26473127945

Committed 26 May 2026 08:25PM UTC coverage: 80.855% (-0.5%) from 81.333%

Build # 26473127945

Build Type

Pull #3877

github

Committed by

web-flow

Commit Message

Merge e16d17e3a into dfb6c5699

Pull Request Pull Request #3877: Add VTKHDF output support for all structured mesh types (#3620)

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75.05

/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()) {
#ifdef OPENMC_MPI
    // pass command line args, empty MPI communicator, and number of threads.
    // 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
    // pass command line args, empty MPI communicator, and number of threads
    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[14];
  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]);
  for (int i = 13; 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};

  // 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_Type_create_struct(14, 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);
          strcpy(openmc_err_msg, msg.c_str());
          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::path_statepoint_c = settings::path_statepoint.c_str();
          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);
          strcpy(openmc_err_msg, msg.c_str());
          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"};
              strcpy(openmc_err_msg, msg.c_str());
              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."};
          strcpy(openmc_err_msg, msg.c_str());
          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."};
          strcpy(openmc_err_msg, msg.c_str());
          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)	5,335✔
46	{
47	using namespace openmc;	5,335✔
48
49	#ifdef OPENMC_MPI
50	// Check if intracomm was passed
51	MPI_Comm comm;	1,866✔
52	if (intracomm) {	1,866✔
53	comm = static_cast<const MPI_Comm>(intracomm);	1,778✔
54	} else {
55	comm = MPI_COMM_WORLD;
56	}
57
58	// Initialize MPI for C++
59	initialize_mpi(comm);	1,866✔
60	#endif
61
62	// Parse command-line arguments
63	int err = parse_command_line(argc, argv);	5,335✔
64	if (err)	5,314✔
65	return err;
66
67	#ifdef OPENMC_LIBMESH_ENABLED
68	const int n_threads = num_threads();
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()) {
73	#ifdef OPENMC_MPI
74	// pass command line args, empty MPI communicator, and number of threads.
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 =
78	make_unique<libMesh::LibMeshInit>(argc, argv, comm, n_threads);
79	#else
80	// pass command line args, empty MPI communicator, and number of threads
81	settings::libmesh_init =
82	make_unique<libMesh::LibMeshInit>(argc, argv, 0, n_threads);
83	#endif
84
85	settings::libmesh_comm = &(settings::libmesh_init->comm());
86	}
87
88	#endif
89
90	// Start total and initialization timer
91	simulation::time_total.start();	5,307✔
92	simulation::time_initialize.start();	5,307✔
93
94	#ifdef _OPENMP
95	// If OMP_SCHEDULE is not set, default to a static schedule
96	char* envvar = std::getenv("OMP_SCHEDULE");	1,618✔
97	if (!envvar) {	1,618!
98	omp_set_schedule(omp_sched_static, 0);	1,618✔
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);	5,307✔
105	openmc::openmc_set_stride(DEFAULT_STRIDE);	5,307✔
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);	5,307✔
113	if (std::setlocale(LC_ALL, "C") == NULL) {	5,307!
114	fatal_error("Cannot set locale to C.");	×
115	}
116
117	// Read XML input files
118	if (!read_model_xml())	5,307✔
119	read_separate_xml_files();	862✔
120
121	if (!settings::properties_file.empty()) {	5,237✔
122	openmc_properties_import(settings::properties_file.c_str());	7✔
123	}
124
125	// Reset locale to previous state
126	if (std::setlocale(LC_ALL, prev_locale.c_str()) == NULL) {	5,237!
127	fatal_error("Cannot reset locale.");	×
128	}
129
130	// Write some initial output under the header if needed
131	initial_output();	5,237✔
132
133	// Check for particle restart run
