25930342666

Committed 15 May 2026 04:56PM UTC coverage: 81.414% (+0.09%) from 81.324%

Build # 25930342666

Build Type

Pull #3734

github

Committed by

web-flow

Commit Message

Merge 0af48acaf into d56cda254

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

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17919 of 25855 branches covered (69.31%)

Branch coverage included in aggregate %.

275 of 305 new or added lines in 18 files covered. (90.16%)

1321 existing lines in 29 files now uncovered.

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75.67

/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[11];
  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]);
  for (int i = 10; i >= 0; --i) {
    disp[i] -= disp[0];
  }

  int blocks[] {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1};
  MPI_Datatype types[] {MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE,
    MPI_DOUBLE, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_LONG, MPI_LONG};
  MPI_Type_create_struct(11, 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
        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;
}

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"));

  // 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();

  // 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)	8,540✔
46	{
47	using namespace openmc;	8,540✔
48
49	#ifdef OPENMC_MPI
50	// Check if intracomm was passed
51	MPI_Comm comm;	3,759✔
52	if (intracomm) {	3,759✔
53	comm = static_cast<const MPI_Comm>(intracomm);	3,561✔
54	} else {
55	comm = MPI_COMM_WORLD;	47✔
56	}
57
58	// Initialize MPI for C++
59	initialize_mpi(comm);	3,759✔
60	#endif
61
62	// Parse command-line arguments
63	int err = parse_command_line(argc, argv);	8,540✔
64	if (err)	8,507✔
65	return err;
66
67	#ifdef OPENMC_LIBMESH_ENABLED
68	const int n_threads = num_threads();	1,595✔
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()) {	1,595!
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 =	918✔
78	make_unique<libMesh::LibMeshInit>(argc, argv, comm, n_threads);	1,836✔
79	#else
80	// pass command line args, empty MPI communicator, and number of threads
81	settings::libmesh_init =	677✔
82	make_unique<libMesh::LibMeshInit>(argc, argv, 0, n_threads);	1,354✔
83	#endif
84
85	settings::libmesh_comm = &(settings::libmesh_init->comm());	1,595✔
86	}
87
88	#endif
89
90	// Start total and initialization timer
91	simulation::time_total.start();	8,496✔
92	simulation::time_initialize.start();	8,496✔
93
94	#ifdef _OPENMP
95	// If OMP_SCHEDULE is not set, default to a static schedule
96	char* envvar = std::getenv("OMP_SCHEDULE");	4,846✔
97	if (!envvar) {	4,846!
98	omp_set_schedule(omp_sched_static, 0);	4,846✔
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);	8,496✔
105	openmc::openmc_set_stride(DEFAULT_STRIDE);	8,496✔
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);	8,496✔
113	if (std::setlocale(LC_ALL, "C") == NULL) {	8,496!
114	fatal_error("Cannot set locale to C.");	×
115	}
116
117	// Read XML input files
118	if (!read_model_xml())	8,496✔
119	read_separate_xml_files();	1,382✔
120
121	if (!settings::properties_file.empty()) {	8,403✔
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) {	8,403!
127	fatal_error("Cannot reset locale.");	×
128	}
129
130	// Write some initial output under the header if needed
131	initial_output();	8,403✔
132
133	// Check for particle restart run
134	if (settings::particle_restart_run)	8,403✔
135	settings::run_mode = RunMode::PARTICLE;	41✔
