename)); } read_geometry_xml(root.child("geometry")); diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py index 342d7dca90..5bfe912a44 100644 --- a/tests/regression_tests/model_xml/test.py +++ b/tests/regression_tests/model_xml/test.py @@ -91,6 +91,7 @@ def test_input_arg(run_in_tmpdir): # run by specifying that single file openmc.run(input_file='pincell.xml') - # now ensure we get an error for an incorrect filename + # now ensure we get an error for an incorrect filename, + # even in the presence of other, valid XML files with pytest.raises(RuntimeError): openmc.run(input_file='ex-em-ell.xml') \ No newline at end of file From 1e6cb68ea420558f6f120e830602b8938f2c1319 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Wed, 23 Nov 2022 23:14:30 -0600 Subject: [PATCH 185/265] Addressing a few more comments in C++ code --- src/initialize.cpp | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/initialize.cpp b/src/initialize.cpp index 68436f07e4..87e839dfdf 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -358,8 +358,12 @@ bool read_model_xml() { fatal_error( fmt::format("No node present in the {} file.", xml_filename)); } + + // find materials node this object cannot be used after being passed to the + // cross section reading function below auto materials_node = root.child("materials"); read_cross_sections_xml(materials_node); + read_materials_xml(root.child("materials")); // Read geometry @@ -411,7 +415,7 @@ void read_separate_xml_files() } void initial_output() { - // handle some final output + // write initial output if (settings::run_mode == RunMode::PLOTTING) { // Read plots.xml if it exists if (mpi::master && settings::verbosity >= 5) From 7a203fbf7266f365d3d209461687402edcb3b56b Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Wed, 23 Nov 2022 23:16:57 -0600 Subject: [PATCH 186/265] Correcting parenthesis --- src/initialize.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/initialize.cpp b/src/initialize.cpp index 87e839dfdf..a6a6b5a776 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -348,7 +348,7 @@ bool read_model_xml() { auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml", "tallies.xml", "plots.xml"}; for (const auto& input : other_inputs) { if (file_exists(settings::path_input + input)) { - warning((fmt::format("Other XML file input(s) are present. These file will be ignored in favor of the {} file.", xml_filename)); + warning((fmt::format("Other XML file input(s) are present. These file will be ignored in favor of the {} file.", xml_filename))); break; } } From fe47d565fd7fddb464e3e67907936211bc76a857 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Wed, 23 Nov 2022 23:17:11 -0600 Subject: [PATCH 187/265] Spot check in error message from failed run --- tests/regression_tests/model_xml/test.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py index 5bfe912a44..0dc2cc2898 100644 --- a/tests/regression_tests/model_xml/test.py +++ b/tests/regression_tests/model_xml/test.py @@ -93,5 +93,6 @@ def test_input_arg(run_in_tmpdir): # now ensure we get an error for an incorrect filename, # even in the presence of other, valid XML files - with pytest.raises(RuntimeError): - openmc.run(input_file='ex-em-ell.xml') \ No newline at end of file + with pytest.raises(RuntimeError) as execinfo: + openmc.run(input_file='ex-em-ell.xml') + assert 'ex-em-ell.xml' in execinfo.value \ No newline at end of file From 6f7a6febd3fe01531979d2276f1c40fb6f8430f7 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Fri, 25 Nov 2022 08:22:57 -0600 Subject: [PATCH 188/265] Updating model XML file format w/ indentation. --- openmc/_xml.py | 28 ++++-- openmc/material.py | 27 +++-- openmc/model/model.py | 7 +- .../model_xml/inputs_true.dat | 99 ++++++++++++------- 4 files changed, 111 insertions(+), 50 deletions(-) diff --git a/openmc/_xml.py b/openmc/_xml.py index 32679fd89e..b4e08c7519 100644 --- a/openmc/_xml.py +++ b/openmc/_xml.py @@ -1,22 +1,36 @@ -def clean_indentation(element, level=0, spaces_per_level=2): - """ - copy and paste from https://effbot.org/zone/element-lib.htm#prettyprint - it basically walks your tree and adds spaces and newlines so the tree is - printed in a nice way +def clean_indentation(element, level=0, spaces_per_level=2, trailing_indent=True): + """Set indentation of XML element and its sub-elements. + Copied and pastee from https://effbot.org/zone/element-lib.htm#prettyprint. + It walks your tree and adds spaces and newlines so the tree is + printed in a nice way. + + Parameters + ---------- + level : int + Indentation level for the element passed in (default 0) + spaces_per_level : int + Number of spaces per indentation level (default 2) + trailing_indent : bool + Whether or not to include an indentation after closing the element + """ i = "\n" + level*spaces_per_level*" " + # ensure there's awlays some tail for the element passed in + if not element.tail: + element.tail = "" + if len(element): if not element.text or not element.text.strip(): element.text = i + spaces_per_level*" " - if not element.tail or not element.tail.strip(): + if trailing_indent and (not element.tail or not element.tail.strip()): element.tail = i for sub_element in element: clean_indentation(sub_element, level+1, spaces_per_level) if not sub_element.tail or not sub_element.tail.strip(): sub_element.tail = i else: - if level and (not element.tail or not element.tail.strip()): + if trailing_indent and level and (not element.tail or not element.tail.strip()): element.tail = i diff --git a/openmc/material.py b/openmc/material.py index c335968002..332f8c9659 100644 --- a/openmc/material.py +++ b/openmc/material.py @@ -1449,7 +1449,7 @@ class Materials(cv.CheckedList): for material in self: material.make_isotropic_in_lab() - def _write_xml(self, file, header=True): + def _write_xml(self, file, header=True, level=0, spaces_per_level=2, trailing_indent=True): """Writes XML content of the materials to an open file handle. Parameters @@ -1458,33 +1458,46 @@ class Materials(cv.CheckedList): Open file handle to write content into. header : bool Whether or not to write the XML header + level : int + Indentation level of materials element + spaces_per_level : int + Number of spaces per indentation + trailing_indentation : bool + Whether or not to write a trailing indentation for the materials element + """ + indentation = level*spaces_per_level*' ' # Write the header and the opening tag for the root element. if header: file.write("\n") - file.write('\n') + file.write(indentation+'\n') # Write the element. if self.cross_sections is not None: element = ET.Element('cross_sections') element.text = str(self.cross_sections) - clean_indentation(element, level=1) + clean_indentation(element, level=level+1) element.tail = element.tail.strip(' ') - file.write(' ') + file.write((level+1)*spaces_per_level*' ') reorder_attributes(element) # TODO: Remove when support is Python 3.8+ ET.ElementTree(element).write(file, encoding='unicode') # Write the elements. for material in sorted(self, key=lambda x: x.id): element = material.to_xml_element() - clean_indentation(element, level=1) + clean_indentation(element, level=level+1) element.tail = element.tail.strip(' ') - file.write(' ') + file.write((level+1)*spaces_per_level*' ') reorder_attributes(element) # TODO: Remove when support is Python 3.8+ ET.ElementTree(element).write(file, encoding='unicode') # Write the closing tag for the root element. - file.write('\n') + file.write(indentation+'\n') + + # Write a trailing indentation for the next element + # at this level if needed + if trailing_indent: + file.write(indentation) def export_to_xml(self, path: PathLike = 'materials.xml'): diff --git a/openmc/model/model.py b/openmc/model/model.py index 15effd3e4c..9c38d27c32 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -552,6 +552,9 @@ class Model: settings_element = self.settings.to_xml_element(memo) geometry_element = self.geometry.to_xml_element() + xml.clean_indentation(geometry_element, level=1) + xml.clean_indentation(settings_element, level=1) + # If a materials collection was specified, export it. Otherwise, look # for all materials in the geometry and use that to automatically build # a collection. @@ -567,16 +570,18 @@ class Model: fh.write("\n") # Write the materials collection to the open XML file first. # This will write the XML header also - materials._write_xml(fh, False) + materials._write_xml(fh, False, level=1) # Write remaining elements as a tree ET.ElementTree(geometry_element).write(fh, encoding='unicode') ET.ElementTree(settings_element).write(fh, encoding='unicode') if self.tallies: tallies_element = self.tallies.to_xml_element(memo) + xml.clean_indentation(tallies_element, level=1, trailing_indent=self.plots) ET.ElementTree(tallies_element).write(fh, encoding='unicode') if self.plots: plots_element = self.plots.to_xml_element() + xml.clean_indentation(plots_element, level=1, trailing_indent=False) ET.ElementTree(plots_element).write(fh, encoding='unicode') fh.write("\n") diff --git a/tests/regression_tests/model_xml/inputs_true.dat b/tests/regression_tests/model_xml/inputs_true.dat index 5aedbfa143..c408026316 100644 --- a/tests/regression_tests/model_xml/inputs_true.dat +++ b/tests/regression_tests/model_xml/inputs_true.dat @@ -1,38 +1,67 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - eigenvalue - 10000 - 10 - 5 - - - -4.0 -4.0 -4.0 4.0 4.0 4.0 - - - + + + + + + + + + + + + + + + + + fixed source + 10000 + 1 + + + 0 0 0 + + + + 14000000.0 1.0 + + + ttb + true + + 1000.0 + + + + + 16 + + + neutron photon electron positron + + + 1 2 + current + + + 2 + Al27 total + total (n,gamma) + tracklength + + + 2 + Al27 total + total heating (n,gamma) + collision + + + 2 + Al27 total + total heating (n,gamma) + analog + + From 5d1ead2e6a88affe5900067412e0464171cba8e4 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Sat, 26 Nov 2022 00:46:12 -0600 Subject: [PATCH 189/265] Addressing some more PR comments. A couple of typo fixes too. --- openmc/_xml.py | 2 +- openmc/model/model.py | 2 +- src/initialize.cpp | 6 +----- tests/regression_tests/adj_cell_rotation/__init__.py | 2 -- tests/regression_tests/energy_laws/__init__.py | 1 - tests/regression_tests/lattice_multiple/__init__.py | 1 - tests/regression_tests/model_xml/test.py | 8 ++++---- tests/regression_tests/photon_production/__init__.py | 1 - 8 files changed, 7 insertions(+), 16 deletions(-) diff --git a/openmc/_xml.py b/openmc/_xml.py index b4e08c7519..450c8a99bf 100644 --- a/openmc/_xml.py +++ b/openmc/_xml.py @@ -11,7 +11,7 @@ def clean_indentation(element, level=0, spaces_per_level=2, trailing_indent=True spaces_per_level : int Number of spaces per indentation level (default 2) trailing_indent : bool - Whether or not to include an indentation after closing the element + Whether or not to add indentation after closing the element """ i = "\n" + level*spaces_per_level*" " diff --git a/openmc/model/model.py b/openmc/model/model.py index 9c38d27c32..145a2151bc 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -469,7 +469,7 @@ class Model: Whether or not to remove redundant surfaces from the geometry when exporting. filename : str - Name of the single XML file to create (only used :math:`separate_xmls` if False) + Name of the single XML file to create (only used :math:`separate_xmls` is False) .. versionadded:: 0.13.1 diff --git a/src/initialize.cpp b/src/initialize.cpp index a6a6b5a776..212b2f7bdc 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -359,11 +359,7 @@ bool read_model_xml() { fmt::format("No node present in the {} file.", xml_filename)); } - // find materials node this object cannot be used after being passed to the - // cross section reading function below - auto materials_node = root.child("materials"); - read_cross_sections_xml(materials_node); - + read_cross_sections_xml(root.child("materials")); read_materials_xml(root.child("materials")); // Read geometry diff --git a/tests/regression_tests/adj_cell_rotation/__init__.py b/tests/regression_tests/adj_cell_rotation/__init__.py index 7efe448659..e69de29bb2 100644 --- a/tests/regression_tests/adj_cell_rotation/__init__.py +++ b/tests/regression_tests/adj_cell_rotation/__init__.py @@ -1,2 +0,0 @@ - -from .test import model \ No newline at end of file diff --git a/tests/regression_tests/energy_laws/__init__.py b/tests/regression_tests/energy_laws/__init__.py index 29fbfcc0c2..e69de29bb2 100644 --- a/tests/regression_tests/energy_laws/__init__.py +++ b/tests/regression_tests/energy_laws/__init__.py @@ -1 +0,0 @@ -from .test import model \ No newline at end of file diff --git a/tests/regression_tests/lattice_multiple/__init__.py b/tests/regression_tests/lattice_multiple/__init__.py index 29fbfcc0c2..e69de29bb2 100644 --- a/tests/regression_tests/lattice_multiple/__init__.py +++ b/tests/regression_tests/lattice_multiple/__init__.py @@ -1 +0,0 @@ -from .test import model \ No newline at end of file diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py index 0dc2cc2898..52f67f76fd 100644 --- a/tests/regression_tests/model_xml/test.py +++ b/tests/regression_tests/model_xml/test.py @@ -9,10 +9,10 @@ from tests.testing_harness import PyAPITestHarness, colorize # use a few models from other tests to make sure the same results are # produced when using a single model.xml file as input -from ..adj_cell_rotation import model as adj_cell_rotation_model -from ..lattice_multiple import model as lattice_mult_model -from ..energy_laws import model as energy_laws_model -from ..photon_production import model as photon_prod_model +from ..adj_cell_rotation.test import model as adj_cell_rotation_model +from ..lattice_multiple.test import model as lattice_mult_model +from ..energy_laws.test import model as energy_laws_model +from ..photon_production.test import model as photon_prod_model class ModelXMLTestHarness(PyAPITestHarness): diff --git a/tests/regression_tests/photon_production/__init__.py b/tests/regression_tests/photon_production/__init__.py index 29fbfcc0c2..e69de29bb2 100644 --- a/tests/regression_tests/photon_production/__init__.py +++ b/tests/regression_tests/photon_production/__init__.py @@ -1 +0,0 @@ -from .test import model \ No newline at end of file From e7f95b0c7a5fc0c1548183f38606ce158c2eb31c Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Mon, 28 Nov 2022 00:44:05 -0600 Subject: [PATCH 190/265] Docstring correction and a note about the recursion --- openmc/_xml.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/openmc/_xml.py b/openmc/_xml.py index 450c8a99bf..6d298638da 100644 --- a/openmc/_xml.py +++ b/openmc/_xml.py @@ -1,6 +1,6 @@ def clean_indentation(element, level=0, spaces_per_level=2, trailing_indent=True): """Set indentation of XML element and its sub-elements. - Copied and pastee from https://effbot.org/zone/element-lib.htm#prettyprint. + Copied and pasted from https://effbot.org/zone/element-lib.htm#prettyprint. It walks your tree and adds spaces and newlines so the tree is printed in a nice way. @@ -26,6 +26,8 @@ def clean_indentation(element, level=0, spaces_per_level=2, trailing_indent=True if trailing_indent and (not element.tail or not element.tail.strip()): element.tail = i for sub_element in element: + # `trailing_indent` intentionally not passed to the recursive call. + # it only applies to the element for the initial of this function. clean_indentation(sub_element, level+1, spaces_per_level) if not sub_element.tail or not sub_element.tail.strip(): sub_element.tail = i From b3225be24d384ba834fab6f003ff7ba39e9d99b1 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Mon, 28 Nov 2022 20:03:42 -0600 Subject: [PATCH 191/265] Adding executor tests --- tests/unit_tests/test_model.py | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/tests/unit_tests/test_model.py b/tests/unit_tests/test_model.py index 87557ddc53..5d4765d657 100644 --- a/tests/unit_tests/test_model.py +++ b/tests/unit_tests/test_model.py @@ -1,5 +1,6 @@ from math import pi from pathlib import Path +import os import numpy as np import pytest @@ -546,4 +547,23 @@ def test_model_xml(run_in_tmpdir): # make sure we can also export this again to separate # XML files - new_model.export_to_xml(separate_xmls=True) \ No newline at end of file + new_model.export_to_xml(separate_xmls=True) + +def test_model_exec(run_in_tmpdir): + + pincell_model = openmc.examples.pwr_pin_cell() + + pincell_model.export_to_xml(filename='pwr_pincell.xml', separate_xmls=False) + + openmc.run(input_file='pwr_pincell.xml') + + with pytest.raises(RuntimeError, match='ex-em-ell.xml'): + openmc.run(input_file='ex-em-ell.xml') + + # test that a file in a different directory can be used + os.mkdir('inputs') + pincell_model.export_to_xml(directory='./inputs', filename='pincell.xml', separate_xmls=False) + openmc.run(input_file='./inputs/pincell.xml') + + with pytest.raises(RuntimeError, match='input_dir'): + openmc.run(input_file='input_dir/pincell.xml') \ No newline at end of file From 72ff942226e8fb60801328a64530ad1cd94b1da0 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Mon, 28 Nov 2022 20:04:45 -0600 Subject: [PATCH 192/265] Checking RuntimeError message correctly --- tests/regression_tests/model_xml/test.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py index 52f67f76fd..51c25a603b 100644 --- a/tests/regression_tests/model_xml/test.py +++ b/tests/regression_tests/model_xml/test.py @@ -93,6 +93,5 @@ def test_input_arg(run_in_tmpdir): # now ensure we get an error for an incorrect filename, # even in the presence of other, valid XML files - with pytest.raises(RuntimeError) as execinfo: - openmc.run(input_file='ex-em-ell.xml') - assert 'ex-em-ell.xml' in execinfo.value \ No newline at end of file + with pytest.raises(RuntimeError, match='ex-em-ell.xml'): + openmc.run(input_file='ex-em-ell.xml') \ No newline at end of file From 7f5d2a583932206bc681a8555d658334d74ebc9d Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Mon, 28 Nov 2022 23:54:26 -0600 Subject: [PATCH 193/265] Refactoring model_xml regression tests a bit and adding input checking --- .../adj_cell_rotation_inputs_true.dat | 38 +++++++++++ .../model_xml/energy_laws_inputs_true.dat | 23 +++++++ .../lattice_multiple_inputs_true.dat | 53 +++++++++++++++ .../photon_production_inputs_true.dat | 67 +++++++++++++++++++ tests/regression_tests/model_xml/test.py | 42 ++++++------ 5 files changed, 201 insertions(+), 22 deletions(-) create mode 100644 tests/regression_tests/model_xml/adj_cell_rotation_inputs_true.dat create mode 100644 tests/regression_tests/model_xml/energy_laws_inputs_true.dat create mode 100644 tests/regression_tests/model_xml/lattice_multiple_inputs_true.dat create mode 100644 tests/regression_tests/model_xml/photon_production_inputs_true.dat diff --git a/tests/regression_tests/model_xml/adj_cell_rotation_inputs_true.dat b/tests/regression_tests/model_xml/adj_cell_rotation_inputs_true.dat new file mode 100644 index 0000000000..3b14f304ea --- /dev/null +++ b/tests/regression_tests/model_xml/adj_cell_rotation_inputs_true.dat @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + eigenvalue + 10000 + 10 + 5 + + + -4.0 -4.0 -4.0 4.0 4.0 4.0 + + + + diff --git a/tests/regression_tests/model_xml/energy_laws_inputs_true.dat b/tests/regression_tests/model_xml/energy_laws_inputs_true.dat new file mode 100644 index 0000000000..62485ff72a --- /dev/null +++ b/tests/regression_tests/model_xml/energy_laws_inputs_true.dat @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + + + eigenvalue + 1000 + 10 + 5 + + diff --git a/tests/regression_tests/model_xml/lattice_multiple_inputs_true.dat b/tests/regression_tests/model_xml/lattice_multiple_inputs_true.dat new file mode 100644 index 0000000000..d828b25f6b --- /dev/null +++ b/tests/regression_tests/model_xml/lattice_multiple_inputs_true.dat @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + 1.2 1.2 + 1 + 2 2 + -1.2 -1.2 + +2 1 +1 1 + + + 2.4 2.4 + 2 2 + -2.4 -2.4 + +4 4 +4 4 + + + + + + + + + + eigenvalue + 1000 + 10 + 5 + + diff --git a/tests/regression_tests/model_xml/photon_production_inputs_true.dat b/tests/regression_tests/model_xml/photon_production_inputs_true.dat new file mode 100644 index 0000000000..9e60033bec --- /dev/null +++ b/tests/regression_tests/model_xml/photon_production_inputs_true.dat @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + fixed source + 10000 + 1 + + + 0 0 0 + + + + 14000000.0 1.0 + + + ttb + true + + 1000.0 + + + + + 1 + + + neutron photon electron positron + + + 1 2 + current + + + 2 + Al27 total + total (n,gamma) + tracklength + + + 2 + Al27 total + total heating (n,gamma) + collision + + + 2 + Al27 total + total heating (n,gamma) + analog + + + diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py index 51c25a603b..9da5438db6 100644 --- a/tests/regression_tests/model_xml/test.py +++ b/tests/regression_tests/model_xml/test.py @@ -10,9 +10,9 @@ from tests.testing_harness import PyAPITestHarness, colorize # use a few models from other tests to make sure the same results are # produced when using a single model.xml file as input from ..adj_cell_rotation.test import model as adj_cell_rotation_model -from ..lattice_multiple.test import model as lattice_mult_model +from ..lattice_multiple.test import model as lattice_multiple_model from ..energy_laws.test import model as energy_laws_model -from ..photon_production.test import model as photon_prod_model +from ..photon_production.test import model as photon_production_model class ModelXMLTestHarness(PyAPITestHarness): @@ -30,10 +30,10 @@ class ModelXMLTestHarness(PyAPITestHarness): def _get_inputs(self): return open('model.xml').read() - def _compare_inputs(self): - """Skip input comparisons for now - """ - pass + # def _compare_inputs(self): + # """Skip input comparisons for now + # """ + # pass def _compare_results(self): """Make sure the current results agree with the reference.""" @@ -54,25 +54,23 @@ class ModelXMLTestHarness(PyAPITestHarness): os.remove('model.xml') -models = [ - 'adj_cell_rotation_model', - 'lattice_mult_model', - 'energy_laws_model', - 'photon_prod_model' -] -paths = [ - '../adj_cell_rotation', - '../lattice_multiple', - '../energy_laws', - '../photon_production' +test_names = [ + 'adj_cell_rotation', + 'lattice_multiple', + 'energy_laws', + 'photon_production' ] -@pytest.mark.parametrize("model, path", zip(models, paths)) -def test_model_xml(model, path, request): - inputs = path + "/inputs_true.dat" - results = path + "/results_true.dat" - harness = ModelXMLTestHarness(request.getfixturevalue(model), inputs, results) +@pytest.mark.parametrize("test_name", test_names, ids=lambda test: test) +def test_model_xml(test_name, request): + openmc.reset_auto_ids() + + test_path = '../' + test_name + results = test_path + "/results_true.dat" + inputs = test_name + "_inputs_true.dat" + model_name = test_name + "_model" + harness = ModelXMLTestHarness(request.getfixturevalue(model_name), inputs, results) harness.main() def test_input_arg(run_in_tmpdir): From 3f4a9eb7a2056f3136b00b82a814e934f52803e3 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 29 Nov 2022 01:19:38 -0600 Subject: [PATCH 194/265] Reordering geometry XML element attributes --- openmc/geometry.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openmc/geometry.py b/openmc/geometry.py index d036df9c74..afcae1d550 100644 --- a/openmc/geometry.py +++ b/openmc/geometry.py @@ -132,6 +132,7 @@ class Geometry: # Clean the indentation in the file to be user-readable xml.clean_indentation(element) + xml.reorder_attributes(element) # TODO: Remove when support is Python 3.8+ return element @@ -157,7 +158,6 @@ class Geometry: p /= 'geometry.xml' # Write the XML Tree to the geometry.xml file - xml.reorder_attributes(root_element) # TODO: Remove when support is Python 3.8+ tree = ET.ElementTree(root_element) tree.write(str(p), xml_declaration=True, encoding='utf-8') From 83cf6848d0f0fbe0a59798b333542daf3255c7e5 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 29 Nov 2022 11:11:06 -0600 Subject: [PATCH 195/265] Updating expected inputs with reordering --- .../adj_cell_rotation_inputs_true.dat | 20 +++++++++---------- .../model_xml/energy_laws_inputs_true.dat | 2 +- .../lattice_multiple_inputs_true.dat | 16 +++++++-------- .../photon_production_inputs_true.dat | 8 ++++---- 4 files changed, 23 insertions(+), 23 deletions(-) diff --git a/tests/regression_tests/model_xml/adj_cell_rotation_inputs_true.dat b/tests/regression_tests/model_xml/adj_cell_rotation_inputs_true.dat index 3b14f304ea..1c4516f42d 100644 --- a/tests/regression_tests/model_xml/adj_cell_rotation_inputs_true.dat +++ b/tests/regression_tests/model_xml/adj_cell_rotation_inputs_true.dat @@ -13,16 +13,16 @@ - - - - - - - - - - + + + + + + + + + + eigenvalue diff --git a/tests/regression_tests/model_xml/energy_laws_inputs_true.dat b/tests/regression_tests/model_xml/energy_laws_inputs_true.dat index 62485ff72a..c89ccc97ee 100644 --- a/tests/regression_tests/model_xml/energy_laws_inputs_true.dat +++ b/tests/regression_tests/model_xml/energy_laws_inputs_true.dat @@ -12,7 +12,7 @@ - + eigenvalue diff --git a/tests/regression_tests/model_xml/lattice_multiple_inputs_true.dat b/tests/regression_tests/model_xml/lattice_multiple_inputs_true.dat index d828b25f6b..0eed3c2015 100644 --- a/tests/regression_tests/model_xml/lattice_multiple_inputs_true.dat +++ b/tests/regression_tests/model_xml/lattice_multiple_inputs_true.dat @@ -18,8 +18,8 @@ - - + + 1.2 1.2 1 @@ -37,12 +37,12 @@ 4 4 4 4 - - - - - - + + + + + + eigenvalue diff --git a/tests/regression_tests/model_xml/photon_production_inputs_true.dat b/tests/regression_tests/model_xml/photon_production_inputs_true.dat index 9e60033bec..e4fe9a5858 100644 --- a/tests/regression_tests/model_xml/photon_production_inputs_true.dat +++ b/tests/regression_tests/model_xml/photon_production_inputs_true.dat @@ -10,10 +10,10 @@ - - - - + + + + fixed source From 2c27d1065a1e583a3778aa493f70a36724b46306 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 29 Nov 2022 13:45:10 -0600 Subject: [PATCH 196/265] Moving other relevant XML reorder calls and updating expected input again. --- openmc/settings.py | 2 +- openmc/tallies.py | 2 +- .../model_xml/photon_production_inputs_true.dat | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/openmc/settings.py b/openmc/settings.py index 74ec0d54a6..3c1c8c7f5c 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1598,6 +1598,7 @@ class Settings: # Clean the indentation in the file to be user-readable clean_indentation(element) + reorder_attributes(element) # TODO: Remove when support is Python 3.8+ return element @@ -1618,7 +1619,6 @@ class Settings: p /= 'settings.xml' # Write the XML Tree to the settings.xml file - reorder_attributes(root_element) # TODO: Remove when support is Python 3.8+ tree = ET.ElementTree(root_element) tree.write(str(p), xml_declaration=True, encoding='utf-8') diff --git a/openmc/tallies.py b/openmc/tallies.py index e37f04e252..e17e7c99db 100644 --- a/openmc/tallies.py +++ b/openmc/tallies.py @@ -3166,6 +3166,7 @@ class Tallies(cv.CheckedList): # Clean the indentation in the file to be user-readable clean_indentation(element) + reorder_attributes(element) # TODO: Remove when support is Python 3.8+ return element @@ -3187,7 +3188,6 @@ class Tallies(cv.CheckedList): p /= 'tallies.xml' # Write the XML Tree to the tallies.xml file - reorder_attributes(root_element) # TODO: Remove when support is Python 3.8+ tree = ET.ElementTree(root_element) tree.write(str(p), xml_declaration=True, encoding='utf-8') diff --git a/tests/regression_tests/model_xml/photon_production_inputs_true.dat b/tests/regression_tests/model_xml/photon_production_inputs_true.dat index e4fe9a5858..0b2b434681 100644 --- a/tests/regression_tests/model_xml/photon_production_inputs_true.dat +++ b/tests/regression_tests/model_xml/photon_production_inputs_true.dat @@ -23,7 +23,7 @@ 0 0 0 - + 14000000.0 1.0 From cd7c3bf6ba62cd019c378a3a22880e24e847f8ef Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 6 Dec 2022 12:58:32 -0600 Subject: [PATCH 197/265] Updates to import/export methods suggested by @paulromano --- openmc/model/model.py | 43 ++++++++++++++++++++++++++----------------- 1 file changed, 26 insertions(+), 17 deletions(-) diff --git a/openmc/model/model.py b/openmc/model/model.py index 145a2151bc..6ca6f72b62 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -205,15 +205,19 @@ class Model: self._plots.append(plot) @classmethod - def from_xml(cls, *args, path='model.xml', separate_xmls=True, **kwargs): + def from_xml(cls, *args, separate_xmls=True, **kwargs): """Generate geometry from XML file Parameters ---------- - path : str, optional - Path to model XML file + args : list + Positional arguments to be forwarded to + :func:`Model.from_separate_xmls` or :func:`Model.from_model_xml`. separate_xmls : bool - Whether or not to read from a single or separate XML files + Whether or not to read from a single or separate XML files. + kwargs : dict, optional + Keyword arguments to be forwarded to + :func:`Model.from_separate_xmls` or :func:`Model.from_model_xml`. Returns ------- @@ -221,7 +225,7 @@ class Model: Geometry object """ - if separate_xmls or not Path(path).exists(): + if separate_xmls: return cls.from_separate_xmls(*args, **kwargs) else: return cls.from_model_xml(*args, **kwargs) @@ -457,19 +461,19 @@ class Model: depletion_operator.cleanup_when_done = True depletion_operator.finalize() - def export_to_xml(self, directory='.', remove_surfs=False, separate_xmls=True, filename='model.xml'): + def export_to_xml(self, directory='.', remove_surfs=False, separate_xmls=True, path='model.xml'): """Export model to an XML file(s). Parameters ---------- directory : str Directory to write XML files to. If it doesn't exist already, it - will be created. + will be created. Only used if :math:`separate_xmls` is True. remove_surfs : bool Whether or not to remove redundant surfaces from the geometry when exporting. - filename : str - Name of the single XML file to create (only used :math:`separate_xmls` is False) + path : str + Path to an output filename or directory. Only used if :math:`separate_xmls` is False. .. versionadded:: 0.13.1 @@ -477,13 +481,9 @@ class Model: Whether or not to write a single model.xml file or many XML files. """ if separate_xmls: - if filename != 'model.xml': - warnings.warn('Export filename parameter {filename} is ignored ' - 'because the model is being written to separate XML files.') self._export_to_separate_xmls(directory, remove_surfs) else: - filename = Path(directory) / Path(filename) - self._export_to_single_xml(filename, remove_surfs) + self._export_to_single_xml(path, remove_surfs) def _export_to_separate_xmls(self, directory='.', remove_surfs=False): """Export model to separate XML files. @@ -530,16 +530,25 @@ class Model: directory : str Directory to write the model.xml file to. If it doesn't exist already, it will be created. + path : str or Pathlike + Location of the XML file to write. Can be a directory or file path. remove_surfs : bool Whether or not to remove redundant surfaces from the geometry when exporting. .. versionadded:: 0.13.1 """ - # Create directory if required xml_path = Path(path) - if not xml_path.parent.exists: - raise RuntimeError(f'The directory "{xml_path}" does not exist.') + # if the provided path doesn't end with the XML extension, assume the + # input path is meant to be a directory. If the directory does not + # exist, create it and place a 'model.xml' file there. + if not str(xml_path).endswith('.xml') and not xml_path.exists(): + os.mkdir(xml_path) + xml_path /= 'model.xml' + # if this is an XML file location and the file's parent directory does + # not exist, create it before continuing + elif not xml_path.parent.exists(): + os.mkdir(xml_path.parent) if remove_surfs: warnings.warn("remove_surfs kwarg will be deprecated soon, please " From