21043561037

Committed 15 Jan 2026 07:23PM UTC coverage: 81.388% (-0.7%) from 82.044%

Build # 21043561037

Build Type

Pull #3734

github

Committed by

web-flow

Commit Message

Merge 5e79b7b6f into 179048b80

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

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156 of 179 new or added lines in 12 files covered. (87.15%)

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75.65

/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();

  // 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)	3,578✔
46	{
47	using namespace openmc;
48
49	#ifdef OPENMC_MPI
50	// Check if intracomm was passed
51	MPI_Comm comm;
52	if (intracomm) {	1,694✔
53	comm = static_cast<const MPI_Comm>(intracomm);	1,603✔
54	} else {
55	comm = MPI_COMM_WORLD;	91✔
56	}
57
58	// Initialize MPI for C++
59	initialize_mpi(comm);	1,694✔
60	#endif
61
62	// Parse command-line arguments
63	int err = parse_command_line(argc, argv);	3,578✔
64	if (err)	3,563✔
65	return err;	5✔
66
67	#ifdef OPENMC_LIBMESH_ENABLED
68	const int n_threads = num_threads();	1,463✔
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()) {	1,463!
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);	843✔
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);	620✔
83	#endif
84
85	settings::libmesh_comm = &(settings::libmesh_init->comm());	1,463✔
86	}
87
88	#endif
89
90	// Start total and initialization timer
91	simulation::time_total.start();	3,558✔
92	simulation::time_initialize.start();	3,558✔
93
94	#ifdef _OPENMP
95	// If OMP_SCHEDULE is not set, default to a static schedule
96	char* envvar = std::getenv("OMP_SCHEDULE");	1,463✔
97	if (!envvar) {	1,463!
98	omp_set_schedule(omp_sched_static, 0);	1,463✔
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);	3,558✔
105	openmc::openmc_set_stride(DEFAULT_STRIDE);	3,558✔
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);	3,558✔
113	if (std::setlocale(LC_ALL, "C") == NULL) {	3,558!
114	fatal_error("Cannot set locale to C.");	×
115	}
116
117	// Read XML input files
118	if (!read_model_xml())	3,558✔
119	read_separate_xml_files();	610✔
120
121	// Reset locale to previous state
122	if (std::setlocale(LC_ALL, prev_locale.c_str()) == NULL) {	3,528!
123	fatal_error("Cannot reset locale.");	×
124	}
125
126	// Write some initial output under the header if needed
127	initial_output();	3,528✔
128
129	// Check for particle restart run
130	if (settings::particle_restart_run)	3,528✔
131	settings::run_mode = RunMode::PARTICLE;	19✔
132
133	// Stop initialization timer
134	simulation::time_initialize.stop();	3,528✔
135	simulation::time_total.stop();	3,528✔
136
137	return 0;	3,528✔
138	}	3,528✔
139
140	namespace openmc {
141
142	#ifdef OPENMC_MPI
143	void initialize_mpi(MPI_Comm intracomm)	1,694✔
144	{
145	mpi::intracomm = intracomm;	1,694✔
146
147	// Initialize MPI
148	int flag;
149	MPI_Initialized(&flag);	1,694✔
150	if (!flag)	1,694✔
151	MPI_Init(nullptr, nullptr);	1,391✔
152
153	// Determine number of processes and rank for each
154	MPI_Comm_size(intracomm, &mpi::n_procs);	1,694✔
155	MPI_Comm_rank(intracomm, &mpi::rank);	1,694✔
156	mpi::master = (mpi::rank == 0);	1,694✔
157
158	// Create bank datatype
159	SourceSite b;	1,694✔
160	MPI_Aint disp[11];
161	MPI_Get_address(&b.r, &disp[0]);	1,694✔
162	MPI_Get_address(&b.u, &disp[1]);	1,694✔
163	MPI_Get_address(&b.E, &disp[2]);	1,694✔
164	MPI_Get_address(&b.time, &disp[3]);	1,694✔
165	MPI_Get_address(&b.wgt, &disp[4]);	1,694✔
166	MPI_Get_address(&b.delayed_group, &disp[5]);	1,694✔
167	MPI_Get_address(&b.surf_id, &disp[6]);	1,694✔
168	MPI_Get_address(&b.particle, &disp[7]);	1,694✔
169	MPI_Get_address(&b.parent_nuclide, &disp[8]);	1,694✔
170	MPI_Get_address(&b.parent_id, &disp[9]);	1,694✔
171	MPI_Get_address(&b.progeny_id, &disp[10]);	1,694✔
172	for (int i = 10; i >= 0; --i) {	20,328✔
173	disp[i] -= disp[0];	18,634✔
174	}
175
176	int blocks[] {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1};	1,694✔
177	MPI_Datatype types[] {MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE,	1,694✔