136
137	// Stop initialization timer
138	simulation::time_initialize.stop();	8,403✔
139	simulation::time_total.stop();	8,403✔
140
141	return 0;	8,403✔
142	}	8,414✔
143
144	namespace openmc {
145
146	#ifdef OPENMC_MPI
147	void initialize_mpi(MPI_Comm intracomm)	3,759✔
148	{
149	mpi::intracomm = intracomm;	3,759✔
150
151	// Initialize MPI
152	int flag;	3,759✔
153	MPI_Initialized(&flag);	3,759✔
154	if (!flag)	3,759✔
155	MPI_Init(nullptr, nullptr);	3,075✔
156
157	// Determine number of processes and rank for each
158	MPI_Comm_size(intracomm, &mpi::n_procs);	3,759✔
159	MPI_Comm_rank(intracomm, &mpi::rank);	3,759✔
160	mpi::master = (mpi::rank == 0);	3,759✔
161
162	// Create bank datatype
163	SourceSite b;	3,759✔
164	MPI_Aint disp[11];	3,759✔
165	MPI_Get_address(&b.r, &disp[0]);	3,759✔
166	MPI_Get_address(&b.u, &disp[1]);	3,759✔
167	MPI_Get_address(&b.E, &disp[2]);	3,759✔
168	MPI_Get_address(&b.time, &disp[3]);	3,759✔
169	MPI_Get_address(&b.wgt, &disp[4]);	3,759✔
170	MPI_Get_address(&b.delayed_group, &disp[5]);	3,759✔
171	MPI_Get_address(&b.surf_id, &disp[6]);	3,759✔
172	MPI_Get_address(&b.particle, &disp[7]);	3,759✔
173	MPI_Get_address(&b.parent_nuclide, &disp[8]);	3,759✔
174	MPI_Get_address(&b.parent_id, &disp[9]);	3,759✔
175	MPI_Get_address(&b.progeny_id, &disp[10]);	3,759✔
176	for (int i = 10; i >= 0; --i) {	45,108✔
177	disp[i] -= disp[0];	41,349✔
178	}
179
180	int blocks[] {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1};	3,759✔
181	MPI_Datatype types[] {MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE,	3,759✔
182	MPI_DOUBLE, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_LONG, MPI_LONG};
183	MPI_Type_create_struct(11, blocks, disp, types, &mpi::source_site);	3,759✔
184	MPI_Type_commit(&mpi::source_site);	3,759✔
185
186	CollisionTrackSite bc;	3,759✔
187	MPI_Aint dispc[16];	3,759✔
188	MPI_Get_address(&bc.r, &dispc[0]); // double	3,759✔
189	MPI_Get_address(&bc.u, &dispc[1]); // double	3,759✔
190	MPI_Get_address(&bc.E, &dispc[2]); // double	3,759✔
191	MPI_Get_address(&bc.dE, &dispc[3]); // double	3,759✔
192	MPI_Get_address(&bc.time, &dispc[4]); // double	3,759✔
193	MPI_Get_address(&bc.wgt, &dispc[5]); // double	3,759✔
194	MPI_Get_address(&bc.event_mt, &dispc[6]); // int	3,759✔
195	MPI_Get_address(&bc.delayed_group, &dispc[7]); // int	3,759✔
196	MPI_Get_address(&bc.cell_id, &dispc[8]); // int	3,759✔
197	MPI_Get_address(&bc.nuclide_id, &dispc[9]); // int	3,759✔
198	MPI_Get_address(&bc.material_id, &dispc[10]); // int	3,759✔
199	MPI_Get_address(&bc.universe_id, &dispc[11]); // int	3,759✔
200	MPI_Get_address(&bc.n_collision, &dispc[12]); // int	3,759✔
201	MPI_Get_address(&bc.particle, &dispc[13]); // int	3,759✔
202	MPI_Get_address(&bc.parent_id, &dispc[14]); // int64_t	3,759✔
203	MPI_Get_address(&bc.progeny_id, &dispc[15]); // int64_t	3,759✔
204	for (int i = 15; i >= 0; --i) {	63,903✔
205	dispc[i] -= dispc[0];	60,144✔
206	}
207
208	int blocksc[] = {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};	3,759✔
209	MPI_Datatype typesc[] = {MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE,	3,759✔
210	MPI_DOUBLE, MPI_DOUBLE, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_INT,
211	MPI_INT, MPI_INT, MPI_INT, MPI_INT64_T, MPI_INT64_T};
212
213	MPI_Type_create_struct(	3,759✔
214	16, blocksc, dispc, typesc, &mpi::collision_track_site);
215	MPI_Type_commit(&mpi::collision_track_site);	3,759✔
216	}	3,759✔
217	#endif // OPENMC_MPI
218
219	int parse_command_line(int argc, char* argv[])	8,540✔
220	{