ef2f690e3d4c7bb1f700f189bdaad88689fa5b16 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 6 Dec 2022 12:59:08 -0600 Subject: [PATCH 198/265] Updating handling of single XML input to leverage existing settings::path_input --- src/initialize.cpp | 42 +++++++++++++++++++----------------------- src/settings.cpp | 3 ++- 2 files changed, 21 insertions(+), 24 deletions(-) diff --git a/src/initialize.cpp b/src/initialize.cpp index 212b2f7bdc..c0333e01c0 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -181,9 +181,6 @@ int parse_command_line(int argc, char* argv[]) } else if (arg == "-e" || arg == "--event") { settings::event_based = true; - } else if (arg == "-i" || arg == "--input") { - i += 1; - args_xml_filename = std::string(argv[i]); } else if (arg == "-r" || arg == "--restart") { i += 1; // Check what type of file this is @@ -295,27 +292,24 @@ int parse_command_line(int argc, char* argv[]) } bool read_model_xml() { - // get verbosity from settings node + std::string model_filename = settings::path_input; - std::string xml_filename = "model.xml"; - if (!args_xml_filename.empty()) xml_filename = args_xml_filename; - std::string model_filename = settings::path_input + xml_filename; - - // check that the model file exists. If it does not and a custom filename was - // supplied by the user report an error - if (!file_exists(model_filename)) { - if (!args_xml_filename.empty()) { - fatal_error(fmt::format("The input file '{}' specified on the command line does not exist", args_xml_filename)); - } - return false; + // if the path input isn't an existing file, assume its a directory + // and append the default model.xml filename + if (!file_exists(settings::path_input)) { + model_filename += "/model.xml"; + if (!file_exists(model_filename)) + return false; } - // attempt to open the document + // try to process the path input as an XML file pugi::xml_document doc; - auto result = doc.load_file(model_filename.c_str()); - if (!result) { - fatal_error("Error processing model.xml file."); + // if the input is a file, try to read it + if (!doc.load_file(model_filename.c_str())) { + fatal_error(fmt::format( + "Error reading from single XML input file '{}'", model_filename)); } + pugi::xml_node root = doc.document_element(); // Read settings @@ -348,15 +342,17 @@ bool read_model_xml() { auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml", "tallies.xml", "plots.xml"}; for (const auto& input : other_inputs) { if (file_exists(settings::path_input + input)) { - warning((fmt::format("Other XML file input(s) are present. These file will be ignored in favor of the {} file.", xml_filename))); + warning((fmt::format("Other XML file input(s) are present. These file " + "will be ignored in favor of the {} file.", + model_filename))); break; } } // Read materials and cross sections if (!check_for_node(root, "materials")) { - fatal_error( - fmt::format("No node present in the {} file.", xml_filename)); + fatal_error(fmt::format( + "No node present in the {} file.", model_filename)); } read_cross_sections_xml(root.child("materials")); @@ -365,7 +361,7 @@ bool read_model_xml() { // Read geometry if (!check_for_node(root, "geometry")) { fatal_error(fmt::format( - "No node present in the model.xml_file.", xml_filename)); + "No node present in the model.xml_file.", model_filename)); } read_geometry_xml(root.child("geometry")); diff --git a/src/settings.cpp b/src/settings.cpp index 3048862e3f..74d45543d8 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -222,7 +222,8 @@ void read_settings_xml() { fmt::format("Settings XML file '{}' does not exist! In order " "to run OpenMC, you first need a set of input files; at a " "minimum, this " - "includes settings.xml, geometry.xml, and materials.xml. " + "includes settings.xml, geometry.xml, and materials.xml " + "or a single XML file containing all of these files. " "Please consult " "the user's guide at https://docs.openmc.org for further " "information.", From 574845b18b1de2d2fa9fa8415d7770e18d411bd6 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 6 Dec 2022 13:09:04 -0600 Subject: [PATCH 199/265] Moving Model.from_separate_xmls back to Model.from_xml. --- openmc/model/model.py | 78 +++++++++++++++---------------------------- 1 file changed, 26 insertions(+), 52 deletions(-) diff --git a/openmc/model/model.py b/openmc/model/model.py index 6ca6f72b62..34cc085b84 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -205,30 +205,40 @@ class Model: self._plots.append(plot) @classmethod - def from_xml(cls, *args, separate_xmls=True, **kwargs): - """Generate geometry from XML file + def from_xml(cls, geometry='geometry.xml', materials='materials.xml', + settings='settings.xml', tallies='tallies.xml', + plots='plots.xml'): + """Create model from existing XML files Parameters ---------- - args : list - Positional arguments to be forwarded to - :func:`Model.from_separate_xmls` or :func:`Model.from_model_xml`. - separate_xmls : bool - Whether or not to read from a single or separate XML files. - kwargs : dict, optional - Keyword arguments to be forwarded to - :func:`Model.from_separate_xmls` or :func:`Model.from_model_xml`. + geometry : str + Path to geometry.xml file + materials : str + Path to materials.xml file + settings : str + Path to settings.xml file + tallies : str + Path to tallies.xml file + + .. versionadded:: 0.13.0 + plots : str + Path to plots.xml file + + .. versionadded:: 0.13.0 Returns ------- - openmc.Geometry - Geometry object + openmc.model.Model + Model created from XML files """ - if separate_xmls: - return cls.from_separate_xmls(*args, **kwargs) - else: - return cls.from_model_xml(*args, **kwargs) + materials = openmc.Materials.from_xml(materials) + geometry = openmc.Geometry.from_xml(geometry, materials) + settings = openmc.Settings.from_xml(settings) + tallies = openmc.Tallies.from_xml(tallies) if Path(tallies).exists() else None + plots = openmc.Plots.from_xml(plots) if Path(plots).exists() else None + return cls(geometry, materials, settings, tallies, plots) @classmethod def from_model_xml(cls, path='model.xml'): @@ -265,42 +275,6 @@ class Model: return model - @classmethod - def from_separate_xmls(cls, geometry='geometry.xml', materials='materials.xml', - settings='settings.xml', tallies='tallies.xml', - plots='plots.xml'): - """Create model from existing XML files - - Parameters - ---------- - geometry : str - Path to geometry.xml file - materials : str - Path to materials.xml file - settings : str - Path to settings.xml file - tallies : str - Path to tallies.xml file - - .. versionadded:: 0.13.0 - plots : str - Path to plots.xml file - - .. versionadded:: 0.13.0 - - Returns - ------- - openmc.model.Model - Model created from XML files - - """ - materials = openmc.Materials.from_xml(materials) - geometry = openmc.Geometry.from_xml(geometry, materials) - settings = openmc.Settings.from_xml(settings) - tallies = openmc.Tallies.from_xml(tallies) if Path(tallies).exists() else None - plots = openmc.Plots.from_xml(plots) if Path(plots).exists() else None - return cls(geometry, materials, settings, tallies, plots) - def init_lib(self, threads=None, geometry_debug=False, restart_file=None, tracks=False, output=True, event_based=None, intracomm=None): """Initializes the model in memory via the C API From 270331aff956b95b1193e121c545345e64d3716c Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 6 Dec 2022 14:39:44 -0600 Subject: [PATCH 200/265] Adding function to check if a path is a directory --- include/openmc/file_utils.h | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/include/openmc/file_utils.h b/include/openmc/file_utils.h index f9c23468df..ae3a26e942 100644 --- a/include/openmc/file_utils.h +++ b/include/openmc/file_utils.h @@ -3,15 +3,31 @@ #include // for ifstream #include +#include namespace openmc { +// TODO: replace with std::filesysem when switch to C++17 is made +//! Determine if a path is a directory +//! \param[in] path Path to check +//! \return Whether the path is a directory +inline bool is_dir(const std::string& path) { + struct stat s; + if (stat(path.c_str(), &s) != 0) return false; + + return s.st_mode & S_IFDIR; +} + //! Determine if a file exists //! \param[in] filename Path to file //! \return Whether file exists inline bool file_exists(const std::string& filename) { + // rule out file being a directory path + if (is_dir(filename)) return false; + std::ifstream s {filename}; + s.seekg(0, std::ios::beg); return s.good(); } From bc1791d367b307656ce31bdfdf7c4b794def44ad Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 6 Dec 2022 14:40:02 -0600 Subject: [PATCH 201/265] Updates to simplify model filename checking --- include/openmc/initialize.h | 2 -- src/initialize.cpp | 30 ++++++++++++++++++------------ 2 files changed, 18 insertions(+), 14 deletions(-) diff --git a/include/openmc/initialize.h b/include/openmc/initialize.h index c37208e5e3..a9b8b336f9 100644 --- a/include/openmc/initialize.h +++ b/include/openmc/initialize.h @@ -21,8 +21,6 @@ void read_separate_xml_files(); //! Write some output that occurs right after initialization void initial_output(); - -std::string args_xml_filename {}; } // namespace openmc #endif // OPENMC_INITIALIZE_H diff --git a/src/initialize.cpp b/src/initialize.cpp index c0333e01c0..b75f410a10 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -282,7 +282,12 @@ int parse_command_line(int argc, char* argv[]) if (argc > 1 && last_flag < argc - 1) { settings::path_input = std::string(argv[last_flag + 1]); - // Add slash at end of directory if it isn't there + // check that the path is either a valid directory or file + if (!is_dir(settings::path_input) && !file_exists(settings::path_input)) { + fatal_error(fmt::format("The specified path '{}' does not exist.", settings::path_input)); + } + + // Add slash at end of directory if it isn't the if (!ends_with(settings::path_input, "/")) { settings::path_input += "/"; } @@ -294,13 +299,17 @@ int parse_command_line(int argc, char* argv[]) bool read_model_xml() { std::string model_filename = settings::path_input; - // if the path input isn't an existing file, assume its a directory - // and append the default model.xml filename - if (!file_exists(settings::path_input)) { - model_filename += "/model.xml"; - if (!file_exists(model_filename)) - return false; - } + // some string cleanup + // a trailing "/" is applied to path_input if it's present, + // remove it for the first attempt at reading the input file + if (ends_with(model_filename, "/")) model_filename.pop_back(); + if (model_filename.length() == 0) model_filename = "."; + + // if the current filename is a directory, append the default model filename + if (is_dir(model_filename)) model_filename += "/model.xml"; + + // if this file doesn't exist, stop here + if (!file_exists(model_filename)) return false; // try to process the path input as an XML file pugi::xml_document doc; @@ -330,10 +339,7 @@ bool read_model_xml() { title(); } - if (!args_xml_filename.empty()) - write_message(fmt::format("Reaging user-specified input '{}'...", args_xml_filename), 5); - else - write_message("Reading model XML file...", 5); + write_message(fmt::format("Reading model XML file '{}' ...", model_filename), 5); read_settings_xml(settings_root); From 5634d8318ad110ee20f79d69ab277f7134a0d277 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 6 Dec 2022 14:40:59 -0600 Subject: [PATCH 202/265] Changing name of input argument for Python executor --- openmc/executor.py | 35 ++++++++++++++++++----------------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/openmc/executor.py b/openmc/executor.py index b143132139..9267366e89 100644 --- a/openmc/executor.py +++ b/openmc/executor.py @@ -9,7 +9,7 @@ from .plots import _get_plot_image def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None, plot=False, restart_file=None, threads=None, tracks=False, event_based=None, - openmc_exec='openmc', mpi_args=None, input_file=None): + openmc_exec='openmc', mpi_args=None, path_input=None): """Converts user-readable flags in to command-line arguments to be run with the OpenMC executable via subprocess. @@ -42,7 +42,7 @@ def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None, mpi_args : list of str, optional MPI execute command and any additional MPI arguments to pass, e.g. ['mpiexec', '-n', '8']. - input_file : str or Pathlike + path_input : str or Pathlike Name of a single XML input file for the OpenMC executable to read. .. versionadded:: 0.13.0 @@ -84,8 +84,8 @@ def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None, if mpi_args is not None: args = mpi_args + args - if input_file is not None: - args += ['-i', input_file] + if path_input is not None: + args += [path_input] return args @@ -95,6 +95,7 @@ def _run(args, output, cwd): p = subprocess.Popen(args, cwd=cwd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True) + print(args) # Capture and re-print OpenMC output in real-time lines = [] while True: @@ -123,7 +124,7 @@ def _run(args, output, cwd): raise RuntimeError(error_msg) -def plot_geometry(output=True, openmc_exec='openmc', cwd='.', input_file=None): +def plot_geometry(output=True, openmc_exec='openmc', cwd='.', path_input=None): """Run OpenMC in plotting mode Parameters @@ -134,7 +135,7 @@ def plot_geometry(output=True, openmc_exec='openmc', cwd='.', input_file=None): Path to OpenMC executable cwd : str, optional Path to working directory to run in - input_file : str + path_input : str Name of a single XML input file for the OpenMC executable to read. Raises @@ -144,12 +145,12 @@ def plot_geometry(output=True, openmc_exec='openmc', cwd='.', input_file=None): """ args = [openmc_exec, '-p'] - if input_file is not None: - args += ['-i', input_file] + if path_input is not None: + args += ['-i', path_input] _run([openmc_exec, '-p'], output, cwd) -def plot_inline(plots, openmc_exec='openmc', cwd='.', input_file=None): +def plot_inline(plots, openmc_exec='openmc', cwd='.', path_input=None): """Display plots inline in a Jupyter notebook. .. versionchanged:: 0.13.0 @@ -165,7 +166,7 @@ def plot_inline(plots, openmc_exec='openmc', cwd='.', input_file=None): Path to OpenMC executable cwd : str, optional Path to working directory to run in - input_file : str + path_input : str Name of a single XML input file for the OpenMC executable to read. Raises @@ -183,7 +184,7 @@ def plot_inline(plots, openmc_exec='openmc', cwd='.', input_file=None): openmc.Plots(plots).export_to_xml(cwd) # Run OpenMC in geometry plotting mode - plot_geometry(False, openmc_exec, cwd, input_file) + plot_geometry(False, openmc_exec, cwd, path_input) if plots is not None: images = [_get_plot_image(p, cwd) for p in plots] @@ -192,7 +193,7 @@ def plot_inline(plots, openmc_exec='openmc', cwd='.', input_file=None): def calculate_volumes(threads=None, output=True, cwd='.', openmc_exec='openmc', mpi_args=None, - input_file=None): + path_input=None): """Run stochastic volume calculations in OpenMC. This function runs OpenMC in stochastic volume calculation mode. To specify @@ -223,7 +224,7 @@ def calculate_volumes(threads=None, output=True, cwd='.', cwd : str, optional Path to working directory to run in. Defaults to the current working directory. - input_file : str or Pathlike + path_input : str or Pathlike Name of a single XML input file for the OpenMC executable to read. Raises @@ -239,7 +240,7 @@ def calculate_volumes(threads=None, output=True, cwd='.', args = _process_CLI_arguments(volume=True, threads=threads, openmc_exec=openmc_exec, mpi_args=mpi_args, - input_file=input_file) + path_input=path_input) _run(args, output, cwd) @@ -247,7 +248,7 @@ def calculate_volumes(threads=None, output=True, cwd='.', def run(particles=None, threads=None, geometry_debug=False, restart_file=None, tracks=False, output=True, cwd='.', openmc_exec='openmc', mpi_args=None, event_based=False, - input_file=None): + path_input=None): """Run an OpenMC simulation. Parameters @@ -282,7 +283,7 @@ def run(particles=None, threads=None, geometry_debug=False, .. versionadded:: 0.12 - input_file : str or Pathlike + path_input : str or Pathlike Name of a single XML input file for the OpenMC executable to read. Raises @@ -296,6 +297,6 @@ def run(particles=None, threads=None, geometry_debug=False, volume=False, geometry_debug=geometry_debug, particles=particles, restart_file=restart_file, threads=threads, tracks=tracks, event_based=event_based, openmc_exec=openmc_exec, mpi_args=mpi_args, - input_file=input_file) + path_input=path_input) _run(args, output, cwd) From d639d1dc1b2796e9fae599d74283b9f125e3801a Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 6 Dec 2022 14:41:11 -0600 Subject: [PATCH 203/265] Docstring correction --- openmc/model/model.py | 1 - 1 file changed, 1 deletion(-) diff --git a/openmc/model/model.py b/openmc/model/model.py index 34cc085b84..a7a6f2d7da 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -450,7 +450,6 @@ class Model: Path to an output filename or directory. Only used if :math:`separate_xmls` is False. .. versionadded:: 0.13.1 - separate_xmls : bool Whether or not to write a single model.xml file or many XML files. """ From 939adbe70e2c73e2d503260bc5a912812d1b0087 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 6 Dec 2022 14:41:26 -0600 Subject: [PATCH 204/265] Updating tests to reflect changes to API --- tests/regression_tests/model_xml/test.py | 12 +++++++++--- tests/unit_tests/test_model.py | 14 +++++++------- 2 files changed, 16 insertions(+), 10 deletions(-) diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py index 9da5438db6..8aa9e5c2e2 100644 --- a/tests/regression_tests/model_xml/test.py +++ b/tests/regression_tests/model_xml/test.py @@ -1,6 +1,8 @@ from difflib import unified_diff +import glob import filecmp import os +from pathlib import Path import openmc import pytest @@ -83,13 +85,17 @@ def test_input_arg(run_in_tmpdir): pincell.export_to_xml(separate_xmls=True) openmc.run() + # make sure the executable isn't falling back on the separate XMLs + [os.remove(f) for f in glob.glob('*.xml')] # now export to a single XML file with a custom name - pincell.export_to_xml(filename='pincell.xml', separate_xmls=False) + pincell.export_to_xml(path='pincell.xml', separate_xmls=False) + assert Path('pincell.xml').exists() # run by specifying that single file - openmc.run(input_file='pincell.xml') + openmc.run(path_input='pincell.xml') # now ensure we get an error for an incorrect filename, # even in the presence of other, valid XML files + pincell.export_to_xml(separate_xmls=True) with pytest.raises(RuntimeError, match='ex-em-ell.xml'): - openmc.run(input_file='ex-em-ell.xml') \ No newline at end of file + openmc.run(path_input='ex-em-ell.xml') \ No newline at end of file diff --git a/tests/unit_tests/test_model.py b/tests/unit_tests/test_model.py index 5d4765d657..11a88d76ce 100644 --- a/tests/unit_tests/test_model.py +++ b/tests/unit_tests/test_model.py @@ -543,7 +543,7 @@ def test_model_xml(run_in_tmpdir): # now write and read a model.xml file pwr_model.export_to_xml(separate_xmls=False) - new_model = openmc.Model.from_xml(separate_xmls=False) + new_model = openmc.Model.from_model_xml() # make sure we can also export this again to separate # XML files @@ -553,17 +553,17 @@ def test_model_exec(run_in_tmpdir): pincell_model = openmc.examples.pwr_pin_cell() - pincell_model.export_to_xml(filename='pwr_pincell.xml', separate_xmls=False) + pincell_model.export_to_xml(path='pwr_pincell.xml', separate_xmls=False) - openmc.run(input_file='pwr_pincell.xml') + openmc.run(path_input='pwr_pincell.xml') with pytest.raises(RuntimeError, match='ex-em-ell.xml'): - openmc.run(input_file='ex-em-ell.xml') + openmc.run(path_input='ex-em-ell.xml') # test that a file in a different directory can be used os.mkdir('inputs') - pincell_model.export_to_xml(directory='./inputs', filename='pincell.xml', separate_xmls=False) - openmc.run(input_file='./inputs/pincell.xml') + pincell_model.export_to_xml(path='./inputs/pincell.xml', separate_xmls=False) + openmc.run(path_input='./inputs/pincell.xml') with pytest.raises(RuntimeError, match='input_dir'): - openmc.run(input_file='input_dir/pincell.xml') \ No newline at end of file + openmc.run(path_input='input_dir/pincell.xml') \ No newline at end of file From 7fdfed22f37e2c50913ba96adce55da98daf4c40 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 6 Dec 2022 21:49:46 -0600 Subject: [PATCH 205/265] Some cleanup of file utils --- include/openmc/file_utils.h | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/include/openmc/file_utils.h b/include/openmc/file_utils.h index ae3a26e942..439af6ee08 100644 --- a/include/openmc/file_utils.h +++ b/include/openmc/file_utils.h @@ -7,7 +7,7 @@ namespace openmc { -// TODO: replace with std::filesysem when switch to C++17 is made +// TODO: replace with std::filesystem when switch to C++17 is made //! Determine if a path is a directory //! \param[in] path Path to check //! \return Whether the path is a directory @@ -27,7 +27,6 @@ inline bool file_exists(const std::string& filename) if (is_dir(filename)) return false; std::ifstream s {filename}; - s.seekg(0, std::ios::beg); return s.good(); } From 55d77cf06c86726d9ebaf7abcb8de232b01af505 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 6 Dec 2022 21:50:08 -0600 Subject: [PATCH 206/265] Small improvements to read_model_xml --- src/initialize.cpp | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/src/initialize.cpp b/src/initialize.cpp index b75f410a10..041712d5a2 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -284,7 +284,9 @@ int parse_command_line(int argc, char* argv[]) // check that the path is either a valid directory or file if (!is_dir(settings::path_input) && !file_exists(settings::path_input)) { - fatal_error(fmt::format("The specified path '{}' does not exist.", settings::path_input)); + fatal_error(fmt::format( + "The path specified to the OpenMC executable '{}' does not exist.", + settings::path_input)); } // Add slash at end of directory if it isn't the @@ -297,13 +299,14 @@ int parse_command_line(int argc, char* argv[]) } bool read_model_xml() { - std::string model_filename = settings::path_input; + std::string model_filename = + settings::path_input.empty() ? "." : settings::path_input; // some string cleanup - // a trailing "/" is applied to path_input if it's present, + // a trailing "/" is applied to path_input if it's specified, // remove it for the first attempt at reading the input file - if (ends_with(model_filename, "/")) model_filename.pop_back(); - if (model_filename.length() == 0) model_filename = "."; + if (ends_with(model_filename, "/")) + model_filename.pop_back(); // if the current filename is a directory, append the default model filename if (is_dir(model_filename)) model_filename += "/model.xml"; @@ -313,7 +316,6 @@ bool read_model_xml() { // try to process the path input as an XML file pugi::xml_document doc; - // if the input is a file, try to read it if (!doc.load_file(model_filename.c_str())) { fatal_error(fmt::format( "Error reading from single XML input file '{}'", model_filename)); From 7873b4d6c1bfb983a7ec4c87ad29b492d4bbb088 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 6 Dec 2022 21:50:49 -0600 Subject: [PATCH 207/265] Update tests/regression_tests/model_xml/test.py Co-authored-by: Paul Romano --- tests/regression_tests/model_xml/test.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py index 8aa9e5c2e2..d040f4649f 100644 --- a/tests/regression_tests/model_xml/test.py +++ b/tests/regression_tests/model_xml/test.py @@ -32,11 +32,6 @@ class ModelXMLTestHarness(PyAPITestHarness): def _get_inputs(self): return open('model.xml').read() - # def _compare_inputs(self): - # """Skip input comparisons for now - # """ - # pass - def _compare_results(self): """Make sure the current results agree with the reference.""" compare = filecmp.cmp('results_test.dat', self.results_true) From f2c28706a6eaf2206da5ff73867c279946b55f4b Mon Sep 17 00:00:00 2001 From: Thomas Kittelmann Date: Wed, 7 Dec 2022 10:12:23 +0100 Subject: [PATCH 208/265] Apply suggestions from code review Co-authored-by: Paul Romano --- CMakeLists.txt | 2 -- docs/source/usersguide/materials.rst | 14 ++++---- openmc/material.py | 43 +++++++++++++------------ tests/regression_tests/ncrystal/test.py | 29 ++++++++--------- tools/ci/gha-install.py | 4 +-- tools/ci/gha-script.sh | 6 ++-- 6 files changed, 47 insertions(+), 51 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 2815230d43..5c4d489e3f 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -497,8 +497,6 @@ if(OPENMC_USE_NCRYSTAL) target_link_libraries(libopenmc NCrystal::NCrystal) endif() - - #=============================================================================== # openmc executable #=============================================================================== diff --git a/docs/source/usersguide/materials.rst b/docs/source/usersguide/materials.rst index a3c05f4211..fbf9effd89 100644 --- a/docs/source/usersguide/materials.rst +++ b/docs/source/usersguide/materials.rst @@ -101,19 +101,17 @@ you would need to add hydrogen and oxygen to a material and then assign the .. _usersguide_naming: ------------------- +------------------------- Adding NCrystal materials ------------------- +------------------------- Additional support for thermal scattering can be added by using NCrystal_. The :meth:`Material.from_ncrystal` class method generates a :class:`openmc.Material` object from an `NCrystal configuration string `_. -Temperature, material composition and density are passed from the configuration string +Temperature, material composition, and density are passed from the configuration string and the `NCMAT file `_ -that define the material, e.g: +that define the material, e.g.:: -:: - mat = openmc.Material.from_ncrystal('Al_sg225.ncmat;temp=300K') defines a material containing polycrystalline alumnium, @@ -126,12 +124,12 @@ defines a material containing polycrystalline alumnium, defines an oriented germanium single crystal with 40 arcsec mosaicity. -NCrystal only handles low energy neutron interactions. Other interaction are +NCrystal only handles low energy neutron interactions. Other interactions are provided by standard ACE files. NCrystal_ comes with a `predefined library `_ but more materials can be added by creating NCMAT files or on-the-fly in the configuration string. -.. warning:: Currently, NCrystal_ materials cannot be modified after created. +.. warning:: Currently, NCrystal_ materials cannot be modified after they are created. Density, temperature and composition should be defined in the configuration string or the NCMAT file. diff --git a/openmc/material.py b/openmc/material.py index de4a22cb8e..298731c92c 100644 --- a/openmc/material.py +++ b/openmc/material.py @@ -336,11 +336,12 @@ class Material(IDManagerMixin): @classmethod def from_ncrystal(cls, cfg, material_id=None, name=''): - """Create material from NCrystal configuration string. Density, - temperature, and material composition, and (ultimately) thermal neutron - scattering, will be automatically be provided by NCrystal based on this - string. The name and material_id parameters are simply passed on to the - Material constructor. + """Create material from NCrystal configuration string. + + Density, temperature, and material composition, and (ultimately) thermal + neutron scattering will be automatically be provided by NCrystal based + on this string. The name and material_id parameters are simply passed on + to the Material constructor. Parameters ---------- @@ -363,41 +364,41 @@ class Material(IDManagerMixin): import NCrystal nc_mat = NCrystal.createInfo(cfg) - def openmc_natabund( Z ): + def openmc_natabund(Z): #nc_mat.getFlattenedComposition might need natural abundancies. #This call-back function is used so NCrystal can flatten composition #using OpenMC's natural abundancies. In practice this function will #only get invoked in the unlikely case where a material is specified #by referring both to natural elements and specific isotopes of the #same element. - elem_name = openmc.data.ATOMIC_SYMBOL.get( Z, None ) + elem_name = openmc.data.ATOMIC_SYMBOL.get(Z) if not elem_name: raise ValueError( f'Element with Z={Z} is not known' ) - l = [] - for iso_name,abund in openmc.data.isotopes( elem_name ): - l.append( ( int(iso_name[ len(elem_name) : ]), abund ) ) - return l + return [ + (int(iso_name[len(elem_name):]), abund) + for iso_name, abund in openmc.data.isotopes(elem_name) + ] - flat_compos = nc_mat.getFlattenedComposition( preferNaturalElements = True, - naturalAbundProvider = openmc_natabund ) + flat_compos = nc_mat.getFlattenedComposition(preferNaturalElements = True, + naturalAbundProvider=openmc_natabund) # Create the Material - material = cls( material_id = material_id, - name = name, - temperature = nc_mat.getTemperature() ) + material = cls(material_id=material_id, + name=name, + temperature=nc_mat.getTemperature()) for Z, A_vals in flat_compos: - elemname = openmc.data.ATOMIC_SYMBOL.get(Z,None) + elemname = openmc.data.ATOMIC_SYMBOL.get(Z) if not elemname: raise ValueError(f'Element with Z={Z} is not known') for A, frac in A_vals: if A: - material.add_nuclide( elemname + str(A), frac, 'ao' ) + material.add_nuclide(f'{elemname}{A}', frac) else: - material.add_element( elemname, frac, 'ao' ) + material.add_element(elemname, frac) - material.set_density( 'g/cm3', nc_mat.getDensity() ) - material._ncrystal_cfg = NCrystal.normaliseCfg( cfg ) + material.set_density('g/cm3', nc_mat.getDensity()) + material._ncrystal_cfg = NCrystal.normaliseCfg(cfg) return material diff --git a/tests/regression_tests/ncrystal/test.py b/tests/regression_tests/ncrystal/test.py index 0a47d634df..3137515d4a 100644 --- a/tests/regression_tests/ncrystal/test.py +++ b/tests/regression_tests/ncrystal/test.py @@ -10,7 +10,7 @@ pytestmark = pytest.mark.skipif( reason="NCrystal materials are not enabled.") def compute_angular_distribution(cfg, E0, N): - """Return a openmc.model.Model() object for a monoenergetic pencil + """Return an openmc.Model() object for a monoenergetic pencil beam hitting a 1 mm sphere filled with the material defined by the cfg string, and compute the angular distribution""" @@ -23,17 +23,16 @@ def compute_angular_distribution(cfg, E0, N): sample_sphere = openmc.Sphere(r=0.1) outer_sphere = openmc.Sphere(r=100, boundary_type="vacuum") - cell1 = openmc.Cell(region= -sample_sphere, fill=m1) - cell2_region= +sample_sphere&-outer_sphere - cell2 = openmc.Cell(region= cell2_region, fill=None) - uni1 = openmc.Universe(cells=[cell1, cell2]) - geometry = openmc.Geometry(uni1) + cell1 = openmc.Cell(region=-sample_sphere, fill=m1) + cell2_region= +sample_sphere & -outer_sphere + cell2 = openmc.Cell(region=cell2_region, fill=None) + geometry = openmc.Geometry([cell1, cell2]) # Source definition source = openmc.Source() - source.space = openmc.stats.Point(xyz = (0,0,-20)) - source.angle = openmc.stats.Monodirectional(reference_uvw = (0,0,1)) + source.space = openmc.stats.Point((0, 0, -20)) + source.angle = openmc.stats.Monodirectional(reference_uvw=(0, 0, 1)) source.energy = openmc.stats.Discrete([E0], [1.0]) # Execution settings @@ -48,13 +47,13 @@ def compute_angular_distribution(cfg, E0, N): tally1 = openmc.Tally(name="angular distribution") tally1.scores = ["current"] - filter1 = openmc.filter.SurfaceFilter(sample_sphere) - filter2 = openmc.filter.PolarFilter(np.linspace(0,np.pi,180+1)) - filter3 = openmc.filter.CellFromFilter(cell1) + filter1 = openmc.SurfaceFilter(sample_sphere) + filter2 = openmc.PolarFilter(np.linspace(0, np.pi, 180+1)) + filter3 = openmc.CellFromFilter(cell1) tally1.filters = [filter1, filter2, filter3] tallies = openmc.Tallies([tally1]) - return openmc.model.Model(geometry, materials, settings, tallies) + return openmc.Model(geometry, materials, settings, tallies) class NCrystalTest(PyAPITestHarness): @@ -62,9 +61,9 @@ class NCrystalTest(PyAPITestHarness): """Digest info in the statepoint and return as a string.""" # Read the statepoint file. - sp = openmc.StatePoint(self._sp_name) - tal = sp.get_tally(name='angular distribution') - df = tal.get_pandas_dataframe() + with openmc.StatePoint(self._sp_name) as sp: + tal = sp.get_tally(name='angular distribution') + df = tal.get_pandas_dataframe() return df.to_string() def test_ncrystal(): diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py index f5779c9351..ac10bb3f65 100644 --- a/tools/ci/gha-install.py +++ b/tools/ci/gha-install.py @@ -56,8 +56,8 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrys if ncrystal: cmake_cmd.append('-DOPENMC_USE_NCRYSTAL=ON') - ncrystal_cmake_path = os.environ.get('HOME')+'/ncrystal_inst/lib/cmake' - cmake_cmd.append('-DCMAKE_PREFIX_PATH=' + ncrystal_cmake_path) + ncrystal_cmake_path = os.environ.get('HOME') + '/ncrystal_inst/lib/cmake' + cmake_cmd.append(f'-DCMAKE_PREFIX_PATH={ncrystal_cmake_path}') # Build in coverage mode for coverage testing cmake_cmd.append('-DOPENMC_ENABLE_COVERAGE=on') diff --git a/tools/ci/gha-script.sh b/tools/ci/gha-script.sh index 85fdef49f5..1f1c3a1ebe 100755 --- a/tools/ci/gha-script.sh +++ b/tools/ci/gha-script.sh @@ -16,9 +16,9 @@ fi # Check NCrystal installation if [[ $NCRYSTAL = 'y' ]]; then - # Change environmental variables - eval $( "${HOME}/ncrystal_inst/bin/ncrystal-config" --setup ) - nctool --test + # Change environmental variables + eval $( "${HOME}/ncrystal_inst/bin/ncrystal-config" --setup ) + nctool --test fi # Run regression and unit tests From a86e74f59a27236a4705ab0b4dc8c79736cd2c56 Mon Sep 17 00:00:00 2001 From: Thomas Kittelmann Date: Wed, 7 Dec 2022 12:51:31 +0100 Subject: [PATCH 209/265] Rename compute_angular_distribution to pencil_beam_model --- tests/regression_tests/ncrystal/test.