178	MPI_DOUBLE, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_LONG, MPI_LONG};
179	MPI_Type_create_struct(11, blocks, disp, types, &mpi::source_site);	1,694✔
180	MPI_Type_commit(&mpi::source_site);	1,694✔
181
182	CollisionTrackSite bc;	1,694✔
183	MPI_Aint dispc[16];
184	MPI_Get_address(&bc.r, &dispc[0]); // double	1,694✔
185	MPI_Get_address(&bc.u, &dispc[1]); // double	1,694✔
186	MPI_Get_address(&bc.E, &dispc[2]); // double	1,694✔
187	MPI_Get_address(&bc.dE, &dispc[3]); // double	1,694✔
188	MPI_Get_address(&bc.time, &dispc[4]); // double	1,694✔
189	MPI_Get_address(&bc.wgt, &dispc[5]); // double	1,694✔
190	MPI_Get_address(&bc.event_mt, &dispc[6]); // int	1,694✔
191	MPI_Get_address(&bc.delayed_group, &dispc[7]); // int	1,694✔
192	MPI_Get_address(&bc.cell_id, &dispc[8]); // int	1,694✔
193	MPI_Get_address(&bc.nuclide_id, &dispc[9]); // int	1,694✔
194	MPI_Get_address(&bc.material_id, &dispc[10]); // int	1,694✔
195	MPI_Get_address(&bc.universe_id, &dispc[11]); // int	1,694✔
196	MPI_Get_address(&bc.n_collision, &dispc[12]); // int	1,694✔
197	MPI_Get_address(&bc.particle, &dispc[13]); // int	1,694✔
198	MPI_Get_address(&bc.parent_id, &dispc[14]); // int64_t	1,694✔
199	MPI_Get_address(&bc.progeny_id, &dispc[15]); // int64_t	1,694✔
200	for (int i = 15; i >= 0; --i) {	28,798✔
201	dispc[i] -= dispc[0];	27,104✔
202	}
203
204	int blocksc[] = {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};	1,694✔
205	MPI_Datatype typesc[] = {MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE, MPI_DOUBLE,	1,694✔
206	MPI_DOUBLE, MPI_DOUBLE, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_INT,
207	MPI_INT, MPI_INT, MPI_INT, MPI_INT64_T, MPI_INT64_T};
208
209	MPI_Type_create_struct(	1,694✔
210	16, blocksc, dispc, typesc, &mpi::collision_track_site);
211	MPI_Type_commit(&mpi::collision_track_site);	1,694✔
212	}	1,694✔
213	#endif // OPENMC_MPI
214
215	int parse_command_line(int argc, char* argv[])	3,578✔
216	{
217	int last_flag = 0;	3,578✔
218	for (int i = 1; i < argc; ++i) {	4,049✔
219	std::string arg {argv[i]};	476✔
220	if (arg[0] == '-') {	476✔
221	if (arg == "-p" \|\| arg == "--plot") {	431!
222	settings::run_mode = RunMode::PLOTTING;	53✔
223	settings::check_overlaps = true;	53✔
224
225	} else if (arg == "-n" \|\| arg == "--particles") {	378!
226	i += 1;	×
227	settings::n_particles = std::stoll(argv[i]);	×
228
229	} else if (arg == "-q" \|\| arg == "--verbosity") {	378!
230	i += 1;	×
231	settings::verbosity = std::stoi(argv[i]);	×
232	if (settings::verbosity > 10 \|\| settings::verbosity < 1) {	×
233	auto msg = fmt::format("Invalid verbosity: {}.", settings::verbosity);	×
234	strcpy(openmc_err_msg, msg.c_str());	×
235	return OPENMC_E_INVALID_ARGUMENT;	×
236	}	×
237
238	} else if (arg == "-e" \|\| arg == "--event") {	378!
UNCOV 239	settings::event_based = true;	×
240	} else if (arg == "-r" \|\| arg == "--restart") {	378!
241	i += 1;	48✔
242	// Check what type of file this is
243	hid_t file_id = file_open(argv[i], 'r', true);	48✔
244	std::string filetype;	48✔
245	read_attribute(file_id, "filetype", filetype);	48✔
246	file_close(file_id);	48✔
247
248	// Set path and flag for type of run
249	if (filetype == "statepoint") {	48✔
250	settings::path_statepoint = argv[i];	29✔
251	settings::path_statepoint_c = settings::path_statepoint.c_str();	29✔
252	settings::restart_run = true;	29✔
253	} else if (filetype == "particle restart") {	19!
254	settings::path_particle_restart = argv[i];	19✔
255	settings::particle_restart_run = true;	19✔
256	} else {
257	auto msg =
258	fmt::format("Unrecognized file after restart flag: {}.", filetype);	×
259	strcpy(openmc_err_msg, msg.c_str());	×
260	return OPENMC_E_INVALID_ARGUMENT;	×
261	}	×
262
263	// If its a restart run check for additional source file
264	if (settings::restart_run && i + 1 < argc) {	48!
265	// Check if it has extension we can read
266	if (ends_with(argv[i + 1], ".h5")) {	×
267
268	// Check file type is a source file
269	file_id = file_open(argv[i + 1], 'r', true);	×
270	read_attribute(file_id, "filetype", filetype);	×