221	int last_flag = 0;	8,540✔
222	for (int i = 1; i < argc; ++i) {	9,860✔
223	std::string arg {argv[i]};	1,331✔
224	if (arg[0] == '-') {	1,331✔
225	if (arg == "-p" \|\| arg == "--plot") {	2,337!
226	settings::run_mode = RunMode::PLOTTING;	119✔
227	settings::check_overlaps = true;	119✔
228
229	} else if (arg == "-n" \|\| arg == "--particles") {	2,218!
230	i += 1;	×
231	settings::n_particles = std::stoll(argv[i]);	×
232
233	} else if (arg == "-q" \|\| arg == "--verbosity") {	2,218!
234	i += 1;	×
235	settings::verbosity = std::stoi(argv[i]);	×
236	if (settings::verbosity > 10 \|\| settings::verbosity < 1) {	×
237	auto msg = fmt::format("Invalid verbosity: {}.", settings::verbosity);	×
238	strcpy(openmc_err_msg, msg.c_str());	×
239	return OPENMC_E_INVALID_ARGUMENT;	×
240	}	×
241
242	} else if (arg == "-e" \|\| arg == "--event") {	2,005!
243	settings::event_based = true;	213✔
244	} else if (arg == "-r" \|\| arg == "--restart") {	1,688!
245	i += 1;	104✔
246	// Check what type of file this is
247	hid_t file_id = file_open(argv[i], 'r', true);	104✔
248	std::string filetype;	104✔
249	read_attribute(file_id, "filetype", filetype);	104✔
250	file_close(file_id);	104✔
251
252	// Set path and flag for type of run
253	if (filetype == "statepoint") {	104✔
254	settings::path_statepoint = argv[i];	63✔
255	settings::path_statepoint_c = settings::path_statepoint.c_str();	63✔
256	settings::restart_run = true;	63✔
257	} else if (filetype == "particle restart") {	41!
258	settings::path_particle_restart = argv[i];	41✔
259	settings::particle_restart_run = true;	41✔
260	} else {
261	auto msg =	×
262	fmt::format("Unrecognized file after restart flag: {}.", filetype);	×
263	strcpy(openmc_err_msg, msg.c_str());	×
264	return OPENMC_E_INVALID_ARGUMENT;	×
265	}	×
266
267	// If its a restart run check for additional source file
268	if (settings::restart_run && i + 1 < argc) {	104!
269	// Check if it has extension we can read
270	if (ends_with(argv[i + 1], ".h5")) {	×
271
272	// Check file type is a source file
273	file_id = file_open(argv[i + 1], 'r', true);	×
274	read_attribute(file_id, "filetype", filetype);	×
275	file_close(file_id);	×
276	if (filetype != "source") {	×
277	std::string msg {	×
278	"Second file after restart flag must be a source file"};	×
279	strcpy(openmc_err_msg, msg.c_str());	×
280	return OPENMC_E_INVALID_ARGUMENT;	×
281	}	×
282
283	// It is a source file
284	settings::path_sourcepoint = argv[i + 1];	104!
285	i += 1;
286
287	} else {
288	// Source is in statepoint file
289	settings::path_sourcepoint = settings::path_statepoint;	×
290	}
291
292	} else {
293	// Source is assumed to be in statepoint file
294	settings::path_sourcepoint = settings::path_statepoint;	208✔
295	}
296
297	} else if (arg == "-g" \|\| arg == "--geometry-debug") {	1,688!
298	settings::check_overlaps = true;	×
299	} else if (arg == "-c" \|\| arg == "--volume") {	965✔
300	settings::run_mode = RunMode::VOLUME;	701✔
301	} else if (arg == "-s" \|\| arg == "--threads") {	158!
302	// Read number of threads
303	i += 1;	24✔
304
305	#ifdef _OPENMP
306	// Read and set number of OpenMP threads
307	int n_threads = std::stoi(argv[i]);	26✔
308	if (n_threads < 1) {	13!
309	std::string msg {"Number of threads must be positive."};	×
310	strcpy(openmc_err_msg, msg.c_str());
311	return OPENMC_E_INVALID_ARGUMENT;
312	}
313	omp_set_num_threads(n_threads);	13✔
314	#else
315	if (mpi::master) {	11✔
316	warning("Ignoring number of threads specified on command line.");	20✔
317	}
318	#endif
319