134	if (settings::particle_restart_run)	5,237✔
135	settings::run_mode = RunMode::PARTICLE;	34✔
136
137	// Stop initialization timer
138	simulation::time_initialize.stop();	5,237✔
139	simulation::time_total.stop();	5,237✔
140
141	return 0;	5,237✔
142	}	5,244✔
143
144	namespace openmc {
145
146	#ifdef OPENMC_MPI
147	void initialize_mpi(MPI_Comm intracomm)	1,866✔
148	{
149	mpi::intracomm = intracomm;	1,866✔
150
151	// Initialize MPI
152	int flag;	1,866✔
153	MPI_Initialized(&flag);	1,866✔
154	if (!flag)	1,866✔
155	MPI_Init(nullptr, nullptr);	1,536✔
156
157	// Determine number of processes and rank for each
158	MPI_Comm_size(intracomm, &mpi::n_procs);	1,866✔
159	MPI_Comm_rank(intracomm, &mpi::rank);	1,866✔
160	mpi::master = (mpi::rank == 0);	1,866✔
161
162	// Create bank datatype
163	SourceSite b;	1,866✔
164	MPI_Aint disp[14];	1,866✔
165	MPI_Get_address(&b.r, &disp[0]);	1,866✔
166	MPI_Get_address(&b.u, &disp[1]);	1,866✔
167	MPI_Get_address(&b.E, &disp[2]);	1,866✔
168	MPI_Get_address(&b.time, &disp[3]);	1,866✔
169	MPI_Get_address(&b.wgt, &disp[4]);	1,866✔
170	MPI_Get_address(&b.delayed_group, &disp[5]);	1,866✔
171	MPI_Get_address(&b.surf_id, &disp[6]);	1,866✔
172	MPI_Get_address(&b.particle, &disp[7]);	1,866✔
173	MPI_Get_address(&b.parent_nuclide, &disp[8]);	1,866✔
174	MPI_Get_address(&b.parent_id, &disp[9]);	1,866✔
175	MPI_Get_address(&b.progeny_id, &disp[10]);	1,866✔
176	MPI_Get_address(&b.wgt_born, &disp[11]);	1,866✔
177	MPI_Get_address(&b.wgt_ww_born, &disp[12]);	1,866✔
178	MPI_Get_address(&b.n_split, &disp[13]);	1,866✔
179	for (int i = 13; i >= 0; --i) {	27,990✔
180	disp[i] -= disp[0];	26,124✔
181	}
182
183	// Block counts for each field
184	int blocks[] = {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};	1,866✔
185
186	// Types for each field
187	MPI_Datatype types[] = {	1,866✔
188	MPI_DOUBLE, // r (3 doubles)
189	MPI_DOUBLE, // u (3 doubles)
190	MPI_DOUBLE, // E
191	MPI_DOUBLE, // time
192	MPI_DOUBLE, // wgt
193	MPI_INT, // delayed_group
194	MPI_INT, // surf_id
195	MPI_INT, // particle (enum)
196	MPI_INT, // parent_nuclide
197	MPI_INT64_T, // parent_id
198	MPI_INT64_T, // progeny_id
199	MPI_DOUBLE, // wgt_born
200	MPI_DOUBLE, // wgt_ww_born
201	MPI_INT64_T // n_split
202	};
203
204	MPI_Type_create_struct(14, blocks, disp, types, &mpi::source_site);	1,866✔
205	MPI_Type_commit(&mpi::source_site);	1,866✔
206
207	CollisionTrackSite bc;	1,866✔
208	MPI_Aint dispc[16];	1,866✔
209	MPI_Get_address(&bc.r, &dispc[0]); // double	1,866✔
210	MPI_Get_address(&bc.u, &dispc[1]); // double	1,866✔
211	MPI_Get_address(&bc.E, &dispc[2]); // double	1,866✔
212	MPI_Get_address(&bc.dE, &dispc[3]); // double	1,866✔
213	MPI_Get_address(&bc.time, &dispc[4]); // double	1,866✔
214	MPI_Get_address(&bc.wgt, &dispc[5]); // double	1,866✔
215	MPI_Get_address(&bc.event_mt, &dispc[6]); // int	1,866✔
216	MPI_Get_address(&bc.delayed_group, &dispc[7]); // int	1,866✔
217	MPI_Get_address(&bc.cell_id, &dispc[8]); // int	1,866✔
218	MPI_Get_address(&bc.nuclide_id, &dispc[9]); // int	1,866✔
219	MPI_Get_address(&bc.material_id, &dispc[10]); // int	1,866✔
220	MPI_Get_address(&bc.universe_id, &dispc[11]); // int	1,866✔
221	MPI_Get_address(&bc.n_collision, &dispc[12]); // int	1,866✔
222	MPI_Get_address(&bc.particle, &dispc[13]); // int	1,866✔
223	MPI_Get_address(&bc.parent_id, &dispc[14]); // int64_t	1,866✔
224	MPI_Get_address(&bc.progeny_id, &dispc[15]); // int64_t	1,866✔
225	for (int i = 15; i >= 0; --i) {	31,722✔
226	dispc[i] -= dispc[0];	29,856✔
227	}
228
229	int blocksc[] = {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};	1,866✔
230	MPI_Datatype typesc[] = {MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE,	1,866✔
231	MPI_DOUBLE, MPI_DOUBLE, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_INT,
232	MPI_INT, MPI_INT, MPI_INT, MPI_INT64_T, MPI_INT64_T};
233
234	MPI_Type_create_struct(	1,866✔
235	16, blocksc, dispc, typesc, &mpi::collision_track_site);
236	MPI_Type_commit(&mpi::collision_track_site);	1,866✔
