33839677304

Committed 04 Sep 2026 05:13AM UTC coverage: 81.383% (+0.02%) from 81.366%

Build # 33839677304

Build Type

Pull #3734

github

Committed by

web-flow

Commit Message

Merge 06d4586ae into 4cf988693

Pull Request Pull Request #3734: Specify temperature from a field (structured mesh only)

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294 of 312 new or added lines in 16 files covered. (94.23%)

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75.44

/src/initialize.cpp

#include "openmc/initialize.h"

#include <clocale>
#include <cstddef>
#include <cstdlib> // for getenv
#include <cstring>
#include <string>

#ifdef _OPENMP
#include <omp.h>
#endif
#include <fmt/core.h>

#include "openmc/capi.h"
#include "openmc/chain.h"
#include "openmc/constants.h"
#include "openmc/cross_sections.h"
#include "openmc/error.h"
#include "openmc/file_utils.h"
#include "openmc/geometry_aux.h"
#include "openmc/hdf5_interface.h"
#include "openmc/material.h"
#include "openmc/memory.h"
#include "openmc/message_passing.h"
#include "openmc/mgxs_interface.h"
#include "openmc/nuclide.h"
#include "openmc/openmp_interface.h"
#include "openmc/output.h"
#include "openmc/plot.h"
#include "openmc/random_lcg.h"
#include "openmc/settings.h"
#include "openmc/simulation.h"
#include "openmc/string_utils.h"
#include "openmc/summary.h"
#include "openmc/tallies/tally.h"
#include "openmc/thermal.h"
#include "openmc/timer.h"
#include "openmc/vector.h"
#include "openmc/weight_windows.h"

#ifdef OPENMC_LIBMESH_ENABLED
#include "libmesh/libmesh.h"
#endif

int openmc_init(int argc, char* argv[], const void* intracomm)
{
  using namespace openmc;

#ifdef OPENMC_MPI
  // Check if intracomm was passed
  MPI_Comm comm;
  if (intracomm) {
    comm = *static_cast<const MPI_Comm*>(intracomm);
  } else {
    comm = MPI_COMM_WORLD;
  }

  // Initialize MPI for C++
  initialize_mpi(comm);
#endif

  // Parse command-line arguments
  int err = parse_command_line(argc, argv);
  if (err)
    return err;

#ifdef OPENMC_LIBMESH_ENABLED
  const int n_threads = num_threads();
  // initialize libMesh if it hasn't been initialized already
  // (if initialized externally, the libmesh_init object needs to be provided
  // also)
  if (!settings::libmesh_init && !libMesh::initialized()) {
#if defined(OPENMC_MPI) && defined(LIBMESH_HAVE_MPI)
    // Pass command line arguments, the OpenMC communicator, and thread count.
    // Because libMesh was not initialized, we assume that OpenMC is the primary
    // application and that its main MPI comm should be used.
    settings::libmesh_init =
      make_unique<libMesh::LibMeshInit>(argc, argv, comm, n_threads);
#else
    // libMesh was built without MPI, so use its serial communicator.
    settings::libmesh_init =
      make_unique<libMesh::LibMeshInit>(argc, argv, 0, n_threads);
#endif

    settings::libmesh_comm = &(settings::libmesh_init->comm());
  }

#endif

  // Start total and initialization timer
  simulation::time_total.start();
  simulation::time_initialize.start();

#ifdef _OPENMP
  // If OMP_SCHEDULE is not set, default to a static schedule
  char* envvar = std::getenv("OMP_SCHEDULE");
  if (!envvar) {
    omp_set_schedule(omp_sched_static, 0);
  }
#endif

  // Initialize random number generator -- if the user specifies a seed and/or
  // stride, it will be re-initialized later
  openmc::openmc_set_seed(DEFAULT_SEED);
  openmc::openmc_set_stride(DEFAULT_STRIDE);

  // Copy previous locale and set locale to C. This is a workaround for an issue
  // whereby when openmc_init is called from the plotter, the Qt application
  // framework first calls std::setlocale, which affects how pugixml reads
  // floating point numbers due to a bug:
  // https://github.com/zeux/pugixml/issues/469
  std::string prev_locale = std::setlocale(LC_ALL, nullptr);
  if (std::setlocale(LC_ALL, "C") == NULL) {
    fatal_error("Cannot set locale to C.");
  }

  // Read XML input files
  if (!read_model_xml())
    read_separate_xml_files();

  if (!settings::properties_file.empty()) {
    openmc_properties_import(settings::properties_file.c_str());
  }

  // Reset locale to previous state
  if (std::setlocale(LC_ALL, prev_locale.c_str()) == NULL) {
    fatal_error("Cannot reset locale.");
  }

  // Write some initial output under the header if needed
  initial_output();

  // Check for particle restart run
  if (settings::particle_restart_run)
    settings::run_mode = RunMode::PARTICLE;

  // Stop initialization timer
  simulation::time_initialize.stop();
  simulation::time_total.stop();

  return 0;
}

namespace openmc {

#ifdef OPENMC_MPI
void initialize_mpi(MPI_Comm intracomm)
{
  mpi::intracomm = intracomm;

  // Initialize MPI
  int flag;
  MPI_Initialized(&flag);
  if (!flag)
    MPI_Init(nullptr, nullptr);

  // Determine number of processes and rank for each
  MPI_Comm_size(intracomm, &mpi::n_procs);
  MPI_Comm_rank(intracomm, &mpi::rank);
  mpi::master = (mpi::rank == 0);

