#include "openmc/dagmc.h"

#include <array>

#include <cassert>

#include "openmc/constants.h"

#include "openmc/container_util.h"

#include "openmc/error.h"

#include "openmc/file_utils.h"

#include "openmc/geometry.h"

#include "openmc/geometry_aux.h"

#include "openmc/hdf5_interface.h"

#include "openmc/material.h"

#include "openmc/settings.h"

#include "openmc/string_utils.h"

#ifdef OPENMC_UWUW_ENABLED

#include "uwuw.hpp"

#endif

#include <fmt/core.h>

#include <algorithm>

#include <filesystem>

#include <fstream>

#include <sstream>

#include <string>

namespace openmc {

#ifdef OPENMC_DAGMC_ENABLED

const bool DAGMC_ENABLED = true;

#else

const bool DAGMC_ENABLED = false;

#endif

#ifdef OPENMC_UWUW_ENABLED

const bool UWUW_ENABLED = true;

#else

const bool UWUW_ENABLED = false;

#endif

} // namespace openmc

#ifdef OPENMC_DAGMC_ENABLED

namespace openmc {

//==============================================================================

// DAGMC Universe implementation

//==============================================================================

DAGUniverse::DAGUniverse(pugi::xml_node node)

{

MaterialOverrides material_overrides;

TemperatureOverrides temperature_overrides;

DensityOverrides density_overrides;

if (check_for_node(node, "id")) {

id_ = std::stoi(get_node_value(node, "id"));

} else {

fatal_error("Must specify the id of the DAGMC universe");

}

if (check_for_node(node, "filename")) {

filename_ = get_node_value(node, "filename");

std::filesystem::path p(filename_);

if (p.is_relative()) {

std::filesystem::path d(dir_name(settings::path_input));

filename_ = (d / p).string();

}

} else {

fatal_error("Must specify a file for the DAGMC universe");

}

adjust_geometry_ids_ = false;

if (check_for_node(node, "auto_geom_ids")) {

adjust_geometry_ids_ = get_node_value_bool(node, "auto_geom_ids");

}

adjust_material_ids_ = false;

if (check_for_node(node, "auto_mat_ids")) {

adjust_material_ids_ = get_node_value_bool(node, "auto_mat_ids");

}

if (check_for_node(node, "length_multiplier")) {

length_multiplier_ = std::stod(get_node_value(node, "length_multiplier"));

}

// Get material assignment overrides from nested DAGMC cell elements.

if (node.child("cell")) {

for (pugi::xml_node cell_node : node.children("cell")) {

if (!check_for_node(cell_node, "id")) {

fatal_error(

"Must specify id for each DAGMC cell override in <dagmc_universe>.");

}

int32_t cell_id = std::stoi(get_node_value(cell_node, "id"));

if (check_for_node(cell_node, "region")) {

fatal_error(fmt::format(

"DAGMC cell {} override cannot specify a region.", cell_id));

}

if (check_for_node(cell_node, "fill")) {

fatal_error(fmt::format(

"DAGMC cell {} override currently only supports material fills.",

cell_id));

}

if (check_for_node(cell_node, "universe")) {

fatal_error(fmt::format(

"DAGMC cell {} override cannot specify a universe.", cell_id));

}

if (check_for_node(cell_node, "translation") ||

check_for_node(cell_node, "rotation")) {

fatal_error(fmt::format(

"DAGMC cell {} override does not support translation or rotation.",

cell_id));

}

if (!check_for_node(cell_node, "material")) {

fatal_error(fmt::format(

"DAGMC cell {} override must specify material.", cell_id));

}

auto inserted = material_overrides.emplace(

cell_id, parse_cell_material_xml(cell_node, cell_id));

if (!inserted.second) {

fatal_error(fmt::format(

"Duplicate DAGMC cell override specified for cell {}", cell_id));

}

if (check_for_node(cell_node, "temperature")) {

temperature_overrides.emplace(

cell_id, parse_cell_temperature_xml(cell_node, cell_id));

}

if (check_for_node(cell_node, "density")) {

density_overrides.emplace(

cell_id, parse_cell_density_xml(cell_node, cell_id));

}

}

} else if (check_for_node(node, "material_overrides")) {

if (node.child("cell")) {

fatal_error("DAGMCUniverse cannot specify both <material_overrides> and "

"<cell> sub-elements. Use <cell> elements only.");

}

warning("DAGMCUniverse <material_overrides> is deprecated. Use nested "

"<cell> elements under <dagmc_universe> instead.");

for (pugi::xml_node co :

node.child("material_overrides").children("cell_override")) {

int32_t cell_id = std::stoi(get_node_value(co, "id"));

std::istringstream iss(co.child("material_ids").text().get());

vector<int32_t> mats;

for (std::string s; iss >> s;) {

mats.push_back(s == "void" ? MATERIAL_VOID : std::stoi(s));

}

material_overrides.emplace(cell_id, mats);

}

}

initialize(material_overrides, temperature_overrides, density_overrides);