320	} else if (arg == "-?" \|\| arg == "-h" \|\| arg == "--help") {	201!
321	print_usage();	×
322	return OPENMC_E_UNASSIGNED;	×
323
324	} else if (arg == "-v" \|\| arg == "--version") {	123!
325	print_version();	11✔
326	print_build_info();	11✔
327	return OPENMC_E_UNASSIGNED;	11✔
328
329	} else if (arg == "-t" \|\| arg == "--track") {	56!
330	settings::write_all_tracks = true;	56✔
331
332	} else {
333	fmt::print(stderr, "Unknown option: {}\n", argv[i]);	×
334	print_usage();	×
335	return OPENMC_E_UNASSIGNED;	×
336	}
337
338	last_flag = i;
339	}
340	}	1,331✔
341
342	// Determine directory where XML input files are
343	if (argc > 1 && last_flag < argc - 1) {	8,529✔
344	settings::path_input = std::string(argv[last_flag + 1]);	103✔
345
346	// check that the path is either a valid directory or file
347	if (!dir_exists(settings::path_input) &&	193✔
348	!file_exists(settings::path_input)) {	90✔
349	fatal_error(fmt::format(	39✔
350	"The path specified to the OpenMC executable '{}' does not exist.",
351	settings::path_input));
352	}
353
354	// Add slash at end of directory if it isn't there
355	if (!ends_with(settings::path_input, "/") &&	210!
356	dir_exists(settings::path_input)) {	70✔
357	settings::path_input += "/";	8,507✔
358	}
359	}
360
361	return 0;
362	}
363
364	bool read_model_xml()	8,496✔
365	{
366	std::string model_filename = settings::path_input;	8,496✔
367
368	// if the current filename is a directory, append the default model filename
369	if (model_filename.empty() \|\| dir_exists(model_filename))	8,496✔
370	model_filename += "model.xml";	8,439✔
371
372	// if this file doesn't exist, stop here
373	if (!file_exists(model_filename))	8,496✔
374	return false;
375
376	// try to process the path input as an XML file
377	pugi::xml_document doc;	7,114✔
378	if (!doc.load_file(model_filename.c_str())) {	7,114!
379	fatal_error(fmt::format(	×
380	"Error reading from single XML input file '{}'", model_filename));
381	}
382
383	pugi::xml_node root = doc.document_element();	7,114✔
384
385	// Read settings
386	if (!check_for_node(root, "settings")) {	7,114!
387	fatal_error("No <settings> node present in the model.xml file.");	×
388	}
389	auto settings_root = root.child("settings");	7,114✔
390
391	// Verbosity
392	if (check_for_node(settings_root, "verbosity") && settings::verbosity == -1) {	7,114!
393	settings::verbosity = std::stoi(get_node_value(settings_root, "verbosity"));	60✔
394	} else if (settings::verbosity == -1) {	7,084!
395	settings::verbosity = 7;	7,084✔
396	}
397
398	// To this point, we haven't displayed any output since we didn't know what
399	// the verbosity is. Now that we checked for it, show the title if necessary
400	if (mpi::master) {	7,114✔
401	if (settings::verbosity >= 2)	6,322✔
402	title();	6,300✔
403	}
404
405	write_message(	7,114✔
406	fmt::format("Reading model XML file '{}' ...", model_filename), 5);	8,447✔
407
408	// Read chain data before settings so DecaySpectrum source distributions can
409	// resolve nuclides while sources are constructed.
410	read_chain_file_xml();	7,114✔
411
412	read_settings_xml(settings_root);	7,114✔
413
414	// If other XML files are present, display warning
415	// that they will be ignored
416	auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml",	7,060✔
417	"tallies.xml", "plots.xml"};	7,060✔
418	for (const auto& input : other_inputs) {	41,566✔
419	if (file_exists(settings::path_input + input)) {	34,696✔
420	warning((fmt::format("Other XML file input(s) are present. These files "	225✔
