22694846817

Committed 04 Mar 2026 11:42PM UTC coverage: 81.537% (-0.2%) from 81.69%

Build # 22694846817

Build Type

Pull #3808

github

Committed by

web-flow

Commit Message

Merge 41317cfa2 into 2bd06660c

Pull Request Pull Request #3808: Add properties to settings w/ documentation, c++ loading of filename, and python round-trip test

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82 of 92 new or added lines in 8 files covered. (89.13%)

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74.95

/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(),
      settings::read_temperatures, settings::read_densities);
  }

  // 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_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 data from chain file
  read_chain_file_xml();

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

  // Read data from chain file
  read_chain_file_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)	8,251✔
46	{
47	using namespace openmc;	8,251✔
48
49	#ifdef OPENMC_MPI
50	// Check if intracomm was passed
51	MPI_Comm comm;	3,631✔
52	if (intracomm) {	3,631✔
53	comm = static_cast<const MPI_Comm>(intracomm);	3,433✔
54	} else {
55	comm = MPI_COMM_WORLD;	47✔
56	}
57
58	// Initialize MPI for C++
59	initialize_mpi(comm);	3,631✔
60	#endif
61
62	// Parse command-line arguments
63	int err = parse_command_line(argc, argv);	8,251✔
64	if (err)	8,218✔
65	return err;
66
67	#ifdef OPENMC_LIBMESH_ENABLED
68	const int n_threads = num_threads();	1,540✔
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()) {	1,540!
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 =	886✔
78	make_unique<libMesh::LibMeshInit>(argc, argv, comm, n_threads);	1,772✔
79	#else
80	// pass command line args, empty MPI communicator, and number of threads
81	settings::libmesh_init =	654✔
82	make_unique<libMesh::LibMeshInit>(argc, argv, 0, n_threads);	1,308✔
83	#endif
84
85	settings::libmesh_comm = &(settings::libmesh_init->comm());	1,540✔
86	}
87
88	#endif
89
90	// Start total and initialization timer
91	simulation::time_total.start();	8,207✔
92	simulation::time_initialize.start();	8,207✔
93
94	#ifdef _OPENMP
95	// If OMP_SCHEDULE is not set, default to a static schedule
96	char* envvar = std::getenv("OMP_SCHEDULE");	4,681✔
97	if (!envvar) {	4,681!
98	omp_set_schedule(omp_sched_static, 0);	4,681✔
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);	8,207✔
105	openmc::openmc_set_stride(DEFAULT_STRIDE);	8,207✔
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);	8,207✔
113	if (std::setlocale(LC_ALL, "C") == NULL) {	8,207!
114	fatal_error("Cannot set locale to C.");	×
115	}
116
117	// Read XML input files
118	if (!read_model_xml())	8,207✔
119	read_separate_xml_files();	1,349✔
120
121	if (!settings::properties_file.empty()) {	8,114!
NEW 122	openmc_properties_import(settings::properties_file.c_str(),	×
123	settings::read_temperatures, settings::read_densities);
124	}
125
126	// Reset locale to previous state
127	if (std::setlocale(LC_ALL, prev_locale.c_str()) == NULL) {	8,114!
128	fatal_error("Cannot reset locale.");	×
129	}
130
131	// Write some initial output under the header if needed
132	initial_output();	8,114✔
133
134	// Check for particle restart run
135	if (settings::particle_restart_run)	8,114✔
136	settings::run_mode = RunMode::PARTICLE;	41✔
137
138	// Stop initialization timer
139	simulation::time_initialize.stop();	8,114✔
