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 01/66] 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 521b46cfc..7be54dc3e 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 b251a3ca8..55f8ae20d 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 d3d00571a..06ca5990a 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 262b3a884..a1db07291 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 1e061b235..ba1a30e30 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 e99eec52c..1fe62961d 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 30dfa5ed5..d7fae8361 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 bcdcf7ecf..9eff4aed7 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 eb0d4936c..3f3e97054 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 02/66] 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 1fe62961d..0a293eb0f 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 03/66] 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 55f8ae20d..eef557088 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 9eff4aed7..948307521 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 04/66] 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 eef557088..10e64773e 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 05/66] 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 06ca5990a..d3d00571a 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 06/66] 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 7be54dc3e..7080accfd 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 10e64773e..30d8ffb7d 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 a1db07291..109f7caff 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 0a293eb0f..15d1f8ac9 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 d7fae8361..13acbba1f 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 948307521..bad499772 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 07/66] 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 30d8ffb7d..47e3e6a16 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 109f7caff..23995e7af 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 ba1a30e30..9bb447005 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 13acbba1f..e894084e2 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 bad499772..e19640314 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 3f3e97054..87c24eedd 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 08/66] 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 e894084e2..9531e9f43 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 09/66] 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 7080accfd..2815230d4 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 10/66] 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 15d1f8ac9..de4a22cb8 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 11/66] 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 23995e7af..806297c4e 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 12/66] 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 9531e9f43..32f5f2e86 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 13/66] 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 000000000..c18087f23 --- /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 14/66] 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 74be9ba0b..9e5ba1ffd 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 15/66] 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 8b43f1a2a..ab5a8c5af 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 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 16/66] 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 3396d7f25..c700b3f2d 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 17/66] 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 000000000..e69de29bb diff --git a/tests/regression_tests/ncrystal/inputs_true.dat b/tests/regression_tests/ncrystal/inputs_true.dat new file mode 100644 index 000000000..7a3f20eb3 --- /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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000000000..3ef0306fd --- /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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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 000000000..51a0f07b7 --- /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 18/66] 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 ab5a8c5af..1886a772b 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 19/66] 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 9bb447005..b01c75d45 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 c14b0d9c2..55e2ec11b 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 87c24eedd..be7228d68 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 51a0f07b7..0a47d634d 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 20/66] 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 e267c0d8e..321f18874 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 21/66] 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 aa40eb90b..e5390be1e 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 22/66] 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 c700b3f2d..64e4fac3d 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 1886a772b..1eaae846c 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 23/66] 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 c18087f23..5f577b8da 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 4c69ba70b..f3a29273f 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 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 24/66] 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 5f577b8da..78a1a44f2 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 25/66] 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 78a1a44f2..715e4da94 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 26/66] 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 715e4da94..8e75cc60a 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 27/66] 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 8e75cc60a..c080c16d8 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 ${INST_DIR}/setup.sh From 3e6bb9d5f669d2729fa96acdb4894ed1d338f2c5 Mon Sep 17 00:00:00 2001 From: Jose Ignacio Marquez Damian <22483345+marquezj@users.noreply.github.com> Date: Mon, 28 Nov 2022 08:51:23 -0300 Subject: [PATCH 28/66] Upgrade installation script to NCrystal 3.5.0 --- tools/ci/gha-install-ncrystal.sh | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh index c080c16d8..18472dfa6 100755 --- a/tools/ci/gha-install-ncrystal.sh +++ b/tools/ci/gha-install-ncrystal.sh @@ -21,13 +21,12 @@ cmake \ "${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 29/66] 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 18472dfa6..1bcc89627 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 30/66] 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 1bcc89627..390b7dba5 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 31/66] 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 f3a29273f..95fe70abe 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 32/66] 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 95fe70abe..f5779c935 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 33/66] 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 c791167e9..4c125b529 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 34/66] 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 d0e2beb82..162e3aad7 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 35/66] 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 4c125b529..85fdef49f 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 36/66] 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 64e4fac3d..0b87913e5 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 1eaae846c..a3c05f421 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 390b7dba5..16f77e13e 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 f2c28706a6eaf2206da5ff73867c279946b55f4b Mon Sep 17 00:00:00 2001 From: Thomas Kittelmann Date: Wed, 7 Dec 2022 10:12:23 +0100 Subject: [PATCH 37/66] 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 2815230d4..5c4d489e3 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 a3c05f421..fbf9effd8 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 de4a22cb8..298731c92 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 0a47d634d..3137515d4 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 f5779c935..ac10bb3f6 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 85fdef49f..1f1c3a1eb 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 38/66] 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 3137515d4..2a789dac7 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 ecfa94e0ff0c50a83c8db61444e5cad888b16c7a Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 8 Sep 2022 14:25:22 -0500 Subject: [PATCH 39/66] 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 960abec2f..1eaf90c97 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 c433ffe2c..78ee6f775 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 06c581b42..91cbe4196 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 55bfb4f09..d5521d998 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 0db842201..d00242438 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 f9b9d0694..d526bc53f 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 508c76ac4..0be70cdba 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 e0574d76d..2d4c13963 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 a2431cf1c..ac9d7f14e 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 e6213e5f0..48f6bfc9b 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 f439cedc3..372ed3510 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 b84b91a7f..2e9673d5f 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 196c8d770..d5ae4bddb 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 c47f888c8..2d49c0626 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 37e024fe2..f88be2602 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 40/66] 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 15a1128f8..c93b42b88 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 b688e6d23..18c501372 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 96199ec2a..d21f361e6 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 d7d5907a2..f90eab134 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 41/66] 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 f08333279..ae329dd7e 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 42/66] 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 f90eab134..bc3633c8c 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 577157b846ac6885251ade59456967e4102d6b24 Mon Sep 17 00:00:00 2001 From: shimwell Date: Sat, 24 Dec 2022 22:40:34 +0000 Subject: [PATCH 43/66] 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 a43899daa..eb7fa8200 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 9db112fd2..843c01def 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 44/66] 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 16760868e..e2d18d085 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 45/66] 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 2aa538012..8169ca4d2 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 1c2e1b70e..eebe0f895 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 46/66] 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 8169ca4d2..cea362ed8 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 47/66] 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 eebe0f895..4185e9a44 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 48/66] 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 000000000..a3f1ff666 --- /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 49/66] 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 336982ac6..760a08e90 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 50/66] 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 000000000..4fe6e044a --- /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 51/66] 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 2c155980e..79af65879 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 52/66] 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 1dee3f90e..4737ff47b 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 5326ad6de..8db9bb628 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 000000000..36038d50c --- /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 806297c4e..382f0f0dd 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 fb5f8387a..9cd430deb 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 25014c448..2d55d6a04 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 000000000..b39f62d90 --- /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 c1ef282f7..46bf37aa9 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 6f6e4e090..9174d4114 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 53/66] 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 0b87913e5..2cafa8691 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 9e5ba1ffd..537dda824 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 fbf9effd8..83af55805 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 382f0f0dd..6e7327d38 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 2a789dac7..cb6421b03 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 54/66] 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 68ec199c3..7844ec131 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 55/66] 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 36038d50c..5a3882df9 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 9cd430deb..90f1e8c29 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 2d55d6a04..74a8d7e35 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 46bf37aa9..7cb8040f6 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 9174d4114..2fda352ce 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 56/66] 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 a43899daa..f9aecca9c 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 9db112fd2..f8c523071 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 57/66] 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 eb7fa8200..a9817fbbb 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 843c01def..0e952ab0f 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 58/66] 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 1ea66d1f6..15e86ca61 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 59/66] merge conflict --- openmc/settings.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/openmc/settings.py b/openmc/settings.py index 6f3ef5ab4..6271e05dc 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 60/66] 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 71ca61d54..6dff76838 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 90f1e8c29..806288efe 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 6271e05dc..3f5873c0a 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 0c2c62310..59294b28c 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 134e2d6b9..99ed44b11 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 6386ce52b..1b822f3b9 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 61/66] 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 3f5873c0a..2210b23a2 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 62/66] 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 2210b23a2..79d28c44b 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 63/66] 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 cea362ed8..a8e1178f4 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 4185e9a44..cef77f160 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 64/66] 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 79d28c44b..911131387 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 65/66] 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 911131387..9330d99b6 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 66/66] 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 9330d99b6..22a83509f 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