  // Create bank datatype
  SourceSite b;
  MPI_Aint disp[15];
  MPI_Get_address(&b.r, &disp[0]);
  MPI_Get_address(&b.u, &disp[1]);
  MPI_Get_address(&b.E, &disp[2]);
  MPI_Get_address(&b.time, &disp[3]);
  MPI_Get_address(&b.wgt, &disp[4]);
  MPI_Get_address(&b.delayed_group, &disp[5]);
  MPI_Get_address(&b.surf_id, &disp[6]);
  MPI_Get_address(&b.particle, &disp[7]);
  MPI_Get_address(&b.parent_nuclide, &disp[8]);
  MPI_Get_address(&b.parent_id, &disp[9]);
  MPI_Get_address(&b.progeny_id, &disp[10]);
  MPI_Get_address(&b.wgt_born, &disp[11]);
  MPI_Get_address(&b.wgt_ww_born, &disp[12]);
  MPI_Get_address(&b.n_split, &disp[13]);
  MPI_Get_address(&b.n_collision, &disp[14]);
  for (int i = 14; i >= 0; --i) {
    disp[i] -= disp[0];
  }

  // Block counts for each field
  int blocks[] = {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};

  // Types for each field
  MPI_Datatype types[] = {
    MPI_DOUBLE,  // r (3 doubles)
    MPI_DOUBLE,  // u (3 doubles)
    MPI_DOUBLE,  // E
    MPI_DOUBLE,  // time
    MPI_DOUBLE,  // wgt
    MPI_INT,     // delayed_group
    MPI_INT,     // surf_id
    MPI_INT,     // particle (enum)
    MPI_INT,     // parent_nuclide
    MPI_INT64_T, // parent_id
    MPI_INT64_T, // progeny_id
    MPI_DOUBLE,  // wgt_born
    MPI_DOUBLE,  // wgt_ww_born
    MPI_INT64_T, // n_split
    MPI_INT      // n_collision
  };

  MPI_Type_create_struct(15, blocks, disp, types, &mpi::source_site);
  MPI_Type_commit(&mpi::source_site);

  CollisionTrackSite bc;
  MPI_Aint dispc[16];
  MPI_Get_address(&bc.r, &dispc[0]);             // double
  MPI_Get_address(&bc.u, &dispc[1]);             // double
  MPI_Get_address(&bc.E, &dispc[2]);             // double
  MPI_Get_address(&bc.dE, &dispc[3]);            // double
  MPI_Get_address(&bc.time, &dispc[4]);          // double
  MPI_Get_address(&bc.wgt, &dispc[5]);           // double
  MPI_Get_address(&bc.event_mt, &dispc[6]);      // int
  MPI_Get_address(&bc.delayed_group, &dispc[7]); // int
  MPI_Get_address(&bc.cell_id, &dispc[8]);       // int
  MPI_Get_address(&bc.nuclide_id, &dispc[9]);    // int
  MPI_Get_address(&bc.material_id, &dispc[10]);  // int
  MPI_Get_address(&bc.universe_id, &dispc[11]);  // int
  MPI_Get_address(&bc.n_collision, &dispc[12]);  // int
  MPI_Get_address(&bc.particle, &dispc[13]);     // int
  MPI_Get_address(&bc.parent_id, &dispc[14]);    // int64_t
  MPI_Get_address(&bc.progeny_id, &dispc[15]);   // int64_t
  for (int i = 15; i >= 0; --i) {
    dispc[i] -= dispc[0];
  }

  int blocksc[] = {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};
  MPI_Datatype typesc[] = {MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE,
    MPI_DOUBLE, MPI_DOUBLE, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_INT,
    MPI_INT, MPI_INT, MPI_INT, MPI_INT64_T, MPI_INT64_T};

  MPI_Type_create_struct(
    16, blocksc, dispc, typesc, &mpi::collision_track_site);
  MPI_Type_commit(&mpi::collision_track_site);
}
#endif // OPENMC_MPI

int parse_command_line(int argc, char* argv[])
{
  int last_flag = 0;
  for (int i = 1; i < argc; ++i) {
    std::string arg {argv[i]};
    if (arg[0] == '-') {
      if (arg == "-p" || arg == "--plot") {
        settings::run_mode = RunMode::PLOTTING;
        settings::check_overlaps = true;

      } else if (arg == "-n" || arg == "--particles") {
        i += 1;
        settings::n_particles = std::stoll(argv[i]);

      } else if (arg == "-q" || arg == "--verbosity") {
        i += 1;
        settings::verbosity = std::stoi(argv[i]);
        if (settings::verbosity > 10 || settings::verbosity < 1) {
          auto msg = fmt::format("Invalid verbosity: {}.", settings::verbosity);
          set_errmsg(msg);
          return OPENMC_E_INVALID_ARGUMENT;
        }

      } else if (arg == "-e" || arg == "--event") {
        settings::event_based = true;
      } else if (arg == "-r" || arg == "--restart") {
        i += 1;
        // Check what type of file this is
        hid_t file_id = file_open(argv[i], 'r', true);
        std::string filetype;
        read_attribute(file_id, "filetype", filetype);
        file_close(file_id);

        // Set path and flag for type of run
        if (filetype == "statepoint") {
          settings::path_statepoint = argv[i];
          settings::restart_run = true;
        } else if (filetype == "particle restart") {
          settings::path_particle_restart = argv[i];
          settings::particle_restart_run = true;
        } else {
          auto msg =
            fmt::format("Unrecognized file after restart flag: {}.", filetype);
          set_errmsg(msg);
          return OPENMC_E_INVALID_ARGUMENT;
        }

        // If its a restart run check for additional source file
        if (settings::restart_run && i + 1 < argc) {
          // Check if it has extension we can read
          if (ends_with(argv[i + 1], ".h5")) {