140	simulation::time_total.stop();	8,114✔
141
142	return 0;	8,114✔
143	}	8,125✔
144
145	namespace openmc {
146
147	#ifdef OPENMC_MPI
148	void initialize_mpi(MPI_Comm intracomm)	3,631✔
149	{
150	mpi::intracomm = intracomm;	3,631✔
151
152	// Initialize MPI
153	int flag;	3,631✔
154	MPI_Initialized(&flag);	3,631✔
155	if (!flag)	3,631✔
156	MPI_Init(nullptr, nullptr);	2,987✔
157
158	// Determine number of processes and rank for each
159	MPI_Comm_size(intracomm, &mpi::n_procs);	3,631✔
160	MPI_Comm_rank(intracomm, &mpi::rank);	3,631✔
161	mpi::master = (mpi::rank == 0);	3,631✔
162
163	// Create bank datatype
164	SourceSite b;	3,631✔
165	MPI_Aint disp[11];	3,631✔
166	MPI_Get_address(&b.r, &disp[0]);	3,631✔
167	MPI_Get_address(&b.u, &disp[1]);	3,631✔
168	MPI_Get_address(&b.E, &disp[2]);	3,631✔
169	MPI_Get_address(&b.time, &disp[3]);	3,631✔
170	MPI_Get_address(&b.wgt, &disp[4]);	3,631✔
171	MPI_Get_address(&b.delayed_group, &disp[5]);	3,631✔
172	MPI_Get_address(&b.surf_id, &disp[6]);	3,631✔
173	MPI_Get_address(&b.particle, &disp[7]);	3,631✔
174	MPI_Get_address(&b.parent_nuclide, &disp[8]);	3,631✔
175	MPI_Get_address(&b.parent_id, &disp[9]);	3,631✔
176	MPI_Get_address(&b.progeny_id, &disp[10]);	3,631✔
177	for (int i = 10; i >= 0; --i) {	43,572✔
178	disp[i] -= disp[0];	39,941✔
179	}
180
181	int blocks[] {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1};	3,631✔
182	MPI_Datatype types[] {MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE,	3,631✔
183	MPI_DOUBLE, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_LONG, MPI_LONG};
184	MPI_Type_create_struct(11, blocks, disp, types, &mpi::source_site);	3,631✔
185	MPI_Type_commit(&mpi::source_site);	3,631✔
186
187	CollisionTrackSite bc;	3,631✔
188	MPI_Aint dispc[16];	3,631✔
189	MPI_Get_address(&bc.r, &dispc[0]); // double	3,631✔
190	MPI_Get_address(&bc.u, &dispc[1]); // double	3,631✔
191	MPI_Get_address(&bc.E, &dispc[2]); // double	3,631✔
192	MPI_Get_address(&bc.dE, &dispc[3]); // double	3,631✔
193	MPI_Get_address(&bc.time, &dispc[4]); // double	3,631✔
194	MPI_Get_address(&bc.wgt, &dispc[5]); // double	3,631✔
195	MPI_Get_address(&bc.event_mt, &dispc[6]); // int	3,631✔
196	MPI_Get_address(&bc.delayed_group, &dispc[7]); // int	3,631✔
197	MPI_Get_address(&bc.cell_id, &dispc[8]); // int	3,631✔
198	MPI_Get_address(&bc.nuclide_id, &dispc[9]); // int	3,631✔
199	MPI_Get_address(&bc.material_id, &dispc[10]); // int	3,631✔
200	MPI_Get_address(&bc.universe_id, &dispc[11]); // int	3,631✔
201	MPI_Get_address(&bc.n_collision, &dispc[12]); // int	3,631✔
202	MPI_Get_address(&bc.particle, &dispc[13]); // int	3,631✔
203	MPI_Get_address(&bc.parent_id, &dispc[14]); // int64_t	3,631✔
204	MPI_Get_address(&bc.progeny_id, &dispc[15]); // int64_t	3,631✔
205	for (int i = 15; i >= 0; --i) {	61,727✔
206	dispc[i] -= dispc[0];	58,096✔
207	}
208
209	int blocksc[] = {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};	3,631✔
210	MPI_Datatype typesc[] = {MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE,	3,631✔
211	MPI_DOUBLE, MPI_DOUBLE, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_INT,
212	MPI_INT, MPI_INT, MPI_INT, MPI_INT64_T, MPI_INT64_T};
213
214	MPI_Type_create_struct(	3,631✔
215	16, blocksc, dispc, typesc, &mpi::collision_track_site);
216	MPI_Type_commit(&mpi::collision_track_site);	3,631✔
217	}	3,631✔
218	#endif // OPENMC_MPI
219
220	int parse_command_line(int argc, char* argv[])	8,251✔