237	}	1,866✔
238	#endif // OPENMC_MPI
239
240	int parse_command_line(int argc, char* argv[])	5,335✔
241	{
242	int last_flag = 0;	5,335✔
243	for (int i = 1; i < argc; ++i) {	6,046✔
244	std::string arg {argv[i]};	718✔
245	if (arg[0] == '-') {	718✔
246	if (arg == "-p" \|\| arg == "--plot") {	1,233!
247	settings::run_mode = RunMode::PLOTTING;	77✔
248	settings::check_overlaps = true;	77✔
249
250	} else if (arg == "-n" \|\| arg == "--particles") {	1,156!
251	i += 1;	×
252	settings::n_particles = std::stoll(argv[i]);	×
253
254	} else if (arg == "-q" \|\| arg == "--verbosity") {	1,156!
255	i += 1;	×
256	settings::verbosity = std::stoi(argv[i]);	×
257	if (settings::verbosity > 10 \|\| settings::verbosity < 1) {	×
258	auto msg = fmt::format("Invalid verbosity: {}.", settings::verbosity);	×
259	strcpy(openmc_err_msg, msg.c_str());	×
260	return OPENMC_E_INVALID_ARGUMENT;	×
261	}	×
262
263	} else if (arg == "-e" \|\| arg == "--event") {	1,156!
UNCOV 264	settings::event_based = true;	×
265	} else if (arg == "-r" \|\| arg == "--restart") {	1,083!
266	i += 1;	73✔
267	// Check what type of file this is
268	hid_t file_id = file_open(argv[i], 'r', true);	73✔
269	std::string filetype;	73✔
270	read_attribute(file_id, "filetype", filetype);	73✔
271	file_close(file_id);	73✔
272
273	// Set path and flag for type of run
274	if (filetype == "statepoint") {	73✔
275	settings::path_statepoint = argv[i];	39✔
276	settings::path_statepoint_c = settings::path_statepoint.c_str();	39✔
277	settings::restart_run = true;	39✔
278	} else if (filetype == "particle restart") {	34!
279	settings::path_particle_restart = argv[i];	34✔
280	settings::particle_restart_run = true;	34✔
281	} else {
282	auto msg =	×
283	fmt::format("Unrecognized file after restart flag: {}.", filetype);	×
284	strcpy(openmc_err_msg, msg.c_str());	×
285	return OPENMC_E_INVALID_ARGUMENT;	×
286	}	×
287
288	// If its a restart run check for additional source file
289	if (settings::restart_run && i + 1 < argc) {	73!
290	// Check if it has extension we can read
291	if (ends_with(argv[i + 1], ".h5")) {	×
292
293	// Check file type is a source file
294	file_id = file_open(argv[i + 1], 'r', true);	×
295	read_attribute(file_id, "filetype", filetype);	×
296	file_close(file_id);	×
297	if (filetype != "source") {	×
298	std::string msg {	×
299	"Second file after restart flag must be a source file"};	×
300	strcpy(openmc_err_msg, msg.c_str());	×
301	return OPENMC_E_INVALID_ARGUMENT;	×
302	}	×
303
304	// It is a source file
305	settings::path_sourcepoint = argv[i + 1];	73!
306	i += 1;
307
308	} else {
309	// Source is in statepoint file
310	settings::path_sourcepoint = settings::path_statepoint;	×
311	}
312
313	} else {
314	// Source is assumed to be in statepoint file
315	settings::path_sourcepoint = settings::path_statepoint;	146✔
316	}
317
318	} else if (arg == "-g" \|\| arg == "--geometry-debug") {	1,083!
319	settings::check_overlaps = true;	×
320	} else if (arg == "-c" \|\| arg == "--volume") {	618✔
321	settings::run_mode = RunMode::VOLUME;	448✔
322	} else if (arg == "-s" \|\| arg == "--threads") {	98!
323	// Read number of threads
324	if (i + 1 >= argc) {	16!
325	std::string msg {"Number of threads not specified."};	×
326	strcpy(openmc_err_msg, msg.c_str());	×
327	return OPENMC_E_INVALID_ARGUMENT;	×
328	}	×
329	i += 1;	16✔
330
331	#ifdef _OPENMP
332	// Read and set number of OpenMP threads
333	int n_threads = std::stoi(argv[i]);	10✔
334	if (n_threads < 1) {	5!
335	std::string msg {"Number of threads must be positive."};	×
336	strcpy(openmc_err_msg, msg.c_str());
337	return OPENMC_E_INVALID_ARGUMENT;
338	}
339	omp_set_num_threads(n_threads);	5✔
340	#else
341	if (mpi::master) {	11✔
342	warning("Ignoring number of threads specified on command line.");	20✔
343	}
344	#endif
345
346	} else if (arg == "-?" \|\| arg == "-h" \|\| arg == "--help") {	123!
347	print_usage();	×
348	return OPENMC_E_UNASSIGNED;	×
349