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/regression_tests/ncrystal/test.py b/tests/regression_tests/ncrystal/test.py index 3137515d4a..2a789dac78 100644 --- a/tests/regression_tests/ncrystal/test.py +++ b/tests/regression_tests/ncrystal/test.py @@ -9,7 +9,7 @@ pytestmark = pytest.mark.skipif( not openmc.lib._ncrystal_enabled(), reason="NCrystal materials are not enabled.") -def compute_angular_distribution(cfg, E0, N): +def pencil_beam_model(cfg, E0, N): """Return an openmc.Model() object for a monoenergetic pencil beam hitting a 1 mm sphere filled with the material defined by the cfg string, and compute the angular distribution""" @@ -71,6 +71,6 @@ def test_ncrystal(): T = 293.6 # K E0 = 0.012 # eV cfg = 'Al_sg225.ncmat' - test = compute_angular_distribution(cfg, E0, NParticles) + test = pencil_beam_model(cfg, E0, NParticles) harness = NCrystalTest('statepoint.10.h5', model=test) harness.main() From ef13643f297dfe030c644d7a776fd85be54afdaa Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Wed, 7 Dec 2022 08:28:13 -0600 Subject: [PATCH 210/265] Some housekeeping in the Python classes --- openmc/model/model.py | 8 ++------ openmc/settings.py | 38 ++++++++++++++++++++++++++------------ 2 files changed, 28 insertions(+), 18 deletions(-) diff --git a/openmc/model/model.py b/openmc/model/model.py index a7a6f2d7da..1fdd127300 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -496,13 +496,10 @@ class Model: self.plots.export_to_xml(d) def _export_to_single_xml(self, path='model.xml', remove_surfs=False): - """Export model to XML files. + """Export model to a single XML file. Parameters ---------- - directory : str - Directory to write the model.xml file to. If it doesn't exist already, it - will be created. path : str or Pathlike Location of the XML file to write. Can be a directory or file path. remove_surfs : bool @@ -530,8 +527,7 @@ class Model: # Can be used to modify tallies in case any surfaces are redundant redundant_surfaces = self.geometry.remove_redundant_surfaces() - memo = set() - settings_element = self.settings.to_xml_element(memo) + settings_element = self.settings.to_xml_element() geometry_element = self.geometry.to_xml_element() xml.clean_indentation(geometry_element, level=1) diff --git a/openmc/settings.py b/openmc/settings.py index 3c1c8c7f5c..3f56f729f3 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1073,7 +1073,7 @@ class Settings: subelement = ET.SubElement(element, key) subelement.text = str(value) - def _create_entropy_mesh_subelement(self, root, memo=None): + def _create_entropy_mesh_subelement(self, root, mesh_memo=None): if self.entropy_mesh is not None: # use default heuristic for entropy mesh if not set by user if self.entropy_mesh.dimension is None: @@ -1085,13 +1085,20 @@ class Settings: d = len(self.entropy_mesh.lower_left) self.entropy_mesh.dimension = (n,)*d + # add mesh ID to this element + subelement = ET.SubElement(root, "entropy_mesh") + subelement.text = str(self.entropy_mesh.id) + + # If this mesh has already been written outside the + # settings element, skip writing it again + if mesh_memo and self.entropy_mesh.id in mesh_memo: + return + # See if a element already exists -- if not, add it path = f"./mesh[@id='{self.entropy_mesh.id}']" if root.find(path) is None: root.append(self.entropy_mesh.to_xml_element()) - - subelement = ET.SubElement(root, "entropy_mesh") - subelement.text = str(self.entropy_mesh.id) + if mesh_memo is not None: mesh_memo.add(self.entropy_mesh.id) def _create_trigger_subelement(self, root): if self._trigger_active is not None: @@ -1207,20 +1214,21 @@ class Settings: elem = ET.SubElement(root, "write_initial_source") elem.text = str(self._write_initial_source).lower() - def _create_weight_windows_subelement(self, root, memo=None): + def _create_weight_windows_subelement(self, root, mesh_memo=None): for ww in self._weight_windows: # Add weight window information root.append(ww.to_xml_element()) - # check the memo for a mesh - if memo and ww.mesh.id in memo: + # if this mesh has already been written, + # skip writing the mesh element + if mesh_memo and ww.mesh.id in mesh_memo: continue # See if a element already exists -- if not, add it path = f"./mesh[@id='{ww.mesh.id}']" if root.find(path) is None: root.append(ww.mesh.to_xml_element()) - if memo is not None: memo.add(ww.mesh.id) + if mesh_memo is not None: mesh_memo.add(ww.mesh.id) if self._weight_windows_on is not None: elem = ET.SubElement(root, "weight_windows_on") @@ -1544,10 +1552,16 @@ class Settings: if text is not None: self.max_tracks = int(text) - def to_xml_element(self, memo=None): + def to_xml_element(self, mesh_memo=None): """Create a 'settings' element to be written to an XML file. - """ + Parameters + ---------- + mesh_memo : set of ints + A set of mesh IDs to keep track of whether a mesh has already been written. + """ + # create a memo object if one isn't passed in already + mesh_memo = mesh_memo if mesh_memo else set() # Reset xml element tree element = ET.Element("settings") @@ -1574,7 +1588,7 @@ class Settings: self._create_seed_subelement(element) self._create_survival_biasing_subelement(element) self._create_cutoff_subelement(element) - self._create_entropy_mesh_subelement(element, memo) + self._create_entropy_mesh_subelement(element, mesh_memo) self._create_trigger_subelement(element) self._create_no_reduce_subelement(element) self._create_verbosity_subelement(element) @@ -1592,7 +1606,7 @@ class Settings: self._create_material_cell_offsets_subelement(element) self._create_log_grid_bins_subelement(element) self._create_write_initial_source_subelement(element) - self._create_weight_windows_subelement(element, memo) + self._create_weight_windows_subelement(element, mesh_memo) self._create_max_splits_subelement(element) self._create_max_tracks_subelement(element) From 9c942db45eaca790dc0f7f142b801381d2574daa Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Wed, 7 Dec 2022 10:10:22 -0600 Subject: [PATCH 211/265] Correct use of mesh memo in single XML export --- openmc/model/model.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/openmc/model/model.py b/openmc/model/model.py index 1fdd127300..a54cd60763 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -527,7 +527,9 @@ class Model: # Can be used to modify tallies in case any surfaces are redundant redundant_surfaces = self.geometry.remove_redundant_surfaces() - settings_element = self.settings.to_xml_element() + # provide a memo to track which meshes have been written + mesh_memo = set() + settings_element = self.settings.to_xml_element(mesh_memo) geometry_element = self.geometry.to_xml_element() xml.clean_indentation(geometry_element, level=1) @@ -554,7 +556,7 @@ class Model: ET.ElementTree(settings_element).write(fh, encoding='unicode') if self.tallies: - tallies_element = self.tallies.to_xml_element(memo) + tallies_element = self.tallies.to_xml_element(mesh_memo) xml.clean_indentation(tallies_element, level=1, trailing_indent=self.plots) ET.ElementTree(tallies_element).write(fh, encoding='unicode') if self.plots: From 916863f82ae304ff6f936701cbb058c5e7c2583a Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Wed, 7 Dec 2022 11:02:10 -0600 Subject: [PATCH 212/265] Renaming and docstring/comment updates --- include/openmc/file_utils.h | 8 +++++--- include/openmc/geometry_aux.h | 2 +- openmc/settings.py | 2 -- src/initialize.cpp | 6 ++++-- 4 files changed, 10 insertions(+), 8 deletions(-) diff --git a/include/openmc/file_utils.h b/include/openmc/file_utils.h index 439af6ee08..cb52b33c89 100644 --- a/include/openmc/file_utils.h +++ b/include/openmc/file_utils.h @@ -11,7 +11,8 @@ namespace openmc { //! Determine if a path is a directory //! \param[in] path Path to check //! \return Whether the path is a directory -inline bool is_dir(const std::string& path) { +inline bool dir_exists(const std::string& path) +{ struct stat s; if (stat(path.c_str(), &s) != 0) return false; @@ -23,8 +24,9 @@ inline bool is_dir(const std::string& path) { //! \return Whether file exists inline bool file_exists(const std::string& filename) { - // rule out file being a directory path - if (is_dir(filename)) return false; + // rule out file being a path to a directory + if (dir_exists(filename)) + return false; std::ifstream s {filename}; return s.good(); diff --git a/include/openmc/geometry_aux.h b/include/openmc/geometry_aux.h index a4c506c31a..cf62debc04 100644 --- a/include/openmc/geometry_aux.h +++ b/include/openmc/geometry_aux.h @@ -24,7 +24,7 @@ extern std::unordered_map universe_level_counts; void read_geometry_xml(); //! Read geometry from XML node -//! \param[in] root node of geometry XML element +//! \param[in] root node of geometry XML element void read_geometry_xml(pugi::xml_node root); //============================================================================== diff --git a/openmc/settings.py b/openmc/settings.py index 3f56f729f3..294aea7a3b 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1560,8 +1560,6 @@ class Settings: mesh_memo : set of ints A set of mesh IDs to keep track of whether a mesh has already been written. """ - # create a memo object if one isn't passed in already - mesh_memo = mesh_memo if mesh_memo else set() # Reset xml element tree element = ET.Element("settings") diff --git a/src/initialize.cpp b/src/initialize.cpp index 041712d5a2..3b332c3b27 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -283,7 +283,8 @@ int parse_command_line(int argc, char* argv[]) settings::path_input = std::string(argv[last_flag + 1]); // check that the path is either a valid directory or file - if (!is_dir(settings::path_input) && !file_exists(settings::path_input)) { + if (!dir_exists(settings::path_input) && + !file_exists(settings::path_input)) { fatal_error(fmt::format( "The path specified to the OpenMC executable '{}' does not exist.", settings::path_input)); @@ -309,7 +310,8 @@ bool read_model_xml() { model_filename.pop_back(); // if the current filename is a directory, append the default model filename - if (is_dir(model_filename)) model_filename += "/model.xml"; + if (dir_exists(model_filename)) + model_filename += "/model.xml"; // if this file doesn't exist, stop here if (!file_exists(model_filename)) return false; From 145594ebb8697ff2c711b6a8f57abbfedfebf8c7 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Mon, 12 Dec 2022 20:23:49 -0600 Subject: [PATCH 213/265] Apply @paulromano suggestions from code review Co-authored-by: Paul Romano --- openmc/_xml.py | 2 +- openmc/executor.py | 3 +-- openmc/material.py | 1 - openmc/model/model.py | 2 +- src/initialize.cpp | 4 ++-- tests/regression_tests/model_xml/test.py | 3 ++- 6 files changed, 7 insertions(+), 8 deletions(-) diff --git a/openmc/_xml.py b/openmc/_xml.py index 6d298638da..aeaeb45b52 100644 --- a/openmc/_xml.py +++ b/openmc/_xml.py @@ -16,7 +16,7 @@ def clean_indentation(element, level=0, spaces_per_level=2, trailing_indent=True """ i = "\n" + level*spaces_per_level*" " - # ensure there's awlays some tail for the element passed in + # ensure there's always some tail for the element passed in if not element.tail: element.tail = "" diff --git a/openmc/executor.py b/openmc/executor.py index 9267366e89..38421ecc2c 100644 --- a/openmc/executor.py +++ b/openmc/executor.py @@ -95,7 +95,6 @@ def _run(args, output, cwd): p = subprocess.Popen(args, cwd=cwd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True) - print(args) # Capture and re-print OpenMC output in real-time lines = [] while True: @@ -146,7 +145,7 @@ def plot_geometry(output=True, openmc_exec='openmc', cwd='.', path_input=None): """ args = [openmc_exec, '-p'] if path_input is not None: - args += ['-i', path_input] + args += [path_input] _run([openmc_exec, '-p'], output, cwd) diff --git a/openmc/material.py b/openmc/material.py index 332f8c9659..aa778cab64 100644 --- a/openmc/material.py +++ b/openmc/material.py @@ -1548,7 +1548,6 @@ class Materials(cv.CheckedList): return materials - @classmethod def from_xml(cls, path: PathLike = 'materials.xml'): """Generate materials collection from XML file diff --git a/openmc/model/model.py b/openmc/model/model.py index a54cd60763..9983d5c60c 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -259,7 +259,7 @@ class Model: materials = {str(m.id): m for m in model.materials} model.geometry = openmc.Geometry.from_xml_element(root.find('geometry'), materials) - # gather meshses from other classes before reading the tally node + # gather meshes from other classes before reading the tally node meshes = {} if model.settings.entropy_mesh is not None: meshes[model.settings.entropy_mesh.id] = model.settings.entropy_mesh diff --git a/src/initialize.cpp b/src/initialize.cpp index 3b332c3b27..0c137795bb 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -352,7 +352,7 @@ bool read_model_xml() { auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml", "tallies.xml", "plots.xml"}; for (const auto& input : other_inputs) { if (file_exists(settings::path_input + input)) { - warning((fmt::format("Other XML file input(s) are present. These file " + warning((fmt::format("Other XML file input(s) are present. These files " "will be ignored in favor of the {} file.", model_filename))); break; @@ -371,7 +371,7 @@ bool read_model_xml() { // Read geometry if (!check_for_node(root, "geometry")) { fatal_error(fmt::format( - "No node present in the model.xml_file.", model_filename)); + "No node present in the {} file.", model_filename)); } read_geometry_xml(root.child("geometry")); diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py index d040f4649f..fbff02357f 100644 --- a/tests/regression_tests/model_xml/test.py +++ b/tests/regression_tests/model_xml/test.py @@ -81,7 +81,8 @@ def test_input_arg(run_in_tmpdir): openmc.run() # make sure the executable isn't falling back on the separate XMLs - [os.remove(f) for f in glob.glob('*.xml')] + for f in glob.glob('*.xml'): + os.remove(f) # now export to a single XML file with a custom name pincell.export_to_xml(path='pincell.xml', separate_xmls=False) assert Path('pincell.xml').exists() From f3bcad37b72629cfc64e857aebdbe7c38461cabb Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Mon, 12 Dec 2022 21:18:48 -0600 Subject: [PATCH 214/265] Addressing comments from @paulromano --- openmc/executor.py | 32 ++++++----- openmc/geometry.py | 19 ++++--- openmc/model/model.py | 33 ++---------- openmc/settings.py | 68 +++++++++++++----------- tests/regression_tests/model_xml/test.py | 11 ++-- tests/unit_tests/test_model.py | 10 ++-- 6 files changed, 85 insertions(+), 88 deletions(-) diff --git a/openmc/executor.py b/openmc/executor.py index 38421ecc2c..22862a7cf9 100644 --- a/openmc/executor.py +++ b/openmc/executor.py @@ -43,7 +43,8 @@ def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None, MPI execute command and any additional MPI arguments to pass, e.g. ['mpiexec', '-n', '8']. path_input : str or Pathlike - Name of a single XML input file for the OpenMC executable to read. + Path to a single XML file or a directory containing XML files for the + OpenMC executable to read. .. versionadded:: 0.13.0 @@ -135,7 +136,8 @@ def plot_geometry(output=True, openmc_exec='openmc', cwd='.', path_input=None): cwd : str, optional Path to working directory to run in path_input : str - Name of a single XML input file for the OpenMC executable to read. + Path to a single XML file or a directory containing XML files for the + OpenMC executable to read. Raises ------ @@ -146,7 +148,7 @@ def plot_geometry(output=True, openmc_exec='openmc', cwd='.', path_input=None): args = [openmc_exec, '-p'] if path_input is not None: args += [path_input] - _run([openmc_exec, '-p'], output, cwd) + _run(args, output, cwd) def plot_inline(plots, openmc_exec='openmc', cwd='.', path_input=None): @@ -166,7 +168,8 @@ def plot_inline(plots, openmc_exec='openmc', cwd='.', path_input=None): cwd : str, optional Path to working directory to run in path_input : str - Name of a single XML input file for the OpenMC executable to read. + Path to a single XML file or a directory containing XML files for the + OpenMC executable to read. Raises ------ @@ -224,7 +227,9 @@ def calculate_volumes(threads=None, output=True, cwd='.', Path to working directory to run in. Defaults to the current working directory. path_input : str or Pathlike - Name of a single XML input file for the OpenMC executable to read. + Path to a single XML file or a directory containing XML files for the + OpenMC executable to read. + Raises ------ @@ -256,17 +261,17 @@ def run(particles=None, threads=None, geometry_debug=False, Number of particles to simulate per generation. threads : int, optional Number of OpenMP threads. If OpenMC is compiled with OpenMP threading - enabled, the default is implementation-dependent but is usually equal - to the number of hardware threads available (or a value set by the + enabled, the default is implementation-dependent but is usually equal to + the number of hardware threads available (or a value set by the :envvar:`OMP_NUM_THREADS` environment variable). geometry_debug : bool, optional Turn on geometry debugging during simulation. Defaults to False. restart_file : str, optional Path to restart file to use tracks : bool, optional - Enables the writing of particles tracks. The number of particle - tracks written to tracks.h5 is limited to 1000 unless - Settings.max_tracks is set. Defaults to False. + Enables the writing of particles tracks. The number of particle tracks + written to tracks.h5 is limited to 1000 unless Settings.max_tracks is + set. Defaults to False. output : bool Capture OpenMC output from standard out cwd : str, optional @@ -275,15 +280,16 @@ def run(particles=None, threads=None, geometry_debug=False, openmc_exec : str, optional Path to OpenMC executable. Defaults to 'openmc'. mpi_args : list of str, optional - MPI execute command and any additional MPI arguments to pass, - e.g. ['mpiexec', '-n', '8']. + MPI execute command and any additional MPI arguments to pass, e.g. + ['mpiexec', '-n', '8']. event_based : bool, optional Turns on event-based parallelism, instead of default history-based .. versionadded:: 0.12 path_input : str or Pathlike - Name of a single XML input file for the OpenMC executable to read. + Path to a single XML file or a directory containing XML files for the + OpenMC executable to read. Raises ------ diff --git a/openmc/geometry.py b/openmc/geometry.py index afcae1d550..a43899daaf 100644 --- a/openmc/geometry.py +++ b/openmc/geometry.py @@ -179,6 +179,11 @@ class Geometry: Geometry object """ + mats = dict() + if materials is not None: + mats.update({str(m.id): m for m in materials}) + mats['void'] = None + # Helper function for keeping a cache of Universe instances universes = {} def get_universe(univ_id): @@ -236,7 +241,7 @@ class Geometry: child_of[u].append(lat) for e in elem.findall('cell'): - c = openmc.Cell.from_xml_element(e, surfaces, materials, get_universe) + c = openmc.Cell.from_xml_element(e, surfaces, mats, get_universe) if c.fill_type in ('universe', 'lattice'): child_of[c.fill].append(c) @@ -266,17 +271,15 @@ class Geometry: Geometry object """ - tree = ET.parse(path) - root = tree.getroot() - - # Create dictionary to easily look up materials + # Create dictionary to easily look up materials if materials is None: filename = Path(path).parent / 'materials.xml' materials = openmc.Materials.from_xml(str(filename)) - mats = {str(m.id): m for m in materials} - mats['void'] = None - return cls.from_xml_element(root, mats) + tree = ET.parse(path) + root = tree.getroot() + + return cls.from_xml_element(root, materials) def find(self, point): """Find cells/universes/lattices which contain a given point diff --git a/openmc/model/model.py b/openmc/model/model.py index 9983d5c60c..a8dc1ce484 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -256,8 +256,7 @@ class Model: model.settings = openmc.Settings.from_xml_element(root.find('settings')) model.materials = openmc.Materials.from_xml_element(root.find('materials')) - materials = {str(m.id): m for m in model.materials} - model.geometry = openmc.Geometry.from_xml_element(root.find('geometry'), materials) + model.geometry = openmc.Geometry.from_xml_element(root.find('geometry'), model.materials) # gather meshes from other classes before reading the tally node meshes = {} @@ -435,30 +434,7 @@ class Model: depletion_operator.cleanup_when_done = True depletion_operator.finalize() - def export_to_xml(self, directory='.', remove_surfs=False, separate_xmls=True, path='model.xml'): - """Export model to an XML file(s). - - Parameters - ---------- - directory : str - Directory to write XML files to. If it doesn't exist already, it - will be created. Only used if :math:`separate_xmls` is True. - remove_surfs : bool - Whether or not to remove redundant surfaces from the geometry when - exporting. - path : str - Path to an output filename or directory. Only used if :math:`separate_xmls` is False. - - .. versionadded:: 0.13.1 - separate_xmls : bool - Whether or not to write a single model.xml file or many XML files. - """ - if separate_xmls: - self._export_to_separate_xmls(directory, remove_surfs) - else: - self._export_to_single_xml(path, remove_surfs) - - def _export_to_separate_xmls(self, directory='.', remove_surfs=False): + def export_to_xml(self, directory='.', remove_surfs=False): """Export model to separate XML files. Parameters @@ -495,13 +471,14 @@ class Model: if self.plots: self.plots.export_to_xml(d) - def _export_to_single_xml(self, path='model.xml', remove_surfs=False): + def export_to_model_xml(self, path='model.xml', remove_surfs=False): """Export model to a single XML file. Parameters ---------- path : str or Pathlike - Location of the XML file to write. Can be a directory or file path. + Location of the XML file to write (default is 'model.xml'). Can be a + directory or file path. remove_surfs : bool Whether or not to remove redundant surfaces from the geometry when exporting. diff --git a/openmc/settings.py b/openmc/settings.py index 294aea7a3b..8f6d3ec078 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1074,31 +1074,33 @@ class Settings: subelement.text = str(value) def _create_entropy_mesh_subelement(self, root, mesh_memo=None): - if self.entropy_mesh is not None: - # use default heuristic for entropy mesh if not set by user - if self.entropy_mesh.dimension is None: - if self.particles is None: - raise RuntimeError("Number of particles must be set in order to " \ - "use entropy mesh dimension heuristic") - else: - n = ceil((self.particles / 20.0)**(1.0 / 3.0)) - d = len(self.entropy_mesh.lower_left) - self.entropy_mesh.dimension = (n,)*d + if self.entropy_mesh is None: + return - # add mesh ID to this element - subelement = ET.SubElement(root, "entropy_mesh") - subelement.text = str(self.entropy_mesh.id) + # use default heuristic for entropy mesh if not set by user + if self.entropy_mesh.dimension is None: + if self.particles is None: + raise RuntimeError("Number of particles must be set in order to " \ + "use entropy mesh dimension heuristic") + else: + n = ceil((self.particles / 20.0)**(1.0 / 3.0)) + d = len(self.entropy_mesh.lower_left) + self.entropy_mesh.dimension = (n,)*d - # If this mesh has already been written outside the - # settings element, skip writing it again - if mesh_memo and self.entropy_mesh.id in mesh_memo: - return + # add mesh ID to this element + subelement = ET.SubElement(root, "entropy_mesh") + subelement.text = str(self.entropy_mesh.id) - # See if a element already exists -- if not, add it - path = f"./mesh[@id='{self.entropy_mesh.id}']" - if root.find(path) is None: - root.append(self.entropy_mesh.to_xml_element()) - if mesh_memo is not None: mesh_memo.add(self.entropy_mesh.id) + # If this mesh has already been written outside the + # settings element, skip writing it again + if mesh_memo and self.entropy_mesh.id in mesh_memo: + return + + # See if a element already exists -- if not, add it + path = f"./mesh[@id='{self.entropy_mesh.id}']" + if root.find(path) is None: + root.append(self.entropy_mesh.to_xml_element()) + if mesh_memo is not None: mesh_memo.add(self.entropy_mesh.id) def _create_trigger_subelement(self, root): if self._trigger_active is not None: @@ -1149,15 +1151,21 @@ class Settings: element = ET.SubElement(root, "track") element.text = ' '.join(map(str, itertools.chain(*self._track))) - def _create_ufs_mesh_subelement(self, root): - if self.ufs_mesh is not None: - # See if a element already exists -- if not, add it - path = f"./mesh[@id='{self.ufs_mesh.id}']" - if root.find(path) is None: - root.append(self.ufs_mesh.to_xml_element()) + def _create_ufs_mesh_subelement(self, root, mesh_memo=None): + if self.ufs_mesh is None: + return - subelement = ET.SubElement(root, "ufs_mesh") - subelement.text = str(self.ufs_mesh.id) + subelement = ET.SubElement(root, "ufs_mesh") + subelement.text = str(self.ufs_mesh.id) + + if mesh_memo and self.ufs_mesh.id in mesh_memo: + return + + # See if a element already exists -- if not, add it + path = f"./mesh[@id='{self.ufs_mesh.id}']" + if root.find(path) is None: + root.append(self.ufs_mesh.to_xml_element()) + if mesh_memo is not None: mesh_memo.add(self.ufs_mesh.id) def _create_resonance_scattering_subelement(self, root): res = self.resonance_scattering diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py index fbff02357f..c67a72ed37 100644 --- a/tests/regression_tests/model_xml/test.py +++ b/tests/regression_tests/model_xml/test.py @@ -27,7 +27,7 @@ class ModelXMLTestHarness(PyAPITestHarness): self.results_true = 'results_true.dat' if results_true is None else results_true def _build_inputs(self): - self._model.export_to_xml(separate_xmls=False) + self._model.export_to_model_xml() def _get_inputs(self): return open('model.xml').read() @@ -77,21 +77,24 @@ def test_input_arg(run_in_tmpdir): pincell.settings.particles = 100 # export to separate XML files and run - pincell.export_to_xml(separate_xmls=True) + pincell.export_to_xml() openmc.run() # make sure the executable isn't falling back on the separate XMLs for f in glob.glob('*.xml'): os.remove(f) # now export to a single XML file with a custom name - pincell.export_to_xml(path='pincell.xml', separate_xmls=False) + pincell.export_to_model_xml('pincell.xml') assert Path('pincell.xml').exists() # run by specifying that single file openmc.run(path_input='pincell.xml') + # check that this works for plotting too + openmc.plot_geometry(path_input='pincell.xml') + # now ensure we get an error for an incorrect filename, # even in the presence of other, valid XML files - pincell.export_to_xml(separate_xmls=True) + pincell.export_to_model_xml() with pytest.raises(RuntimeError, match='ex-em-ell.xml'): openmc.run(path_input='ex-em-ell.xml') \ No newline at end of file diff --git a/tests/unit_tests/test_model.py b/tests/unit_tests/test_model.py index 11a88d76ce..6c483aeb94 100644 --- a/tests/unit_tests/test_model.py +++ b/tests/unit_tests/test_model.py @@ -542,18 +542,18 @@ def test_model_xml(run_in_tmpdir): pwr_model.geometry.export_to_xml('geometry_ref.xml') # now write and read a model.xml file - pwr_model.export_to_xml(separate_xmls=False) + pwr_model.export_to_model_xml() new_model = openmc.Model.from_model_xml() # make sure we can also export this again to separate # XML files - new_model.export_to_xml(separate_xmls=True) + new_model.export_to_xml() -def test_model_exec(run_in_tmpdir): +def test_single_xml_exec(run_in_tmpdir): pincell_model = openmc.examples.pwr_pin_cell() - pincell_model.export_to_xml(path='pwr_pincell.xml', separate_xmls=False) + pincell_model.export_to_model_xml('pwr_pincell.xml') openmc.run(path_input='pwr_pincell.xml') @@ -562,7 +562,7 @@ def test_model_exec(run_in_tmpdir): # test that a file in a different directory can be used os.mkdir('inputs') - pincell_model.export_to_xml(path='./inputs/pincell.xml', separate_xmls=False) + pincell_model.export_to_model_xml('./inputs/pincell.xml') openmc.run(path_input='./inputs/pincell.xml') with pytest.raises(RuntimeError, match='input_dir'): From 43687e5194f854d6d2a9fdf6287ec0c9b45bf3a1 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Mon, 12 Dec 2022 21:40:48 -0600 Subject: [PATCH 215/265] Improve comment on recursion arguments --- openmc/_xml.