271	file_close(file_id);	×
272	if (filetype != "source") {	×
273	std::string msg {
274	"Second file after restart flag must be a source file"};	×
275	strcpy(openmc_err_msg, msg.c_str());	×
276	return OPENMC_E_INVALID_ARGUMENT;	×
277	}	×
278
279	// It is a source file
280	settings::path_sourcepoint = argv[i + 1];	×
281	i += 1;	×
282
283	} else {
284	// Source is in statepoint file
285	settings::path_sourcepoint = settings::path_statepoint;	×
286	}
287
288	} else {	×
289	// Source is assumed to be in statepoint file
290	settings::path_sourcepoint = settings::path_statepoint;	48✔
291	}
292
293	} else if (arg == "-g" \|\| arg == "--geometry-debug") {	378!
294	settings::check_overlaps = true;	×
295	} else if (arg == "-c" \|\| arg == "--volume") {	330✔
296	settings::run_mode = RunMode::VOLUME;	289✔
297	} else if (arg == "-s" \|\| arg == "--threads") {	41!
298	// Read number of threads
299	i += 1;	10✔
300
301	#ifdef _OPENMP
302	// Read and set number of OpenMP threads
303	int n_threads = std::stoi(argv[i]);	3✔
304	if (n_threads < 1) {	3!
305	std::string msg {"Number of threads must be positive."};	×
306	strcpy(openmc_err_msg, msg.c_str());
307	return OPENMC_E_INVALID_ARGUMENT;
308	}
309	omp_set_num_threads(n_threads);	3✔
310	#else
311	if (mpi::master) {	7✔
312	warning("Ignoring number of threads specified on command line.");	6✔
313	}
314	#endif
315
316	} else if (arg == "-?" \|\| arg == "-h" \|\| arg == "--help") {	31!
317	print_usage();	×
318	return OPENMC_E_UNASSIGNED;	×
319
320	} else if (arg == "-v" \|\| arg == "--version") {	31!
321	print_version();	5✔
322	print_build_info();	5✔
323	return OPENMC_E_UNASSIGNED;	5✔
324
325	} else if (arg == "-t" \|\| arg == "--track") {	26!
326	settings::write_all_tracks = true;	26✔
327
328	} else {
329	fmt::print(stderr, "Unknown option: {}\n", argv[i]);	×
330	print_usage();	×
331	return OPENMC_E_UNASSIGNED;	×
332	}
333
334	last_flag = i;	426✔
335	}
336	}	476✔
337
338	// Determine directory where XML input files are
339	if (argc > 1 && last_flag < argc - 1) {	3,573✔
340	settings::path_input = std::string(argv[last_flag + 1]);	45✔
341
342	// check that the path is either a valid directory or file
343	if (!dir_exists(settings::path_input) &&	85✔
344	!file_exists(settings::path_input)) {	40✔
345	fatal_error(fmt::format(	15✔
346	"The path specified to the OpenMC executable '{}' does not exist.",
347	settings::path_input));
348	}
349
350	// Add slash at end of directory if it isn't there
351	if (!ends_with(settings::path_input, "/") &&	60!
352	dir_exists(settings::path_input)) {	30✔
353	settings::path_input += "/";	5✔
354	}
355	}
356
357	return 0;	3,558✔
358	}
359
360	bool read_model_xml()	3,558✔
361	{
362	std::string model_filename = settings::path_input;	3,558✔
363
364	// if the current filename is a directory, append the default model filename
365	if (model_filename.empty() \|\| dir_exists(model_filename))	3,558✔
366	model_filename += "model.xml";	3,533✔
367
368	// if this file doesn't exist, stop here
369	if (!file_exists(model_filename))	3,558✔
370	return false;	610✔
371
372	// try to process the path input as an XML file
373	pugi::xml_document doc;	2,948✔
374	if (!doc.load_file(model_filename.c_str())) {	2,948!
375	fatal_error(fmt::format(	×
376	"Error reading from single XML input file '{}'", model_filename));
377	}
378
379	pugi::xml_node root = doc.document_element();	2,948✔
380
381	// Read settings
382	if (!check_for_node(root, "settings")) {	2,948!
383	fatal_error("No <settings> node present in the model.xml file.");	×
384	}
385	auto settings_root = root.child("settings");	2,948✔
386
387	// Verbosity
388	if (check_for_node(settings_root, "verbosity") && settings::verbosity == -1) {	2,948!
389	settings::verbosity = std::stoi(get_node_value(settings_root, "verbosity"));	14✔
390	} else if (settings::verbosity == -1) {	2,934!
391	settings::verbosity = 7;	2,934✔
392	}
393
394	// To this point, we haven't displayed any output since we didn't know what
395	// the verbosity is. Now that we checked for it, show the title if necessary