            // Check file type is a source file
            file_id = file_open(argv[i + 1], 'r', true);
            read_attribute(file_id, "filetype", filetype);
            file_close(file_id);
            if (filetype != "source") {
              std::string msg {
                "Second file after restart flag must be a source file"};
              set_errmsg(msg);
              return OPENMC_E_INVALID_ARGUMENT;
            }

            // It is a source file
            settings::path_sourcepoint = argv[i + 1];
            i += 1;

          } else {
            // Source is in statepoint file
            settings::path_sourcepoint = settings::path_statepoint;
          }

        } else {
          // Source is assumed to be in statepoint file
          settings::path_sourcepoint = settings::path_statepoint;
        }

      } else if (arg == "-g" || arg == "--geometry-debug") {
        settings::check_overlaps = true;
      } else if (arg == "-c" || arg == "--volume") {
        settings::run_mode = RunMode::VOLUME;
      } else if (arg == "-s" || arg == "--threads") {
        // Read number of threads
        if (i + 1 >= argc) {
          std::string msg {"Number of threads not specified."};
          set_errmsg(msg);
          return OPENMC_E_INVALID_ARGUMENT;
        }
        i += 1;

#ifdef _OPENMP
        // Read and set number of OpenMP threads
        int n_threads = std::stoi(argv[i]);
        if (n_threads < 1) {
          std::string msg {"Number of threads must be positive."};
          set_errmsg(msg);
          return OPENMC_E_INVALID_ARGUMENT;
        }
        omp_set_num_threads(n_threads);
#else
        if (mpi::master) {
          warning("Ignoring number of threads specified on command line.");
        }
#endif

      } else if (arg == "-?" || arg == "-h" || arg == "--help") {
        print_usage();
        return OPENMC_E_UNASSIGNED;

      } else if (arg == "-v" || arg == "--version") {
        print_version();
        print_build_info();
        return OPENMC_E_UNASSIGNED;

      } else if (arg == "-t" || arg == "--track") {
        settings::write_all_tracks = true;

      } else {
        fmt::print(stderr, "Unknown option: {}\n", argv[i]);
        print_usage();
        return OPENMC_E_UNASSIGNED;
      }

      last_flag = i;
    }
  }

  // Determine directory where XML input files are
  if (argc > 1 && last_flag < argc - 1) {
    settings::path_input = std::string(argv[last_flag + 1]);

    // check that the path is either a valid directory or file
    if (!dir_exists(settings::path_input) &&
        !file_exists(settings::path_input)) {
      fatal_error(fmt::format(
        "The path specified to the OpenMC executable '{}' does not exist.",
        settings::path_input));
    }

    // Add slash at end of directory if it isn't there
    if (!ends_with(settings::path_input, "/") &&
        dir_exists(settings::path_input)) {
      settings::path_input += "/";
    }
  }

  return 0;
}

// TODO: Pulse-height tallies require per-history scoring across the full
// particle tree (parent + all descendants). The shared secondary bank
// transports each secondary as an independent Particle, breaking this
// assumption. A proper fix would defer pulse-height scoring: save
// (root_source_id, cell, pht_storage) per particle, then aggregate by
// root_source_id after all secondary generations complete before scoring
// into the histogram. For now, disable shared secondary when pulse-height
// tallies are present.
static void check_pulse_height_compatibility()
{
  if (settings::use_shared_secondary_bank) {
    for (const auto& t : model::tallies) {
      if (t->type_ == TallyType::PULSE_HEIGHT) {
        settings::use_shared_secondary_bank = false;
        warning("Pulse-height tallies are not yet compatible with the shared "
                "secondary bank. Disabling shared secondary bank.");
        break;
      }
    }
  }
}

bool read_model_xml()
{
  std::string model_filename = settings::path_input;

  // if the current filename is a directory, append the default model filename
  if (model_filename.empty() || dir_exists(model_filename))
    model_filename += "model.xml";

  // if this file doesn't exist, stop here
  if (!file_exists(model_filename))
    return false;

  // try to process the path input as an XML file
  pugi::xml_document doc;
  if (!doc.load_file(model_filename.c_str())) {
    fatal_error(fmt::format(
      "Error reading from single XML input file '{}'", model_filename));
  }

  pugi::xml_node root = doc.document_element();

  // Read settings
  if (!check_for_node(root, "settings")) {
    fatal_error("No <settings> node present in the model.xml file.");
  }
  auto settings_root = root.child("settings");

  // Verbosity
  if (check_for_node(settings_root, "verbosity") && settings::verbosity == -1) {
    settings::verbosity = std::stoi(get_node_value(settings_root, "verbosity"));
  } else if (settings::verbosity == -1) {
    settings::verbosity = 7;
  }

  // To this point, we haven't displayed any output since we didn't know what
  // the verbosity is. Now that we checked for it, show the title if necessary
  if (mpi::master) {
    if (settings::verbosity >= 2)
      title();
  }

  write_message(
    fmt::format("Reading model XML file '{}' ...", model_filename), 5);

  // Read chain data before settings so DecaySpectrum source distributions can
  // resolve nuclides while sources are constructed.
  read_chain_file_xml();

  read_settings_xml(settings_root);

  // If other XML files are present, display warning
  // that they will be ignored
  auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml",
    "tallies.xml", "plots.xml"};
  for (const auto& input : other_inputs) {
    if (file_exists(settings::path_input + input)) {
      warning((fmt::format("Other XML file input(s) are present. These files "
                           "may be ignored in favor of the {} file.",
        model_filename)));
      break;
    }
  }