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/openmc/_xml.py b/openmc/_xml.py index aeaeb45b52..2a33d4b8d7 100644 --- a/openmc/_xml.py +++ b/openmc/_xml.py @@ -26,8 +26,10 @@ def clean_indentation(element, level=0, spaces_per_level=2, trailing_indent=True if trailing_indent and (not element.tail or not element.tail.strip()): element.tail = i for sub_element in element: - # `trailing_indent` intentionally not passed to the recursive call. - # it only applies to the element for the initial of this function. + # `trailing_indent` is intentionally not forwarded to the recursive + # call. Any child element of the topmost clement should add + # indentation at the end to ensure its parent's indentation is + # correct. clean_indentation(sub_element, level+1, spaces_per_level) if not sub_element.tail or not sub_element.tail.strip(): sub_element.tail = i From 2eca57a299ce91b9ddb68b8d6b40313ad6ddd708 Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Tue, 13 Dec 2022 23:16:57 -0600 Subject: [PATCH 216/265] Adding mesh memo to Settings.from_xml_element --- openmc/model/model.py | 4 ++-- openmc/settings.py | 25 ++++++++++++++++++------- openmc/tallies.py | 4 ++++ 3 files changed, 24 insertions(+), 9 deletions(-) diff --git a/openmc/model/model.py b/openmc/model/model.py index a8dc1ce484..7c6d9b828c 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -254,12 +254,12 @@ class Model: model = cls() - model.settings = openmc.Settings.from_xml_element(root.find('settings')) + meshes = {} + model.settings = openmc.Settings.from_xml_element(root.find('settings'), meshes) model.materials = openmc.Materials.from_xml_element(root.find('materials')) model.geometry = openmc.Geometry.from_xml_element(root.find('geometry'), model.materials) # gather meshes from other classes before reading the tally node - meshes = {} if model.settings.entropy_mesh is not None: meshes[model.settings.entropy_mesh.id] = model.settings.entropy_mesh diff --git a/openmc/settings.py b/openmc/settings.py index 8f6d3ec078..65ca719572 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1417,13 +1417,15 @@ class Settings: if value is not None: self.cutoff[key] = float(value) - def _entropy_mesh_from_xml_element(self, root): + def _entropy_mesh_from_xml_element(self, root, meshes=None): text = get_text(root, 'entropy_mesh') if text is not None: path = f"./mesh[@id='{int(text)}']" elem = root.find(path) if elem is not None: self.entropy_mesh = RegularMesh.from_xml_element(elem) + if meshes is not None and self.entropy_mesh is not None: + meshes[self.entropy_mesh.id] = self.entropy_mesh def _trigger_from_xml_element(self, root): elem = root.find('trigger') @@ -1483,13 +1485,15 @@ class Settings: values = [int(x) for x in text.split()] self.track = list(zip(values[::3], values[1::3], values[2::3])) - def _ufs_mesh_from_xml_element(self, root): + def _ufs_mesh_from_xml_element(self, root, meshes=None): text = get_text(root, 'ufs_mesh') if text is not None: path = f"./mesh[@id='{int(text)}']" elem = root.find(path) if elem is not None: self.ufs_mesh = RegularMesh.from_xml_element(elem) + if meshes is not None and self.ufs_mesh is not None: + meshes[self.ufs_mesh.id] = self.ufs_mesh def _resonance_scattering_from_xml_element(self, root): elem = root.find('resonance_scattering') @@ -1541,7 +1545,7 @@ class Settings: if text is not None: self.write_initial_source = text in ('true', '1') - def _weight_windows_from_xml_element(self, root): + def _weight_windows_from_xml_element(self, root, meshes=None): for elem in root.findall('weight_windows'): ww = WeightWindows.from_xml_element(elem, root) self.weight_windows.append(ww) @@ -1550,6 +1554,9 @@ class Settings: if text is not None: self.weight_windows_on = text in ('true', '1') + if meshes is not None and self.weight_windows: + meshes.update({ww.mesh.id: ww.mesh for ww in self.weight_windows}) + def _max_splits_from_xml_element(self, root): text = get_text(root, 'max_splits') if text is not None: @@ -1643,13 +1650,17 @@ class Settings: tree.write(str(p), xml_declaration=True, encoding='utf-8') @classmethod - def from_xml_element(cls, elem): + def from_xml_element(cls, elem, meshes=None): """Generate settings from XML element Parameters ---------- elem : xml.etree.ElementTree.Element XML element + meshes : dict or None + A dictionary with mesh IDs as keys and mesh instances as values that + have already been read from XML. Pre-existing meshes are used + and new meshes are added to when creating tally objects. Returns ------- @@ -1683,7 +1694,7 @@ class Settings: settings._seed_from_xml_element(elem) settings._survival_biasing_from_xml_element(elem) settings._cutoff_from_xml_element(elem) - settings._entropy_mesh_from_xml_element(elem) + settings._entropy_mesh_from_xml_element(elem, meshes) settings._trigger_from_xml_element(elem) settings._no_reduce_from_xml_element(elem) settings._verbosity_from_xml_element(elem) @@ -1691,7 +1702,7 @@ class Settings: settings._temperature_from_xml_element(elem) settings._trace_from_xml_element(elem) settings._track_from_xml_element(elem) - settings._ufs_mesh_from_xml_element(elem) + settings._ufs_mesh_from_xml_element(elem, meshes) settings._resonance_scattering_from_xml_element(elem) settings._create_fission_neutrons_from_xml_element(elem) settings._delayed_photon_scaling_from_xml_element(elem) @@ -1700,7 +1711,7 @@ class Settings: settings._material_cell_offsets_from_xml_element(elem) settings._log_grid_bins_from_xml_element(elem) settings._write_initial_source_from_xml_element(elem) - settings._weight_windows_from_xml_element(elem) + settings._weight_windows_from_xml_element(elem, meshes) settings._max_splits_from_xml_element(elem) settings._max_tracks_from_xml_element(elem) diff --git a/openmc/tallies.py b/openmc/tallies.py index e17e7c99db..b22cc4cf0a 100644 --- a/openmc/tallies.py +++ b/openmc/tallies.py @@ -3199,6 +3199,10 @@ class Tallies(cv.CheckedList): ---------- elem : xml.etree.ElementTree.Element XML element + meshes : dict or None + A dictionary with mesh IDs as keys and mesh instances as values that + have already been read from XML. Pre-existing meshes are used + and new meshes are added to when creating tally objects. Returns ------- From 2b7fa8fdd2dbe313e14cf2d789f9cad1260d964e Mon Sep 17 00:00:00 2001 From: erkn Date: Tue, 20 Dec 2022 23:58:22 +0100 Subject: [PATCH 217/265] Revert "enable mcpl from the python layer" This reverts commit e3f1bdaca1f5144563c4ceac45f10e4b0b5b7963. There is now a check in the cpp-layer if the file is named .mcpl --- openmc/source.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/openmc/source.py b/openmc/source.py index fdb2d5bc25..48e14f6f71 100644 --- a/openmc/source.py +++ b/openmc/source.py @@ -223,10 +223,7 @@ class Source: if self.particle != 'neutron': element.set("particle", self.particle) if self.file is not None: - if (self.file.endswith('.mcpl')): - element.set("mcpl", self.file) - else: - element.set("file", self.file) + element.set("file", self.file) if self.library is not None: element.set("library", self.library) if self.parameters is not None: From 1ab9aa4b6fddf4e6b7216b7fe993d8c672c22468 Mon Sep 17 00:00:00 2001 From: erkn Date: Wed, 21 Dec 2022 00:14:43 +0100 Subject: [PATCH 218/265] script for installing mcpl as a ci-thing --- tools/ci/gha-install-mcpl.sh | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100755 tools/ci/gha-install-mcpl.sh diff --git a/tools/ci/gha-install-mcpl.sh b/tools/ci/gha-install-mcpl.sh new file mode 100755 index 0000000000..9b8609398a --- /dev/null +++ b/tools/ci/gha-install-mcpl.sh @@ -0,0 +1,7 @@ +#!/bin/bash +set -ex +cd $HOME +git clone https://github.com/mctools/mcpl +cd mcpl +mkdir build && cd build +cmake .. && make 2>/dev/null && sudo make install From 9865a129c49ad2b07628d152a2d8865ad6936fd6 Mon Sep 17 00:00:00 2001 From: erkn Date: Wed, 21 Dec 2022 00:22:38 +0100 Subject: [PATCH 219/265] optionally install mcpl depending on environment var --- tools/ci/gha-install.py | 8 ++++++-- tools/ci/gha-install.sh | 5 +++++ 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py index 4c69ba70b0..ea317b5f0a 100644 --- a/tools/ci/gha-install.py +++ b/tools/ci/gha-install.py @@ -19,7 +19,7 @@ def which(program): return None -def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False): +def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, mcpl=False): # Create build directory and change to it shutil.rmtree('build', ignore_errors=True) os.mkdir('build') @@ -54,6 +54,9 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False): libmesh_path = os.environ.get('HOME') + '/LIBMESH' cmake_cmd.append('-DCMAKE_PREFIX_PATH=' + libmesh_path) + if mcpl: + cmake_cmd.append('-DOPENMC_USE_MCPL=ON') + # Build in coverage mode for coverage testing cmake_cmd.append('-DOPENMC_ENABLE_COVERAGE=on') @@ -71,9 +74,10 @@ def main(): phdf5 = (os.environ.get('PHDF5') == 'y') dagmc = (os.environ.get('DAGMC') == 'y') libmesh = (os.environ.get('LIBMESH') == 'y') + mcpl = (os.environ.get('MCPL') == 'y') # Build and install - install(omp, mpi, phdf5, dagmc, libmesh) + install(omp, mpi, phdf5, dagmc, libmesh, mcpl) if __name__ == '__main__': main() diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh index aa40eb90b1..68e825d486 100755 --- a/tools/ci/gha-install.sh +++ b/tools/ci/gha-install.sh @@ -27,6 +27,11 @@ if [[ $LIBMESH = 'y' ]]; then ./tools/ci/gha-install-libmesh.sh fi +# Install mcpl if needed +if [[ $MCPL = 'y' ]]; then + ./tools/ci/gha-install-mcpl.sh +fi + # For MPI configurations, make sure mpi4py and h5py are built against the # correct version of MPI if [[ $MPI == 'y' ]]; then From a50776219fe659be4572a918d4e19bfb9596a5f3 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Wed, 21 Dec 2022 11:33:36 +0100 Subject: [PATCH 220/265] resolve conflict w. develop --- src/source.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/source.cpp b/src/source.cpp index af108f3fa9..19d1c2a9db 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -234,7 +234,7 @@ SourceSite IndependentSource::sample(uint64_t* seed) const auto id = (domain_type_ == DomainType::CELL) ? model::cells[coord.cell]->id_ : model::universes[coord.universe]->id_; - if (found = contains(domain_ids_, id)) + if ((found = contains(domain_ids_, id))) break; } } From ff48f53595144aa0ecbc1f44f2d28428a7306633 Mon Sep 17 00:00:00 2001 From: erkn Date: Thu, 22 Dec 2022 12:04:29 +0100 Subject: [PATCH 221/265] skip mcpl-test if it is not enabled patterned after the dagmc-tests This required the MCPL_ENABLED symbol to be unmangled --- include/openmc/source.h | 1 + tests/regression_tests/source_mcpl_file/test.py | 7 +++++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/include/openmc/source.h b/include/openmc/source.h index bb7e2d55f7..051167b3f6 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -32,6 +32,7 @@ constexpr double EXTSRC_REJECT_FRACTION {0.05}; //============================================================================== // Global variables //============================================================================== +extern "C" const bool MCPL_ENABLED; class Source; diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index a005fc2d83..0b8e79104e 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -1,10 +1,13 @@ #!/usr/bin/env python - +import openmc.lib +import pytest import glob import os from tests.testing_harness import * - +pytestmark = pytest.mark.skipif( + not openmc.lib._mcpl_enabled(), + reason="MCPL is not enabled.") settings1=""" From fe19cfcdd25966c3ab5cce056b9337c50e3e7743 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Thu, 22 Dec 2022 17:16:16 +0100 Subject: [PATCH 222/265] set seed to get a deterministic test and set result --- tests/regression_tests/source_mcpl_file/results_true.dat | 2 +- tests/regression_tests/source_mcpl_file/settings.xml | 1 + tests/regression_tests/source_mcpl_file/test.py | 1 + 3 files changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/regression_tests/source_mcpl_file/results_true.dat b/tests/regression_tests/source_mcpl_file/results_true.dat index 19460623f5..e8f4a20a08 100644 --- a/tests/regression_tests/source_mcpl_file/results_true.dat +++ b/tests/regression_tests/source_mcpl_file/results_true.dat @@ -1,2 +1,2 @@ k-combined: -3.039964E-01 3.654869E-04 +3.004254E-01 8.027600E-04 diff --git a/tests/regression_tests/source_mcpl_file/settings.xml b/tests/regression_tests/source_mcpl_file/settings.xml index 47b010bffe..2e511461f3 100644 --- a/tests/regression_tests/source_mcpl_file/settings.xml +++ b/tests/regression_tests/source_mcpl_file/settings.xml @@ -1,5 +1,6 @@ + 1234 diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index 0b8e79104e..e87479c5a4 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -11,6 +11,7 @@ pytestmark = pytest.mark.skipif( settings1=""" + 1234 From e9c6b03b9e2f5fb50875c64a8a33db8eda1059dd Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Thu, 22 Dec 2022 17:17:50 +0100 Subject: [PATCH 223/265] remove dead code --- tests/regression_tests/source_mcpl_file/test.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index e87479c5a4..6492783197 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -93,9 +93,6 @@ class SourceFileTestHarness(TestHarness): def _cleanup(self): TestHarness._cleanup(self) output = glob.glob(os.path.join(os.getcwd(), 'source.*')) - #for f in output: - # if os.path.exists(f): - # os.remove(f) with open('settings.xml','w') as fh: fh.write(settings1) From 4d7797c25b3932aaa166b4a6b12c4ffebd48d925 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Thu, 22 Dec 2022 17:18:37 +0100 Subject: [PATCH 224/265] mistake assigning the wrong variable --- src/settings.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/settings.cpp b/src/settings.cpp index 5e8eb0e58f..b0829c1bad 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -656,7 +656,7 @@ void read_settings_xml() source_write = get_node_value_bool(node_sp, "write"); } if (check_for_node(node_sp, "mcpl")) { - source_write = get_node_value_bool(node_sp, "mcpl"); + source_mcpl_write = get_node_value_bool(node_sp, "mcpl"); } if (check_for_node(node_sp, "overwrite_latest")) { source_latest = get_node_value_bool(node_sp, "overwrite_latest"); From 51d3a0c2ce6079f18ea479c7efc158148236f5a7 Mon Sep 17 00:00:00 2001 From: Erik B Knudsen Date: Thu, 22 Dec 2022 17:19:56 +0100 Subject: [PATCH 225/265] check for mcpl-input is in the cpp-layer now --- tests/regression_tests/source_mcpl_file/test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index 6492783197..60e0ad50f8 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -35,7 +35,7 @@ settings2 = """ 1000 - source.10.{0} + source.10.{0} """ From 28521c8384c6e68b6ee0f52a7a44425b4a6306bd Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 22 Dec 2022 10:53:40 -0600 Subject: [PATCH 226/265] Use vector::push_back for building MCPL FileSource --- src/source.cpp | 42 +++++++++++++++++++++++------------------- 1 file changed, 23 insertions(+), 19 deletions(-) diff --git a/src/source.cpp b/src/source.cpp index 19d1c2a9db..4ab087e125 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -335,9 +335,8 @@ FileSource::FileSource(mcpl_file_t mcpl_file) { size_t n_sites = mcpl_hdr_nparticles(mcpl_file); - sites_.resize(n_sites); for (int i = 0; i < n_sites; i++) { - SourceSite site_; + SourceSite site; const mcpl_particle_t* mcpl_particle; // extract particle from mcpl-file @@ -351,36 +350,41 @@ FileSource::FileSource(mcpl_file_t mcpl_file) switch (pdg) { case 2112: - site_.particle = ParticleType::neutron; + site.particle = ParticleType::neutron; break; case 22: - site_.particle = ParticleType::photon; + site.particle = ParticleType::photon; break; case 11: - site_.particle = ParticleType::electron; + site.particle = ParticleType::electron; break; case -11: - site_.particle = ParticleType::positron; + site.particle = ParticleType::positron; break; } - // particle is good, convert to openmc-formalism - site_.r.x = mcpl_particle->position[0]; - site_.r.y = mcpl_particle->position[1]; - site_.r.z = mcpl_particle->position[2]; - - site_.u.x = mcpl_particle->direction[0]; - site_.u.y = mcpl_particle->direction[1]; - site_.u.z = mcpl_particle->direction[2]; + // Copy position and direction + site.r.x = mcpl_particle->position[0]; + site.r.y = mcpl_particle->position[1]; + site.r.z = mcpl_particle->position[2]; + site.u.x = mcpl_particle->direction[0]; + site.u.y = mcpl_particle->direction[1]; + site.u.z = mcpl_particle->direction[2]; // mcpl stores kinetic energy in MeV - site_.E = mcpl_particle->ekin * 1e6; + site.E = mcpl_particle->ekin * 1e6; // mcpl stores time in ms - site_.time = mcpl_particle->time * 1e-3; - site_.wgt = mcpl_particle->weight; - site_.delayed_group = 0; - sites_[i] = site_; + site.time = mcpl_particle->time * 1e-3; + site.wgt = mcpl_particle->weight; + sites_.push_back(site); } + + // Check that some sites were read + if (sites_.empty()) { + fatal_error("MCPL file contained no neutron, photon, electron, or positron " + "source particles."); + } + mcpl_close_file(mcpl_file); } #endif // OPENMC_MCPL From 987293cfffb2934359b0c1f0dcd685eb8140fd63 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 22 Dec 2022 10:57:11 -0600 Subject: [PATCH 227/265] Small fixes and formatting changes --- docs/source/io_formats/settings.rst | 8 ++-- include/openmc/state_point.h | 3 +- openmc/settings.py | 2 +- src/settings.cpp | 17 ++++--- src/simulation.cpp | 10 ++--- src/state_point.cpp | 70 ++++++++++++++--------------- 6 files changed, 57 insertions(+), 53 deletions(-) diff --git a/docs/source/io_formats/settings.rst b/docs/source/io_formats/settings.rst index a162e8de6d..7174c5317a 100644 --- a/docs/source/io_formats/settings.rst +++ b/docs/source/io_formats/settings.rst @@ -768,10 +768,10 @@ certain surfaces and write out the source bank in a separate file called *Default*: None :mcpl: - An optional boolean which indicates if the banked particles should - be written to a file in the MCPL-format (documented in mcpl_). - instead of the native hdf5-based format.If activated the output - output file name is altered to ``surface_source.mcpl`` + An optional boolean which indicates if the banked particles should be + written to a file in the MCPL-format (documented in mcpl_). instead of the + native HDF5-based format. If activated the output file name is changed to + ``surface_source.mcpl``. *Default*: false diff --git a/include/openmc/state_point.h b/include/openmc/state_point.h index 698ed2c93a..7301275542 100644 --- a/include/openmc/state_point.h +++ b/include/openmc/state_point.h @@ -26,7 +26,8 @@ void restart_set_keff(); void write_unstructured_mesh_results(); #ifdef OPENMC_MCPL -void write_mcpl_source_point(const char* filename, bool surf_source_bank = false); +void write_mcpl_source_point( + const char* filename, bool surf_source_bank = false); void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank); #endif diff --git a/openmc/settings.py b/openmc/settings.py index b2c184f780..fd622870c5 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1349,7 +1349,7 @@ class Settings: elif key in ('max_particles'): value = int(value) elif key == 'mcpl': - value = True + value = value in ('true', '1') self.surf_source_write[key] = value def _confidence_intervals_from_xml_element(self, root): diff --git a/src/settings.cpp b/src/settings.cpp index b0829c1bad..de298c58d1 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -432,12 +432,15 @@ void read_settings_xml() if (check_for_node(node, "file")) { auto path = get_node_value(node, "file", false, true); #ifdef OPENMC_MCPL - if ( (path.size() >= 5 && path.compare(path.size()-5,5,".mcpl")==0 ) || - (path.size() >= 8 && path.compare(path.size()-8,8,".mcpl.gz")==0 ) ) { - model::external_sources.push_back(make_unique(mcpl_open_file(path.c_str()))); - } else -#endif + if (ends_with(path, ".mcpl") || ends_with(path, ".mcpl.gz")) { + model::external_sources.push_back( + make_unique(mcpl_open_file(path.c_str()))); + } else { model::external_sources.push_back(make_unique(path)); + } +#else + model::external_sources.push_back(make_unique(path)); +#endif } else if (check_for_node(node, "library")) { // Get shared library path and parameters auto path = get_node_value(node, "library", false, true); @@ -689,8 +692,8 @@ void read_settings_xml() std::stoll(get_node_value(node_ssw, "max_particles")); } #ifdef OPENMC_MCPL - if(check_for_node(node_ssw, "mcpl")){ - surf_mcpl_write=true; + if (check_for_node(node_ssw, "mcpl")) { + surf_mcpl_write = true; } #endif } diff --git a/src/simulation.cpp b/src/simulation.cpp index d7cc2237d5..2c1d1c988b 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -390,7 +390,7 @@ void finalize_batch() if (settings::run_mode == RunMode::EIGENVALUE) { // Write out a separate source point if it's been specified for this batch #ifdef OPENMC_MCPL - if(! settings::source_mcpl_write) { + if (!settings::source_mcpl_write) { #endif if (contains(settings::sourcepoint_batch, simulation::current_batch) && settings::source_write && settings::source_separate) { @@ -405,8 +405,8 @@ void finalize_batch() #ifdef OPENMC_MCPL } else { if (contains(settings::sourcepoint_batch, simulation::current_batch) && - settings::source_mcpl_write && settings::source_separate) { - write_mcpl_source_point(nullptr); + settings::source_mcpl_write && settings::source_separate) { + write_mcpl_source_point(nullptr); } // Write a continously-overwritten source point if requested. @@ -425,12 +425,12 @@ void finalize_batch() write_source_point(filename.c_str(), true); } #ifdef OPENMC_MCPL - if(settings::surf_mcpl_write && simulation::current_batch == settings::n_batches){ + if (settings::surf_mcpl_write && + simulation::current_batch == settings::n_batches) { auto filename = settings::path_output + "surface_source.mcpl"; write_mcpl_source_point(filename.c_str(), true); } #endif - } void initialize_generation() diff --git a/src/state_point.cpp b/src/state_point.cpp index 3ee5f13b39..9dd0f13747 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -604,7 +604,7 @@ void write_source_point(const char* filename, bool surf_source_bank) } #ifdef OPENMC_MCPL -void write_mcpl_source_point(const char *filename, bool surf_source_bank) +void write_mcpl_source_point(const char* filename, bool surf_source_bank) { std::string filename_; if (filename) { @@ -622,21 +622,21 @@ void write_mcpl_source_point(const char *filename, bool surf_source_bank) std::string line; if (mpi::master) { file_id = mcpl_create_outfile(filename_.c_str()); - if (VERSION_DEV){ - line=fmt::format("OpenMC {0}.{1}.{2}-development",VERSION_MAJOR,VERSION_MINOR,VERSION_RELEASE); + if (VERSION_DEV) { + line = fmt::format("OpenMC {0}.{1}.{2}-development", VERSION_MAJOR, + VERSION_MINOR, VERSION_RELEASE); } else { - line=fmt::format("OpenMC {0}.{1}.{2}",VERSION_MAJOR,VERSION_MINOR,VERSION_RELEASE); + line = fmt::format( + "OpenMC {0}.{1}.{2}", VERSION_MAJOR, VERSION_MINOR, VERSION_RELEASE); } - mcpl_hdr_set_srcname(file_id,line.c_str()); + mcpl_hdr_set_srcname(file_id, line.c_str()); } write_mcpl_source_bank(file_id, surf_source_bank); if (mpi::master) { - //change this - this is h5 specific mcpl_close_outfile(file_id); } - } #endif @@ -768,7 +768,7 @@ void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) vector surf_source_index_vector; vector surf_source_bank_vector; - if(surf_source_bank) { + if (surf_source_bank) { surf_source_index_vector = calculate_surf_source_size(); dims_size = surf_source_index_vector[mpi::n_procs]; count_size = simulation::surf_source_bank.size(); @@ -790,55 +790,56 @@ void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) vector temp_source {source_bank->begin(), source_bank->end()}; #endif - //loop over the other nodes and receive data - then write those. + // loop over the other nodes and receive data - then write those. for (int i = 0; i < mpi::n_procs; ++i) { // number of particles for node node i size_t count[] { static_cast((*bank_index)[i + 1] - (*bank_index)[i])}; #ifdef OPENMC_MPI - if (i>0) + if (i > 0) MPI_Recv(source_bank->data(), count[0], mpi::source_site, i, i, mpi::intracomm, MPI_STATUS_IGNORE); #endif // now write the source_bank data again. - for (vector::iterator _site=source_bank->begin(); _site!=source_bank->end();_site++){ + for (vector::iterator _site = source_bank->begin(); + _site != source_bank->end(); _site++) { // particle is now at the iterator // write it to the mcpl-file mcpl_particle_t p; - p.position[0]=_site->r.x; - p.position[1]=_site->r.y; - p.position[2]=_site->r.z; + p.position[0] = _site->r.x; + p.position[1] = _site->r.y; + p.position[2] = _site->r.z; // mcpl requires that the direction vector is unit length // which is also the case in openmc - p.direction[0]=_site->u.x; - p.direction[1]=_site->u.y; - p.direction[2]=_site->u.z; + p.direction[0] = _site->u.x; + p.direction[1] = _site->u.y; + p.direction[2] = _site->u.z; // mcpl stores kinetic energy in MeV - p.ekin=_site->E*1e-6; + p.ekin = _site->E * 1e-6; - p.time=_site->time*1e3; + p.time = _site->time * 1e3; - p.weight=_site->wgt; + p.weight = _site->wgt; - switch(_site->particle){ - case ParticleType::neutron: - p.pdgcode=2112; - break; - case ParticleType::photon: - p.pdgcode=22; - break; - case ParticleType::electron: - p.pdgcode=11; - break; - case ParticleType::positron: - p.pdgcode=-11; - break; + switch (_site->particle) { + case ParticleType::neutron: + p.pdgcode = 2112; + break; + case ParticleType::photon: + p.pdgcode = 22; + break; + case ParticleType::electron: + p.pdgcode = 11; + break; + case ParticleType::positron: + p.pdgcode = -11; + break; } - mcpl_add_particle(file_id,&p); + mcpl_add_particle(file_id, &p); } } #ifdef OPENMC_MPI @@ -851,7 +852,6 @@ void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) mpi::intracomm); #endif } - } #endif From a3065b479c0a47caae6229fa8657da59668be1e9 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 22 Dec 2022 11:33:29 -0600 Subject: [PATCH 228/265] Move FileSource MCPL reading to mcpl_interface.h/cpp --- CMakeLists.txt | 1 + include/openmc/mcpl_interface.h | 25 +++++++++ include/openmc/source.h | 10 +--- src/mcpl_interface.cpp | 93 +++++++++++++++++++++++++++++++++ src/settings.cpp | 11 ++-- src/source.cpp | 69 ------------------------ 6 files changed, 126 insertions(+), 83 deletions(-) create mode 100644 include/openmc/mcpl_interface.h create mode 100644 src/mcpl_interface.cpp diff --git a/CMakeLists.txt b/CMakeLists.txt index 24018eb0f1..af3a5b4af8 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -331,6 +331,7 @@ list(APPEND libopenmc_SOURCES src/lattice.cpp src/material.cpp src/math_functions.cpp + src/mcpl_interface.cpp src/mesh.cpp src/message_passing.cpp src/mgxs.cpp diff --git a/include/openmc/mcpl_interface.h b/include/openmc/mcpl_interface.h new file mode 100644 index 0000000000..89dab16bcb --- /dev/null +++ b/include/openmc/mcpl_interface.h @@ -0,0 +1,25 @@ +#ifndef OPENMC_MCPL_INTERFACE_H +#define OPENMC_MCPL_INTERFACE_H + +#include "openmc/particle_data.h" + +#include +#include + +#ifdef OPENMC_MCPL +#include +#endif + +namespace openmc { + +extern "C" const bool MCPL_ENABLED; + +//! Get a vector of source sites from an MCPL file +// +//! \param[in] path Path to MCPL file +//! \return Vector of source sites +vector mcpl_source_sites(std::string path); + +} // namespace openmc + +#endif // OPENMC_MCPL_INTERFACE_H diff --git a/include/openmc/source.h b/include/openmc/source.h index 051167b3f6..96d659dcb3 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -14,10 +14,6 @@ #include "openmc/particle.h" #include "openmc/vector.h" -#ifdef OPENMC_MCPL -#include -#endif - namespace openmc { //============================================================================== @@ -32,7 +28,6 @@ constexpr double EXTSRC_REJECT_FRACTION {0.05}; //============================================================================== // Global variables //============================================================================== -extern "C" const bool MCPL_ENABLED; class Source; @@ -107,9 +102,8 @@ class FileSource : public Source { public: // Constructors explicit FileSource(std::string path); -#ifdef OPENMC_MCPL - explicit FileSource(mcpl_file_t mcpl_file); -#endif + explicit FileSource(const vector& sites) : sites_ {sites} {} + // Methods SourceSite sample(uint64_t* seed) const override; diff --git a/src/mcpl_interface.cpp b/src/mcpl_interface.cpp new file mode 100644 index 0000000000..d55cc5af7c --- /dev/null +++ b/src/mcpl_interface.cpp @@ -0,0 +1,93 @@ +#include "openmc/mcpl_interface.h" + +#include "openmc/error.h" + +#ifdef OPENMC_MCPL +#include +#endif + +namespace openmc { + +#ifdef OPENMC_MCPL +const bool MCPL_ENABLED = true; +#else +const bool MCPL_ENABLED = false; +#endif + +#ifdef OPENMC_MCPL +SourceSite mcpl_particle_to_site(const mcpl_particle* particle) +{ + SourceSite site; + + switch (particle->pdgcode) { + case 2112: + site.particle = ParticleType::neutron; + break; + case 22: + site.particle = ParticleType::photon; + break; + case 11: + site.particle = ParticleType::electron; + break; + case -11: + site.particle = ParticleType::positron; + break; + } + + // Copy position and direction + site.r.x = mcpl_particle->position[0]; + site.r.y = mcpl_particle->position[1]; + site.r.z = mcpl_particle->position[2]; + site.u.x = mcpl_particle->direction[0]; + site.u.y = mcpl_particle->direction[1]; + site.u.z = mcpl_particle->direction[2]; + + // mcpl stores kinetic energy in MeV + site.E = mcpl_particle->ekin * 1e6; + // mcpl stores time in ms + site.time = mcpl_particle->time * 1e-3; + site.wgt = mcpl_particle->weight; + + return site; +} +#endif + +vector mcpl_source_sites(std::string path) +{ + vector sites; + +#ifdef OPENMC_MCPL + size_t n_sites = mcpl_hdr_nparticles(mcpl_file); + + for (int i = 0; i < n_sites; i++) { + SourceSite site; + + // Extract particle from mcpl-file, checking if it is a neutron, photon, + // electron, or positron. Otherwise skip. + const mcpl_particle_t* particle; + int pdg = 0; + while (pdg != 2112 && pdg != 22 && pdg != 11 && pdg != -11) { + particle = mcpl_read(mcpl_file); + pdg = mcpl_particle->pdgcode; + } + + // Convert to source site and add to vector + sites.push_back(mcpl_particle_to_site(particle)); + } + + // Check that some sites were read + if (sites_.empty()) { + fatal_error("MCPL file contained no neutron, photon, electron, or positron " + "source particles."); + } + + mcpl_close_file(mcpl_file); +#else + fatal_error( + "Your build of OpenMC does not support reading MCPL source files."); +#endif + + return sites; +} + +} // namespace openmc diff --git a/src/settings.cpp b/src/settings.cpp index de298c58d1..bc31e2c4d0 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -18,6 +18,7 @@ #include "openmc/eigenvalue.h" #include "openmc/error.h" #include "openmc/file_utils.h" +#include "openmc/mcpl_interface.h" #include "openmc/mesh.h" #include "openmc/message_passing.h" #include "openmc/output.h" @@ -431,16 +432,14 @@ void read_settings_xml() for (pugi::xml_node node : root.children("source")) { if (check_for_node(node, "file")) { auto path = get_node_value(node, "file", false, true); -#ifdef OPENMC_MCPL if (ends_with(path, ".mcpl") || ends_with(path, ".mcpl.gz")) { - model::external_sources.push_back( - make_unique(mcpl_open_file(path.c_str()))); +#ifdef OPENMC_MCPL + auto sites = mcpl_source_sites(path); + model::external_sources.push_back(make_unique(sites)); +#endif } else { model::external_sources.push_back(make_unique(path)); } -#else - model::external_sources.push_back(make_unique(path)); -#endif } else if (check_for_node(node, "library")) { // Get shared library path and parameters auto path = get_node_value(node, "library", false, true); diff --git a/src/source.cpp b/src/source.cpp index 4ab087e125..d201e3c033 100644 --- a/src/source.cpp +++ b/src/source.cpp @@ -33,22 +33,12 @@ #include "openmc/state_point.h" #include "openmc/xml_interface.h" -#ifdef OPENMC_MCPL -#include -#endif - namespace openmc { //============================================================================== // Global variables //============================================================================== -#ifdef OPENMC_MCPL -const bool MCPL_ENABLED = true; -#else -const bool MCPL_ENABLED = false; -#endif - namespace model { vector> external_sources; @@ -330,65 +320,6 @@ FileSource::FileSource(std::string path) file_close(file_id); } -#ifdef OPENMC_MCPL -FileSource::FileSource(mcpl_file_t mcpl_file) -{ - size_t n_sites = mcpl_hdr_nparticles(mcpl_file); - - for (int i = 0; i < n_sites; i++) { - SourceSite site; - - const mcpl_particle_t* mcpl_particle; - // extract particle from mcpl-file - mcpl_particle = mcpl_read(mcpl_file); - // check if it is a neutron, photon, electron, or positron. Otherwise skip. - int pdg = mcpl_particle->pdgcode; - while (pdg != 2112 && pdg != 22 && pdg != 11 && pdg != -11) { - mcpl_particle = mcpl_read(mcpl_file); - pdg = mcpl_particle->pdgcode; - } - - switch (pdg) { - case 2112: - site.particle = ParticleType::neutron; - break; - case 22: - site.particle = ParticleType::photon; - break; - case 11: - site.particle = ParticleType::electron; - break; - case -11: - site.particle = ParticleType::positron; - break; - } - - // Copy position and direction - site.r.x = mcpl_particle->position[0]; - site.r.y = mcpl_particle->position[1]; - site.r.z = mcpl_particle->position[2]; - site.u.x = mcpl_particle->direction[0]; - site.u.y = mcpl_particle->direction[1]; - site.u.z = mcpl_particle->direction[2]; - - // mcpl stores kinetic energy in MeV - site.E = mcpl_particle->ekin * 1e6; - // mcpl stores time in ms - site.time = mcpl_particle->time * 1e-3; - site.wgt = mcpl_particle->weight; - sites_.push_back(site); - } - - // Check that some sites were read - if (sites_.empty()) { - fatal_error("MCPL file contained no neutron, photon, electron, or positron " - "source particles."); - } - - mcpl_close_file(mcpl_file); -} -#endif // OPENMC_MCPL - SourceSite FileSource::sample(uint64_t* seed) const { size_t i_site = sites_.size() * prn(seed); From 361b3486efa4c078e87a1c29f76e6ab4a1edc58e Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 22 Dec 2022 12:27:56 -0600 Subject: [PATCH 229/265] Move remainder of MCPL-related code to mcpl_interface.h/cpp --- CMakeLists.txt | 1 + include/openmc/mcpl_interface.h | 19 +++- include/openmc/state_point.h | 10 -- src/mcpl_interface.cpp | 185 +++++++++++++++++++++++++++++--- src/settings.cpp | 18 +++- src/simulation.cpp | 7 +- src/state_point.cpp | 140 ------------------------ 7 files changed, 201 insertions(+), 179 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index af3a5b4af8..466816b300 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -164,6 +164,7 @@ endif() #=============================================================================== if (OPENMC_USE_MCPL) find_package(MCPL REQUIRED) + message(STATUS "Found MCPL: ${MCPL_DIR} (found version \"${MCPL_VERSION}\")") endif() #=============================================================================== diff --git a/include/openmc/mcpl_interface.h b/include/openmc/mcpl_interface.h index 89dab16bcb..c931f17743 100644 --- a/include/openmc/mcpl_interface.h +++ b/include/openmc/mcpl_interface.h @@ -6,20 +6,31 @@ #include #include -#ifdef OPENMC_MCPL -#include -#endif - namespace openmc { +//============================================================================== +// Constants +//============================================================================== + extern "C" const bool MCPL_ENABLED; +//============================================================================== +// Functions +//============================================================================== + //! Get a vector of source sites from an MCPL file // //! \param[in] path Path to MCPL file //! \return Vector of source sites vector mcpl_source_sites(std::string path); +//! Write an MCPL source file +// +//! \param[in] filename Path to MCPL file +//! \param[in] surf_source_bank Whether to use the surface source bank +void write_mcpl_source_point( + const char* filename, bool surf_source_bank = false); + } // namespace openmc #endif // OPENMC_MCPL_INTERFACE_H diff --git a/include/openmc/state_point.h b/include/openmc/state_point.h index 7301275542..5ada2bf88d 100644 --- a/include/openmc/state_point.h +++ b/include/openmc/state_point.h @@ -9,10 +9,6 @@ #include "openmc/particle.h" #include "openmc/vector.h" -#ifdef OPENMC_MCPL -#include -#endif - namespace openmc { void load_state_point(); @@ -25,11 +21,5 @@ void write_tally_results_nr(hid_t file_id); void restart_set_keff(); void write_unstructured_mesh_results(); -#ifdef OPENMC_MCPL -void write_mcpl_source_point( - const char* filename, bool surf_source_bank = false); -void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank); -#endif - } // namespace openmc #endif // OPENMC_STATE_POINT_H diff --git a/src/mcpl_interface.cpp b/src/mcpl_interface.cpp index d55cc5af7c..e9bc648303 100644 --- a/src/mcpl_interface.cpp +++ b/src/mcpl_interface.cpp @@ -1,6 +1,13 @@ #include "openmc/mcpl_interface.h" +#include "openmc/bank.h" #include "openmc/error.h" +#include "openmc/message_passing.h" +#include "openmc/settings.h" +#include "openmc/simulation.h" +#include "openmc/state_point.h" + +#include #ifdef OPENMC_MCPL #include @@ -8,14 +15,22 @@ namespace openmc { +//============================================================================== +// Constants +//============================================================================== + #ifdef OPENMC_MCPL const bool MCPL_ENABLED = true; #else const bool MCPL_ENABLED = false; #endif +//============================================================================== +// Functions +//============================================================================== + #ifdef OPENMC_MCPL -SourceSite mcpl_particle_to_site(const mcpl_particle* particle) +SourceSite mcpl_particle_to_site(const mcpl_particle_t* particle) { SourceSite site; @@ -35,40 +50,42 @@ SourceSite mcpl_particle_to_site(const mcpl_particle* particle) } // Copy position and direction - site.r.x = mcpl_particle->position[0]; - site.r.y = mcpl_particle->position[1]; - site.r.z = mcpl_particle->position[2]; - site.u.x = mcpl_particle->direction[0]; - site.u.y = mcpl_particle->direction[1]; - site.u.z = mcpl_particle->direction[2]; + site.r.x = particle->position[0]; + site.r.y = particle->position[1]; + site.r.z = particle->position[2]; + site.u.x = particle->direction[0]; + site.u.y = particle->direction[1]; + site.u.z = particle->direction[2]; // mcpl stores kinetic energy in MeV - site.E = mcpl_particle->ekin * 1e6; + site.E = particle->ekin * 1e6; // mcpl stores time in ms - site.time = mcpl_particle->time * 1e-3; - site.wgt = mcpl_particle->weight; + site.time = particle->time * 1e-3; + site.wgt = particle->weight; return site; } #endif +//============================================================================== + vector mcpl_source_sites(std::string path) { vector sites; #ifdef OPENMC_MCPL + // Open MCPL file and determine number of particles + auto mcpl_file = mcpl_open_file(path.c_str()); size_t n_sites = mcpl_hdr_nparticles(mcpl_file); for (int i = 0; i < n_sites; i++) { - SourceSite site; - // Extract particle from mcpl-file, checking if it is a neutron, photon, // electron, or positron. Otherwise skip. const mcpl_particle_t* particle; int pdg = 0; while (pdg != 2112 && pdg != 22 && pdg != 11 && pdg != -11) { particle = mcpl_read(mcpl_file); - pdg = mcpl_particle->pdgcode; + pdg = particle->pdgcode; } // Convert to source site and add to vector @@ -76,7 +93,7 @@ vector mcpl_source_sites(std::string path) } // Check that some sites were read - if (sites_.empty()) { + if (sites.empty()) { fatal_error("MCPL file contained no neutron, photon, electron, or positron " "source particles."); } @@ -90,4 +107,144 @@ vector mcpl_source_sites(std::string path) return sites; } +//============================================================================== + +#ifdef OPENMC_MCPL +void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) +{ + int64_t dims_size = settings::n_particles; + int64_t count_size = simulation::work_per_rank; + + // Set vectors for source bank and starting bank index of each process + vector* bank_index = &simulation::work_index; + vector* source_bank = &simulation::source_bank; + vector surf_source_index_vector; + vector surf_source_bank_vector; + + if (surf_source_bank) { + surf_source_index_vector = calculate_surf_source_size(); + dims_size = surf_source_index_vector[mpi::n_procs]; + count_size = simulation::surf_source_bank.size(); + + bank_index = &surf_source_index_vector; + + // Copy data in a SharedArray into a vector. + surf_source_bank_vector.resize(count_size); + surf_source_bank_vector.assign(simulation::surf_source_bank.data(), + simulation::surf_source_bank.data() + count_size); + source_bank = &surf_source_bank_vector; + } + + if (mpi::master) { + // Particles are writeen to disk from the master node only + + // Save source bank sites since the array is overwritten below +#ifdef OPENMC_MPI + vector temp_source {source_bank->begin(), source_bank->end()}; +#endif + + // loop over the other nodes and receive data - then write those. + for (int i = 0; i < mpi::n_procs; ++i) { + // number of particles for node node i + size_t count[] { + static_cast((*bank_index)[i + 1] - (*bank_index)[i])}; + +#ifdef OPENMC_MPI + if (i > 0) + MPI_Recv(source_bank->data(), count[0], mpi::source_site, i, i, + mpi::intracomm, MPI_STATUS_IGNORE); +#endif + // now write the source_bank data again. + for (vector::iterator _site = source_bank->begin(); + _site != source_bank->end(); _site++) { + // particle is now at the iterator + // write it to the mcpl-file + mcpl_particle_t p; + p.position[0] = _site->r.x; + p.position[1] = _site->r.y; + p.position[2] = _site->r.z; + + // mcpl requires that the direction vector is unit length + // which is also the case in openmc + p.direction[0] = _site->u.x; + p.direction[1] = _site->u.y; + p.direction[2] = _site->u.z; + + // mcpl stores kinetic energy in MeV + p.ekin = _site->E * 1e-6; + + p.time = _site->time * 1e3; + + p.weight = _site->wgt; + + switch (_site->particle) { + case ParticleType::neutron: + p.pdgcode = 2112; + break; + case ParticleType::photon: + p.pdgcode = 22; + break; + case ParticleType::electron: + p.pdgcode = 11; + break; + case ParticleType::positron: + p.pdgcode = -11; + break; + } + + mcpl_add_particle(file_id, &p); + } + } +#ifdef OPENMC_MPI + // Restore state of source bank + std::copy(temp_source.begin(), temp_source.end(), source_bank->begin()); +#endif + } else { +#ifdef OPENMC_MPI + MPI_Send(source_bank->data(), count_size, mpi::source_site, 0, mpi::rank, + mpi::intracomm); +#endif + } +} +#endif + +//============================================================================== + +void write_mcpl_source_point(const char* filename, bool surf_source_bank) +{ + std::string filename_; + if (filename) { + filename_ = filename; + } else { + // Determine width for zero padding + int w = std::to_string(settings::n_max_batches).size(); + + filename_ = fmt::format("{0}source.{1:0{2}}.mcpl", settings::path_output, + simulation::current_batch, w); + } + +#ifdef OPENMC_MCPL + mcpl_outfile_t file_id; + + std::string line; + if (mpi::master) { + file_id = mcpl_create_outfile(filename_.c_str()); + if (VERSION_DEV) { + line = fmt::format("OpenMC {0}.{1}.{2}-development", VERSION_MAJOR, + VERSION_MINOR, VERSION_RELEASE); + } else { + line = fmt::format( + "OpenMC {0}.{1}.{2}", VERSION_MAJOR, VERSION_MINOR, VERSION_RELEASE); + } + mcpl_hdr_set_srcname(file_id, line.c_str()); + } + + write_mcpl_source_bank(file_id, surf_source_bank); + + if (mpi::master) { + mcpl_close_outfile(file_id); + } +#endif +} + } // namespace openmc diff --git a/src/settings.cpp b/src/settings.cpp index bc31e2c4d0..cb39d0c8b2 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -433,10 +433,8 @@ void read_settings_xml() if (check_for_node(node, "file")) { auto path = get_node_value(node, "file", false, true); if (ends_with(path, ".mcpl") || ends_with(path, ".mcpl.gz")) { -#ifdef OPENMC_MCPL auto sites = mcpl_source_sites(path); model::external_sources.push_back(make_unique(sites)); -#endif } else { model::external_sources.push_back(make_unique(path)); } @@ -659,6 +657,12 @@ void read_settings_xml() } if (check_for_node(node_sp, "mcpl")) { source_mcpl_write = get_node_value_bool(node_sp, "mcpl"); + + // Make sure MCPL support is enabled + if (source_mcpl_write && !MCPL_ENABLED) { + fatal_error( + "Your build of OpenMC does not support writing MCPL source files."); + } } if (check_for_node(node_sp, "overwrite_latest")) { source_latest = get_node_value_bool(node_sp, "overwrite_latest"); @@ -690,11 +694,15 @@ void read_settings_xml() max_surface_particles = std::stoll(get_node_value(node_ssw, "max_particles")); } -#ifdef OPENMC_MCPL if (check_for_node(node_ssw, "mcpl")) { - surf_mcpl_write = true; + surf_mcpl_write = get_node_value_bool(node_ssw, "mcpl"); + + // Make sure MCPL support is enabled + if (surf_mcpl_write && !MCPL_ENABLED) { + fatal_error("Your build of OpenMC does not support writing MCPL " + "surface source files."); + } } -#endif } // If source is not separate and is to be written out in the statepoint file, diff --git a/src/simulation.cpp b/src/simulation.cpp index 2c1d1c988b..497b26124b 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -8,6 +8,7 @@ #include "openmc/event.h" #include "openmc/geometry_aux.h" #include "openmc/material.h" +#include "openmc/mcpl_interface.h" #include "openmc/message_passing.h" #include "openmc/nuclide.h" #include "openmc/output.h" @@ -389,9 +390,7 @@ void finalize_batch() if (settings::run_mode == RunMode::EIGENVALUE) { // Write out a separate source point if it's been specified for this batch -#ifdef OPENMC_MCPL if (!settings::source_mcpl_write) { -#endif if (contains(settings::sourcepoint_batch, simulation::current_batch) && settings::source_write && settings::source_separate) { write_source_point(nullptr); @@ -402,7 +401,6 @@ void finalize_batch() auto filename = settings::path_output + "source.h5"; write_source_point(filename.c_str()); } -#ifdef OPENMC_MCPL } else { if (contains(settings::sourcepoint_batch, simulation::current_batch) && settings::source_mcpl_write && settings::source_separate) { @@ -415,7 +413,6 @@ void finalize_batch() write_mcpl_source_point(filename.c_str()); } } -#endif } // Write out surface source if requested. @@ -424,13 +421,11 @@ void finalize_batch() auto filename = settings::path_output + "surface_source.h5"; write_source_point(filename.c_str(), true); } -#ifdef OPENMC_MCPL if (settings::surf_mcpl_write && simulation::current_batch == settings::n_batches) { auto filename = settings::path_output + "surface_source.mcpl"; write_mcpl_source_point(filename.c_str(), true); } -#endif } void initialize_generation() diff --git a/src/state_point.cpp b/src/state_point.cpp index 9dd0f13747..470dd77182 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -28,10 +28,6 @@ #include "openmc/timer.h" #include "openmc/vector.h" -#ifdef OPENMC_MCPL -#include -#endif - namespace openmc { extern "C" int openmc_statepoint_write(const char* filename, bool* write_source) @@ -603,43 +599,6 @@ void write_source_point(const char* filename, bool surf_source_bank) file_close(file_id); } -#ifdef OPENMC_MCPL -void write_mcpl_source_point(const char* filename, bool surf_source_bank) -{ - std::string filename_; - if (filename) { - filename_ = filename; - } else { - // Determine width for zero padding - int w = std::to_string(settings::n_max_batches).size(); - - filename_ = fmt::format("{0}source.{1:0{2}}.mcpl", settings::path_output, - simulation::current_batch, w); - } - - mcpl_outfile_t file_id; - - std::string line; - if (mpi::master) { - file_id = mcpl_create_outfile(filename_.c_str()); - if (VERSION_DEV) { - line = fmt::format("OpenMC {0}.{1}.{2}-development", VERSION_MAJOR, - VERSION_MINOR, VERSION_RELEASE); - } else { - line = fmt::format( - "OpenMC {0}.{1}.{2}", VERSION_MAJOR, VERSION_MINOR, VERSION_RELEASE); - } - mcpl_hdr_set_srcname(file_id, line.c_str()); - } - - write_mcpl_source_bank(file_id, surf_source_bank); - - if (mpi::master) { - mcpl_close_outfile(file_id); - } -} -#endif - void write_source_bank(hid_t group_id, bool surf_source_bank) { hid_t banktype = h5banktype(); @@ -756,105 +715,6 @@ void write_source_bank(hid_t group_id, bool surf_source_bank) H5Tclose(banktype); } -#ifdef OPENMC_MCPL -void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) -{ - int64_t dims_size = settings::n_particles; - int64_t count_size = simulation::work_per_rank; - - // Set vectors for source bank and starting bank index of each process - vector* bank_index = &simulation::work_index; - vector* source_bank = &simulation::source_bank; - vector surf_source_index_vector; - vector surf_source_bank_vector; - - if (surf_source_bank) { - surf_source_index_vector = calculate_surf_source_size(); - dims_size = surf_source_index_vector[mpi::n_procs]; - count_size = simulation::surf_source_bank.size(); - - bank_index = &surf_source_index_vector; - - // Copy data in a SharedArray into a vector. - surf_source_bank_vector.resize(count_size); - surf_source_bank_vector.assign(simulation::surf_source_bank.data(), - simulation::surf_source_bank.data() + count_size); - source_bank = &surf_source_bank_vector; - } - - if (mpi::master) { - // Particles are writeen to disk from the master node only - - // Save source bank sites since the array is overwritten below -#ifdef OPENMC_MPI - vector temp_source {source_bank->begin(), source_bank->end()}; -#endif - - // loop over the other nodes and receive data - then write those. - for (int i = 0; i < mpi::n_procs; ++i) { - // number of particles for node node i - size_t count[] { - static_cast((*bank_index)[i + 1] - (*bank_index)[i])}; - -#ifdef OPENMC_MPI - if (i > 0) - MPI_Recv(source_bank->data(), count[0], mpi::source_site, i, i, - mpi::intracomm, MPI_STATUS_IGNORE); -#endif - // now write the source_bank data again. - for (vector::iterator _site = source_bank->begin(); - _site != source_bank->end(); _site++) { - // particle is now at the iterator - // write it to the mcpl-file - mcpl_particle_t p; - p.position[0] = _site->r.x; - p.position[1] = _site->r.y; - p.position[2] = _site->r.z; - - // mcpl requires that the direction vector is unit length - // which is also the case in openmc - p.direction[0] = _site->u.x; - p.direction[1] = _site->u.y; - p.direction[2] = _site->u.z; - - // mcpl stores kinetic energy in MeV - p.ekin = _site->E * 1e-6; - - p.time = _site->time * 1e3; - - p.weight = _site->wgt; - - switch (_site->particle) { - case ParticleType::neutron: - p.pdgcode = 2112; - break; - case ParticleType::photon: - p.pdgcode = 22; - break; - case ParticleType::electron: - p.pdgcode = 11; - break; - case ParticleType::positron: - p.pdgcode = -11; - break; - } - - mcpl_add_particle(file_id, &p); - } - } -#ifdef OPENMC_MPI - // Restore state of source bank - std::copy(temp_source.begin(), temp_source.end(), source_bank->begin()); -#endif - } else { -#ifdef OPENMC_MPI - MPI_Send(source_bank->data(), count_size, mpi::source_site, 0, mpi::rank, - mpi::intracomm); -#endif - } -} -#endif - // Determine member names of a compound HDF5 datatype std::string dtype_member_names(hid_t dtype_id) { From 9ae44b3fd1e9c6e26c3f5089c9382a7fe97eb48e Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 22 Dec 2022 12:43:31 -0600 Subject: [PATCH 230/265] Rearragne MCPL source writing logic --- src/simulation.cpp | 42 +++++++++++++++++++----------------------- 1 file changed, 19 insertions(+), 23 deletions(-) diff --git a/src/simulation.cpp b/src/simulation.cpp index 497b26124b..2f07f8124f 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -390,27 +390,23 @@ void finalize_batch() if (settings::run_mode == RunMode::EIGENVALUE) { // Write out a separate source point if it's been specified for this batch - if (!settings::source_mcpl_write) { - if (contains(settings::sourcepoint_batch, simulation::current_batch) && - settings::source_write && settings::source_separate) { + if (contains(settings::sourcepoint_batch, simulation::current_batch) && + settings::source_write && settings::source_separate) { + if (settings::source_mcpl_write) { + write_mcpl_source_point(nullptr); + } else { write_source_point(nullptr); } + } - // Write a continously-overwritten source point if requested. - if (settings::source_latest) { - auto filename = settings::path_output + "source.h5"; - write_source_point(filename.c_str()); - } - } else { - if (contains(settings::sourcepoint_batch, simulation::current_batch) && - settings::source_mcpl_write && settings::source_separate) { - write_mcpl_source_point(nullptr); - } - - // Write a continously-overwritten source point if requested. - if (settings::source_latest && settings::source_mcpl_write) { + // Write a continously-overwritten source point if requested. + if (settings::source_latest) { + if (settings::source_mcpl_write) { auto filename = settings::path_output + "source.mcpl"; write_mcpl_source_point(filename.c_str()); + } else { + auto filename = settings::path_output + "source.h5"; + write_source_point(filename.c_str()); } } } @@ -418,13 +414,13 @@ void finalize_batch() // Write out surface source if requested. if (settings::surf_source_write && simulation::current_batch == settings::n_batches) { - auto filename = settings::path_output + "surface_source.h5"; - write_source_point(filename.c_str(), true); - } - if (settings::surf_mcpl_write && - simulation::current_batch == settings::n_batches) { - auto filename = settings::path_output + "surface_source.mcpl"; - write_mcpl_source_point(filename.c_str(), true); + if (settings::surf_mcpl_write) { + auto filename = settings::path_output + "surface_source.mcpl"; + write_mcpl_source_point(filename.c_str(), true); + } else { + auto filename = settings::path_output + "surface_source.h5"; + write_source_point(filename.c_str(), true); + } } } From eeab41a19d8bbe1617f6abb63ff8bb2f89dd24f3 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 22 Dec 2022 14:03:26 -0600 Subject: [PATCH 231/265] Build against MCPL in CI by default --- tools/ci/gha-install.py | 12 ++++-------- tools/ci/gha-install.sh | 6 ++---- 2 files changed, 6 insertions(+), 12 deletions(-) diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py index ea317b5f0a..83e5afac79 100644 --- a/tools/ci/gha-install.py +++ b/tools/ci/gha-install.py @@ -19,14 +19,14 @@ def which(program): return None -def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, mcpl=False): +def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False): # Create build directory and change to it shutil.rmtree('build', ignore_errors=True) os.mkdir('build') os.chdir('build') - # Build in debug mode by default - cmake_cmd = ['cmake', '-DCMAKE_BUILD_TYPE=Debug'] + # Build in debug mode by default with support for MCPL + cmake_cmd = ['cmake', '-DCMAKE_BUILD_TYPE=Debug', '-DOPENMC_USE_MCPL=on'] # Turn off OpenMP if specified if not omp: @@ -54,9 +54,6 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, mcpl= libmesh_path = os.environ.get('HOME') + '/LIBMESH' cmake_cmd.append('-DCMAKE_PREFIX_PATH=' + libmesh_path) - if mcpl: - cmake_cmd.append('-DOPENMC_USE_MCPL=ON') - # Build in coverage mode for coverage testing cmake_cmd.append('-DOPENMC_ENABLE_COVERAGE=on') @@ -74,10 +71,9 @@ def main(): phdf5 = (os.environ.get('PHDF5') == 'y') dagmc = (os.environ.get('DAGMC') == 'y') libmesh = (os.environ.get('LIBMESH') == 'y') - mcpl = (os.environ.get('MCPL') == 'y') # Build and install - install(omp, mpi, phdf5, dagmc, libmesh, mcpl) + install(omp, mpi, phdf5, dagmc, libmesh) if __name__ == '__main__': main() diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh index 68e825d486..75fa0ca703 100755 --- a/tools/ci/gha-install.sh +++ b/tools/ci/gha-install.sh @@ -27,10 +27,8 @@ if [[ $LIBMESH = 'y' ]]; then ./tools/ci/gha-install-libmesh.sh fi -# Install mcpl if needed -if [[ $MCPL = 'y' ]]; then - ./tools/ci/gha-install-mcpl.sh -fi +# Install MCPL +./tools/ci/gha-install-mcpl.sh # For MPI configurations, make sure mpi4py and h5py are built against the # correct version of MPI From 47848b79abe964be913095397d1d5aaf2780d28c Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 22 Dec 2022 14:34:37 -0600 Subject: [PATCH 232/265] Allow Settings.sourcepoint['mcpl'] to be set --- docs/source/io_formats/settings.rst | 14 +++++++++++--- openmc/settings.py | 12 ++++++++++-- tests/unit_tests/test_settings.py | 4 ++-- 3 files changed, 23 insertions(+), 7 deletions(-) diff --git a/docs/source/io_formats/settings.rst b/docs/source/io_formats/settings.rst index 7174c5317a..01b1852ca2 100644 --- a/docs/source/io_formats/settings.rst +++ b/docs/source/io_formats/settings.rst @@ -732,6 +732,14 @@ attributes/sub-elements: *Default*: false + :mcpl: + If this element is set to "true", the source point file containing the + source bank will be written as an MCPL_ file name ``source.mcpl`` instead of + an HDF5 file. This option is only applicable if the ```` element + is set to true. + + *Default*: false + ------------------------------ ```` Element ------------------------------ @@ -769,13 +777,13 @@ certain surfaces and write out the source bank in a separate file called :mcpl: An optional boolean which indicates if the banked particles should be - written to a file in the MCPL-format (documented in mcpl_). instead of the - native HDF5-based format. If activated the output file name is changed to + written to a file in the MCPL_-format instead of the native HDF5-based + format. If activated the output file name is changed to ``surface_source.mcpl``. *Default*: false - .. _mcpl: https://mctools.github.io/mcpl/mcpl.pdf + .. _MCPL: https://mctools.github.io/mcpl/mcpl.pdf ------------------------------ ```` Element diff --git a/openmc/settings.py b/openmc/settings.py index fd622870c5..cc0ca29645 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -156,6 +156,7 @@ class Settings: :separate: bool indicating whether the source should be written as a separate file :write: bool indicating whether or not to write the source + :mcpl: bool indicating whether to write the source as an MCPL file statepoint : dict Options for writing state points. Acceptable keys are: @@ -620,6 +621,8 @@ class Settings: cv.check_type('sourcepoint write', value, bool) elif key == 'overwrite': cv.check_type('sourcepoint overwrite', value, bool) + elif key == 'mcpl': + cv.check_type('sourcepoint mcpl', value, bool) else: raise ValueError(f"Unknown key '{key}' encountered when " "setting sourcepoint options.") @@ -1019,6 +1022,11 @@ class Settings: subelement = ET.SubElement(element, "overwrite_latest") subelement.text = str(self._sourcepoint['overwrite']).lower() + if 'mcpl' in self._sourcepoint: + subelement = ET.SubElement(element, "mcpl") + subelement.text = str(self._sourcepoint['mcpl']).lower() + + def _create_surf_source_read_subelement(self, root): if self._surf_source_read: element = ET.SubElement(root, "surf_source_read") @@ -1319,10 +1327,10 @@ class Settings: def _sourcepoint_from_xml_element(self, root): elem = root.find('source_point') if elem is not None: - for key in ('separate', 'write', 'overwrite_latest', 'batches'): + for key in ('separate', 'write', 'overwrite_latest', 'batches', 'mcpl'): value = get_text(elem, key) if value is not None: - if key in ('separate', 'write'): + if key in ('separate', 'write', 'mcpl'): value = value in ('true', '1') elif key == 'overwrite_latest': value = value in ('true', '1') diff --git a/tests/unit_tests/test_settings.py b/tests/unit_tests/test_settings.py index 7678711a43..f1ae581923 100644 --- a/tests/unit_tests/test_settings.py +++ b/tests/unit_tests/test_settings.py @@ -17,7 +17,7 @@ def test_export_to_xml(run_in_tmpdir): s.output = {'summary': True, 'tallies': False, 'path': 'here'} s.verbosity = 7 s.sourcepoint = {'batches': [50, 150, 500, 1000], 'separate': True, - 'write': True, 'overwrite': True} + 'write': True, 'overwrite': True, 'mcpl': True} s.statepoint = {'batches': [50, 150, 500, 1000]} s.surf_source_read = {'path': 'surface_source_1.h5'} s.surf_source_write = {'surface_ids': [2], 'max_particles': 200} @@ -75,7 +75,7 @@ def test_export_to_xml(run_in_tmpdir): assert s.output == {'summary': True, 'tallies': False, 'path': 'here'} assert s.verbosity == 7 assert s.sourcepoint == {'batches': [50, 150, 500, 1000], 'separate': True, - 'write': True, 'overwrite': True} + 'write': True, 'overwrite': True, 'mcpl': True} assert s.statepoint == {'batches': [50, 150, 500, 1000]} assert s.surf_source_read == {'path': 'surface_source_1.h5'} assert s.surf_source_write == {'surface_ids': [2], 'max_particles': 200} From 731eff8817520773670d8a56c3ee4fbf7962cca9 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 22 Dec 2022 14:43:58 -0600 Subject: [PATCH 233/265] Update source_mcpl_file test result --- tests/regression_tests/source_mcpl_file/results_true.dat | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression_tests/source_mcpl_file/results_true.dat b/tests/regression_tests/source_mcpl_file/results_true.dat index e8f4a20a08..5651efde70 100644 --- a/tests/regression_tests/source_mcpl_file/results_true.dat +++ b/tests/regression_tests/source_mcpl_file/results_true.dat @@ -1,2 +1,2 @@ k-combined: -3.004254E-01 8.027600E-04 +2.943088E-01 2.093028E-03 From ddbd61cc97ee2767d81f93b62542a3d367be1c85 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 22 Dec 2022 14:49:47 -0600 Subject: [PATCH 234/265] Formatting fixes --- CMakeLists.txt | 1 + openmc/settings.py | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 466816b300..c6c2257830 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -162,6 +162,7 @@ endif() #=============================================================================== # MCPL #=============================================================================== + if (OPENMC_USE_MCPL) find_package(MCPL REQUIRED) message(STATUS "Found MCPL: ${MCPL_DIR} (found version \"${MCPL_VERSION}\")") diff --git a/openmc/settings.py b/openmc/settings.py index cc0ca29645..e445655ca2 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1026,7 +1026,6 @@ class Settings: subelement = ET.SubElement(element, "mcpl") subelement.text = str(self._sourcepoint['mcpl']).lower() - def _create_surf_source_read_subelement(self, root): if self._surf_source_read: element = ET.SubElement(root, "surf_source_read") From 25f2bd50f9005cf8fa05ea055ebce0384d488106 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 22 Dec 2022 18:27:42 -0600 Subject: [PATCH 235/265] Several small fixes --- openmc/_xml.py | 2 +- openmc/model/model.py | 12 ++++-------- openmc/settings.py | 5 +++-- 3 files changed, 8 insertions(+), 11 deletions(-) diff --git a/openmc/_xml.py b/openmc/_xml.py index 2a33d4b8d7..6799a4e2d8 100644 --- a/openmc/_xml.py +++ b/openmc/_xml.py @@ -27,7 +27,7 @@ def clean_indentation(element, level=0, spaces_per_level=2, trailing_indent=True element.tail = i for sub_element in element: # `trailing_indent` is intentionally not forwarded to the recursive - # call. Any child element of the topmost clement should add + # call. Any child element of the topmost element should add # indentation at the end to ensure its parent's indentation is # correct. clean_indentation(sub_element, level+1, spaces_per_level) diff --git a/openmc/model/model.py b/openmc/model/model.py index 7c6d9b828c..2f44890844 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -244,6 +244,8 @@ class Model: def from_model_xml(cls, path='model.xml'): """Create model from single XML file + .. vesionadded:: 0.13.3 + Parameters ---------- path : str or Pathlike @@ -259,13 +261,6 @@ class Model: model.materials = openmc.Materials.from_xml_element(root.find('materials')) model.geometry = openmc.Geometry.from_xml_element(root.find('geometry'), model.materials) - # gather meshes from other classes before reading the tally node - if model.settings.entropy_mesh is not None: - meshes[model.settings.entropy_mesh.id] = model.settings.entropy_mesh - - for ww in model.settings.weight_windows: - meshes[ww.mesh.id] = ww.mesh - if root.find('tallies'): model.tallies = openmc.Tallies.from_xml_element(root.find('tallies'), meshes) @@ -474,6 +469,8 @@ class Model: def export_to_model_xml(self, path='model.xml', remove_surfs=False): """Export model to a single XML file. + .. versionadded:: 0.13.3 + Parameters ---------- path : str or Pathlike @@ -483,7 +480,6 @@ class Model: Whether or not to remove redundant surfaces from the geometry when exporting. - .. versionadded:: 0.13.1 """ xml_path = Path(path) # if the provided path doesn't end with the XML extension, assume the diff --git a/openmc/settings.py b/openmc/settings.py index 65ca719572..4e6f144fee 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1100,7 +1100,8 @@ class Settings: path = f"./mesh[@id='{self.entropy_mesh.id}']" if root.find(path) is None: root.append(self.entropy_mesh.to_xml_element()) - if mesh_memo is not None: mesh_memo.add(self.entropy_mesh.id) + if mesh_memo is not None: + mesh_memo.add(self.entropy_mesh.id) def _create_trigger_subelement(self, root): if self._trigger_active is not None: @@ -1609,7 +1610,7 @@ class Settings: self._create_temperature_subelements(element) self._create_trace_subelement(element) self._create_track_subelement(element) - self._create_ufs_mesh_subelement(element) + self._create_ufs_mesh_subelement(element, mesh_memo) self._create_resonance_scattering_subelement(element) self._create_volume_calcs_subelement(element) self._create_create_fission_neutrons_subelement(element) From