221	{
222	int last_flag = 0;	8,251✔
223	for (int i = 1; i < argc; ++i) {	9,540✔
224	std::string arg {argv[i]};	1,300✔
225	if (arg[0] == '-') {	1,300✔
226	if (arg == "-p" \|\| arg == "--plot") {	2,275!
227	settings::run_mode = RunMode::PLOTTING;	119✔
228	settings::check_overlaps = true;	119✔
229
230	} else if (arg == "-n" \|\| arg == "--particles") {	2,156!
231	i += 1;	×
232	settings::n_particles = std::stoll(argv[i]);	×
233
234	} else if (arg == "-q" \|\| arg == "--verbosity") {	2,156!
235	i += 1;	×
236	settings::verbosity = std::stoi(argv[i]);	×
237	if (settings::verbosity > 10 \|\| settings::verbosity < 1) {	×
238	auto msg = fmt::format("Invalid verbosity: {}.", settings::verbosity);	×
239	strcpy(openmc_err_msg, msg.c_str());	×
240	return OPENMC_E_INVALID_ARGUMENT;	×
241	}	×
242
243	} else if (arg == "-e" \|\| arg == "--event") {	1,952!
244	settings::event_based = true;	204✔
245	} else if (arg == "-r" \|\| arg == "--restart") {	1,644!
246	i += 1;	104✔
247	// Check what type of file this is
248	hid_t file_id = file_open(argv[i], 'r', true);	104✔
249	std::string filetype;	104✔
250	read_attribute(file_id, "filetype", filetype);	104✔
251	file_close(file_id);	104✔
252
253	// Set path and flag for type of run
254	if (filetype == "statepoint") {	104✔
255	settings::path_statepoint = argv[i];	63✔
256	settings::path_statepoint_c = settings::path_statepoint.c_str();	63✔
257	settings::restart_run = true;	63✔
258	} else if (filetype == "particle restart") {	41!
259	settings::path_particle_restart = argv[i];	41✔
260	settings::particle_restart_run = true;	41✔
261	} else {
UNCOV 262	auto msg =	×
263	fmt::format("Unrecognized file after restart flag: {}.", filetype);	×
264	strcpy(openmc_err_msg, msg.c_str());	×
265	return OPENMC_E_INVALID_ARGUMENT;	×
266	}	×
267
268	// If its a restart run check for additional source file
269	if (settings::restart_run && i + 1 < argc) {	104!
270	// Check if it has extension we can read
271	if (ends_with(argv[i + 1], ".h5")) {	×
272
273	// Check file type is a source file
274	file_id = file_open(argv[i + 1], 'r', true);	×
275	read_attribute(file_id, "filetype", filetype);	×
276	file_close(file_id);	×
277	if (filetype != "source") {	×
UNCOV 278	std::string msg {	×
279	"Second file after restart flag must be a source file"};	×
280	strcpy(openmc_err_msg, msg.c_str());	×
281	return OPENMC_E_INVALID_ARGUMENT;	×
282	}	×
283
284	// It is a source file
285	settings::path_sourcepoint = argv[i + 1];	104!
286	i += 1;
287
288	} else {
289	// Source is in statepoint file
290	settings::path_sourcepoint = settings::path_statepoint;	×
291	}
292
293	} else {
294	// Source is assumed to be in statepoint file
295	settings::path_sourcepoint = settings::path_statepoint;	208✔
296	}
297
298	} else if (arg == "-g" \|\| arg == "--geometry-debug") {	1,644!
299	settings::check_overlaps = true;	×
300	} else if (arg == "-c" \|\| arg == "--volume") {	943✔
301	settings::run_mode = RunMode::VOLUME;	679✔
302	} else if (arg == "-s" \|\| arg == "--threads") {	158!
303	// Read number of threads
304	i += 1;	24✔
305
306	#ifdef _OPENMP
307	// Read and set number of OpenMP threads
308	int n_threads = std::stoi(argv[i]);	26✔
309	if (n_threads < 1) {	13!
310	std::string msg {"Number of threads must be positive."};	×
311	strcpy(openmc_err_msg, msg.c_str());
312	return OPENMC_E_INVALID_ARGUMENT;
313	}
314	omp_set_num_threads(n_threads);	13✔