  // Read materials and cross sections
  if (!check_for_node(root, "materials")) {
    fatal_error(fmt::format(
      "No <materials> node present in the {} file.", model_filename));
  }

  if (settings::run_mode != RunMode::PLOTTING) {
    read_cross_sections_xml(root.child("materials"));
  }
  read_materials_xml(root.child("materials"));

  // Read geometry
  if (!check_for_node(root, "geometry")) {
    fatal_error(fmt::format(
      "No <geometry> node present in the {} file.", model_filename));
  }
  read_geometry_xml(root.child("geometry"));

  // Final geometry setup and assign temperatures
  finalize_geometry();

  // Finalize cross sections having assigned temperatures
  finalize_cross_sections();

  // Compute cell density multipliers now that material densities
  // have been finalized (from geometry_aux.h)
  finalize_cell_densities();

  if (check_for_node(root, "tallies"))
    read_tallies_xml(root.child("tallies"));

  check_pulse_height_compatibility();

  // Initialize distribcell_filters
  prepare_distribcell();

  if (check_for_node(root, "plots")) {
    read_plots_xml(root.child("plots"));
  } else {
    // When no <plots> element is present in the model.xml file, check for a
    // regular plots.xml file
    std::string filename = settings::path_input + "plots.xml";
    if (file_exists(filename)) {
      read_plots_xml();
    }
  }

  finalize_variance_reduction();

  return true;
}

void read_separate_xml_files()
{
  // Read chain data before settings so DecaySpectrum source distributions can
  // resolve nuclides while sources are constructed.
  read_chain_file_xml();

  read_settings_xml();
  if (settings::run_mode != RunMode::PLOTTING) {
    read_cross_sections_xml();
  }

  read_materials_xml();
  read_geometry_xml();

  // Final geometry setup and assign temperatures
  finalize_geometry();

  // Finalize cross sections having assigned temperatures
  finalize_cross_sections();

  // Compute cell density multipliers now that material densities
  // have been finalized (from geometry_aux.h)
  finalize_cell_densities();

  read_tallies_xml();

  check_pulse_height_compatibility();

  // Initialize distribcell_filters
  prepare_distribcell();

  // Read the plots.xml regardless of plot mode in case plots are requested
  // via the API
  read_plots_xml();

  finalize_variance_reduction();
}

void initial_output()
{
  // write initial output
  if (settings::run_mode == RunMode::PLOTTING) {
    // Read plots.xml if it exists
    if (mpi::master && settings::verbosity >= 5)
      print_plot();

  } else {
    // Write summary information
    if (mpi::master && settings::output_summary)
      write_summary();

    // Warn if overlap checking is on
    if (mpi::master && settings::check_overlaps) {
      warning("Cell overlap checking is ON.");
    }
  }
}