a0d8541a0164e19732ff3ce50b94ae9f83e0da13 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 22 Dec 2022 22:27:03 -0600 Subject: [PATCH 236/265] Make sure OpenMCConfig.cmake.in includes MCPL --- cmake/OpenMCConfig.cmake.in | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/cmake/OpenMCConfig.cmake.in b/cmake/OpenMCConfig.cmake.in index d0e2beb827..1e35083050 100644 --- a/cmake/OpenMCConfig.cmake.in +++ b/cmake/OpenMCConfig.cmake.in @@ -25,3 +25,7 @@ endif() if(@OPENMC_USE_MPI@) find_package(MPI REQUIRED) endif() + +if(@OPENMC_USE_MCPL@) + find_package(MCPL REQUIRED) +endif() From ecfa94e0ff0c50a83c8db61444e5cad888b16c7a Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 8 Sep 2022 14:25:22 -0500 Subject: [PATCH 237/265] Rename gnd_name to gnds_name. Change GND to GNDS in comments --- docs/source/pythonapi/data.rst | 2 +- docs/source/usersguide/scripts.rst | 4 ++-- openmc/data/ace.py | 4 ++-- openmc/data/data.py | 19 +++++++++++-------- openmc/data/decay.py | 2 +- openmc/data/endf.py | 12 ++++++------ openmc/data/multipole.py | 4 ++-- openmc/data/neutron.py | 4 ++-- openmc/data/reaction.py | 2 +- openmc/data/thermal.py | 10 +++++----- openmc/deplete/chain.py | 16 ++++++++-------- openmc/deplete/nuclide.py | 2 +- openmc/nuclide.py | 2 +- scripts/openmc-update-inputs | 5 ++--- tests/unit_tests/test_data_misc.py | 12 ++++++------ 15 files changed, 51 insertions(+), 49 deletions(-) diff --git a/docs/source/pythonapi/data.rst b/docs/source/pythonapi/data.rst index 960abec2fe..1eaf90c972 100644 --- a/docs/source/pythonapi/data.rst +++ b/docs/source/pythonapi/data.rst @@ -66,7 +66,7 @@ Core Functions decay_energy decay_photon_energy dose_coefficients - gnd_name + gnds_name half_life isotopes kalbach_slope diff --git a/docs/source/usersguide/scripts.rst b/docs/source/usersguide/scripts.rst index c433ffe2c3..78ee6f7758 100644 --- a/docs/source/usersguide/scripts.rst +++ b/docs/source/usersguide/scripts.rst @@ -157,9 +157,9 @@ geometry.xml added. Any 'surfaces' attributes/elements on a cell will be renamed 'region'. materials.xml - Nuclide names will be changed from ACE aliases (e.g., Am-242m) to HDF5/GND + Nuclide names will be changed from ACE aliases (e.g., Am-242m) to HDF5/GNDS names (e.g., Am242_m1). Thermal scattering table names will be changed from - ACE aliases (e.g., HH2O) to HDF5/GND names (e.g., c_H_in_H2O). + ACE aliases (e.g., HH2O) to HDF5/GNDS names (e.g., c_H_in_H2O). ---------------------- ``openmc-update-mgxs`` diff --git a/openmc/data/ace.py b/openmc/data/ace.py index 06c581b426..91cbe41960 100644 --- a/openmc/data/ace.py +++ b/openmc/data/ace.py @@ -24,7 +24,7 @@ import numpy as np import openmc.checkvalue as cv from openmc.mixin import EqualityMixin -from .data import ATOMIC_SYMBOL, gnd_name, EV_PER_MEV, K_BOLTZMANN +from .data import ATOMIC_SYMBOL, gnds_name, EV_PER_MEV, K_BOLTZMANN from .endf import ENDF_FLOAT_RE @@ -88,7 +88,7 @@ def get_metadata(zaid, metastable_scheme='nndc'): # Determine name element = ATOMIC_SYMBOL[Z] - name = gnd_name(Z, mass_number, metastable) + name = gnds_name(Z, mass_number, metastable) return (name, element, Z, mass_number, metastable) diff --git a/openmc/data/data.py b/openmc/data/data.py index 55bfb4f096..d5521d9980 100644 --- a/openmc/data/data.py +++ b/openmc/data/data.py @@ -197,8 +197,8 @@ NEUTRON_MASS = 1.00866491595 # Used in atomic_mass function as a cache _ATOMIC_MASS = {} -# Regex for GND nuclide names (used in zam function) -_GND_NAME_RE = re.compile(r'([A-Zn][a-z]*)(\d+)((?:_[em]\d+)?)') +# Regex for GNDS nuclide names (used in zam function) +_GNDS_NAME_RE = re.compile(r'([A-Zn][a-z]*)(\d+)((?:_[em]\d+)?)') # Used in half_life function as a cache _HALF_LIFE = {} @@ -436,8 +436,11 @@ def water_density(temperature, pressure=0.1013): return coeff / pi / gamma1_pi -def gnd_name(Z, A, m=0): - """Return nuclide name using GND convention +def gnds_name(Z, A, m=0): + """Return nuclide name using GNDS convention + + .. versionchanged:: 0.14.0 + Function name changed from ``gnd_name`` to ``gnds_name`` Parameters ---------- @@ -451,7 +454,7 @@ def gnd_name(Z, A, m=0): Returns ------- str - Nuclide name in GND convention, e.g., 'Am242_m1' + Nuclide name in GNDS convention, e.g., 'Am242_m1' """ if m > 0: @@ -502,7 +505,7 @@ def zam(name): Parameters ---------- name : str - Name of nuclide using GND convention, e.g., 'Am242_m1' + Name of nuclide using GNDS convention, e.g., 'Am242_m1' Returns ------- @@ -511,10 +514,10 @@ def zam(name): """ try: - symbol, A, state = _GND_NAME_RE.match(name).groups() + symbol, A, state = _GNDS_NAME_RE.match(name).groups() except AttributeError: raise ValueError(f"'{name}' does not appear to be a nuclide name in " - "GND format") + "GNDS format") if symbol not in ATOMIC_NUMBER: raise ValueError(f"'{symbol}' is not a recognized element symbol") diff --git a/openmc/data/decay.py b/openmc/data/decay.py index 0db8422010..d002424385 100644 --- a/openmc/data/decay.py +++ b/openmc/data/decay.py @@ -144,7 +144,7 @@ class FissionProductYields(EqualityMixin): # Assign basic nuclide properties self.nuclide = { - 'name': ev.gnd_name, + 'name': ev.gnds_name, 'atomic_number': ev.target['atomic_number'], 'mass_number': ev.target['mass_number'], 'isomeric_state': ev.target['isomeric_state'] diff --git a/openmc/data/endf.py b/openmc/data/endf.py index f9b9d06941..d526bc53f5 100644 --- a/openmc/data/endf.py +++ b/openmc/data/endf.py @@ -12,7 +12,7 @@ import re import numpy as np -from .data import gnd_name +from .data import gnds_name from .function import Tabulated1D try: from ._endf import float_endf @@ -520,10 +520,10 @@ class Evaluation: self.reaction_list.append((mf, mt, nc, mod)) @property - def gnd_name(self): - return gnd_name(self.target['atomic_number'], - self.target['mass_number'], - self.target['isomeric_state']) + def gnds_name(self): + return gnds_name(self.target['atomic_number'], + self.target['mass_number'], + self.target['isomeric_state']) class Tabulated2D: @@ -531,7 +531,7 @@ class Tabulated2D: This is a dummy class that is not really used other than to store the interpolation information for a two-dimensional function. Once we refactor - to adopt GND-like data containers, this will probably be removed or + to adopt GNDS-like data containers, this will probably be removed or extended. Parameters diff --git a/openmc/data/multipole.py b/openmc/data/multipole.py index 508c76ac43..0be70cdba2 100644 --- a/openmc/data/multipole.py +++ b/openmc/data/multipole.py @@ -748,12 +748,12 @@ class WindowedMultipole(EqualityMixin): Parameters ---------- name : str - Name of the nuclide using the GND naming convention + Name of the nuclide using the GNDS naming convention Attributes ---------- name : str - Name of the nuclide using the GND naming convention + Name of the nuclide using the GNDS naming convention spacing : float The width of each window in sqrt(E)-space. For example, the frst window will end at (sqrt(E_min) + spacing)**2 and the second window at diff --git a/openmc/data/neutron.py b/openmc/data/neutron.py index e0574d76d4..2d4c139635 100644 --- a/openmc/data/neutron.py +++ b/openmc/data/neutron.py @@ -44,7 +44,7 @@ class IncidentNeutron(EqualityMixin): Parameters ---------- name : str - Name of the nuclide using the GND naming convention + Name of the nuclide using the GNDS naming convention atomic_number : int Number of protons in the target nucleus mass_number : int @@ -75,7 +75,7 @@ class IncidentNeutron(EqualityMixin): Metastable state of the target nucleus. A value of zero indicates ground state. name : str - Name of the nuclide using the GND naming convention + Name of the nuclide using the GNDS naming convention reactions : collections.OrderedDict Contains the cross sections, secondary angle and energy distributions, and other associated data for each reaction. The keys are the MT values diff --git a/openmc/data/reaction.py b/openmc/data/reaction.py index a2431cf1ce..ac9d7f14e9 100644 --- a/openmc/data/reaction.py +++ b/openmc/data/reaction.py @@ -555,7 +555,7 @@ def _get_activation_products(ev, rx): Z, A = divmod(items[2], 1000) excited_state = items[3] - # Get GND name for product + # Get GNDS name for product symbol = ATOMIC_SYMBOL[Z] if excited_state > 0: name = '{}{}_e{}'.format(symbol, A, excited_state) diff --git a/openmc/data/thermal.py b/openmc/data/thermal.py index e6213e5f0d..48f6bfc9b3 100644 --- a/openmc/data/thermal.py +++ b/openmc/data/thermal.py @@ -104,7 +104,7 @@ def get_thermal_name(name): Returns ------- str - GND-format thermal scattering name + GNDS-format thermal scattering name """ if name in _THERMAL_NAMES: @@ -396,7 +396,7 @@ class ThermalScattering(EqualityMixin): Parameters ---------- name : str - Name of the material using GND convention, e.g. c_H_in_H2O + Name of the material using GNDS convention, e.g. c_H_in_H2O atomic_weight_ratio : float Atomic mass ratio of the target nuclide. kTs : Iterable of float @@ -415,7 +415,7 @@ class ThermalScattering(EqualityMixin): Inelastic scattering cross section derived in the incoherent approximation name : str - Name of the material using GND convention, e.g. c_H_in_H2O + Name of the material using GNDS convention, e.g. c_H_in_H2O temperatures : Iterable of str List of string representations the temperatures of the target nuclide in the data set. The temperatures are strings of the temperature, @@ -491,7 +491,7 @@ class ThermalScattering(EqualityMixin): ACE table to read from. If given as a string, it is assumed to be the filename for the ACE file. name : str - GND-conforming name of the material, e.g. c_H_in_H2O. If none is + GNDS-conforming name of the material, e.g. c_H_in_H2O. If none is passed, the appropriate name is guessed based on the name of the ACE table. @@ -596,7 +596,7 @@ class ThermalScattering(EqualityMixin): ACE table to read from. If given as a string, it is assumed to be the filename for the ACE file. name : str - GND-conforming name of the material, e.g. c_H_in_H2O. If none is + GNDS-conforming name of the material, e.g. c_H_in_H2O. If none is passed, the appropriate name is guessed based on the name of the ACE table. diff --git a/openmc/deplete/chain.py b/openmc/deplete/chain.py index f439cedc34..372ed35108 100644 --- a/openmc/deplete/chain.py +++ b/openmc/deplete/chain.py @@ -15,7 +15,7 @@ from numbers import Real, Integral from warnings import warn from openmc.checkvalue import check_type, check_greater_than -from openmc.data import gnd_name, zam, DataLibrary +from openmc.data import gnds_name, zam, DataLibrary from openmc.exceptions import DataError from .nuclide import FissionYieldDistribution @@ -135,14 +135,14 @@ def replace_missing(product, decay_data): Parameters ---------- product : str - Name of product in GND format, e.g. 'Y86_m1'. + Name of product in GNDS format, e.g. 'Y86_m1'. decay_data : dict Dictionary of decay data Returns ------- product : str - Replacement for missing product in GND format. + Replacement for missing product in GNDS format. """ # Determine atomic number, mass number, and metastable state @@ -213,7 +213,7 @@ def replace_missing_fpy(actinide, fpy_data, decay_data): # Check if metastable state has data (e.g., Am242m) Z, A, m = zam(actinide) if m == 0: - metastable = gnd_name(Z, A, 1) + metastable = gnds_name(Z, A, 1) if metastable in fpy_data: return metastable @@ -222,7 +222,7 @@ def replace_missing_fpy(actinide, fpy_data, decay_data): while isotone in decay_data: Z += 1 A += 1 - isotone = gnd_name(Z, A, 0) + isotone = gnds_name(Z, A, 0) if isotone in fpy_data: return isotone @@ -231,7 +231,7 @@ def replace_missing_fpy(actinide, fpy_data, decay_data): while isotone in decay_data: Z -= 1 A -= 1 - isotone = gnd_name(Z, A, 0) + isotone = gnds_name(Z, A, 0) if isotone in fpy_data: return isotone @@ -357,7 +357,7 @@ class Chain: reactions = {} for f in neutron_files: evaluation = openmc.data.endf.Evaluation(f) - name = evaluation.gnd_name + name = evaluation.gnds_name reactions[name] = {} for mf, mt, nc, mod in evaluation.reaction_list: if mf == 3: @@ -904,7 +904,7 @@ class Chain: ground_target = grounds.get(parent_name) if ground_target is None: pz, pa, pm = zam(parent_name) - ground_target = gnd_name(pz, pa + 1, 0) + ground_target = gnds_name(pz, pa + 1, 0) new_ratios[ground_target] = ground_br parent.add_reaction(reaction, ground_target, rxn_Q, ground_br) diff --git a/openmc/deplete/nuclide.py b/openmc/deplete/nuclide.py index b84b91a7ff..2e9673d5f7 100644 --- a/openmc/deplete/nuclide.py +++ b/openmc/deplete/nuclide.py @@ -82,7 +82,7 @@ class Nuclide: Parameters ---------- name : str, optional - GND name of this nuclide, e.g. ``"He4"``, ``"Am242_m1"`` + GNDS name of this nuclide, e.g. ``"He4"``, ``"Am242_m1"`` Attributes ---------- diff --git a/openmc/nuclide.py b/openmc/nuclide.py index 196c8d7701..d5ae4bddbb 100644 --- a/openmc/nuclide.py +++ b/openmc/nuclide.py @@ -26,7 +26,7 @@ class Nuclide(str): if name.endswith('m'): name = name[:-1] + '_m1' - msg = ('OpenMC nuclides follow the GND naming convention. ' + msg = ('OpenMC nuclides follow the GNDS naming convention. ' f'Nuclide "{orig_name}" is being renamed as "{name}".') warnings.warn(msg) diff --git a/scripts/openmc-update-inputs b/scripts/openmc-update-inputs index c47f888c83..2d49c0626e 100755 --- a/scripts/openmc-update-inputs +++ b/scripts/openmc-update-inputs @@ -4,7 +4,6 @@ """ import argparse -from difflib import get_close_matches from itertools import chain from random import randint from shutil import move @@ -27,8 +26,8 @@ geometry.xml: Lattices containing 'outside' attributes/tags will be replaced will be renamed 'region'. materials.xml: Nuclide names will be changed from ACE aliases (e.g., Am-242m) to - HDF5/GND names (e.g., Am242_m1). Thermal scattering table names will be - changed from ACE aliases (e.g., HH2O) to HDF5/GND names (e.g., c_H_in_H2O). + HDF5/GNDS names (e.g., Am242_m1). Thermal scattering table names will be + changed from ACE aliases (e.g., HH2O) to HDF5/GNDS names (e.g., c_H_in_H2O). """ diff --git a/tests/unit_tests/test_data_misc.py b/tests/unit_tests/test_data_misc.py index 37e024fe23..f88be2602d 100644 --- a/tests/unit_tests/test_data_misc.py +++ b/tests/unit_tests/test_data_misc.py @@ -101,12 +101,12 @@ def test_water_density(): assert dens(500.0, 3.0) == pytest.approx(1e-3/0.120241800e-2, 1e-6) -def test_gnd_name(): - assert openmc.data.gnd_name(1, 1) == 'H1' - assert openmc.data.gnd_name(40, 90) == ('Zr90') - assert openmc.data.gnd_name(95, 242, 0) == ('Am242') - assert openmc.data.gnd_name(95, 242, 1) == ('Am242_m1') - assert openmc.data.gnd_name(95, 242, 10) == ('Am242_m10') +def test_gnds_name(): + assert openmc.data.gnds_name(1, 1) == 'H1' + assert openmc.data.gnds_name(40, 90) == ('Zr90') + assert openmc.data.gnds_name(95, 242, 0) == ('Am242') + assert openmc.data.gnds_name(95, 242, 1) == ('Am242_m1') + assert openmc.data.gnds_name(95, 242, 10) == ('Am242_m10') def test_isotopes(): From a5bdbd3adbc18ec429647c4b0ae9cee7098d7025 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Fri, 23 Dec 2022 00:04:45 -0600 Subject: [PATCH 238/265] Address a few warnings from tests --- openmc/mgxs/mgxs.py | 4 ++-- tests/regression_tests/diff_tally/test.py | 5 ++--- tests/regression_tests/surface_tally/test.py | 5 ++--- tests/unit_tests/test_mesh_to_vtk.py | 4 ++-- 4 files changed, 8 insertions(+), 10 deletions(-) diff --git a/openmc/mgxs/mgxs.py b/openmc/mgxs/mgxs.py index 15a1128f89..c93b42b88b 100644 --- a/openmc/mgxs/mgxs.py +++ b/openmc/mgxs/mgxs.py @@ -925,7 +925,7 @@ class MGXS: # Tabulate the atomic number densities for all nuclides elif nuclides == 'all': nuclides = self.get_nuclides() - densities = np.zeros(self.num_nuclides, dtype=np.float) + densities = np.zeros(self.num_nuclides, dtype=float) for i, nuclide in enumerate(nuclides): densities[i] += self.get_nuclide_density(nuclide) @@ -3019,7 +3019,7 @@ class DiffusionCoefficient(TransportXS): new_filt = openmc.EnergyFilter(old_filt.values) p1_tally.filters[-2] = new_filt - p1_tally = p1_tally.get_slice(filters=[openmc.LegendreFilter], + p1_tally = p1_tally.get_slice(filters=[openmc.LegendreFilter], filter_bins=[('P1',)],squeeze=True) p1_tally._scores = ['scatter-1'] total_xs = self.tallies['total'] / self.tallies['flux (tracklength)'] diff --git a/tests/regression_tests/diff_tally/test.py b/tests/regression_tests/diff_tally/test.py index b688e6d233..18c5013722 100644 --- a/tests/regression_tests/diff_tally/test.py +++ b/tests/regression_tests/diff_tally/test.py @@ -103,9 +103,8 @@ class DiffTallyTestHarness(PyAPITestHarness): sp = openmc.StatePoint(statepoint) # Extract the tally data as a Pandas DataFrame. - df = pd.DataFrame() - for t in sp.tallies.values(): - df = df.append(t.get_pandas_dataframe(), ignore_index=True) + tally_dfs = [t.get_pandas_dataframe() for t in sp.tallies.values()] + df = pd.concat(tally_dfs, ignore_index=True) # Extract the relevant data as a CSV string. cols = ('d_material', 'd_nuclide', 'd_variable', 'score', 'mean', diff --git a/tests/regression_tests/surface_tally/test.py b/tests/regression_tests/surface_tally/test.py index 96199ec2a4..d21f361e64 100644 --- a/tests/regression_tests/surface_tally/test.py +++ b/tests/regression_tests/surface_tally/test.py @@ -164,9 +164,8 @@ class SurfaceTallyTestHarness(PyAPITestHarness): sp = openmc.StatePoint(self._sp_name) # Extract the tally data as a Pandas DataFrame. - df = pd.DataFrame() - for t in sp.tallies.values(): - df = df.append(t.get_pandas_dataframe(), ignore_index=True) + tally_dfs = [t.get_pandas_dataframe() for t in sp.tallies.values()] + df = pd.concat(tally_dfs, ignore_index=True) # Extract the relevant data as a CSV string. cols = ('mean', 'std. dev.') diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py index d7d5907a22..f90eab134b 100644 --- a/tests/unit_tests/test_mesh_to_vtk.py +++ b/tests/unit_tests/test_mesh_to_vtk.py @@ -77,8 +77,8 @@ def test_write_data_to_vtk_size_mismatch(mesh): # by regex. These are needed to make the test string match the error message # string when using the match argument as that uses regular expression expected_error_msg = ( - f"The size of the dataset 'label' \({len(data)}\) should be equal to " - f"the number of mesh cells \({mesh.num_mesh_cells}\)" + f"The size of the dataset 'label' ({len(data)}) should be equal to " + f"the number of mesh cells ({mesh.num_mesh_cells})" ) with pytest.raises(ValueError, match=expected_error_msg): mesh.write_data_to_vtk(filename="out.vtk", datasets={"label": data}) From f9c6765eca0026291bf760cb8f33866fe367034b Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Mon, 12 Dec 2022 21:39:39 -0600 Subject: [PATCH 239/265] Update intersphinx URLs --- docs/source/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index f083332799..ae329dd7ed 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -247,7 +247,7 @@ napoleon_use_ivar = True intersphinx_mapping = { 'python': ('https://docs.python.org/3', None), 'numpy': ('https://numpy.org/doc/stable/', None), - 'scipy': ('https://docs.scipy.org/doc/scipy/reference', None), + 'scipy': ('https://docs.scipy.org/doc/scipy/', None), 'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None), - 'matplotlib': ('https://matplotlib.org/', None) + 'matplotlib': ('https://matplotlib.org/stable/', None) } From a178f5f85a95d3eb519da91b9e462ae5d906be0c Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Fri, 23 Dec 2022 10:55:58 -0600 Subject: [PATCH 240/265] Use raw f-string in test_mesh_to_vtk.py --- tests/unit_tests/test_mesh_to_vtk.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py index f90eab134b..bc3633c8c0 100644 --- a/tests/unit_tests/test_mesh_to_vtk.py +++ b/tests/unit_tests/test_mesh_to_vtk.py @@ -77,8 +77,8 @@ def test_write_data_to_vtk_size_mismatch(mesh): # by regex. These are needed to make the test string match the error message # string when using the match argument as that uses regular expression expected_error_msg = ( - f"The size of the dataset 'label' ({len(data)}) should be equal to " - f"the number of mesh cells ({mesh.num_mesh_cells})" + fr"The size of the dataset 'label' \({len(data)}\) should be equal to " + fr"the number of mesh cells \({mesh.num_mesh_cells}\)" ) with pytest.raises(ValueError, match=expected_error_msg): mesh.write_data_to_vtk(filename="out.vtk", datasets={"label": data}) From 954a2bdcdaf47cfbf778f0e07e0c4ab3fba17175 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Fri, 23 Dec 2022 11:12:22 -0600 Subject: [PATCH 241/265] Fix source definition in source_mcpl_file test --- include/openmc/mcpl_interface.h | 2 +- src/mcpl_interface.cpp | 31 +++++++++---------- .../source_mcpl_file/results_true.dat | 2 +- .../source_mcpl_file/settings.xml | 1 - .../regression_tests/source_mcpl_file/test.py | 3 +- 5 files changed, 17 insertions(+), 22 deletions(-) diff --git a/include/openmc/mcpl_interface.h b/include/openmc/mcpl_interface.h index c931f17743..64f15c13ab 100644 --- a/include/openmc/mcpl_interface.h +++ b/include/openmc/mcpl_interface.h @@ -2,9 +2,9 @@ #define OPENMC_MCPL_INTERFACE_H #include "openmc/particle_data.h" +#include "openmc/vector.h" #include -#include namespace openmc { diff --git a/src/mcpl_interface.cpp b/src/mcpl_interface.cpp index e9bc648303..a388914782 100644 --- a/src/mcpl_interface.cpp +++ b/src/mcpl_interface.cpp @@ -6,6 +6,7 @@ #include "openmc/settings.h" #include "openmc/simulation.h" #include "openmc/state_point.h" +#include "openmc/vector.h" #include @@ -57,9 +58,8 @@ SourceSite mcpl_particle_to_site(const mcpl_particle_t* particle) site.u.y = particle->direction[1]; site.u.z = particle->direction[2]; - // mcpl stores kinetic energy in MeV + // MCPL stores kinetic energy in [MeV], time in [ms] site.E = particle->ekin * 1e6; - // mcpl stores time in ms site.time = particle->time * 1e-3; site.wgt = particle->weight; @@ -155,29 +155,26 @@ void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) mpi::intracomm, MPI_STATUS_IGNORE); #endif // now write the source_bank data again. - for (vector::iterator _site = source_bank->begin(); - _site != source_bank->end(); _site++) { + for (const auto& site : *source_bank) { // particle is now at the iterator // write it to the mcpl-file mcpl_particle_t p; - p.position[0] = _site->r.x; - p.position[1] = _site->r.y; - p.position[2] = _site->r.z; + p.position[0] = site.r.x; + p.position[1] = site.r.y; + p.position[2] = site.r.z; // mcpl requires that the direction vector is unit length // which is also the case in openmc - p.direction[0] = _site->u.x; - p.direction[1] = _site->u.y; - p.direction[2] = _site->u.z; + p.direction[0] = site.u.x; + p.direction[1] = site.u.y; + p.direction[2] = site.u.z; - // mcpl stores kinetic energy in MeV - p.ekin = _site->E * 1e-6; + // MCPL stores kinetic energy in [MeV], time in [ms] + p.ekin = site.E * 1e-6; + p.time = site.time * 1e3; + p.weight = site.wgt; - p.time = _site->time * 1e3; - - p.weight = _site->wgt; - - switch (_site->particle) { + switch (site.particle) { case ParticleType::neutron: p.pdgcode = 2112; break; diff --git a/tests/regression_tests/source_mcpl_file/results_true.dat b/tests/regression_tests/source_mcpl_file/results_true.dat index 5651efde70..0a98e9d8cc 100644 --- a/tests/regression_tests/source_mcpl_file/results_true.dat +++ b/tests/regression_tests/source_mcpl_file/results_true.dat @@ -1,2 +1,2 @@ k-combined: -2.943088E-01 2.093028E-03 +3.009416E-01 3.229999E-03 diff --git a/tests/regression_tests/source_mcpl_file/settings.xml b/tests/regression_tests/source_mcpl_file/settings.xml index 2e511461f3..47b010bffe 100644 --- a/tests/regression_tests/source_mcpl_file/settings.xml +++ b/tests/regression_tests/source_mcpl_file/settings.xml @@ -1,6 +1,5 @@ - 1234 diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py index 60e0ad50f8..84ec005ae1 100644 --- a/tests/regression_tests/source_mcpl_file/test.py +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -11,7 +11,6 @@ pytestmark = pytest.mark.skipif( settings1=""" - 1234 @@ -35,7 +34,7 @@ settings2 = """ 1000 - source.10.{0} + source.10.{} """ From 577157b846ac6885251ade59456967e4102d6b24 Mon Sep 17 00:00:00 2001 From: shimwell Date: Sat, 24 Dec 2022 22:40:34 +0000 Subject: [PATCH 242/265] allowing xml file for materials --- openmc/geometry.py | 29 +++++++++++++++++++---------- tests/unit_tests/test_geometry.py | 19 ++++++++++++++++++- 2 files changed, 37 insertions(+), 11 deletions(-) diff --git a/openmc/geometry.py b/openmc/geometry.py index a43899daaf..eb7fa8200a 100644 --- a/openmc/geometry.py +++ b/openmc/geometry.py @@ -1,3 +1,5 @@ +import os +import typing from collections import OrderedDict, defaultdict from collections.abc import Iterable from copy import deepcopy @@ -7,7 +9,7 @@ import warnings import openmc import openmc._xml as xml -from .checkvalue import check_type, check_less_than, check_greater_than +from .checkvalue import check_type, check_less_than, check_greater_than, PathLike class Geometry: @@ -254,16 +256,20 @@ class Geometry: raise ValueError('Error determining root universe.') @classmethod - def from_xml(cls, path='geometry.xml', materials=None): + def from_xml( + cls, + path: PathLike = 'geometry.xml', + materials: typing.Optional[typing.Union[PathLike, 'openmc.Materials']] = 'materials.xml' + ): """Generate geometry from XML file Parameters ---------- - path : str, optional + path : PathLike, optional Path to geometry XML file - materials : openmc.Materials or None - Materials used to assign to cells. If None, an attempt is made to - generate it from the materials.xml file. + materials : openmc.Materials or or PathLike + Materials used to assign to cells. If PathLike, an attempt is made + to generate materials from the provided xml file. Returns ------- @@ -271,10 +277,13 @@ class Geometry: Geometry object """ - # Create dictionary to easily look up materials - if materials is None: - filename = Path(path).parent / 'materials.xml' - materials = openmc.Materials.from_xml(str(filename)) + + # Using str and os.Pathlike here to avoid error when using just the imported PathLike + # TypeError: Subscripted generics cannot be used with class and instance checks + check_type('materials', materials, (str, os.PathLike, openmc.Materials)) + + if isinstance(materials, (str, os.PathLike)): + materials = openmc.Materials.from_xml(materials) tree = ET.parse(path) root = tree.getroot() diff --git a/tests/unit_tests/test_geometry.py b/tests/unit_tests/test_geometry.py index 9db112fd29..843c01defd 100644 --- a/tests/unit_tests/test_geometry.py +++ b/tests/unit_tests/test_geometry.py @@ -1,4 +1,5 @@ import xml.etree.ElementTree as ET +from pathlib import Path import numpy as np import openmc @@ -274,7 +275,23 @@ def test_from_xml(run_in_tmpdir, mixed_lattice_model): # Export model mixed_lattice_model.export_to_xml() - # Import geometry + mats_from_xml = openmc.Materials.from_xml('materials.xml') + # checking string a Path are both acceptable + for path in ['geometry.xml', Path('geometry.xml')]: + for materials in [mats_from_xml, 'materials.xml']: + # Import geometry from file + geom = openmc.Geometry.from_xml(path=path, materials=materials) + assert isinstance(geom, openmc.Geometry) + ll, ur = geom.bounding_box + assert ll == pytest.approx((-6.0, -6.0, -np.inf)) + assert ur == pytest.approx((6.0, 6.0, np.inf)) + + with pytest.raises(TypeError) as excinfo: + geom = openmc.Geometry.from_xml(path='geometry.xml', materials=None) + assert 'Unable to set "materials" to "None"' in str(excinfo.value) + + + # checking that the default args also work geom = openmc.Geometry.from_xml() assert isinstance(geom, openmc.Geometry) ll, ur = geom.bounding_box From 80dad0f2403176c8fe5a501ec7a29ef0963ddf03 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Sat, 31 Dec 2022 11:32:39 +0700 Subject: [PATCH 243/265] Small fix in plot_xs when S(a,b) tables are present --- openmc/plotter.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openmc/plotter.py b/openmc/plotter.py index 16760868e3..e2d18d0857 100644 --- a/openmc/plotter.py +++ b/openmc/plotter.py @@ -563,7 +563,7 @@ def _calculate_cexs_elem_mat(this, types, temperature=294., for nuclide in nuclides.items(): sabs[nuclide[0]] = None if isinstance(this, openmc.Material): - for sab_name in this._sab: + for sab_name, _ in this._sab: sab = openmc.data.ThermalScattering.from_hdf5( library.get_by_material(sab_name, data_type='thermal')['path']) for nuc in sab.nuclides: From ac2ba93b3a573353a6e2fd051a1a35581f32c257 Mon Sep 17 00:00:00 2001 From: josh Date: Wed, 4 Jan 2023 03:31:07 +0000 Subject: [PATCH 244/265] remove cell deepcopying for creating a fresh instance --- openmc/cell.py | 11 ++++++++--- tests/unit_tests/test_cell.py | 30 ++++++++++++++++++++++++++++++ 2 files changed, 38 insertions(+), 3 deletions(-) diff --git a/openmc/cell.py b/openmc/cell.py index 2aa538012f..8169ca4d24 100644 --- a/openmc/cell.py +++ b/openmc/cell.py @@ -1,6 +1,5 @@ from collections import OrderedDict from collections.abc import Iterable -from copy import deepcopy from math import cos, sin, pi from numbers import Real from xml.etree import ElementTree as ET @@ -519,8 +518,14 @@ class Cell(IDManagerMixin): paths = self._paths self._paths = None - clone = deepcopy(self) - clone.id = None + clone = openmc.Cell() + clone.name = self.name + clone.temperature = self.temperature + clone.volume = self.volume + if self.translation is not None: + clone.translation = self.translation + if self.rotation is not None: + clone.rotation = self.rotation clone._num_instances = None # Restore paths on original instance diff --git a/tests/unit_tests/test_cell.py b/tests/unit_tests/test_cell.py index 1c2e1b70e4..eebe0f895c 100644 --- a/tests/unit_tests/test_cell.py +++ b/tests/unit_tests/test_cell.py @@ -58,24 +58,54 @@ def test_clone(): cyl = openmc.ZCylinder() c = openmc.Cell(fill=m, region=-cyl) c.temperature = 650. + c.translation = (1,2,3) + c.rotation = (4,5,6) + c.volume = 100 c2 = c.clone() assert c2.id != c.id assert c2.fill != c.fill assert c2.region != c.region assert c2.temperature == c.temperature + assert all(c2.translation == c.translation) + assert all(c2.rotation == c.rotation) + assert c2.volume == c.volume c3 = c.clone(clone_materials=False) assert c3.id != c.id assert c3.fill == c.fill assert c3.region != c.region assert c3.temperature == c.temperature + assert all(c2.translation == c.translation) + assert all(c2.rotation == c.rotation) c4 = c.clone(clone_regions=False) assert c4.id != c.id assert c4.fill != c.fill assert c4.region == c.region assert c4.temperature == c.temperature + assert all(c2.translation == c.translation) + assert all(c2.rotation == c.rotation) + + c5 = c.clone(clone_materials=False, clone_regions=False) + assert c5.id != c.id + assert c5.fill == c.fill + assert c5.region == c.region + assert c5.temperature == c.temperature + assert all(c2.translation == c.translation) + assert all(c2.rotation == c.rotation) + + # Mutate the original to ensure the changes are not seen in the clones + c.fill = openmc.Material() + c.region = +openmc.ZCylinder() + c.translation = [-1,-2,-3] + c.rotation = [-4,-5,-6] + c.temperature = 1 + assert c5.fill != c.fill + assert c5.region != c.region + assert c5.temperature != c.temperature + assert all(c2.translation != c.translation) + assert all(c2.rotation != c.rotation) def test_temperature(cell_with_lattice): From affc62f09cdb66bd2fea9ffdf6b44099b1e0afde Mon Sep 17 00:00:00 2001 From: josh Date: Wed, 4 Jan 2023 22:53:55 +0000 Subject: [PATCH 245/265] only reassign temps when not None --- openmc/cell.