396	if (mpi::master) {	2,948✔
397	if (settings::verbosity >= 2)	2,593✔
398	title();	2,583✔
399	}
400
401	write_message(	2,948✔
402	fmt::format("Reading model XML file '{}' ...", model_filename), 5);	4,687✔
403
404	read_settings_xml(settings_root);	2,948✔
405
406	// If other XML files are present, display warning
407	// that they will be ignored
408	auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml",	2,930✔
409	"tallies.xml", "plots.xml"};	2,930✔
410	for (const auto& input : other_inputs) {	17,222✔
411	if (file_exists(settings::path_input + input)) {	14,378✔
412	warning((fmt::format("Other XML file input(s) are present. These files "	86✔
413	"may be ignored in favor of the {} file.",
414	model_filename)));
415	break;	86✔
416	}
417	}
418
419	// Read data from chain file
420	read_chain_file_xml();	2,930✔
421
422	// Read materials and cross sections
423	if (!check_for_node(root, "materials")) {	2,930!
424	fatal_error(fmt::format(	×
425	"No <materials> node present in the {} file.", model_filename));
426	}
427
428	if (settings::run_mode != RunMode::PLOTTING) {	2,930✔
429	read_cross_sections_xml(root.child("materials"));	2,892✔
430	}
431	read_materials_xml(root.child("materials"));	2,930✔
432
433	// Read geometry
434	if (!check_for_node(root, "geometry")) {	2,930!
435	fatal_error(fmt::format(	×
436	"No <geometry> node present in the {} file.", model_filename));
437	}
438	read_geometry_xml(root.child("geometry"));	2,930✔
439
440	// Final geometry setup and assign temperatures
441	finalize_geometry();	2,930✔
442
443	// Finalize cross sections having assigned temperatures
444	finalize_cross_sections();	2,930✔
445
446	// Compute cell density multipliers now that material densities
447	// have been finalized (from geometry_aux.h)
448	finalize_cell_densities();	2,930✔
449
450	if (check_for_node(root, "tallies"))	2,930✔
451	read_tallies_xml(root.child("tallies"));	1,653✔
452
453	// Initialize distribcell_filters
454	prepare_distribcell();	2,924✔
455
456	if (check_for_node(root, "plots")) {	2,924✔
457	read_plots_xml(root.child("plots"));	140✔
458	} else {
459	// When no <plots> element is present in the model.xml file, check for a
460	// regular plots.xml file
461	std::string filename = settings::path_input + "plots.xml";	2,784✔
462	if (file_exists(filename)) {	2,784!
463	read_plots_xml();	×
464	}
465	}	2,784✔
466
467	finalize_variance_reduction();	2,921✔
468
469	return true;	2,921✔
470	}	3,531✔
471
472	void read_separate_xml_files()	610✔
473	{
474	read_settings_xml();	610✔
475	if (settings::run_mode != RunMode::PLOTTING) {	607✔
476	read_cross_sections_xml();	592✔
477	}
478
479	// Read data from chain file
480	read_chain_file_xml();	607✔
481
482	read_materials_xml();	607✔
483	read_geometry_xml();	607✔
484
485	// Final geometry setup and assign temperatures
486	finalize_geometry();	607✔
487
488	// Finalize cross sections having assigned temperatures
489	finalize_cross_sections();	607✔
490
491	// Compute cell density multipliers now that material densities
492	// have been finalized (from geometry_aux.h)
493	finalize_cell_densities();	607✔
494
495	read_tallies_xml();	607✔
496
497	// Initialize distribcell_filters
498	prepare_distribcell();	607✔
499
500	// Read the plots.xml regardless of plot mode in case plots are requested
501	// via the API
502	read_plots_xml();	607✔
503
504	finalize_variance_reduction();	607✔
505	}	607✔
506
507	void initial_output()	3,528✔
508	{
509	// write initial output
510	if (settings::run_mode == RunMode::PLOTTING) {	3,528✔
511	// Read plots.xml if it exists
512	if (mpi::master && settings::verbosity >= 5)	50!
513	print_plot();	40✔
514
515	} else {
516	// Write summary information
517	if (mpi::master && settings::output_summary)	3,478✔
518	write_summary();	2,888✔
519
520	// Warn if overlap checking is on
521	if (mpi::master && settings::check_overlaps) {	3,478!
522	warning("Cell overlap checking is ON.");	×
523	}
524	}
525	}	3,528✔
526
527	} // namespace openmc

openmc-dev / openmc / 21043561037

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