} // namespace openmc

1	#include "openmc/initialize.h"
2
3	#include <clocale>
4	#include <cstddef>
5	#include <cstdlib> // for getenv
6	#include <cstring>
7	#include <string>
8
9	#ifdef _OPENMP
10	#include <omp.h>
11	#endif
12	#include <fmt/core.h>
13
14	#include "openmc/capi.h"
15	#include "openmc/chain.h"
16	#include "openmc/constants.h"
17	#include "openmc/cross_sections.h"
18	#include "openmc/error.h"
19	#include "openmc/file_utils.h"
20	#include "openmc/geometry_aux.h"
21	#include "openmc/hdf5_interface.h"
22	#include "openmc/material.h"
23	#include "openmc/memory.h"
24	#include "openmc/message_passing.h"
25	#include "openmc/mgxs_interface.h"
26	#include "openmc/nuclide.h"
27	#include "openmc/openmp_interface.h"
28	#include "openmc/output.h"
29	#include "openmc/plot.h"
30	#include "openmc/random_lcg.h"
31	#include "openmc/settings.h"
32	#include "openmc/simulation.h"
33	#include "openmc/string_utils.h"
34	#include "openmc/summary.h"
35	#include "openmc/tallies/tally.h"
36	#include "openmc/thermal.h"
37	#include "openmc/timer.h"
38	#include "openmc/vector.h"
39	#include "openmc/weight_windows.h"
40
41	#ifdef OPENMC_LIBMESH_ENABLED
42	#include "libmesh/libmesh.h"
43	#endif
44
45	int openmc_init(int argc, char* argv[], const void* intracomm)	9,376 ✔
46	{
47	using namespace openmc;	9,376 ✔
48
49	#ifdef OPENMC_MPI
50	// Check if intracomm was passed
51	MPI_Comm comm;	4,103 ✔
52	if (intracomm) {	4,103 ✔
53	comm = static_cast<const MPI_Comm>(intracomm);	3,889 ✔
54	} else {
55	comm = MPI_COMM_WORLD;	51 ✔
56	}
57
58	// Initialize MPI for C++
59	initialize_mpi(comm);	4,103 ✔
60	#endif
61
62	// Parse command-line arguments
63	int err = parse_command_line(argc, argv);	9,376 ✔
64	if (err)	9,343 ✔
65	return err;
66
67	#ifdef OPENMC_LIBMESH_ENABLED
68	const int n_threads = num_threads();	1,752 ✔
69	// initialize libMesh if it hasn't been initialized already
70	// (if initialized externally, the libmesh_init object needs to be provided
71	// also)
72	if (!settings::libmesh_init && !libMesh::initialized()) {	1,752 !
73	#if defined(OPENMC_MPI) && defined(LIBMESH_HAVE_MPI)
74	// Pass command line arguments, the OpenMC communicator, and thread count.
75	// Because libMesh was not initialized, we assume that OpenMC is the primary
76	// application and that its main MPI comm should be used.
77	settings::libmesh_init =	1,004 ✔
78	make_unique<libMesh::LibMeshInit>(argc, argv, comm, n_threads);	2,008 ✔
79	#else
80	// libMesh was built without MPI, so use its serial communicator.
81	settings::libmesh_init =	748 ✔
82	make_unique<libMesh::LibMeshInit>(argc, argv, 0, n_threads);	1,496 ✔
83	#endif
84
85	settings::libmesh_comm = &(settings::libmesh_init->comm());	1,752 ✔
86	}
87
88	#endif
89
90	// Start total and initialization timer
91	simulation::time_total.start();	9,332 ✔
92	simulation::time_initialize.start();	9,332 ✔
93
94	#ifdef _OPENMP
95	// If OMP_SCHEDULE is not set, default to a static schedule
96	char* envvar = std::getenv("OMP_SCHEDULE");	5,317 ✔
97	if (!envvar) {	5,317 !
98	omp_set_schedule(omp_sched_static, 0);	5,317 ✔
99	}
100	#endif
101
102	// Initialize random number generator -- if the user specifies a seed and/or
103	// stride, it will be re-initialized later
104	openmc::openmc_set_seed(DEFAULT_SEED);	9,332 ✔
105	openmc::openmc_set_stride(DEFAULT_STRIDE);	9,332 ✔
106
107	// Copy previous locale and set locale to C. This is a workaround for an issue
108	// whereby when openmc_init is called from the plotter, the Qt application
109	// framework first calls std::setlocale, which affects how pugixml reads
110	// floating point numbers due to a bug:
111	// https://github.com/zeux/pugixml/issues/469
112	std::string prev_locale = std::setlocale(LC_ALL, nullptr);	9,332 ✔
113	if (std::setlocale(LC_ALL, "C") == NULL) {	9,332 !
114	fatal_error("Cannot set locale to C.");	×
115	}
116
117	// Read XML input files
118	if (!read_model_xml())	9,332 ✔
119	read_separate_xml_files();	1,423 ✔
120
121	if (!settings::properties_file.empty()) {	9,239 ✔
122	openmc_properties_import(settings::properties_file.c_str());	11 ✔
123	}
124
125	// Reset locale to previous state
126	if (std::setlocale(LC_ALL, prev_locale.c_str()) == NULL) {	9,239 !
127	fatal_error("Cannot reset locale.");	×
128	}
129
130	// Write some initial output under the header if needed
131	initial_output();	9,239 ✔
132
133	// Check for particle restart run
134	if (settings::particle_restart_run)	9,239 ✔
135	settings::run_mode = RunMode::PARTICLE;	56 ✔
136
137	// Stop initialization timer
138	simulation::time_initialize.stop();	9,239 ✔
139	simulation::time_total.stop();	9,239 ✔
140
141	return 0;	9,239 ✔
142	}	9,250 ✔
143
144	namespace openmc {
145
146	#ifdef OPENMC_MPI
147	void initialize_mpi(MPI_Comm intracomm)	4,103 ✔
148	{
149	mpi::intracomm = intracomm;	4,103 ✔
150
151	// Initialize MPI
152	int flag;	4,103 ✔
153	MPI_Initialized(&flag);	4,103 ✔
154	if (!flag)	4,103 ✔
155	MPI_Init(nullptr, nullptr);	3,306 ✔
156
157	// Determine number of processes and rank for each
158	MPI_Comm_size(intracomm, &mpi::n_procs);	4,103 ✔
159	MPI_Comm_rank(intracomm, &mpi::rank);	4,103 ✔