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/openmc/cell.py b/openmc/cell.py index 8169ca4d24..cea362ed8f 100644 --- a/openmc/cell.py +++ b/openmc/cell.py @@ -520,8 +520,9 @@ class Cell(IDManagerMixin): clone = openmc.Cell() clone.name = self.name - clone.temperature = self.temperature clone.volume = self.volume + if self.temperature is not None: + clone.temperature = self.temperature if self.translation is not None: clone.translation = self.translation if self.rotation is not None: From 60f9a4271172d61c2c36dd57ebbe8bc4a02fe587 Mon Sep 17 00:00:00 2001 From: josh Date: Wed, 4 Jan 2023 22:54:26 +0000 Subject: [PATCH 246/265] simplify cell cloning test changes --- tests/unit_tests/test_cell.py | 32 ++++++++++++++------------------ 1 file changed, 14 insertions(+), 18 deletions(-) diff --git a/tests/unit_tests/test_cell.py b/tests/unit_tests/test_cell.py index eebe0f895c..4185e9a44c 100644 --- a/tests/unit_tests/test_cell.py +++ b/tests/unit_tests/test_cell.py @@ -57,43 +57,37 @@ def test_clone(): m = openmc.Material() cyl = openmc.ZCylinder() c = openmc.Cell(fill=m, region=-cyl) - c.temperature = 650. - c.translation = (1,2,3) - c.rotation = (4,5,6) - c.volume = 100 + # Check cloning with all optional params as the defaults c2 = c.clone() assert c2.id != c.id assert c2.fill != c.fill assert c2.region != c.region - assert c2.temperature == c.temperature - assert all(c2.translation == c.translation) - assert all(c2.rotation == c.rotation) - assert c2.volume == c.volume c3 = c.clone(clone_materials=False) assert c3.id != c.id assert c3.fill == c.fill assert c3.region != c.region - assert c3.temperature == c.temperature - assert all(c2.translation == c.translation) - assert all(c2.rotation == c.rotation) c4 = c.clone(clone_regions=False) assert c4.id != c.id assert c4.fill != c.fill assert c4.region == c.region - assert c4.temperature == c.temperature - assert all(c2.translation == c.translation) - assert all(c2.rotation == c.rotation) + + # Add optional properties to the original cell to ensure they're cloned successfully + c.temperature = 650. + c.translation = [1,2,3] + c.rotation = [4,5,6] + c.volume = 100 c5 = c.clone(clone_materials=False, clone_regions=False) assert c5.id != c.id assert c5.fill == c.fill assert c5.region == c.region assert c5.temperature == c.temperature - assert all(c2.translation == c.translation) - assert all(c2.rotation == c.rotation) + assert c5.volume == c.volume + assert all(c5.translation == c.translation) + assert all(c5.rotation == c.rotation) # Mutate the original to ensure the changes are not seen in the clones c.fill = openmc.Material() @@ -101,11 +95,13 @@ def test_clone(): c.translation = [-1,-2,-3] c.rotation = [-4,-5,-6] c.temperature = 1 + c.volume = 1 assert c5.fill != c.fill assert c5.region != c.region assert c5.temperature != c.temperature - assert all(c2.translation != c.translation) - assert all(c2.rotation != c.rotation) + assert c5.volume != c.volume + assert all(c5.translation != c.translation) + assert all(c5.rotation != c.rotation) def test_temperature(cell_with_lattice): From 82429cbb19d4ba10aa771a5493a092cd35711b4f Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Thu, 5 Jan 2023 11:16:16 +0000 Subject: [PATCH 247/265] added test for sab xs appears in xs calc --- tests/unit_tests/test_plotter.py | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 tests/unit_tests/test_plotter.py diff --git a/tests/unit_tests/test_plotter.py b/tests/unit_tests/test_plotter.py new file mode 100644 index 0000000000..a3f1ff6662 --- /dev/null +++ b/tests/unit_tests/test_plotter.py @@ -0,0 +1,27 @@ +import openmc +import numpy as np + + +def test_calculate_cexs_elem_mat_sab(): + """Checks that sab cross sections are included in the + _calculate_cexs_elem_mat method and have the correct shape""" + + mat_1 = openmc.Material() + mat_1.add_element("H", 4.0, "ao") + mat_1.add_element("O", 4.0, "ao") + mat_1.add_element("C", 4.0, "ao") + + mat_1.add_s_alpha_beta("c_C6H6") + mat_1.set_density("g/cm3", 0.865) + + energy_grid, data = openmc.plotter._calculate_cexs_elem_mat( + mat_1, + ["inelastic"], + sab_name="c_C6H6", + ) + + assert isinstance(energy_grid, np.ndarray) + assert isinstance(data, np.ndarray) + assert len(energy_grid) > 1 + assert len(data) == 1 + assert len(data[0]) == len(energy_grid) From 9fac1bb4d25d7399d7c942e8605c7dc01cd4824a Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 5 Jan 2023 12:13:55 -0600 Subject: [PATCH 248/265] Updating note on photon transport limitations --- docs/source/usersguide/settings.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/source/usersguide/settings.rst b/docs/source/usersguide/settings.rst index 336982ac6e..760a08e90c 100644 --- a/docs/source/usersguide/settings.rst +++ b/docs/source/usersguide/settings.rst @@ -474,7 +474,6 @@ selected:: Some features related to photon transport are not currently implemented, including: - * Tallying photon energy deposition. * Generating a photon source from a neutron calculation that can be used for a later fixed source photon calculation. * Photoneutron reactions. From 9615b9f5da9a1bccfd0a693f74c9c0437ec1329a Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 5 Jan 2023 16:04:33 -0600 Subject: [PATCH 249/265] Adding tests for tally triggers. --- tests/unit_tests/test_triggers.py | 75 +++++++++++++++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 tests/unit_tests/test_triggers.py diff --git a/tests/unit_tests/test_triggers.py b/tests/unit_tests/test_triggers.py new file mode 100644 index 0000000000..4fe6e044ab --- /dev/null +++ b/tests/unit_tests/test_triggers.py @@ -0,0 +1,75 @@ + +import openmc + +def test_tally_trigger(run_in_tmpdir): + pincell = openmc.examples.pwr_pin_cell() + + # create a tally filter on the materials + mat_filter = openmc.MaterialFilter(pincell.materials) + + # create a tally with triggers applied + tally = openmc.Tally() + tally.filters = [mat_filter] + tally.scores = ['scatter'] + + trigger = openmc.Trigger('rel_err', 0.05) + trigger.scores = ['scatter'] + + tally.triggers = [trigger] + + pincell.tallies = [tally] + + pincell.settings.trigger_active = True + pincell.settings.trigger_max_batches = 100 + pincell.settings.trigger_batch_interval = 5 + + sp_file = pincell.run() + with openmc.StatePoint(sp_file) as sp: + expected_realizations = sp.n_realizations + + # adding other scores to the tally should not change the + # number of batches required to satisfy the trigger + tally.scores = ['total', 'absorption', 'scatter'] + + sp_file = pincell.run() + + with openmc.StatePoint(sp_file) as sp: + realizations = sp.n_realizations + + assert realizations == expected_realizations + + +def test_tally_trigger_null_score(run_in_tmpdir): + pincell = openmc.examples.pwr_pin_cell() + + # create a tally filter on the materials + mat_filter = openmc.MaterialFilter(pincell.materials) + + # apply a tally with a score that be tallied in this model + tally = openmc.Tally() + tally.filters = [mat_filter] + tally.scores = ['pair-production'] + + trigger = openmc.Trigger('rel_err', 0.05) + trigger.scores = ['pair-production'] + + tally.triggers = [trigger] + + pincell.tallies = [tally] + + pincell.settings.trigger_active = True + pincell.settings.trigger_max_batches = 50 + pincell.settings.trigger_batch_interval = 5 + + sp_file = pincell.run() + + with openmc.StatePoint(sp_file) as sp: + # verify that the tally mean is zero + tally_out = sp.get_tally(id=tally.id) + assert all(tally_out.mean == 0.0) + + # we expect that this simulation will run + # up to the max allowed batches + total_batches = sp.n_realizations + sp.n_inactive + assert total_batches == pincell.settings.trigger_max_batches + From bfcbecdbaa002954c5a25edae670d108ea95369a Mon Sep 17 00:00:00 2001 From: Patrick Shriwise Date: Thu, 5 Jan 2023 16:25:15 -0600 Subject: [PATCH 250/265] Fixing tally triggers. Refs #2342 and #2343 --- src/tallies/trigger.cpp | 87 ++++++++++++++++++++++++----------------- 1 file changed, 51 insertions(+), 36 deletions(-) diff --git a/src/tallies/trigger.cpp b/src/tallies/trigger.cpp index 2c155980e7..79af658793 100644 --- a/src/tallies/trigger.cpp +++ b/src/tallies/trigger.cpp @@ -37,6 +37,10 @@ std::pair get_tally_uncertainty( int n = tally->n_realizations_; auto mean = sum / n; + + // if the result has no contributions, return an invalid pair + if (mean == 0) return {-1 , -1}; + double std_dev = std::sqrt((sum_sq / n - mean * mean) / (n - 1)); double rel_err = (mean != 0.) ? std_dev / std::abs(mean) : 0.; @@ -68,42 +72,49 @@ void check_tally_triggers(double& ratio, int& tally_id, int& score) const auto& results = t.results_; for (auto filter_index = 0; filter_index < results.shape()[0]; ++filter_index) { - for (auto score_index = 0; score_index < results.shape()[1]; - ++score_index) { - // Compute the tally uncertainty metrics. - auto uncert_pair = - get_tally_uncertainty(i_tally, score_index, filter_index); - double std_dev = uncert_pair.first; - double rel_err = uncert_pair.second; + // Compute the tally uncertainty metrics. + auto uncert_pair = + get_tally_uncertainty(i_tally, trigger.score_index, filter_index); - // Pick out the relevant uncertainty metric for this trigger. - double uncertainty; - switch (trigger.metric) { - case TriggerMetric::variance: - uncertainty = std_dev * std_dev; - break; - case TriggerMetric::standard_deviation: - uncertainty = std_dev; - break; - case TriggerMetric::relative_error: - uncertainty = rel_err; - break; - case TriggerMetric::not_active: - UNREACHABLE(); - } + // if there is a score without contributions, set ratio to inf and + // exit early + if (uncert_pair.first == -1) { + ratio = INFINITY; + score = t.scores_[trigger.score_index]; + tally_id = t.id_; + return; + } - // Compute the uncertainty / threshold ratio. - double this_ratio = uncertainty / trigger.threshold; - if (trigger.metric == TriggerMetric::variance) { - this_ratio = std::sqrt(ratio); - } + double std_dev = uncert_pair.first; + double rel_err = uncert_pair.second; - // If this is the most uncertain value, set the output variables. - if (this_ratio > ratio) { - ratio = this_ratio; - score = t.scores_[trigger.score_index]; - tally_id = t.id_; - } + // Pick out the relevant uncertainty metric for this trigger. + double uncertainty; + switch (trigger.metric) { + case TriggerMetric::variance: + uncertainty = std_dev * std_dev; + break; + case TriggerMetric::standard_deviation: + uncertainty = std_dev; + break; + case TriggerMetric::relative_error: + uncertainty = rel_err; + break; + case TriggerMetric::not_active: + UNREACHABLE(); + } + + // Compute the uncertainty / threshold ratio. + double this_ratio = uncertainty / trigger.threshold; + if (trigger.metric == TriggerMetric::variance) { + this_ratio = std::sqrt(ratio); + } + + // If this is the most uncertain value, set the output variables. + if (this_ratio > ratio) { + ratio = this_ratio; + score = t.scores_[trigger.score_index]; + tally_id = t.id_; } } } @@ -181,9 +192,13 @@ void check_triggers() "eigenvalue", keff_ratio); } else { - msg = fmt::format( - "Triggers unsatisfied, max unc./thresh. is {} for {} in tally {}", - tally_ratio, reaction_name(score), tally_id); + if (tally_ratio == INFINITY) { + msg = fmt::format("Triggers unsatisfied, no result tallied for score {} in tally {}", reaction_name(score), tally_id); + } else{ + msg = fmt::format( + "Triggers unsatisfied, max unc./thresh. is {} for {} in tally {}", + tally_ratio, reaction_name(score), tally_id); + } } write_message(msg, 7); From 62af77310897b6de1ef43906a781da0c9fcfe15f Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Mon, 9 Jan 2023 18:16:45 +0700 Subject: [PATCH 251/265] Refactor NCrystal interface code to ncrystal_interface.h/cpp --- CMakeLists.txt | 1 + include/openmc/material.h | 25 ++----- include/openmc/ncrystal_interface.h | 91 +++++++++++++++++++++++ include/openmc/physics.h | 28 +------- include/openmc/settings.h | 8 +-- src/material.cpp | 39 +++------- src/ncrystal_interface.cpp | 108 ++++++++++++++++++++++++++++ src/physics.cpp | 30 ++------ src/settings.cpp | 12 +--- 9 files changed, 229 insertions(+), 113 deletions(-) create mode 100644 include/openmc/ncrystal_interface.h create mode 100644 src/ncrystal_interface.cpp diff --git a/CMakeLists.txt b/CMakeLists.txt index 1dee3f90e7..4737ff47b2 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -348,6 +348,7 @@ list(APPEND libopenmc_SOURCES src/message_passing.cpp src/mgxs.cpp src/mgxs_interface.cpp + src/ncrystal_interface.cpp src/nuclide.cpp src/output.cpp src/particle.cpp diff --git a/include/openmc/material.h b/include/openmc/material.h index 5326ad6ded..8db9bb6283 100644 --- a/include/openmc/material.h +++ b/include/openmc/material.h @@ -12,13 +12,10 @@ #include "openmc/bremsstrahlung.h" #include "openmc/constants.h" #include "openmc/memory.h" // for unique_ptr +#include "openmc/ncrystal_interface.h" #include "openmc/particle.h" #include "openmc/vector.h" -#ifdef NCRYSTAL -#include "NCrystal/NCrystal.hh" -#endif - namespace openmc { //============================================================================== @@ -155,25 +152,17 @@ public: //! \return Temperature in [K] double temperature() const; -#ifdef NCRYSTAL //! Get pointer to NCrystal material object //! \return Pointer to NCrystal material object - std::shared_ptr ncrystal_mat() const - { - return ncrystal_mat_; - }; -#endif + const NCrystalMat& ncrystal_mat() const { return ncrystal_mat_; }; //---------------------------------------------------------------------------- // Data - int32_t id_ {C_NONE}; //!< Unique ID - std::string name_; //!< Name of material - vector nuclide_; //!< Indices in nuclides vector - vector element_; //!< Indices in elements vector -#ifdef NCRYSTAL - std::string ncrystal_cfg_; //!< NCrystal configuration string - std::shared_ptr ncrystal_mat_; -#endif + int32_t id_ {C_NONE}; //!< Unique ID + std::string name_; //!< Name of material + vector nuclide_; //!< Indices in nuclides vector + vector element_; //!< Indices in elements vector + NCrystalMat ncrystal_mat_; //!< NCrystal material object xt::xtensor atom_density_; //!< Nuclide atom density in [atom/b-cm] double density_; //!< Total atom density in [atom/b-cm] double density_gpcc_; //!< Total atom density in [g/cm^3] diff --git a/include/openmc/ncrystal_interface.h b/include/openmc/ncrystal_interface.h new file mode 100644 index 0000000000..36038d50c3 --- /dev/null +++ b/include/openmc/ncrystal_interface.h @@ -0,0 +1,91 @@ +#ifndef OPENMC_NCRYSTAL_INTERFACE_H +#define OPENMC_NCRYSTAL_INTERFACE_H + +#ifdef NCRYSTAL +#include "NCrystal/NCRNG.hh" +#include "NCrystal/NCrystal.hh" +#endif + +#include "openmc/particle.h" + +#include // for uint64_t +#include // for numeric_limits +#include + +namespace openmc { + +//============================================================================== +// Constants +//============================================================================== + +extern "C" const bool NCRYSTAL_ENABLED; + +//============================================================================== +// Wrapper class an NCrystal material +//============================================================================== + +class NCrystalMat { +public: + //---------------------------------------------------------------------------- + // Constructors + NCrystalMat() = default; + explicit NCrystalMat(const std::string& cfg); + + //---------------------------------------------------------------------------- + // Methods + +#ifdef NCRYSTAL + //! Return configuration string + std::string cfg() const; + + //! Get cross section from NCrystal material + // + //! \param[in] p Particle object + //! \return Cross section in [b] + double xs(const Particle& p) const; + + // Process scattering event + // + //! \param[in] p Particle object + void scatter(Particle& p) const; + + //! Whether the object holds a valid NCrystal material + operator bool() const; +#else + + //---------------------------------------------------------------------------- + // Trivial methods when compiling without NCRYSTAL + std::string cfg() const + { + return ""; + } + double xs(const Particle& p) const + { + return -1.0; + } + void scatter(Particle& p) const {} + operator bool() const + { + return false; + } +#endif + +private: + //---------------------------------------------------------------------------- + // Data members (only present when compiling with NCrystal support) +#ifdef NCRYSTAL + std::string cfg_; //!< NCrystal configuration string + std::shared_ptr + ptr_; //!< Pointer to NCrystal material object +#endif +}; + +//============================================================================== +// Functions +//============================================================================== + +void ncrystal_update_micro(double xs, NuclideMicroXS& micro); + +} // namespace openmc + +#endif // OPENMC_NCRYSTAL_INTERFACE_H diff --git a/include/openmc/physics.h b/include/openmc/physics.h index 806297c4ea..382f0f0dd2 100644 --- a/include/openmc/physics.h +++ b/include/openmc/physics.h @@ -8,10 +8,6 @@ #include "openmc/reaction.h" #include "openmc/vector.h" -#ifdef NCRYSTAL -#include "NCrystal/NCRNG.hh" -#endif - namespace openmc { //============================================================================== @@ -100,31 +96,11 @@ void inelastic_scatter(const Nuclide& nuc, const Reaction& rx, Particle& p); void sample_secondary_photons(Particle& p, int i_nuclide); -//！Split or Roulette particles based their weight and the lower weight window -// bound. +// ！Split or Roulette particles based their weight and the lower weight window +// bound. //! \param[in] p, particle to be split or rouletted with the weight window. void split_particle(Particle& p); -#ifdef NCRYSTAL -//============================================================================== -// NCrystal wrapper class for the OpenMC random number generator -//============================================================================== - -class NCrystalRNGWrapper : public NCrystal::RNGStream { -public: - constexpr NCrystalRNGWrapper(uint64_t* seed) noexcept : openmc_seed_(seed) {} - -protected: - double actualGenerate() override - { - return std::max( - std::numeric_limits::min(), prn(openmc_seed_)); - } -private: - uint64_t* openmc_seed_; -}; -#endif - } // namespace openmc #endif // OPENMC_PHYSICS_H diff --git a/include/openmc/settings.h b/include/openmc/settings.h index fb5f8387a1..9cd430deba 100644 --- a/include/openmc/settings.h +++ b/include/openmc/settings.h @@ -20,8 +20,6 @@ namespace openmc { // Global variable declarations //============================================================================== -extern "C" const bool NCRYSTAL_ENABLED; - namespace settings { // Boolean flags @@ -93,6 +91,8 @@ extern int n_log_bins; //!< number of bins for logarithmic energy grid extern int n_batches; //!< number of (inactive+active) batches extern int n_max_batches; //!< Maximum number of batches extern int max_tracks; //!< Maximum number of particle tracks written to file +extern double + ncrystal_max_energy; //!< Energy in eV to switch between NCrystal and ENDF extern ResScatMethod res_scat_method; //!< resonance upscattering method extern double res_scat_energy_min; //!< Min energy in [eV] for res. upscattering extern double res_scat_energy_max; //!< Max energy in [eV] for res. upscattering @@ -124,10 +124,6 @@ extern int trigger_batch_interval; //!< Batch interval for triggers extern "C" int verbosity; //!< How verbose to make output extern double weight_cutoff; //!< Weight cutoff for Russian roulette extern double weight_survive; //!< Survival weight after Russian roulette -#ifdef NCRYSTAL -extern double - ncrystal_max_energy; //!< Energy in eV to switch between NCrystal and ENDF -#endif } // namespace settings //============================================================================== diff --git a/src/material.cpp b/src/material.cpp index 25014c448d..2d55d6a047 100644 --- a/src/material.cpp +++ b/src/material.cpp @@ -60,13 +60,12 @@ Material::Material(pugi::xml_node node) name_ = get_node_value(node, "name"); } -#ifdef NCRYSTAL if (check_for_node(node, "cfg")) { - ncrystal_cfg_ = get_node_value(node, "cfg"); - write_message(5, "NCrystal config string for material #{}: '{}'", this->id(), ncrystal_cfg_); - ncrystal_mat_ = NCrystal::FactImpl::createScatter(ncrystal_cfg_); + auto cfg = get_node_value(node, "cfg"); + write_message( + 5, "NCrystal config string for material #{}: '{}'", this->id(), cfg); + ncrystal_mat_ = NCrystalMat(cfg); } -#endif if (check_for_node(node, "depletable")) { depletable_ = get_node_value_bool(node, "depletable"); @@ -800,19 +799,11 @@ void Material::calculate_neutron_xs(Particle& p) const // Initialize position in i_sab_nuclides int j = 0; -#ifdef NCRYSTAL - double ncrystal_xs = -1; - + // Calculate NCrystal cross section + double ncrystal_xs = -1.0; if (ncrystal_mat_ && p.E() < settings::ncrystal_max_energy) { - // Calculate scattering XS per atom with NCrystal, only once per material - NCrystal::CachePtr dummy_cache; - auto nc_energy = NCrystal::NeutronEnergy {p.E()}; - ncrystal_xs = - ncrystal_mat_ - ->crossSection(dummy_cache, nc_energy, {p.u().x, p.u().y, p.u().z}) - .get(); + ncrystal_xs = ncrystal_mat_.xs(p); } -#endif // Add contribution from each nuclide in material for (int i = 0; i < nuclide_.size(); ++i) { @@ -852,26 +843,16 @@ void Material::calculate_neutron_xs(Particle& p) const int i_nuclide = nuclide_[i]; // Calculate microscopic cross section for this nuclide -#ifdef NCRYSTAL auto& micro {p.neutron_xs(i_nuclide)}; -#else - const auto& micro {p.neutron_xs(i_nuclide)}; -#endif if (p.E() != micro.last_E || p.sqrtkT() != micro.last_sqrtkT || i_sab != micro.index_sab || sab_frac != micro.sab_frac) { data::nuclides[i_nuclide]->calculate_xs(i_sab, i_grid, sab_frac, p); -#ifdef NCRYSTAL + + // If NCrystal is being used, update micro cross section cache if (ncrystal_xs >= 0.0) { - if (micro.thermal > 0 || micro.thermal_elastic > 0) { - fatal_error("S(a,b) treatment and NCrystal are not compatible."); - } data::nuclides[i_nuclide]->calculate_elastic_xs(p); - // remove free atom cross section - // and replace it by scattering cross section per atom from NCrystal - micro.total = micro.total - micro.elastic + ncrystal_xs; - micro.elastic = ncrystal_xs; + ncrystal_update_micro(ncrystal_xs, micro); } -#endif } // ====================================================================== diff --git a/src/ncrystal_interface.cpp b/src/ncrystal_interface.cpp new file mode 100644 index 0000000000..b39f62d902 --- /dev/null +++ b/src/ncrystal_interface.cpp @@ -0,0 +1,108 @@ +#include "openmc/ncrystal_interface.h" + +#include "openmc/error.h" +#include "openmc/material.h" +#include "openmc/random_lcg.h" + +namespace openmc { + +//============================================================================== +// Constants +//============================================================================== + +#ifdef NCRYSTAL +const bool NCRYSTAL_ENABLED = true; +#else +const bool NCRYSTAL_ENABLED = false; +#endif + +//============================================================================== +// NCrystal wrapper class for the OpenMC random number generator +//============================================================================== + +#ifdef NCRYSTAL +class NCrystalRNGWrapper : public NCrystal::RNGStream { +public: + constexpr NCrystalRNGWrapper(uint64_t* seed) noexcept : openmc_seed_(seed) {} + +protected: + double actualGenerate() override + { + return std::max( + std::numeric_limits::min(), prn(openmc_seed_)); + } + +private: + uint64_t* openmc_seed_; +}; +#endif + +//============================================================================== +// NCrystal implementation +//============================================================================== + +NCrystalMat::NCrystalMat(const std::string& cfg) +{ +#ifdef NCRYSTAL + cfg_ = cfg; + ptr_ = NCrystal::FactImpl::createScatter(cfg); +#else + fatal_error("Your build of OpenMC does not support NCrystal materials."); +#endif +} + +#ifdef NCRYSTAL +std::string NCrystalMat::cfg() const +{ + return cfg_; +} + +double NCrystalMat::xs(const Particle& p) const +{ + // Calculate scattering XS per atom with NCrystal, only once per material + NCrystal::CachePtr dummy_cache; + auto nc_energy = NCrystal::NeutronEnergy {p.E()}; + return ptr_->crossSection(dummy_cache, nc_energy, {p.u().x, p.u().y, p.u().z}) + .get(); +} + +void NCrystalMat::scatter(Particle& p) const +{ + NCrystalRNGWrapper rng(p.current_seed()); // Initialize RNG + // create a cache pointer for multi thread physics + NCrystal::CachePtr dummy_cache; + auto nc_energy = NCrystal::NeutronEnergy {p.E()}; + auto outcome = ptr_->sampleScatter( + dummy_cache, rng, nc_energy, {p.u().x, p.u().y, p.u().z}); + + // Modify attributes of particle + p.E() = outcome.ekin.get(); + Direction u_old {p.u()}; + p.u() = + Direction(outcome.direction[0], outcome.direction[1], outcome.direction[2]); + p.mu() = u_old.dot(p.u()); + p.event_mt() = ELASTIC; +} + +NCrystalMat::operator bool() const +{ + return ptr_.get(); +} +#endif + +//============================================================================== +// Functions +//============================================================================== + +void ncrystal_update_micro(double xs, NuclideMicroXS& micro) +{ + if (micro.thermal > 0 || micro.thermal_elastic > 0) { + fatal_error("S(a,b) treatment and NCrystal are not compatible."); + } + // remove free atom cross section + // and replace it by scattering cross section per atom from NCrystal + micro.total = micro.total - micro.elastic + xs; + micro.elastic = xs; +} + +} // namespace openmc diff --git a/src/physics.cpp b/src/physics.cpp index c1ef282f7a..46bf37aa9f 100644 --- a/src/physics.cpp +++ b/src/physics.cpp @@ -10,6 +10,7 @@ #include "openmc/material.h" #include "openmc/math_functions.h" #include "openmc/message_passing.h" +#include "openmc/ncrystal_interface.h" #include "openmc/nuclide.h" #include "openmc/photon.h" #include "openmc/physics_common.h" @@ -138,32 +139,15 @@ void sample_neutron_reaction(Particle& p) if (!p.alive()) return; - // Sample a scattering reaction and determine the secondary energy of the - // exiting neutron - -#ifdef NCRYSTAL - if (model::materials[p.material()]->ncrystal_mat() && - p.E() < settings::ncrystal_max_energy) { - NCrystalRNGWrapper rng(p.current_seed()); // Initialize RNG - // create a cache pointer for multi thread physics - NCrystal::CachePtr dummy_cache; - auto nc_energy = NCrystal::NeutronEnergy {p.E()}; - auto outcome = - model::materials[p.material()]->ncrystal_mat()->sampleScatter( - dummy_cache, rng, nc_energy, {p.u().x, p.u().y, p.u().z}); - p.E_last() = p.E(); - p.E() = outcome.ekin.get(); - Direction u_old {p.u()}; - p.u() = Direction( - outcome.direction[0], outcome.direction[1], outcome.direction[2]); - p.mu() = u_old.dot(p.u()); - p.event_mt() = ELASTIC; + // Sample a scattering reaction and determine the secondary energy of the + // exiting neutron + const auto& ncrystal_mat = model::materials[p.material()]->ncrystal_mat(); + if (ncrystal_mat && p.E() < settings::ncrystal_max_energy) { + ncrystal_mat.scatter(p); } else { scatter(p, i_nuclide); } -#else - scatter(p, i_nuclide); -#endif + // Advance URR seed stream 'N' times after energy changes if (p.E() != p.E_last()) { p.stream() = STREAM_URR_PTABLE; diff --git a/src/settings.cpp b/src/settings.cpp index 6f6e4e090a..9174d41147 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -37,13 +37,6 @@ namespace openmc { // Global variables //============================================================================== -#ifdef NCRYSTAL -const bool NCRYSTAL_ENABLED = true; -#else -const bool NCRYSTAL_ENABLED = false; -#endif - - namespace settings { // Default values for boolean flags @@ -106,6 +99,7 @@ int n_batches; int n_max_batches; int max_splits {1000}; int max_tracks {1000}; +double ncrystal_max_energy {5.0}; ResScatMethod res_scat_method {ResScatMethod::rvs}; double res_scat_energy_min {0.01}; double res_scat_energy_max {1000.0}; @@ -128,10 +122,6 @@ int verbosity {7}; double weight_cutoff {0.25}; double weight_survive {1.0}; -#ifdef NCRYSTAL -double ncrystal_max_energy {5.0}; -#endif - } // namespace settings //============================================================================== From 4eda693133a3a0f6c55eea084ca7ddeb3ab0769d Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Tue, 10 Jan 2023 10:39:22 +0700 Subject: [PATCH 252/265] Style and spacing changes --- docs/source/methods/cross_sections.rst | 27 ++++++++++++++----------- docs/source/usersguide/install.rst | 11 +++++----- docs/source/usersguide/materials.rst | 20 +++++++++--------- include/openmc/physics.h | 5 +++-- tests/regression_tests/ncrystal/test.py | 16 +++++++++------ 5 files changed, 45 insertions(+), 34 deletions(-) diff --git a/docs/source/methods/cross_sections.rst b/docs/source/methods/cross_sections.rst index 0b87913e51..2cafa86916 100644 --- a/docs/source/methods/cross_sections.rst +++ b/docs/source/methods/cross_sections.rst @@ -182,19 +182,22 @@ been selected. There are three methods available: NCrystal materials ------------------ -As an alternative of the standard thermal scattering treatment using :math:`S(\alpha,\beta)` -tables, OpenMC allows to create materials using NCrystal_. In addition to the regular thermal elastic, -and thermal inelastic processes, NCrystal allows the generation of models for materials that -cannot currently included in ACE files such as oriented single crystals (see the `NCrystal paper`_), -and further extend the physics `using plugins`_. Thermal scattering kernels are generated on -the fly from dynamic and structural data, or loaded from :math:`S(\alpha,\beta)` tables converted -from ENDF6 evaluations. These kernels are sampled in a direct way using a fast `rejection algorithm`_ -that does not require previous processing. A `large library`_ of materials is already included in -the NCrystal distribution, and new materials can be easily defined from scratch in the `NCMAT format`_ -or `combining existing files`_. +As an alternative of the standard thermal scattering treatment using +:math:`S(\alpha,\beta)` tables, OpenMC allows to create materials using +NCrystal_. In addition to the regular thermal elastic, and thermal inelastic +processes, NCrystal allows the generation of models for materials that cannot +currently included in ACE files such as oriented single crystals (see the +`NCrystal paper`_), and further extend the physics `using plugins`_. Thermal +scattering kernels are generated on the fly from dynamic and structural data, or +loaded from :math:`S(\alpha,\beta)` tables converted from ENDF6 evaluations. +These kernels are sampled in a direct way using a fast `rejection algorithm`_ +that does not require previous processing. A `large library`_ of materials is +already included in the NCrystal distribution, and new materials can be easily +defined from scratch in the `NCMAT format`_ or `combining existing files`_. -The compositions of the materials defined in NCrystal are passed on to OpenMC all other reactions -except for thermal neutron scattering are handled by continuous energy ACE libraries. +The compositions of the materials defined in NCrystal are passed on to OpenMC +all other reactions except for thermal neutron scattering are handled by +continuous energy ACE libraries. ---------------- Multi-Group Data diff --git a/docs/source/usersguide/install.rst b/docs/source/usersguide/install.rst index 9e5ba1ffd9..537dda8248 100644 --- a/docs/source/usersguide/install.rst +++ b/docs/source/usersguide/install.rst @@ -274,9 +274,10 @@ Prerequisites * NCrystal_ library for defining materials with enhanced thermal neutron transport Adding this option allows the creation of materials from NCrystal, which - replaces the scattering kernel treatment of ACE files with a modular, on-the-fly approach. - To use it `install `_ and - `initialize `_ + replaces the scattering kernel treatment of ACE files with a modular, + on-the-fly approach. To use it `install + `_ and `initialize + `_ NCrystal and turn on the option in the CMake configuration step: cmake -DOPENMC_USE_NCRYSTAL=on .. @@ -374,8 +375,8 @@ OPENMC_USE_DAGMC (Default: off) OPENMC_USE_NCRYSTAL - Turns on support for NCrystal materials. NCrystal must be - `installed `_ and + Turns on support for NCrystal materials. NCrystal must be + `installed `_ and `initialized `_. (Default: off) diff --git a/docs/source/usersguide/materials.rst b/docs/source/usersguide/materials.rst index fbf9effd89..83af558057 100644 --- a/docs/source/usersguide/materials.rst +++ b/docs/source/usersguide/materials.rst @@ -105,12 +105,14 @@ you would need to add hydrogen and oxygen to a material and then assign the Adding NCrystal materials ------------------------- -Additional support for thermal scattering can be added by using NCrystal_. -The :meth:`Material.from_ncrystal` class method generates a :class:`openmc.Material` object from -an `NCrystal configuration string `_. -Temperature, material composition, and density are passed from the configuration string -and the `NCMAT file `_ -that define the material, e.g.:: +Additional support for thermal scattering can be added by using NCrystal_. The +:meth:`Material.from_ncrystal` class method generates a :class:`openmc.Material` +object from an `NCrystal configuration string +`_. +Temperature, material composition, and density are passed from the configuration +string and the `NCMAT file +`_ that define the +material, e.g.:: mat = openmc.Material.from_ncrystal('Al_sg225.ncmat;temp=300K') @@ -125,12 +127,12 @@ defines a material containing polycrystalline alumnium, defines an oriented germanium single crystal with 40 arcsec mosaicity. NCrystal only handles low energy neutron interactions. Other interactions are -provided by standard ACE files. NCrystal_ comes with a `predefined library +provided by standard ACE files. NCrystal_ comes with a `predefined library `_ but more materials can be added by creating NCMAT files or on-the-fly in the configuration string. -.. warning:: Currently, NCrystal_ materials cannot be modified after they are created. - Density, temperature and composition should be defined in the +.. warning:: Currently, NCrystal_ materials cannot be modified after they are created. + Density, temperature and composition should be defined in the configuration string or the NCMAT file. .. _NCrystal: https://github.com/mctools/ncrystal diff --git a/include/openmc/physics.h b/include/openmc/physics.h index 382f0f0dd2..6e7327d381 100644 --- a/include/openmc/physics.h +++ b/include/openmc/physics.h @@ -96,8 +96,9 @@ void inelastic_scatter(const Nuclide& nuc, const Reaction& rx, Particle& p); void sample_secondary_photons(Particle& p, int i_nuclide); -// ！