315	#else
316	if (mpi::master) {	11✔
317	warning("Ignoring number of threads specified on command line.");	20✔
318	}
319	#endif
320
321	} else if (arg == "-?" \|\| arg == "-h" \|\| arg == "--help") {	201!
322	print_usage();	×
323	return OPENMC_E_UNASSIGNED;	×
324
325	} else if (arg == "-v" \|\| arg == "--version") {	123!
326	print_version();	11✔
327	print_build_info();	11✔
328	return OPENMC_E_UNASSIGNED;	11✔
329
330	} else if (arg == "-t" \|\| arg == "--track") {	56!
331	settings::write_all_tracks = true;	56✔
332
333	} else {
334	fmt::print(stderr, "Unknown option: {}\n", argv[i]);	×
335	print_usage();	×
336	return OPENMC_E_UNASSIGNED;	×
337	}
338
339	last_flag = i;
340	}
341	}	1,300✔
342
343	// Determine directory where XML input files are
344	if (argc > 1 && last_flag < argc - 1) {	8,240✔
345	settings::path_input = std::string(argv[last_flag + 1]);	103✔
346
347	// check that the path is either a valid directory or file
348	if (!dir_exists(settings::path_input) &&	193✔
349	!file_exists(settings::path_input)) {	90✔
350	fatal_error(fmt::format(	39✔
351	"The path specified to the OpenMC executable '{}' does not exist.",
352	settings::path_input));
353	}
354
355	// Add slash at end of directory if it isn't there
356	if (!ends_with(settings::path_input, "/") &&	210!
357	dir_exists(settings::path_input)) {	70✔
358	settings::path_input += "/";	8,218✔
359	}
360	}
361
362	return 0;
363	}
364
365	bool read_model_xml()	8,207✔
366	{
367	std::string model_filename = settings::path_input;	8,207✔
368
369	// if the current filename is a directory, append the default model filename
370	if (model_filename.empty() \|\| dir_exists(model_filename))	8,207✔
371	model_filename += "model.xml";	8,150✔
372
373	// if this file doesn't exist, stop here
374	if (!file_exists(model_filename))	8,207✔
375	return false;
376
377	// try to process the path input as an XML file
378	pugi::xml_document doc;	6,858✔
379	if (!doc.load_file(model_filename.c_str())) {	6,858!
380	fatal_error(fmt::format(	×
381	"Error reading from single XML input file '{}'", model_filename));
382	}
383
384	pugi::xml_node root = doc.document_element();	6,858✔
385
386	// Read settings
387	if (!check_for_node(root, "settings")) {	6,858!
388	fatal_error("No <settings> node present in the model.xml file.");	×
389	}
390	auto settings_root = root.child("settings");	6,858✔
391
392	// Verbosity
393	if (check_for_node(settings_root, "verbosity") && settings::verbosity == -1) {	6,858!
394	settings::verbosity = std::stoi(get_node_value(settings_root, "verbosity"));	60✔
395	} else if (settings::verbosity == -1) {	6,828!
396	settings::verbosity = 7;	6,828✔
397	}
398
399	// To this point, we haven't displayed any output since we didn't know what
400	// the verbosity is. Now that we checked for it, show the title if necessary
401	if (mpi::master) {	6,858✔
402	if (settings::verbosity >= 2)	6,102✔
403	title();	6,080✔
404	}
405
406	write_message(	6,858✔
407	fmt::format("Reading model XML file '{}' ...", model_filename), 5);	8,142✔
408
409	read_settings_xml(settings_root);	6,858✔
410
411	// If other XML files are present, display warning
412	// that they will be ignored
413	auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml",	6,804✔
414	"tallies.xml", "plots.xml"};	6,804✔
415	for (const auto& input : other_inputs) {	40,030✔
416	if (file_exists(settings::path_input + input)) {	33,416✔
