address PR comments

src/bank.cpp

@@ -16,15 +16,15 @@ namespace openmc {
 
 namespace simulation {
 
-vector<ParticleBank> source_bank;
+vector<SourceSite> source_bank;
 
-SharedArray<ParticleBank> surf_source_bank;
+SharedArray<SourceSite> surf_source_bank;
 
 // The fission bank is allocated as a SharedArray, rather than a vector, as it will
 // be shared by all threads in the simulation. It will be allocated to a fixed
 // maximum capacity in the init_fission_bank() function. Then, Elements will be
 // added to it by using SharedArray's special thread_safe_append() function.
-SharedArray<ParticleBank> fission_bank;
+SharedArray<SourceSite> fission_bank;
 
 // Each entry in this vector corresponds to the number of progeny produced
 // this generation for the particle located at that index. This vector is
@@ -80,8 +80,8 @@ void sort_fission_bank()
   // We need a scratch vector to make permutation of the fission bank into
   // sorted order easy. Under normal usage conditions, the fission bank is
   // over provisioned, so we can use that as scratch space.
-  ParticleBank* sorted_bank;
-  vector<ParticleBank> sorted_bank_holder;
+  SourceSite* sorted_bank;
+  vector<SourceSite> sorted_bank_holder;
 
   // If there is not enough space, allocate a temporary vector and point to it
   if (simulation::fission_bank.size() > simulation::fission_bank.capacity() / 2) {

src/cross_sections.cpp

@@ -181,8 +181,8 @@ void read_cross_sections_xml()
   }
 }
 
-void read_ce_cross_sections(const vector<std::vector<double>>& nuc_temps,
-  const vector<std::vector<double>>& thermal_temps)
+void read_ce_cross_sections(const vector<vector<double>>& nuc_temps,
+  const vector<vector<double>>& thermal_temps)
 {
   std::unordered_set<std::string> already_read;
 

src/eigenvalue.cpp

@@ -137,7 +137,7 @@ void synchronize_bank()
   // Allocate temporary source bank -- we don't really know how many fission
   // sites were created, so overallocate by a factor of 3
   int64_t index_temp = 0;
-  vector<ParticleBank> temp_sites(3 * simulation::work_per_rank);
+  vector<SourceSite> temp_sites(3 * simulation::work_per_rank);
 
   for (int64_t i = 0; i < simulation::fission_bank.size(); i++ ) {
     const auto& site = simulation::fission_bank[i];

src/geometry_aux.cpp

@@ -191,8 +191,8 @@ assign_temperatures()
 
 //==============================================================================
 
-void get_temperatures(vector<std::vector<double>>& nuc_temps,
-  vector<std::vector<double>>& thermal_temps)
+void get_temperatures(
+  vector<vector<double>>& nuc_temps, vector<vector<double>>& thermal_temps)
 {
   for (const auto& cell : model::cells) {
     // Skip non-material cells.

src/initialize.cpp

@@ -132,7 +132,7 @@ void initialize_mpi(MPI_Comm intracomm)
   mpi::master = (mpi::rank == 0);
 
   // Create bank datatype
-  ParticleBank b;
+  SourceSite b;
   MPI_Aint disp[9];
   MPI_Get_address(&b.r, &disp[0]);
   MPI_Get_address(&b.u, &disp[1]);

src/material.cpp

@@ -1144,9 +1144,9 @@ double sternheimer_adjustment(const vector<double>& f,
   return rho;
 }
 
-double density_effect(const vector<double>& f,
-  const std::vector<double>& e_b_sq, double e_p_sq, double n_conduction,
-  double rho, double E, double tol, int max_iter)
+double density_effect(const vector<double>& f, const vector<double>& e_b_sq,
+  double e_p_sq, double n_conduction, double rho, double E, double tol,
+  int max_iter)
 {
   // Get the total number of oscillators
   int n = f.size();

src/math_functions.cpp

@@ -556,7 +556,7 @@ void calc_zn(int n, double rho, double phi, double zn[]) {
   // ===========================================================================
   // Calculate R_pq(rho)
   // Matrix forms of the coefficients which are easier to work with
-  vector<std::vector<double>> zn_mat(n + 1, std::vector<double>(n + 1));
+  vector<vector<double>> zn_mat(n + 1, vector<double>(n + 1));
 