421	"may be ignored in favor of the {} file.",
422	model_filename)));
423	break;	190✔
424	}
425	}
426
427	// Read materials and cross sections
428	if (!check_for_node(root, "materials")) {	7,060!
UNCOV 429	fatal_error(fmt::format(	×
430	"No <materials> node present in the {} file.", model_filename));
431	}
432
433	if (settings::run_mode != RunMode::PLOTTING) {	7,060✔
434	read_cross_sections_xml(root.child("materials"));	6,974✔
435	}
436	read_materials_xml(root.child("materials"));	7,060✔
437
438	// Read geometry
439	if (!check_for_node(root, "geometry")) {	7,060!
UNCOV 440	fatal_error(fmt::format(	×
441	"No <geometry> node present in the {} file.", model_filename));
442	}
443	read_geometry_xml(root.child("geometry"));	7,060✔
444
445	// Final geometry setup and assign temperatures
446	finalize_geometry();	7,058✔
447
448	// Finalize cross sections having assigned temperatures
449	finalize_cross_sections();	7,058✔
450
451	// Compute cell density multipliers now that material densities
452	// have been finalized (from geometry_aux.h)
453	finalize_cell_densities();	7,058✔
454
455	if (check_for_node(root, "tallies"))	7,058✔
456	read_tallies_xml(root.child("tallies"));	4,168✔
457
458	// Initialize distribcell_filters
459	prepare_distribcell();	7,040✔
460
461	if (check_for_node(root, "plots")) {	7,040✔
462	read_plots_xml(root.child("plots"));	365✔
463	} else {
464	// When no <plots> element is present in the model.xml file, check for a
465	// regular plots.xml file
466	std::string filename = settings::path_input + "plots.xml";	6,675✔
467	if (file_exists(filename)) {	6,675!
UNCOV 468	read_plots_xml();	×
469	}
470	}	6,675✔
471
472	finalize_variance_reduction();	7,031✔
473
474	return true;	7,031✔
475	}	15,444✔
476
477	void read_separate_xml_files()	1,382✔
478	{
479	// Read chain data before settings so DecaySpectrum source distributions can
480	// resolve nuclides while sources are constructed.
481	read_chain_file_xml();	1,382✔
482
483	read_settings_xml();	1,382✔
484	if (settings::run_mode != RunMode::PLOTTING) {	1,372✔
485	read_cross_sections_xml();	1,339✔
486	}
487
488	read_materials_xml();	1,372✔
489	read_geometry_xml();	1,372✔
490
491	// Final geometry setup and assign temperatures
492	finalize_geometry();	1,372✔
493
494	// Finalize cross sections having assigned temperatures
495	finalize_cross_sections();	1,372✔
496
497	// Compute cell density multipliers now that material densities
498	// have been finalized (from geometry_aux.h)
499	finalize_cell_densities();	1,372✔
500
501	read_tallies_xml();	1,372✔
502
503	// Initialize distribcell_filters
504	prepare_distribcell();	1,372✔
505
506	// Read the plots.xml regardless of plot mode in case plots are requested
507	// via the API
508	read_plots_xml();	1,372✔
509
510	finalize_variance_reduction();	1,372✔
511	}	1,372✔
512
513	void initial_output()	8,403✔
514	{
515	// write initial output
516	if (settings::run_mode == RunMode::PLOTTING) {	8,403✔
517	// Read plots.xml if it exists
518	if (mpi::master && settings::verbosity >= 5)	110!
519	print_plot();	88✔
520
521	} else {
522	// Write summary information
523	if (mpi::master && settings::output_summary)	8,293✔
524	write_summary();	6,977✔
525
526	// Warn if overlap checking is on
527	if (mpi::master && settings::check_overlaps) {	8,293!
UNCOV 528	warning("Cell overlap checking is ON.");	×
529	}
530	}
531	}	8,403✔
532
533	} // namespace openmc

openmc-dev / openmc / 25930342666

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