417	warning((fmt::format("Other XML file input(s) are present. These files "	225✔
418	"may be ignored in favor of the {} file.",
419	model_filename)));
420	break;	190✔
421	}
422	}
423
424	// Read data from chain file
425	read_chain_file_xml();	6,804✔
426
427	// Read materials and cross sections
428	if (!check_for_node(root, "materials")) {	6,804!
429	fatal_error(fmt::format(	×
430	"No <materials> node present in the {} file.", model_filename));
431	}
432
433	if (settings::run_mode != RunMode::PLOTTING) {	6,804✔
434	read_cross_sections_xml(root.child("materials"));	6,718✔
435	}
436	read_materials_xml(root.child("materials"));	6,804✔
437
438	// Read geometry
439	if (!check_for_node(root, "geometry")) {	6,804!
440	fatal_error(fmt::format(	×
441	"No <geometry> node present in the {} file.", model_filename));
442	}
443	read_geometry_xml(root.child("geometry"));	6,804✔
444
445	// Final geometry setup and assign temperatures
446	finalize_geometry();	6,802✔
447
448	// Finalize cross sections having assigned temperatures
449	finalize_cross_sections();	6,802✔
450
451	// Compute cell density multipliers now that material densities
452	// have been finalized (from geometry_aux.h)
453	finalize_cell_densities();	6,802✔
454
455	if (check_for_node(root, "tallies"))	6,802✔
456	read_tallies_xml(root.child("tallies"));	3,956✔
457
458	// Initialize distribcell_filters
459	prepare_distribcell();	6,784✔
460
461	if (check_for_node(root, "plots")) {	6,784✔
462	read_plots_xml(root.child("plots"));	343✔
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";	6,441✔
467	if (file_exists(filename)) {	6,441!
468	read_plots_xml();	×
469	}
470	}	6,441✔
471
472	finalize_variance_reduction();	6,775✔
473
474	return true;	6,775✔
475	}	14,899✔
476
477	void read_separate_xml_files()	1,349✔
478	{
479	read_settings_xml();	1,349✔
480	if (settings::run_mode != RunMode::PLOTTING) {	1,339✔
481	read_cross_sections_xml();	1,306✔
482	}
483
484	// Read data from chain file
485	read_chain_file_xml();	1,339✔
486
487	read_materials_xml();	1,339✔
488	read_geometry_xml();	1,339✔
489
490	// Final geometry setup and assign temperatures
491	finalize_geometry();	1,339✔
492
493	// Finalize cross sections having assigned temperatures
494	finalize_cross_sections();	1,339✔
495
496	// Compute cell density multipliers now that material densities
497	// have been finalized (from geometry_aux.h)
498	finalize_cell_densities();	1,339✔
499
500	read_tallies_xml();	1,339✔
501
502	// Initialize distribcell_filters
503	prepare_distribcell();	1,339✔
504
505	// Read the plots.xml regardless of plot mode in case plots are requested
506	// via the API
507	read_plots_xml();	1,339✔
508
509	finalize_variance_reduction();	1,339✔
510	}	1,339✔
511
512	void initial_output()	8,114✔
513	{
514	// write initial output
515	if (settings::run_mode == RunMode::PLOTTING) {	8,114✔
516	// Read plots.xml if it exists
517	if (mpi::master && settings::verbosity >= 5)	110!
518	print_plot();	88✔
519
520	} else {
521	// Write summary information
522	if (mpi::master && settings::output_summary)	8,004✔
523	write_summary();	6,735✔
524
525	// Warn if overlap checking is on
526	if (mpi::master && settings::check_overlaps) {	8,004!
527	warning("Cell overlap checking is ON.");	×
528	}
529	}
530	}	8,114✔
531
532	} // namespace openmc

openmc-dev / openmc / 22694846817

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