Split or Roulette particles based their weight and the lower weight window -// bound. +//! Split or Roulette particles based their weight and the lower weight window +//! bound. +// //! \param[in] p, particle to be split or rouletted with the weight window. void split_particle(Particle& p); diff --git a/tests/regression_tests/ncrystal/test.py b/tests/regression_tests/ncrystal/test.py index 2a789dac78..cb6421b034 100644 --- a/tests/regression_tests/ncrystal/test.py +++ b/tests/regression_tests/ncrystal/test.py @@ -1,3 +1,5 @@ +from math import pi + import numpy as np import openmc import openmc.lib @@ -9,6 +11,7 @@ pytestmark = pytest.mark.skipif( not openmc.lib._ncrystal_enabled(), reason="NCrystal materials are not enabled.") + def pencil_beam_model(cfg, E0, N): """Return an openmc.Model() object for a monoenergetic pencil beam hitting a 1 mm sphere filled with the material defined by @@ -24,7 +27,7 @@ def pencil_beam_model(cfg, E0, N): sample_sphere = openmc.Sphere(r=0.1) outer_sphere = openmc.Sphere(r=100, boundary_type="vacuum") cell1 = openmc.Cell(region=-sample_sphere, fill=m1) - cell2_region= +sample_sphere & -outer_sphere + cell2_region = +sample_sphere & -outer_sphere cell2 = openmc.Cell(region=cell2_region, fill=None) geometry = openmc.Geometry([cell1, cell2]) @@ -48,7 +51,7 @@ def pencil_beam_model(cfg, E0, N): tally1 = openmc.Tally(name="angular distribution") tally1.scores = ["current"] filter1 = openmc.SurfaceFilter(sample_sphere) - filter2 = openmc.PolarFilter(np.linspace(0, np.pi, 180+1)) + filter2 = openmc.PolarFilter(np.linspace(0, pi, 180+1)) filter3 = openmc.CellFromFilter(cell1) tally1.filters = [filter1, filter2, filter3] tallies = openmc.Tallies([tally1]) @@ -66,11 +69,12 @@ class NCrystalTest(PyAPITestHarness): df = tal.get_pandas_dataframe() return df.to_string() + def test_ncrystal(): - NParticles = 100000 - T = 293.6 # K - E0 = 0.012 # eV + n_particles = 100000 + T = 293.6 # K + E0 = 0.012 # eV cfg = 'Al_sg225.ncmat' - test = pencil_beam_model(cfg, E0, NParticles) + test = pencil_beam_model(cfg, E0, n_particles) harness = NCrystalTest('statepoint.10.h5', model=test) harness.main() From c4227f7dc1b30879dd7492730e8dbb02b14006d5 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Tue, 10 Jan 2023 10:39:45 +0700 Subject: [PATCH 253/265] Change Material.from_ncrystal to accept kwargs --- openmc/material.py | 51 +++++++++++++++++++++++----------------------- 1 file changed, 25 insertions(+), 26 deletions(-) diff --git a/openmc/material.py b/openmc/material.py index 68ec199c3c..7844ec131c 100644 --- a/openmc/material.py +++ b/openmc/material.py @@ -99,6 +99,10 @@ class Material(IDManagerMixin): [decay/sec]. .. versionadded:: 0.13.2 + ncrystal_cfg : str + NCrystal configuration string + + .. versionadded:: 0.13.3 """ @@ -141,7 +145,8 @@ class Material(IDManagerMixin): string += '{: <16}\n'.format('\tS(a,b) Tables') - string += '{: <16}=\t{}\n'.format('\tNCrystal conf', self._ncrystal_cfg) + if self._ncrystal_cfg: + string += '{: <16}=\t{}\n'.format('\tNCrystal conf', self._ncrystal_cfg) for sab in self._sab: string += '{: <16}=\t{}\n'.format('\tS(a,b)', sab) @@ -222,6 +227,10 @@ class Material(IDManagerMixin): def volume(self): return self._volume + @property + def ncrystal_cfg(self): + return self._ncrystal_cfg + @name.setter def name(self, name: Optional[str]): if name is not None: @@ -335,9 +344,9 @@ class Material(IDManagerMixin): return material @classmethod - def from_ncrystal(cls, cfg, material_id=None, name=''): + def from_ncrystal(cls, cfg, **kwargs): """Create material from NCrystal configuration string. - + Density, temperature, and material composition, and (ultimately) thermal neutron scattering will be automatically be provided by NCrystal based on this string. The name and material_id parameters are simply passed on @@ -347,12 +356,8 @@ class Material(IDManagerMixin): ---------- cfg : str NCrystal configuration string - material_id : int, optional - Unique identifier for the material. If not specified, an identifier will - automatically be assigned. - name : str, optional - Name of the material. If not specified, the name will be the empty - string. + **kwargs + Keyword arguments passed to :class:`openmc.Material` Returns ------- @@ -371,26 +376,20 @@ class Material(IDManagerMixin): #only get invoked in the unlikely case where a material is specified #by referring both to natural elements and specific isotopes of the #same element. - elem_name = openmc.data.ATOMIC_SYMBOL.get(Z) - if not elem_name: - raise ValueError( f'Element with Z={Z} is not known' ) + elem_name = openmc.data.ATOMIC_SYMBOL[Z] return [ (int(iso_name[len(elem_name):]), abund) for iso_name, abund in openmc.data.isotopes(elem_name) ] - flat_compos = nc_mat.getFlattenedComposition(preferNaturalElements = True, - naturalAbundProvider=openmc_natabund) + flat_compos = nc_mat.getFlattenedComposition( + preferNaturalElements=True, naturalAbundProvider=openmc_natabund) # Create the Material - material = cls(material_id=material_id, - name=name, - temperature=nc_mat.getTemperature()) + material = cls(temperature=nc_mat.getTemperature(), **kwargs) for Z, A_vals in flat_compos: - elemname = openmc.data.ATOMIC_SYMBOL.get(Z) - if not elemname: - raise ValueError(f'Element with Z={Z} is not known') + elemname = openmc.data.ATOMIC_SYMBOL[Z] for A, frac in A_vals: if A: material.add_nuclide(f'{elemname}{A}', frac) @@ -1067,7 +1066,7 @@ class Material(IDManagerMixin): activity[nuclide] = inv_seconds * 1e24 * atoms_per_bcm * multiplier return activity if by_nuclide else sum(activity.values()) - + def get_decay_heat(self, units: str = 'W', by_nuclide: bool = False): """Returns the decay heat of the material or for each nuclide in the material in units of [W], [W/g] or [W/cm3]. @@ -1101,16 +1100,16 @@ class Material(IDManagerMixin): multiplier = 1 elif units == 'W/g': multiplier = 1.0 / self.get_mass_density() - - decayheat = {} + + decayheat = {} for nuclide, atoms_per_bcm in self.get_nuclide_atom_densities().items(): decay_erg = openmc.data.decay_energy(nuclide) inv_seconds = openmc.data.decay_constant(nuclide) decay_erg *= openmc.data.JOULE_PER_EV decayheat[nuclide] = inv_seconds * decay_erg * 1e24 * atoms_per_bcm * multiplier - return decayheat if by_nuclide else sum(decayheat.values()) - + return decayheat if by_nuclide else sum(decayheat.values()) + def get_nuclide_atoms(self): """Return number of atoms of each nuclide in the material @@ -1651,4 +1650,4 @@ class Materials(cv.CheckedList): tree = ET.parse(path) root = tree.getroot() - return cls.from_xml_element(root) \ No newline at end of file + return cls.from_xml_element(root) From e83ced88dc58d0a9fcf83f04390a5284b30d06b9 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Wed, 11 Jan 2023 01:17:53 +0700 Subject: [PATCH 254/265] Change ncrystal_max_energy to be a global constant --- include/openmc/ncrystal_interface.h | 3 +++ include/openmc/settings.h | 2 -- src/material.cpp | 2 +- src/physics.cpp | 2 +- src/settings.cpp | 1 - 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/include/openmc/ncrystal_interface.h b/include/openmc/ncrystal_interface.h index 36038d50c3..5a3882df9c 100644 --- a/include/openmc/ncrystal_interface.h +++ b/include/openmc/ncrystal_interface.h @@ -20,6 +20,9 @@ namespace openmc { extern "C" const bool NCRYSTAL_ENABLED; +//! Energy in [eV] to switch between NCrystal and ENDF +constexpr double NCRYSTAL_MAX_ENERGY {5.0}; + //============================================================================== // Wrapper class an NCrystal material //============================================================================== diff --git a/include/openmc/settings.h b/include/openmc/settings.h index 9cd430deba..90f1e8c297 100644 --- a/include/openmc/settings.h +++ b/include/openmc/settings.h @@ -91,8 +91,6 @@ extern int n_log_bins; //!< number of bins for logarithmic energy grid extern int n_batches; //!< number of (inactive+active) batches extern int n_max_batches; //!< Maximum number of batches extern int max_tracks; //!< Maximum number of particle tracks written to file -extern double - ncrystal_max_energy; //!< Energy in eV to switch between NCrystal and ENDF extern ResScatMethod res_scat_method; //!< resonance upscattering method extern double res_scat_energy_min; //!< Min energy in [eV] for res. upscattering extern double res_scat_energy_max; //!< Max energy in [eV] for res. upscattering diff --git a/src/material.cpp b/src/material.cpp index 2d55d6a047..74a8d7e350 100644 --- a/src/material.cpp +++ b/src/material.cpp @@ -801,7 +801,7 @@ void Material::calculate_neutron_xs(Particle& p) const // Calculate NCrystal cross section double ncrystal_xs = -1.0; - if (ncrystal_mat_ && p.E() < settings::ncrystal_max_energy) { + if (ncrystal_mat_ && p.E() < NCRYSTAL_MAX_ENERGY) { ncrystal_xs = ncrystal_mat_.xs(p); } diff --git a/src/physics.cpp b/src/physics.cpp index 46bf37aa9f..7cb8040f63 100644 --- a/src/physics.cpp +++ b/src/physics.cpp @@ -142,7 +142,7 @@ void sample_neutron_reaction(Particle& p) // Sample a scattering reaction and determine the secondary energy of the // exiting neutron const auto& ncrystal_mat = model::materials[p.material()]->ncrystal_mat(); - if (ncrystal_mat && p.E() < settings::ncrystal_max_energy) { + if (ncrystal_mat && p.E() < NCRYSTAL_MAX_ENERGY) { ncrystal_mat.scatter(p); } else { scatter(p, i_nuclide); diff --git a/src/settings.cpp b/src/settings.cpp index 9174d41147..2fda352ce0 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -99,7 +99,6 @@ int n_batches; int n_max_batches; int max_splits {1000}; int max_tracks {1000}; -double ncrystal_max_energy {5.0}; ResScatMethod res_scat_method {ResScatMethod::rvs}; double res_scat_energy_min {0.01}; double res_scat_energy_max {1000.0}; From a0afa5de441bbd584721bf7f6c029e966675291f Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Tue, 10 Jan 2023 19:04:12 +0000 Subject: [PATCH 255/265] added get_surfaces_by_name method --- openmc/geometry.py | 21 +++++++++++++++++++++ tests/unit_tests/test_geometry.py | 16 ++++++++++++---- 2 files changed, 33 insertions(+), 4 deletions(-) diff --git a/openmc/geometry.py b/openmc/geometry.py index a43899daaf..f9aecca9c7 100644 --- a/openmc/geometry.py +++ b/openmc/geometry.py @@ -525,6 +525,27 @@ class Geometry: """ return self._get_domains_by_name(name, case_sensitive, matching, 'cell') + def get_surfaces_by_name(self, name, case_sensitive=False, matching=False): + """Return a list of surfaces with matching names. + + Parameters + ---------- + name : str + The name to search match + case_sensitive : bool + Whether to distinguish upper and lower case letters in each + surface's name (default is False) + matching : bool + Whether the names must match completely (default is False) + + Returns + ------- + list of openmc.Surface + Surfaces matching the queried name + + """ + return self._get_domains_by_name(name, case_sensitive, matching, 'surface') + def get_cells_by_fill_name(self, name, case_sensitive=False, matching=False): """Return a list of cells with fills with matching names. diff --git a/tests/unit_tests/test_geometry.py b/tests/unit_tests/test_geometry.py index 9db112fd29..f8c5230714 100644 --- a/tests/unit_tests/test_geometry.py +++ b/tests/unit_tests/test_geometry.py @@ -159,12 +159,13 @@ def test_get_by_name(): m2 = openmc.Material(name='Zirconium') m2.add_element('Zr', 1.0) - c1 = openmc.Cell(fill=m1, name='cell1') + s1 = openmc.Sphere(name='surface1') + c1 = openmc.Cell(fill=m1, region=-s1, name='cell1') u1 = openmc.Universe(name='Zircaloy universe', cells=[c1]) - cyl = openmc.ZCylinder() - c2 = openmc.Cell(fill=u1, region=-cyl, name='cell2') - c3 = openmc.Cell(fill=m2, region=+cyl, name='Cell3') + s2 = openmc.ZCylinder(name='surface2') + c2 = openmc.Cell(fill=u1, region=-s2, name='cell2') + c3 = openmc.Cell(fill=m2, region=+s2, name='Cell3') root = openmc.Universe(name='root Universe', cells=[c2, c3]) geom = openmc.Geometry(root) @@ -177,6 +178,13 @@ def test_get_by_name(): mats = geom.get_materials_by_name('zirconium', True, True) assert not mats + surfaces = set(geom.get_surfaces_by_name('surface')) + assert not surfaces ^ {s1, s2} + surfaces = set(geom.get_surfaces_by_name('Surface2', False, True)) + assert not surfaces ^ {s2} + surfaces = geom.get_surfaces_by_name('Surface2', True, True) + assert not surfaces + cells = set(geom.get_cells_by_name('cell')) assert not cells ^ {c1, c2, c3} cells = set(geom.get_cells_by_name('cell', True)) From 2c9df1b77e5828ed410dbd00250856265ec211ca Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Wed, 11 Jan 2023 09:32:02 +0000 Subject: [PATCH 256/265] Apply typo fixes identified incode review by @paulromano Co-authored-by: Paul Romano --- openmc/geometry.py | 2 +- tests/unit_tests/test_geometry.py | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/openmc/geometry.py b/openmc/geometry.py index eb7fa8200a..a9817fbbb8 100644 --- a/openmc/geometry.py +++ b/openmc/geometry.py @@ -267,7 +267,7 @@ class Geometry: ---------- path : PathLike, optional Path to geometry XML file - materials : openmc.Materials or or PathLike + materials : openmc.Materials or PathLike Materials used to assign to cells. If PathLike, an attempt is made to generate materials from the provided xml file. diff --git a/tests/unit_tests/test_geometry.py b/tests/unit_tests/test_geometry.py index 843c01defd..0e952ab0f8 100644 --- a/tests/unit_tests/test_geometry.py +++ b/tests/unit_tests/test_geometry.py @@ -290,7 +290,6 @@ def test_from_xml(run_in_tmpdir, mixed_lattice_model): geom = openmc.Geometry.from_xml(path='geometry.xml', materials=None) assert 'Unable to set "materials" to "None"' in str(excinfo.value) - # checking that the default args also work geom = openmc.Geometry.from_xml() assert isinstance(geom, openmc.Geometry) From 50892c61b7865a92b27e289be88299ad2667343b Mon Sep 17 00:00:00 2001 From: Christopher Fichtlscherer Date: Wed, 11 Jan 2023 13:56:54 -0500 Subject: [PATCH 257/265] unit test and description --- tests/unit_tests/test_settings.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/unit_tests/test_settings.py b/tests/unit_tests/test_settings.py index 1ea66d1f6f..15e86ca619 100644 --- a/tests/unit_tests/test_settings.py +++ b/tests/unit_tests/test_settings.py @@ -49,6 +49,7 @@ def test_export_to_xml(run_in_tmpdir): domains=[openmc.Cell()], samples=1000, lower_left=(-10., -10., -10.), upper_right = (10., 10., 10.)) s.create_fission_neutrons = True + s.create_delayed_neutrons = False s.log_grid_bins = 2000 s.photon_transport = False s.electron_treatment = 'led' @@ -107,6 +108,7 @@ def test_export_to_xml(run_in_tmpdir): 'energy_min': 1.0, 'energy_max': 1000.0, 'nuclides': ['U235', 'U238', 'Pu239']} assert s.create_fission_neutrons + assert not s.create_delayed_neutrons assert s.log_grid_bins == 2000 assert not s.photon_transport assert s.electron_treatment == 'led' From 9d86274fcc790e7ba05d030234ec099ef8c09d15 Mon Sep 17 00:00:00 2001 From: Christopher Fichtlscherer Date: Wed, 11 Jan 2023 14:17:29 -0500 Subject: [PATCH 258/265] merge conflict --- openmc/settings.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/openmc/settings.py b/openmc/settings.py index 6f3ef5ab4f..6271e05dc9 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -224,6 +224,10 @@ class Settings: weight_windows : WeightWindows iterable of WeightWindows Weight windows to use for variance reduction + .. versionadded:: 0.13.3 + create_delayed_neutrons : bool + Whether delayed neutrons are created in fission. + .. versionadded:: 0.13 weight_windows_on : bool Whether weight windows are enabled From e266bb15bfcbbdbaa77a0a30c2c9909f60612bb8 Mon Sep 17 00:00:00 2001 From: Christopher Fichtlscherer Date: Wed, 11 Jan 2023 14:50:06 -0500 Subject: [PATCH 259/265] old changes for delayed neutron feature --- docs/source/io_formats/settings.rst | 11 +++++++++++ include/openmc/settings.h | 1 + openmc/settings.py | 23 +++++++++++++++++++++++ src/finalize.cpp | 1 + src/nuclide.cpp | 4 ++-- src/settings.cpp | 7 +++++++ 6 files changed, 45 insertions(+), 2 deletions(-) diff --git a/docs/source/io_formats/settings.rst b/docs/source/io_formats/settings.rst index 71ca61d540..6dff768381 100644 --- a/docs/source/io_formats/settings.rst +++ b/docs/source/io_formats/settings.rst @@ -32,6 +32,17 @@ standard deviation. *Default*: false +------------------------------------- +```` Element +------------------------------------- + +The ```` element indicates whether delayed neutrons +are created in fission. If this element is set to "true", delayed neutrons +will be created in fission events; otherwise only prompt neutrons will be +created. + + *Default*: true + ------------------------------------- ```` Element ------------------------------------- diff --git a/include/openmc/settings.h b/include/openmc/settings.h index 90f1e8c297..806288efe5 100644 --- a/include/openmc/settings.h +++ b/include/openmc/settings.h @@ -28,6 +28,7 @@ extern bool check_overlaps; //!< check overlaps in geometry? extern bool confidence_intervals; //!< use confidence intervals for results? extern bool create_fission_neutrons; //!< create fission neutrons (fixed source)? +extern bool create_delayed_neutrons; //!< create delayed fission neutrons? extern "C" bool cmfd_run; //!< is a CMFD run? extern bool delayed_photon_scaling; //!< Scale fission photon yield to include delayed diff --git a/openmc/settings.py b/openmc/settings.py index 6271e05dc9..3f5873c0a7 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -300,6 +300,7 @@ class Settings: VolumeCalculation, 'volume calculations') self._create_fission_neutrons = None + self._create_delayed_neutrons = None self._delayed_photon_scaling = None self._material_cell_offsets = None self._log_grid_bins = None @@ -463,6 +464,10 @@ class Settings: def create_fission_neutrons(self) -> bool: return self._create_fission_neutrons + @property + def create_delayed_neutrons(self) -> bool: + return self._create_delayed_neutrons + @property def delayed_photon_scaling(self) -> bool: return self._delayed_photon_scaling @@ -870,6 +875,12 @@ class Settings: create_fission_neutrons, bool) self._create_fission_neutrons = create_fission_neutrons + @create_delayed_neutrons.setter + def create_delayed_neutrons(self, create_delayed_neutrons: bool): + cv.check_type('Whether create only prompt neutrons', + create_delayed_neutrons, bool) + self._create_delayed_neutrons = create_delayed_neutrons + @delayed_photon_scaling.setter def delayed_photon_scaling(self, value: bool): cv.check_type('delayed photon scaling', value, bool) @@ -1211,6 +1222,11 @@ class Settings: elem = ET.SubElement(root, "create_fission_neutrons") elem.text = str(self._create_fission_neutrons).lower() + def _create_create_delayed_neutrons_subelement(self, root): + if self._create_delayed_neutrons is not None: + elem = ET.SubElement(root, "create_delayed_neutrons") + elem.text = str(self._create_delayed_neutrons).lower() + def _create_delayed_photon_scaling_subelement(self, root): if self._delayed_photon_scaling is not None: elem = ET.SubElement(root, "delayed_photon_scaling") @@ -1536,6 +1552,11 @@ class Settings: if text is not None: self.create_fission_neutrons = text in ('true', '1') + def _create_delayed_neutrons_from_xml_element(self, root): + text = get_text(root, 'create_delayed_neutrons') + if text is not None: + self.create_delayed_neutrons = text in ('true', '1') + def _delayed_photon_scaling_from_xml_element(self, root): text = get_text(root, 'delayed_photon_scaling') if text is not None: @@ -1634,6 +1655,7 @@ class Settings: self._create_resonance_scattering_subelement(element) self._create_volume_calcs_subelement(element) self._create_create_fission_neutrons_subelement(element) + self._create_create_delayed_neutrons_subelement(root_element) self._create_delayed_photon_scaling_subelement(element) self._create_event_based_subelement(element) self._create_max_particles_in_flight_subelement(element) @@ -1726,6 +1748,7 @@ class Settings: settings._ufs_mesh_from_xml_element(elem, meshes) settings._resonance_scattering_from_xml_element(elem) settings._create_fission_neutrons_from_xml_element(elem) + settings._create_delayed_neutrons_from_xml_element(root) settings._delayed_photon_scaling_from_xml_element(elem) settings._event_based_from_xml_element(elem) settings._max_particles_in_flight_from_xml_element(elem) diff --git a/src/finalize.cpp b/src/finalize.cpp index 0c2c62310e..59294b28c9 100644 --- a/src/finalize.cpp +++ b/src/finalize.cpp @@ -74,6 +74,7 @@ int openmc_finalize() settings::check_overlaps = false; settings::confidence_intervals = false; settings::create_fission_neutrons = true; + settings::create_delayed_neutrons = true; settings::electron_treatment = ElectronTreatment::LED; settings::delayed_photon_scaling = true; settings::energy_cutoff = {0.0, 1000.0, 0.0, 0.0}; diff --git a/src/nuclide.cpp b/src/nuclide.cpp index 134e2d6b9a..99ed44b112 100644 --- a/src/nuclide.cpp +++ b/src/nuclide.cpp @@ -519,7 +519,7 @@ double Nuclide::nu(double E, EmissionMode mode, int group) const case EmissionMode::prompt: return (*fission_rx_[0]->products_[0].yield_)(E); case EmissionMode::delayed: - if (n_precursor_ > 0) { + if (n_precursor_ > 0 && settings::create_delayed_neutrons) { auto rx = fission_rx_[0]; if (group >= 1 && group < rx->products_.size()) { // If delayed group specified, determine yield immediately @@ -544,7 +544,7 @@ double Nuclide::nu(double E, EmissionMode mode, int group) const return 0.0; } case EmissionMode::total: - if (total_nu_) { + if (total_nu_ && settings::create_delayed_neutrons) { return (*total_nu_)(E); } else { return (*fission_rx_[0]->products_[0].yield_)(E); diff --git a/src/settings.cpp b/src/settings.cpp index 6386ce52bd..1b822f3b96 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -44,6 +44,7 @@ bool assume_separate {false}; bool check_overlaps {false}; bool cmfd_run {false}; bool confidence_intervals {false}; +bool create_delayed_neutrons {true}; bool create_fission_neutrons {true}; bool delayed_photon_scaling {true}; bool entropy_on {false}; @@ -872,6 +873,12 @@ void read_settings_xml(pugi::xml_node root) } } + // Check whether create delayed neutrons in fission + if (check_for_node(root, "create_delayed_neutrons")) { + create_delayed_neutrons = + get_node_value_bool(root, "create_delayed_neutrons"); + } + // Check whether create fission sites if (run_mode == RunMode::FIXED_SOURCE) { if (check_for_node(root, "create_fission_neutrons")) { From 8b1ecaad09546901231dc0890e55fc57622b77bf Mon Sep 17 00:00:00 2001 From: Christopher Fichtlscherer Date: Wed, 11 Jan 2023 15:38:16 -0500 Subject: [PATCH 260/265] deleted white spaces --- openmc/settings.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/openmc/settings.py b/openmc/settings.py index 3f5873c0a7..2210b23a28 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -465,7 +465,7 @@ class Settings: return self._create_fission_neutrons @property - def create_delayed_neutrons(self) -> bool: + def create_delayed_neutrons(self) -> bool: return self._create_delayed_neutrons @property @@ -875,7 +875,7 @@ class Settings: create_fission_neutrons, bool) self._create_fission_neutrons = create_fission_neutrons - @create_delayed_neutrons.setter + @create_delayed_neutrons.setter def create_delayed_neutrons(self, create_delayed_neutrons: bool): cv.check_type('Whether create only prompt neutrons', create_delayed_neutrons, bool) @@ -1222,7 +1222,7 @@ class Settings: elem = ET.SubElement(root, "create_fission_neutrons") elem.text = str(self._create_fission_neutrons).lower() - def _create_create_delayed_neutrons_subelement(self, root): + def _create_create_delayed_neutrons_subelement(self, root): if self._create_delayed_neutrons is not None: elem = ET.SubElement(root, "create_delayed_neutrons") elem.text = str(self._create_delayed_neutrons).lower() @@ -1552,7 +1552,7 @@ class Settings: if text is not None: self.create_fission_neutrons = text in ('true', '1') - def _create_delayed_neutrons_from_xml_element(self, root): + def _create_delayed_neutrons_from_xml_element(self, root): text = get_text(root, 'create_delayed_neutrons') if text is not None: self.create_delayed_neutrons = text in ('true', '1') From 3ba117fcd95afa1f8aba745dd368db705a3a5102 Mon Sep 17 00:00:00 2001 From: Christopher Fichtlscherer Date: Wed, 11 Jan 2023 15:41:31 -0500 Subject: [PATCH 261/265] indentation level change --- openmc/settings.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openmc/settings.py b/openmc/settings.py index 2210b23a28..79d28c44b7 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1222,7 +1222,7 @@ class Settings: elem = ET.SubElement(root, "create_fission_neutrons") elem.text = str(self._create_fission_neutrons).lower() - def _create_create_delayed_neutrons_subelement(self, root): + def _create_create_delayed_neutrons_subelement(self, root): if self._create_delayed_neutrons is not None: elem = ET.SubElement(root, "create_delayed_neutrons") elem.text = str(self._create_delayed_neutrons).lower() From afa490f6a6c98e41062c180eb74fae20ddffdad4 Mon Sep 17 00:00:00 2001 From: Josh May Date: Wed, 11 Jan 2023 13:27:06 -0800 Subject: [PATCH 262/265] Apply suggestions from code review Co-authored-by: Paul Romano --- openmc/cell.py | 3 +-- tests/unit_tests/test_cell.py | 8 ++++---- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/openmc/cell.py b/openmc/cell.py index cea362ed8f..a8e1178f41 100644 --- a/openmc/cell.py +++ b/openmc/cell.py @@ -518,8 +518,7 @@ class Cell(IDManagerMixin): paths = self._paths self._paths = None - clone = openmc.Cell() - clone.name = self.name + clone = openmc.Cell(name=self.name) clone.volume = self.volume if self.temperature is not None: clone.temperature = self.temperature diff --git a/tests/unit_tests/test_cell.py b/tests/unit_tests/test_cell.py index 4185e9a44c..cef77f1608 100644 --- a/tests/unit_tests/test_cell.py +++ b/tests/unit_tests/test_cell.py @@ -76,8 +76,8 @@ def test_clone(): # Add optional properties to the original cell to ensure they're cloned successfully c.temperature = 650. - c.translation = [1,2,3] - c.rotation = [4,5,6] + c.translation = (1., 2., 3.) + c.rotation = (4., 5., 6.) c.volume = 100 c5 = c.clone(clone_materials=False, clone_regions=False) @@ -92,8 +92,8 @@ def test_clone(): # Mutate the original to ensure the changes are not seen in the clones c.fill = openmc.Material() c.region = +openmc.ZCylinder() - c.translation = [-1,-2,-3] - c.rotation = [-4,-5,-6] + c.translation = (-1., -2., -3.) + c.rotation = (-4., -5., -6.) c.temperature = 1 c.volume = 1 assert c5.fill != c.fill From f7c1a57b15ba1fe5bb697db077bf4cd29d595f79 Mon Sep 17 00:00:00 2001 From: Christopher Fichtlscherer Date: Wed, 11 Jan 2023 16:55:27 -0500 Subject: [PATCH 263/265] settings change element --- openmc/settings.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openmc/settings.py b/openmc/settings.py index 79d28c44b7..911131387e 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1655,7 +1655,7 @@ class Settings: self._create_resonance_scattering_subelement(element) self._create_volume_calcs_subelement(element) self._create_create_fission_neutrons_subelement(element) - self._create_create_delayed_neutrons_subelement(root_element) + self._create_create_delayed_neutrons_subelement(element) self._create_delayed_photon_scaling_subelement(element) self._create_event_based_subelement(element) self._create_max_particles_in_flight_subelement(element) From 36249d3742dabfe95ee50e2aac822caf72f1e1a9 Mon Sep 17 00:00:00 2001 From: Christopher Fichtlscherer <29277544+cfichtlscherer@users.noreply.github.com> Date: Thu, 12 Jan 2023 06:25:52 -0500 Subject: [PATCH 264/265] Update openmc/settings.py yes Co-authored-by: Paul Romano --- openmc/settings.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openmc/settings.py b/openmc/settings.py index 911131387e..9330d99b6e 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1748,7 +1748,7 @@ class Settings: settings._ufs_mesh_from_xml_element(elem, meshes) settings._resonance_scattering_from_xml_element(elem) settings._create_fission_neutrons_from_xml_element(elem) - settings._create_delayed_neutrons_from_xml_element(root) + settings._create_delayed_neutrons_from_xml_element(elem) settings._delayed_photon_scaling_from_xml_element(elem) settings._event_based_from_xml_element(elem) settings._max_particles_in_flight_from_xml_element(elem) From a66d4da53f1ce87f6a14902636ab12eb765c895b Mon Sep 17 00:00:00 2001 From: Christopher Fichtlscherer <29277544+cfichtlscherer@users.noreply.github.com> Date: Thu, 12 Jan 2023 06:26:07 -0500 Subject: [PATCH 265/265] Update openmc/settings.py version number Co-authored-by: Paul Romano --- openmc/settings.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/openmc/settings.py b/openmc/settings.py index 9330d99b6e..22a83509f3 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -224,11 +224,11 @@ class Settings: weight_windows : WeightWindows iterable of WeightWindows Weight windows to use for variance reduction - .. versionadded:: 0.13.3 + .. versionadded:: 0.13 create_delayed_neutrons : bool Whether delayed neutrons are created in fission. - .. versionadded:: 0.13 + .. versionadded:: 0.13.3 weight_windows_on : bool Whether weight windows are enabled