160	mpi::master = (mpi::rank == 0);	4,103 ✔
161
162	// Create bank datatype
163	SourceSite b;	4,103 ✔
164	MPI_Aint disp[15];	4,103 ✔
165	MPI_Get_address(&b.r, &disp[0]);	4,103 ✔
166	MPI_Get_address(&b.u, &disp[1]);	4,103 ✔
167	MPI_Get_address(&b.E, &disp[2]);	4,103 ✔
168	MPI_Get_address(&b.time, &disp[3]);	4,103 ✔
169	MPI_Get_address(&b.wgt, &disp[4]);	4,103 ✔
170	MPI_Get_address(&b.delayed_group, &disp[5]);	4,103 ✔
171	MPI_Get_address(&b.surf_id, &disp[6]);	4,103 ✔
172	MPI_Get_address(&b.particle, &disp[7]);	4,103 ✔
173	MPI_Get_address(&b.parent_nuclide, &disp[8]);	4,103 ✔
174	MPI_Get_address(&b.parent_id, &disp[9]);	4,103 ✔
175	MPI_Get_address(&b.progeny_id, &disp[10]);	4,103 ✔
176	MPI_Get_address(&b.wgt_born, &disp[11]);	4,103 ✔
177	MPI_Get_address(&b.wgt_ww_born, &disp[12]);	4,103 ✔
178	MPI_Get_address(&b.n_split, &disp[13]);	4,103 ✔
179	MPI_Get_address(&b.n_collision, &disp[14]);	4,103 ✔
180	for (int i = 14; i >= 0; --i) {	65,648 ✔
181	disp[i] -= disp[0];	61,545 ✔
182	}
183
184	// Block counts for each field
185	int blocks[] = {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};	4,103 ✔
186
187	// Types for each field
188	MPI_Datatype types[] = {	4,103 ✔
189	MPI_DOUBLE, // r (3 doubles)
190	MPI_DOUBLE, // u (3 doubles)
191	MPI_DOUBLE, // E
192	MPI_DOUBLE, // time
193	MPI_DOUBLE, // wgt
194	MPI_INT, // delayed_group
195	MPI_INT, // surf_id
196	MPI_INT, // particle (enum)
197	MPI_INT, // parent_nuclide
198	MPI_INT64_T, // parent_id
199	MPI_INT64_T, // progeny_id
200	MPI_DOUBLE, // wgt_born
201	MPI_DOUBLE, // wgt_ww_born
202	MPI_INT64_T, // n_split
203	MPI_INT // n_collision
204	};
205
206	MPI_Type_create_struct(15, blocks, disp, types, &mpi::source_site);	4,103 ✔
207	MPI_Type_commit(&mpi::source_site);	4,103 ✔
208
209	CollisionTrackSite bc;	4,103 ✔
210	MPI_Aint dispc[16];	4,103 ✔
211	MPI_Get_address(&bc.r, &dispc[0]); // double	4,103 ✔
212	MPI_Get_address(&bc.u, &dispc[1]); // double	4,103 ✔
213	MPI_Get_address(&bc.E, &dispc[2]); // double	4,103 ✔
214	MPI_Get_address(&bc.dE, &dispc[3]); // double	4,103 ✔
215	MPI_Get_address(&bc.time, &dispc[4]); // double	4,103 ✔
216	MPI_Get_address(&bc.wgt, &dispc[5]); // double	4,103 ✔
217	MPI_Get_address(&bc.event_mt, &dispc[6]); // int	4,103 ✔
218	MPI_Get_address(&bc.delayed_group, &dispc[7]); // int	4,103 ✔
219	MPI_Get_address(&bc.cell_id, &dispc[8]); // int	4,103 ✔
220	MPI_Get_address(&bc.nuclide_id, &dispc[9]); // int	4,103 ✔
221	MPI_Get_address(&bc.material_id, &dispc[10]); // int	4,103 ✔
222	MPI_Get_address(&bc.universe_id, &dispc[11]); // int	4,103 ✔
223	MPI_Get_address(&bc.n_collision, &dispc[12]); // int	4,103 ✔
224	MPI_Get_address(&bc.particle, &dispc[13]); // int	4,103 ✔
225	MPI_Get_address(&bc.parent_id, &dispc[14]); // int64_t	4,103 ✔
226	MPI_Get_address(&bc.progeny_id, &dispc[15]); // int64_t	4,103 ✔
227	for (int i = 15; i >= 0; --i) {	69,751 ✔
228	dispc[i] -= dispc[0];	65,648 ✔
229	}
230
231	int blocksc[] = {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};	4,103 ✔
232	MPI_Datatype typesc[] = {MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE,	4,103 ✔
233	MPI_DOUBLE, MPI_DOUBLE, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_INT,
234	MPI_INT, MPI_INT, MPI_INT, MPI_INT64_T, MPI_INT64_T};
235
236	MPI_Type_create_struct(	4,103 ✔
237	16, blocksc, dispc, typesc, &mpi::collision_track_site);
238	MPI_Type_commit(&mpi::collision_track_site);	4,103 ✔
239	}	4,103 ✔
240	#endif // OPENMC_MPI
241
242	int parse_command_line(int argc, char* argv[])	9,376 ✔
243	{
244	int last_flag = 0;	9,376 ✔
245	for (int i = 1; i < argc; ++i) {	10,965 ✔
246	std::string arg {argv[i]};	1,600 ✔
247	if (arg[0] == '-') {	1,600 ✔
248	if (arg == "-p" \|\| arg == "--plot") {	2,875 !
249	settings::run_mode = RunMode::PLOTTING;	119 ✔
250	settings::check_overlaps = true;	119 ✔
251
252	} else if (arg == "-n" \|\| arg == "--particles") {	2,745 !
253	i += 1;	11 ✔
254	settings::n_particles = std::stoll(argv[i]);	22 ✔
255
256	} else if (arg == "-q" \|\| arg == "--verbosity") {	2,734 !
257	i += 1;	×
258	settings::verbosity = std::stoi(argv[i]);	×
259	if (settings::verbosity > 10 \|\| settings::verbosity < 1) {	×
260	auto msg = fmt::format("Invalid verbosity: {}.", settings::verbosity);	×
261	set_errmsg(msg);	×
262	return OPENMC_E_INVALID_ARGUMENT;	×
263	}	×
264
265	} else if (arg == "-e" \|\| arg == "--event") {	2,510 !
266	settings::event_based = true;	224 ✔
267	} else if (arg == "-r" \|\| arg == "--restart") {	2,167 !
268	i += 1;	119 ✔
269	// Check what type of file this is
270	hid_t file_id = file_open(argv[i], 'r', true);	119 ✔
271	std::string filetype;	119 ✔
272	read_attribute(file_id, "filetype", filetype);	119 ✔
273	file_close(file_id);	119 ✔
274
275	// Set path and flag for type of run
276	if (filetype == "statepoint") {	119 ✔
277	settings::path_statepoint = argv[i];	63 ✔
278	settings::restart_run = true;	63 ✔
279	} else if (filetype == "particle restart") {	56 !
280	settings::path_particle_restart = argv[i];	56 ✔
281	settings::particle_restart_run = true;	56 ✔
282	} else {
UNCOV 283	auto msg =	×
284	fmt::format("Unrecognized file after restart flag: {}.", filetype);	×