}

DAGUniverse::DAGUniverse(const std::string& filename, bool auto_geom_ids,

bool auto_mat_ids, double length_multiplier)

: filename_(filename), adjust_geometry_ids_(auto_geom_ids),

adjust_material_ids_(auto_mat_ids), length_multiplier_(length_multiplier)

{

set_id();

initialize();

}

DAGUniverse::DAGUniverse(std::shared_ptr<moab::DagMC> dagmc_ptr,

const std::string& filename, bool auto_geom_ids, bool auto_mat_ids,

double length_multiplier)

: dagmc_instance_(dagmc_ptr), filename_(filename),

adjust_geometry_ids_(auto_geom_ids), adjust_material_ids_(auto_mat_ids),

length_multiplier_(length_multiplier)

{

MaterialOverrides material_overrides;

TemperatureOverrides temperature_overrides;

DensityOverrides density_overrides;

set_id();

init_metadata();

init_geometry(material_overrides, temperature_overrides, density_overrides);

}

void DAGUniverse::set_id()

{

// determine the next universe id

int32_t next_univ_id = 0;

for (const auto& u : model::universes) {

if (u->id_ > next_univ_id)

next_univ_id = u->id_;

}

next_univ_id++;

// set the universe id

id_ = next_univ_id;

}

void DAGUniverse::initialize()

{

MaterialOverrides material_overrides;

TemperatureOverrides temperature_overrides;

initialize(material_overrides, temperature_overrides);

}

void DAGUniverse::initialize(const MaterialOverrides& material_overrides,

const TemperatureOverrides& temperature_overrides,

const DensityOverrides& density_overrides)

{

#ifdef OPENMC_UWUW_ENABLED

// read uwuw materials from the .h5m file if present

read_uwuw_materials();

#endif

init_dagmc();

init_metadata();

init_geometry(material_overrides, temperature_overrides, density_overrides);

}

void DAGUniverse::init_dagmc()

{

// create a new DAGMC instance

dagmc_instance_ = std::make_shared<moab::DagMC>();

// load the DAGMC geometry

if (!file_exists(filename_)) {

fatal_error("Geometry DAGMC file '" + filename_ + "' does not exist!");

}

moab::ErrorCode rval = dagmc_instance_->load_file(filename_.c_str());

MB_CHK_ERR_CONT(rval);

if (length_multiplier_ != 1.0) {

moab::Range verts;

rval =

dagmc_instance_->moab_instance()->get_entities_by_dimension(0, 0, verts);

MB_CHK_ERR_CONT(rval);

for (auto vert : verts) {

std::array<double, 3> coord;

rval =

dagmc_instance_->moab_instance()->get_coords(&vert, 1, coord.data());

MB_CHK_ERR_CONT(rval);

for (auto& c : coord) {

c *= length_multiplier_;

}

rval =

dagmc_instance_->moab_instance()->set_coords(&vert, 1, coord.data());

MB_CHK_ERR_CONT(rval);

}

}

// initialize acceleration data structures

rval = dagmc_instance_->init_OBBTree();

MB_CHK_ERR_CONT(rval);

}

void DAGUniverse::init_metadata()

{

// parse model metadata

dmd_ptr =

std::make_unique<dagmcMetaData>(dagmc_instance_.get(), false, false);

dmd_ptr->load_property_data();

std::vector<std::string> keywords {"temp"};

std::map<std::string, std::string> dum;

std::string delimiters = ":/";

moab::ErrorCode rval;

rval = dagmc_instance_->parse_properties(keywords, dum, delimiters.c_str());

MB_CHK_ERR_CONT(rval);

}

void DAGUniverse::init_geometry(const MaterialOverrides& material_overrides,

const TemperatureOverrides& temperature_overrides,

const DensityOverrides& density_overrides)

{

moab::ErrorCode rval;

// determine the next cell id

int32_t next_cell_id = 0;

for (const auto& c : model::cells) {

if (c->id_ > next_cell_id)

next_cell_id = c->id_;

}

cell_idx_offset_ = model::cells.size();

next_cell_id++;

// initialize cell objects

int n_cells = dagmc_instance_->num_entities(3);

moab::EntityHandle graveyard = 0;

for (int i = 0; i < n_cells; i++) {

moab::EntityHandle vol_handle = dagmc_instance_->entity_by_index(3, i + 1);

// set cell ids using global IDs

auto c = std::make_unique<DAGCell>(dagmc_instance_, i + 1);

c->id_ = adjust_geometry_ids_

? next_cell_id++

: dagmc_instance_->id_by_index(3, c->dag_index());

c->universe_ = this->id_;

c->fill_ = C_NONE; // no fill, single universe

if (dagmc_instance_->is_implicit_complement(vol_handle)) {

c->name_ = "implicit complement";

}

auto in_map = model::cell_map.find(c->id_);

if (in_map == model::cell_map.end()) {

model::cell_map[c->id_] = model::cells.size();