350	} else if (arg == "-v" \|\| arg == "--version") {	75!
351	print_version();	7✔
352	print_build_info();	7✔
353	return OPENMC_E_UNASSIGNED;	7✔
354
355	} else if (arg == "-t" \|\| arg == "--track") {	34!
356	settings::write_all_tracks = true;	34✔
357
358	} else {
359	fmt::print(stderr, "Unknown option: {}\n", argv[i]);	×
360	print_usage();	×
361	return OPENMC_E_UNASSIGNED;	×
362	}
363
364	last_flag = i;
365	}
366	}	718✔
367
368	// Determine directory where XML input files are
369	if (argc > 1 && last_flag < argc - 1) {	5,328✔
370	settings::path_input = std::string(argv[last_flag + 1]);	63✔
371
372	// check that the path is either a valid directory or file
373	if (!dir_exists(settings::path_input) &&	119✔
374	!file_exists(settings::path_input)) {	56✔
375	fatal_error(fmt::format(	21✔
376	"The path specified to the OpenMC executable '{}' does not exist.",
377	settings::path_input));
378	}
379
380	// Add slash at end of directory if it isn't there
381	if (!ends_with(settings::path_input, "/") &&	126!
382	dir_exists(settings::path_input)) {	42✔
383	settings::path_input += "/";	5,314✔
384	}
385	}
386
387	return 0;
388	}
389
390	// TODO: Pulse-height tallies require per-history scoring across the full
391	// particle tree (parent + all descendants). The shared secondary bank
392	// transports each secondary as an independent Particle, breaking this
393	// assumption. A proper fix would defer pulse-height scoring: save
394	// (root_source_id, cell, pht_storage) per particle, then aggregate by
395	// root_source_id after all secondary generations complete before scoring
396	// into the histogram. For now, disable shared secondary when pulse-height
397	// tallies are present.
398	static void check_pulse_height_compatibility()	5,244✔
399	{
400	if (settings::use_shared_secondary_bank) {	5,244✔
401	for (const auto& t : model::tallies) {	334✔
402	if (t->type_ == TallyType::PULSE_HEIGHT) {	195✔
403	settings::use_shared_secondary_bank = false;	18✔
404	warning("Pulse-height tallies are not yet compatible with the shared "	18✔
405	"secondary bank. Disabling shared secondary bank.");
406	break;	18✔
407	}
408	}
409	}
410	}	5,244✔
411
412	bool read_model_xml()	5,307✔
413	{
414	std::string model_filename = settings::path_input;	5,307✔
415
416	// if the current filename is a directory, append the default model filename
417	if (model_filename.empty() \|\| dir_exists(model_filename))	5,307✔
418	model_filename += "model.xml";	5,272✔
419
420	// if this file doesn't exist, stop here
421	if (!file_exists(model_filename))	5,307✔
422	return false;
423
424	// try to process the path input as an XML file
425	pugi::xml_document doc;	4,445✔
426	if (!doc.load_file(model_filename.c_str())) {	4,445!
427	fatal_error(fmt::format(	×
428	"Error reading from single XML input file '{}'", model_filename));
429	}
430
431	pugi::xml_node root = doc.document_element();	4,445✔
432
433	// Read settings
434	if (!check_for_node(root, "settings")) {	4,445!
435	fatal_error("No <settings> node present in the model.xml file.");	×
436	}
437	auto settings_root = root.child("settings");	4,445✔
438
439	// Verbosity
440	if (check_for_node(settings_root, "verbosity") && settings::verbosity == -1) {	4,445!
441	settings::verbosity = std::stoi(get_node_value(settings_root, "verbosity"));	36✔
442	} else if (settings::verbosity == -1) {	4,427!
443	settings::verbosity = 7;	4,427✔
444	}
445
446	// To this point, we haven't displayed any output since we didn't know what
447	// the verbosity is. Now that we checked for it, show the title if necessary
448	if (mpi::master) {	4,445✔
449	if (settings::verbosity >= 2)	4,055✔
450	title();	4,041✔
451	}
452
453	write_message(	4,445✔
454	fmt::format("Reading model XML file '{}' ...", model_filename), 5);	4,445✔
455
456	// Read chain data before settings so DecaySpectrum source distributions can
457	// resolve nuclides while sources are constructed.
458	read_chain_file_xml();	4,445✔
459
460	read_settings_xml(settings_root);	4,445✔