285	set_errmsg(msg);	×
286	return OPENMC_E_INVALID_ARGUMENT;	×
287	}	×
288
289	// If its a restart run check for additional source file
290	if (settings::restart_run && i + 1 < argc) {	119 !
291	// Check if it has extension we can read
UNCOV 292	if (ends_with(argv[i + 1], ".h5")) {	×
293
294	// Check file type is a source file
UNCOV 295	file_id = file_open(argv[i + 1], 'r', true);	×
296	read_attribute(file_id, "filetype", filetype);	×
297	file_close(file_id);	×
298	if (filetype != "source") {	×
299	std::string msg {	×
300	"Second file after restart flag must be a source file"};	×
301	set_errmsg(msg);	×
302	return OPENMC_E_INVALID_ARGUMENT;	×
303	}	×
304
305	// It is a source file
306	settings::path_sourcepoint = argv[i + 1];	119 !
307	i += 1;
308
309	} else {
310	// Source is in statepoint file
UNCOV 311	settings::path_sourcepoint = settings::path_statepoint;	×
312	}
313
314	} else {
315	// Source is assumed to be in statepoint file
316	settings::path_sourcepoint = settings::path_statepoint;	238 ✔
317	}
318
319	} else if (arg == "-g" \|\| arg == "--geometry-debug") {	2,167 !
UNCOV 320	settings::check_overlaps = true;	×
321	} else if (arg == "-c" \|\| arg == "--volume") {	1,219 ✔
322	settings::run_mode = RunMode::VOLUME;	911 ✔
323	} else if (arg == "-s" \|\| arg == "--threads") {	180 !
324	// Read number of threads
325	if (i + 1 >= argc) {	46 !
UNCOV 326	std::string msg {"Number of threads not specified."};	×
327	set_errmsg(msg);	×
328	return OPENMC_E_INVALID_ARGUMENT;	×
329	}	×
330	i += 1;	46 ✔
331
332	#ifdef _OPENMP
333	// Read and set number of OpenMP threads
334	int n_threads = std::stoi(argv[i]);	50 ✔
335	if (n_threads < 1) {	25 !
336	std::string msg {"Number of threads must be positive."};	×
337	set_errmsg(msg);	×
338	return OPENMC_E_INVALID_ARGUMENT;
339	}
340	omp_set_num_threads(n_threads);	25 ✔
341	#else
342	if (mpi::master) {	21 ✔
343	warning("Ignoring number of threads specified on command line.");	40 ✔
344	}
345	#endif
346
347	} else if (arg == "-?" \|\| arg == "-h" \|\| arg == "--help") {	201 !
UNCOV 348	print_usage();	×
349	return OPENMC_E_UNASSIGNED;
350
351	} else if (arg == "-v" \|\| arg == "--version") {	123 !
352	print_version();	11 ✔
353	print_build_info();	11 ✔
354	return OPENMC_E_UNASSIGNED;
355
356	} else if (arg == "-t" \|\| arg == "--track") {	56 !
357	settings::write_all_tracks = true;	56 ✔
358
359	} else {
UNCOV 360	fmt::print(stderr, "Unknown option: {}\n", argv[i]);	×
361	print_usage();	×
362	return OPENMC_E_UNASSIGNED;
363	}
364
365	last_flag = i;
366	}
367	}	1,600 ✔
368
369	// Determine directory where XML input files are
370	if (argc > 1 && last_flag < argc - 1) {	9,365 ✔
371	settings::path_input = std::string(argv[last_flag + 1]);	103 ✔
372
373	// check that the path is either a valid directory or file
374	if (!dir_exists(settings::path_input) &&	193 ✔
375	!file_exists(settings::path_input)) {	90 ✔
376	fatal_error(fmt::format(	39 ✔
377	"The path specified to the OpenMC executable '{}' does not exist.",
378	settings::path_input));
379	}
380
381	// Add slash at end of directory if it isn't there
382	if (!ends_with(settings::path_input, "/") &&	210 !
383	dir_exists(settings::path_input)) {	70 ✔
384	settings::path_input += "/";	9,343 ✔
385	}
386	}
387
388	return 0;
389	}
390
391	// TODO: Pulse-height tallies require per-history scoring across the full
392	// particle tree (parent + all descendants). The shared secondary bank
393	// transports each secondary as an independent Particle, breaking this
394	// assumption. A proper fix would defer pulse-height scoring: save
395	// (root_source_id, cell, pht_storage) per particle, then aggregate by
396	// root_source_id after all secondary generations complete before scoring
397	// into the histogram. For now, disable shared secondary when pulse-height
398	// tallies are present.
399	static void check_pulse_height_compatibility()	9,248 ✔
400	{
401	if (settings::use_shared_secondary_bank) {	9,248 ✔
402	for (const auto& t : model::tallies) {	720 ✔
403	if (t->type_ == TallyType::PULSE_HEIGHT) {	428 ✔
404	settings::use_shared_secondary_bank = false;	45 ✔
405	warning("Pulse-height tallies are not yet compatible with the shared "	45 ✔
406	"secondary bank. Disabling shared secondary bank.");
407	break;	45 ✔
408	}
409	}
410	}
411	}	9,248 ✔
412
413	bool read_model_xml()	9,332 ✔
414	{
415	std::string model_filename = settings::path_input;	9,332 ✔
416
417	// if the current filename is a directory, append the default model filename
418	if (model_filename.empty() \|\| dir_exists(model_filename))	9,332 ✔
419	model_filename += "model.xml";	9,275 ✔
420
421	// if this file doesn't exist, stop here
422	if (!file_exists(model_filename))	9,332 ✔
423	return false;
424
425	// try to process the path input as an XML file
426	pugi::xml_document doc;	7,909 ✔
427	if (!doc.load_file(model_filename.c_str())) {	7,909 !
UNCOV 428	fatal_error(fmt::format(	×
429	"Error reading from single XML input file '{}'", model_filename));
430	}
431
432	pugi::xml_node root = doc.document_element();	7,909 ✔
433
434	// Read settings