   // Fill the main diagonal first (Eq 3.9 in Chong)
   for (int p = 0; p <= n; p++) {

src/mesh.cpp

@@ -284,7 +284,7 @@ int StructuredMesh::n_surface_bins() const
 }
 
 xt::xtensor<double, 1> StructuredMesh::count_sites(
-  const ParticleBank* bank, int64_t length, bool* outside) const
+  const SourceSite* bank, int64_t length, bool* outside) const
 {
   // Determine shape of array for counts
   std::size_t m = this->n_bins();
@@ -938,7 +938,7 @@ RegularMesh::surface_bins_crossed(Position r0,
   }
 }
 
-std::pair<vector<double>, std::vector<double>> RegularMesh::plot(
+std::pair<vector<double>, vector<double>> RegularMesh::plot(
   Position plot_ll, Position plot_ur) const
 {
   // Figure out which axes lie in the plane of the plot.
@@ -988,7 +988,7 @@ void RegularMesh::to_hdf5(hid_t group) const
 }
 
 xt::xtensor<double, 1> RegularMesh::count_sites(
-  const ParticleBank* bank, int64_t length, bool* outside) const
+  const SourceSite* bank, int64_t length, bool* outside) const
 {
   // Determine shape of array for counts
   std::size_t m = this->n_bins();
@@ -1264,7 +1264,7 @@ int RectilinearMesh::get_index_in_direction(double r, int i) const
   return lower_bound_index(grid_[i].begin(), grid_[i].end(), r) + 1;
 }
 
-std::pair<vector<double>, std::vector<double>> RectilinearMesh::plot(
+std::pair<vector<double>, vector<double>> RectilinearMesh::plot(
   Position plot_ll, Position plot_ur) const
 {
   // Figure out which axes lie in the plane of the plot.
@@ -1923,7 +1923,7 @@ int MOABMesh::get_index_from_bin(int bin) const
   return bin;
 }
 
-std::pair<vector<double>, std::vector<double>> MOABMesh::plot(
+std::pair<vector<double>, vector<double>> MOABMesh::plot(
   Position plot_ll, Position plot_ur) const
 {
   // TODO: Implement mesh lines
@@ -2337,7 +2337,7 @@ LibMesh::get_bin_from_element(const libMesh::Elem* elem) const
   return bin;
 }
 
-std::pair<vector<double>, std::vector<double>> LibMesh::plot(
+std::pair<vector<double>, vector<double>> LibMesh::plot(
   Position plot_ll, Position plot_ur) const
 {
   return {};

src/mgxs.cpp

@@ -32,7 +32,7 @@ namespace openmc {
 void Mgxs::init(const std::string& in_name, double in_awr,
   const vector<double>& in_kTs, bool in_fissionable,
   AngleDistributionType in_scatter_format, bool in_is_isotropic,
-  const vector<double>& in_polar, const std::vector<double>& in_azimuthal)
+  const vector<double>& in_polar, const vector<double>& in_azimuthal)
 {
   // Set the metadata
   name = in_name;
@@ -307,7 +307,7 @@ Mgxs::Mgxs(
 //==============================================================================
 
 Mgxs::Mgxs(const std::string& in_name, const vector<double>& mat_kTs,
-  const vector<Mgxs*>& micros, const std::vector<double>& atom_densities,
+  const vector<Mgxs*>& micros, const vector<double>& atom_densities,
   int num_group, int num_delay)
   : num_groups(num_group), num_delayed_groups(num_delay)
 {
@@ -415,8 +415,8 @@ Mgxs::Mgxs(const std::string& in_name, const vector<double>& mat_kTs,
 
 //==============================================================================
 
-void Mgxs::combine(const vector<Mgxs*>& micros,
-  const std::vector<double>& scalars, const vector<int>& micro_ts, int this_t)
+void Mgxs::combine(const vector<Mgxs*>& micros, const vector<double>& scalars,
+  const vector<int>& micro_ts, int this_t)
 {
   // Build the vector of pointers to the xs objects within micros
   vector<XsData*> those_xs(micros.size());

src/mgxs_interface.cpp

@@ -29,8 +29,7 @@ namespace data {
 }
 
 MgxsInterface::MgxsInterface(const std::string& path_cross_sections,
-  const vector<std::string> xs_to_read,
-  const vector<std::vector<double>> xs_temps)
+  const vector<std::string> xs_to_read, const vector<vector<double>> xs_temps)
 {
   read_header(path_cross_sections);
   set_nuclides_and_temperatures(xs_to_read, xs_temps);
@@ -38,7 +37,7 @@ MgxsInterface::MgxsInterface(const std::string& path_cross_sections,
 }
 
 void MgxsInterface::set_nuclides_and_temperatures(
-  vector<std::string> xs_to_read, vector<std::vector<double>> xs_temps)
+  vector<std::string> xs_to_read, vector<vector<double>> xs_temps)
 {
   // Check to remove all duplicates
   xs_to_read_ = xs_to_read;
@@ -148,9 +147,9 @@ void MgxsInterface::create_macro_xs()
 