461
462	// If other XML files are present, display warning
463	// that they will be ignored
464	auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml",	4,403✔
465	"tallies.xml", "plots.xml"};	4,403✔
466	for (const auto& input : other_inputs) {	25,924✔
467	if (file_exists(settings::path_input + input)) {	21,639✔
468	warning((fmt::format("Other XML file input(s) are present. These files "	118✔
469	"may be ignored in favor of the {} file.",
470	model_filename)));
471	break;	118✔
472	}
473	}
474
475	// Read materials and cross sections
476	if (!check_for_node(root, "materials")) {	4,403!
477	fatal_error(fmt::format(	×
478	"No <materials> node present in the {} file.", model_filename));
479	}
480
481	if (settings::run_mode != RunMode::PLOTTING) {	4,403✔
482	read_cross_sections_xml(root.child("materials"));	4,347✔
483	}
484	read_materials_xml(root.child("materials"));	4,403✔
485
486	// Read geometry
487	if (!check_for_node(root, "geometry")) {	4,403!
488	fatal_error(fmt::format(	×
489	"No <geometry> node present in the {} file.", model_filename));
490	}
491	read_geometry_xml(root.child("geometry"));	4,403✔
492
493	// Final geometry setup and assign temperatures
494	finalize_geometry();	4,403✔
495
496	// Finalize cross sections having assigned temperatures
497	finalize_cross_sections();	4,403✔
498
499	// Compute cell density multipliers now that material densities
500	// have been finalized (from geometry_aux.h)
501	finalize_cell_densities();	4,403✔
502
503	if (check_for_node(root, "tallies"))	4,403✔
504	read_tallies_xml(root.child("tallies"));	2,605✔
505
506	check_pulse_height_compatibility();	4,389✔
507
508	// Initialize distribcell_filters
509	prepare_distribcell();	4,389✔
510
511	if (check_for_node(root, "plots")) {	4,389✔
512	read_plots_xml(root.child("plots"));	233✔
513	} else {
514	// When no <plots> element is present in the model.xml file, check for a
515	// regular plots.xml file
516	std::string filename = settings::path_input + "plots.xml";	4,156✔
517	if (file_exists(filename)) {	4,156!
518	read_plots_xml();	×
519	}
520	}	4,156✔
521
522	finalize_variance_reduction();	4,382✔
523
524	return true;	4,382✔
525	}	9,626✔
526
527	void read_separate_xml_files()	862✔
528	{
529	// Read chain data before settings so DecaySpectrum source distributions can
530	// resolve nuclides while sources are constructed.
531	read_chain_file_xml();	862✔
532
533	read_settings_xml();	862✔
534	if (settings::run_mode != RunMode::PLOTTING) {	855✔
535	read_cross_sections_xml();	834✔
536	}
537
538	read_materials_xml();	855✔
539	read_geometry_xml();	855✔
540
541	// Final geometry setup and assign temperatures
542	finalize_geometry();	855✔
543
544	// Finalize cross sections having assigned temperatures
545	finalize_cross_sections();	855✔
546
547	// Compute cell density multipliers now that material densities
548	// have been finalized (from geometry_aux.h)
549	finalize_cell_densities();	855✔
550
551	read_tallies_xml();	855✔
552
553	check_pulse_height_compatibility();	855✔
554
555	// Initialize distribcell_filters
556	prepare_distribcell();	855✔
557
558	// Read the plots.xml regardless of plot mode in case plots are requested
559	// via the API
560	read_plots_xml();	855✔
561
562	finalize_variance_reduction();	855✔
563	}	855✔
564
565	void initial_output()	5,237✔
566	{
567	// write initial output
568	if (settings::run_mode == RunMode::PLOTTING) {	5,237✔
569	// Read plots.xml if it exists
570	if (mpi::master && settings::verbosity >= 5)	70!
571	print_plot();	56✔
572
573	} else {
574	// Write summary information
575	if (mpi::master && settings::output_summary)	5,167✔
576	write_summary();	4,459✔
577
578	// Warn if overlap checking is on
579	if (mpi::master && settings::check_overlaps) {	5,167!
580	warning("Cell overlap checking is ON.");	×
581	}
582	}
583	}	5,237✔
584
585	} // namespace openmc

openmc-dev / openmc / 26473127945

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