435	if (!check_for_node(root, "settings")) {	7,909 !
UNCOV 436	fatal_error("No <settings> node present in the model.xml file.");	×
437	}
438	auto settings_root = root.child("settings");	7,909 ✔
439
440	// Verbosity
441	if (check_for_node(settings_root, "verbosity") && settings::verbosity == -1) {	7,909 !
442	settings::verbosity = std::stoi(get_node_value(settings_root, "verbosity"));	60 ✔
443	} else if (settings::verbosity == -1) {	7,879 !
444	settings::verbosity = 7;	7,879 ✔
445	}
446
447	// To this point, we haven't displayed any output since we didn't know what
448	// the verbosity is. Now that we checked for it, show the title if necessary
449	if (mpi::master) {	7,909 ✔
450	if (settings::verbosity >= 2)	7,064 ✔
451	title();	7,042 ✔
452	}
453
454	write_message(	7,909 ✔
455	fmt::format("Reading model XML file '{}' ...", model_filename), 5);	9,391 ✔
456
457	// Read chain data before settings so DecaySpectrum source distributions can
458	// resolve nuclides while sources are constructed.
459	read_chain_file_xml();	7,909 ✔
460
461	read_settings_xml(settings_root);	7,909 ✔
462
463	// If other XML files are present, display warning
464	// that they will be ignored
465	auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml",	7,855 ✔
466	"tallies.xml", "plots.xml"};	7,855 ✔
467	for (const auto& input : other_inputs) {	46,292 ✔
468	if (file_exists(settings::path_input + input)) {	38,638 ✔
469	warning((fmt::format("Other XML file input(s) are present. These files "	238 ✔
470	"may be ignored in favor of the {} file.",
471	model_filename)));
472	break;	201 ✔
473	}
474	}
475
476	// Read materials and cross sections
477	if (!check_for_node(root, "materials")) {	7,855 !
UNCOV 478	fatal_error(fmt::format(	×
479	"No <materials> node present in the {} file.", model_filename));
480	}
481
482	if (settings::run_mode != RunMode::PLOTTING) {	7,855 ✔
483	read_cross_sections_xml(root.child("materials"));	7,769 ✔
484	}
485	read_materials_xml(root.child("materials"));	7,855 ✔
486
487	// Read geometry
488	if (!check_for_node(root, "geometry")) {	7,855 !
UNCOV 489	fatal_error(fmt::format(	×
490	"No <geometry> node present in the {} file.", model_filename));
491	}
492	read_geometry_xml(root.child("geometry"));	7,855 ✔
493
494	// Final geometry setup and assign temperatures
495	finalize_geometry();	7,853 ✔
496
497	// Finalize cross sections having assigned temperatures
498	finalize_cross_sections();	7,853 ✔
499
500	// Compute cell density multipliers now that material densities
501	// have been finalized (from geometry_aux.h)
502	finalize_cell_densities();	7,853 ✔
503
504	if (check_for_node(root, "tallies"))	7,853 ✔
505	read_tallies_xml(root.child("tallies"));	4,650 ✔
506
507	check_pulse_height_compatibility();	7,835 ✔
508
509	// Initialize distribcell_filters
510	prepare_distribcell();	7,835 ✔
511
512	if (check_for_node(root, "plots")) {	7,835 ✔
513	read_plots_xml(root.child("plots"));	508 ✔
514	} else {
515	// When no <plots> element is present in the model.xml file, check for a
516	// regular plots.xml file
517	std::string filename = settings::path_input + "plots.xml";	7,327 ✔
518	if (file_exists(filename)) {	7,327 !
UNCOV 519	read_plots_xml();	×
520	}
521	}	7,327 ✔
522
523	finalize_variance_reduction();	7,826 ✔
524
525	return true;	7,826 ✔
526	}	17,075 ✔
527
528	void read_separate_xml_files()	1,423 ✔
529	{
530	// Read chain data before settings so DecaySpectrum source distributions can
531	// resolve nuclides while sources are constructed.
532	read_chain_file_xml();	1,423 ✔
533
534	read_settings_xml();	1,423 ✔
535	if (settings::run_mode != RunMode::PLOTTING) {	1,413 ✔
536	read_cross_sections_xml();	1,380 ✔
537	}
538
539	read_materials_xml();	1,413 ✔
540	read_geometry_xml();	1,413 ✔
541
542	// Final geometry setup and assign temperatures
543	finalize_geometry();	1,413 ✔
544
545	// Finalize cross sections having assigned temperatures
546	finalize_cross_sections();	1,413 ✔
547
548	// Compute cell density multipliers now that material densities
549	// have been finalized (from geometry_aux.h)
550	finalize_cell_densities();	1,413 ✔
551
552	read_tallies_xml();	1,413 ✔
553
554	check_pulse_height_compatibility();	1,413 ✔
555
556	// Initialize distribcell_filters
557	prepare_distribcell();	1,413 ✔
558
559	// Read the plots.xml regardless of plot mode in case plots are requested
560	// via the API
561	read_plots_xml();	1,413 ✔
562
563	finalize_variance_reduction();	1,413 ✔
564	}	1,413 ✔
565
566	void initial_output()	9,239 ✔
567	{
568	// write initial output
569	if (settings::run_mode == RunMode::PLOTTING) {	9,239 ✔
570	// Read plots.xml if it exists
571	if (mpi::master && settings::verbosity >= 5)	110 !
572	print_plot();	88 ✔
573
574	} else {
575	// Write summary information
576	if (mpi::master && settings::output_summary)	9,129 ✔
577	write_summary();	7,708 ✔
578
579	// Warn if overlap checking is on
580	if (mpi::master && settings::check_overlaps) {	9,129 !
UNCOV 581	warning("Cell overlap checking is ON.");	×
582	}
583	}
584	}	9,239 ✔
585
586	} // namespace openmc

openmc-dev / openmc / 33839677304

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