 //==============================================================================
 
-vector<std::vector<double>> MgxsInterface::get_mat_kTs()
+vector<vector<double>> MgxsInterface::get_mat_kTs()
 {
-  vector<std::vector<double>> kTs(model::materials.size());
+  vector<vector<double>> kTs(model::materials.size());
 
   for (const auto& cell : model::cells) {
     // Skip non-material cells
@@ -246,8 +245,8 @@ void put_mgxs_header_data_to_globals()
 void set_mg_interface_nuclides_and_temps()
 {
   // Get temperatures from global data
-  vector<std::vector<double>> nuc_temps(data::nuclide_map.size());
-  vector<std::vector<double>> dummy;
+  vector<vector<double>> nuc_temps(data::nuclide_map.size());
+  vector<vector<double>> dummy;
   get_temperatures(nuc_temps, dummy);
 
   // Build vector of nuclide names which are to be read

src/particle.cpp

@@ -50,7 +50,7 @@ void Particle::create_secondary(
   n_bank_second() += 1;
 }
 
-void Particle::from_source(const ParticleBank* src)
+void Particle::from_source(const SourceSite* src)
 {
   // Reset some attributes
   clear();
@@ -368,7 +368,7 @@ Particle::cross_surface()
   }
 
   if (surf->surf_source_ && simulation::current_batch == settings::n_batches) {
-    ParticleBank site;
+    SourceSite site;
     site.r = r();
     site.u = u();
     site.E = E();

src/physics.cpp

@@ -187,7 +187,7 @@ create_fission_sites(Particle& p, int i_nuclide, const Reaction& rx)
 
   for (int i = 0; i < nu; ++i) {
     // Initialize fission site object with particle data
-    ParticleBank site;
+    SourceSite site;
     site.r = p.r();
     site.particle = ParticleType::neutron;
     site.wgt = 1. / weight;
@@ -1015,7 +1015,7 @@ sample_cxs_target_velocity(double awr, double E, Direction u, double kT, uint64_
 }
 
 void sample_fission_neutron(int i_nuclide, const Reaction& rx, double E_in,
-  ParticleBank* site, uint64_t* seed)
+  SourceSite* site, uint64_t* seed)
 {
   // Sample cosine of angle -- fission neutrons are always emitted
   // isotropically. Sometimes in ACE data, fission reactions actually have

src/physics_mg.cpp

@@ -127,7 +127,7 @@ create_fission_sites(Particle& p)
 
   for (int i = 0; i < nu; ++i) {
     // Initialize fission site object with particle data
-    ParticleBank site;
+    SourceSite site;
     site.r = p.r();
     site.particle = ParticleType::neutron;
     site.wgt = 1. / weight;

src/source.cpp

@@ -140,9 +140,9 @@ IndependentSource::IndependentSource(pugi::xml_node node)
   }
 }
 
-ParticleBank IndependentSource::sample(uint64_t* seed) const
+SourceSite IndependentSource::sample(uint64_t* seed) const
 {
-  ParticleBank site;
+  SourceSite site;
 
   // Set weight to one by default
   site.wgt = 1.0;
@@ -262,7 +262,7 @@ FileSource::FileSource(std::string path)
   file_close(file_id);
 }
 
-ParticleBank FileSource::sample(uint64_t* seed) const
+SourceSite FileSource::sample(uint64_t* seed) const
 {
   size_t i_site = sites_.size()*prn(seed);
   return sites_[i_site];
@@ -348,7 +348,7 @@ void initialize_source()
   }
 }
 
-ParticleBank sample_external_source(uint64_t* seed)
+SourceSite sample_external_source(uint64_t* seed)
 {
   // Determine total source strength
   double total_strength = 0.0;
@@ -367,7 +367,7 @@ ParticleBank sample_external_source(uint64_t* seed)
   }
 
   // Sample source site from i-th source distribution
-  ParticleBank site {model::external_sources[i]->sample(seed)};
+  SourceSite site {model::external_sources[i]->sample(seed)};
 
   // If running in MG, convert site.E to group
   if (!settings::run_CE) {

src/state_point.cpp

@@ -512,17 +512,16 @@ hid_t h5banktype() {
   // - openmc/statepoint.py
   // - docs/source/io_formats/statepoint.rst
   // - docs/source/io_formats/source.rst
-  hid_t banktype = H5Tcreate(H5T_COMPOUND, sizeof(struct ParticleBank));
-  H5Tinsert(banktype, "r", HOFFSET(ParticleBank, r), postype);
-  H5Tinsert(banktype, "u", HOFFSET(ParticleBank, u), postype);
-  H5Tinsert(banktype, "E", HOFFSET(ParticleBank, E), H5T_NATIVE_DOUBLE);
-  H5Tinsert(banktype, "wgt", HOFFSET(ParticleBank, wgt), H5T_NATIVE_DOUBLE);
-  H5Tinsert(banktype, "delayed_group", HOFFSET(ParticleBank, delayed_group),
+  hid_t banktype = H5Tcreate(H5T_COMPOUND, sizeof(struct SourceSite));
+  H5Tinsert(banktype, "r", HOFFSET(SourceSite, r), postype);
+  H5Tinsert(banktype, "u", HOFFSET(SourceSite, u), postype);
+  H5Tinsert(banktype, "E", HOFFSET(SourceSite, E), H5T_NATIVE_DOUBLE);
+  H5Tinsert(banktype, "wgt", HOFFSET(SourceSite, wgt), H5T_NATIVE_DOUBLE);
+  H5Tinsert(banktype, "delayed_group", HOFFSET(SourceSite, delayed_group),
     H5T_NATIVE_INT);
+  H5Tinsert(banktype, "surf_id", HOFFSET(SourceSite, surf_id), H5T_NATIVE_INT);
   H5Tinsert(
-    banktype, "surf_id", HOFFSET(ParticleBank, surf_id), H5T_NATIVE_INT);
-  H5Tinsert(
-    banktype, "particle", HOFFSET(ParticleBank, particle), H5T_NATIVE_INT);
+    banktype, "particle", HOFFSET(SourceSite, particle), H5T_NATIVE_INT);
 
   H5Tclose(postype);
   return banktype;
@@ -598,9 +597,9 @@ write_source_bank(hid_t group_id, bool surf_source_bank)
 
   // Set vectors for source bank and starting bank index of each process
   vector<int64_t>* bank_index = &simulation::work_index;
-  vector<ParticleBank>* source_bank = &simulation::source_bank;
+  vector<SourceSite>* source_bank = &simulation::source_bank;
   vector<int64_t> surf_source_index_vector;
-  vector<ParticleBank> surf_source_bank_vector;
+  vector<SourceSite> surf_source_bank_vector;
 
   // Reset dataspace sizes and vectors for surface source bank
   if (surf_source_bank) {
@@ -656,7 +655,7 @@ write_source_bank(hid_t group_id, bool surf_source_bank)
 
     // Save source bank sites since the array is overwritten below
 #ifdef OPENMC_MPI
-    vector<ParticleBank> temp_source {source_bank->begin(), source_bank->end()};
+    vector<SourceSite> temp_source {source_bank->begin(), source_bank->end()};
 #endif
 
     for (int i = 0; i < mpi::n_procs; ++i) {
@@ -714,7 +713,7 @@ std::string dtype_member_names(hid_t dtype_id)
 }
 
 void read_source_bank(
-  hid_t group_id, vector<ParticleBank>& sites, bool distribute)
+  hid_t group_id, vector<SourceSite>& sites, bool distribute)
 {
   hid_t banktype = h5banktype();
 

src/volume_calc.cpp

@@ -98,9 +98,9 @@ vector<VolumeCalculation::Result> VolumeCalculation::execute() const
 {
   // Shared data that is collected from all threads
   int n = domain_ids_.size();
-  vector<std::vector<int>> master_indices(
+  vector<vector<int>> master_indices(
     n); // List of material indices for each domain
-  vector<std::vector<int>> master_hits(
+  vector<vector<int>> master_hits(
     n); // Number of hits for each material in each domain
   int iterations = 0;
 
@@ -121,8 +121,8 @@ vector<VolumeCalculation::Result> VolumeCalculation::execute() const
     #pragma omp parallel
     {
       // Variables that are private to each thread
-      vector<std::vector<int>> indices(n);
-      vector<std::vector<int>> hits(n);
+      vector<vector<int>> indices(n);
+      vector<vector<int>> hits(n);
       Particle p;
 
       // Sample locations and count hits