} else {

warning(fmt::format("DAGMC Cell IDs: {}", dagmc_ids_for_dim(3)));

fatal_error(fmt::format(

"DAGMC Universe {} contains a cell with ID {}, which "

"already exists elsewhere in the geometry. Setting auto_geom_ids "

"to True when initiating the DAGMC Universe may "

"resolve this issue",

this->id_, c->id_));

}

// --- Materials ---

// determine volume material assignment

std::string mat_str = dmd_ptr->get_volume_property("material", vol_handle);

if (mat_str.empty()) {

fatal_error(fmt::format("Volume {} has no material assignment.", c->id_));

}

to_lower(mat_str);

if (mat_str == "graveyard") {

graveyard = vol_handle;

}

if (material_overrides.count(c->id_)) {

override_assign_material(c, material_overrides);

} else if (mat_str == "void" || mat_str == "vacuum" ||

mat_str == "graveyard") {

c->material_.push_back(MATERIAL_VOID);

} else if (uses_uwuw()) {

uwuw_assign_material(vol_handle, c);

} else {

legacy_assign_material(mat_str, c);

}

if (temperature_overrides.count(c->id_)) {

if (c->material_.empty() || c->material_[0] == MATERIAL_VOID) {

fatal_error(fmt::format("DAGMC cell {} was specified with a "

"temperature but no non-void material.",

c->id_));

}

c->sqrtkT_.clear();

const auto& temp_overrides = temperature_overrides.at(c->id_);

c->sqrtkT_.reserve(temp_overrides.size());

for (auto T : temp_overrides) {

c->sqrtkT_.push_back(std::sqrt(K_BOLTZMANN * T));

}

if (settings::verbosity >= 10) {

std::stringstream override_values;

for (size_t i = 0; i < temp_overrides.size(); ++i) {

if (i > 0) {

override_values << " ";

}

override_values << temp_overrides[i];

}

auto msg = fmt::format("Overriding DAGMC cell {} property "

"'temperature [K]' with value(s): {}",

c->id_, override_values.str());

write_message(msg, 10);

}

}

if (density_overrides.count(c->id_)) {

if (c->material_.empty() || c->material_[0] == MATERIAL_VOID) {

fatal_error(fmt::format("DAGMC cell {} was specified with a density "

"but no non-void material.",

c->id_));

}

// density_mult_ holds the true density until materials are finalized,

// at which point it is converted to a proper multiplier (same as CSG).

c->density_mult_ = density_overrides.at(c->id_);

if (settings::verbosity >= 10) {

const auto& dens = density_overrides.at(c->id_);

std::stringstream override_values;

for (size_t i = 0; i < dens.size(); ++i) {

if (i > 0)

override_values << " ";

override_values << dens[i];

}

write_message(fmt::format("Overriding DAGMC cell {} property "

"'density [g/cm³]' with value(s): {}",

c->id_, override_values.str()),

10);

}

}

// check for temperature assignment

std::string temp_value;

// no temperature if void

if (c->material_[0] == MATERIAL_VOID) {

model::cells.emplace_back(std::move(c));

continue;

}

// assign cell temperature if not explicitly overridden

if (c->sqrtkT_.empty()) {

const auto& mat =

model::materials[model::material_map.at(c->material_[0])];

if (dagmc_instance_->has_prop(vol_handle, "temp")) {

rval = dagmc_instance_->prop_value(vol_handle, "temp", temp_value);

MB_CHK_ERR_CONT(rval);

double temp = std::stod(temp_value);

c->sqrtkT_.push_back(std::sqrt(K_BOLTZMANN * temp));

} else if (mat->temperature() > 0.0) {

c->sqrtkT_.push_back(std::sqrt(K_BOLTZMANN * mat->temperature()));

} else {

c->sqrtkT_.push_back(

std::sqrt(K_BOLTZMANN * settings::temperature_default));

}

}

model::cells.emplace_back(std::move(c));

}

// allocate the cell overlap count if necessary

if (settings::check_overlaps) {

model::overlap_check_count.resize(model::cells.size(), 0);

}

has_graveyard_ = graveyard;

// determine the next surface id

int32_t next_surf_id = 0;

for (const auto& s : model::surfaces) {

if (s->id_ > next_surf_id)

next_surf_id = s->id_;

}

surf_idx_offset_ = model::surfaces.size();

next_surf_id++;

// initialize surface objects

int n_surfaces = dagmc_instance_->num_entities(2);

for (int i = 0; i < n_surfaces; i++) {

moab::EntityHandle surf_handle = dagmc_instance_->entity_by_index(2, i + 1);

// set cell ids using global IDs

auto s = std::make_unique<DAGSurface>(dagmc_instance_, i + 1);

s->id_ = adjust_geometry_ids_ ? next_surf_id++

: dagmc_instance_->id_by_index(2, i + 1);

// set surface source attribute if needed

if (contains(settings::source_write_surf_id, s->id_) ||

settings::source_write_surf_id.empty()) {

s->surf_source_ = true;

}

// set BCs

std::string bc_value =

dmd_ptr->get_surface_property("boundary", surf_handle);

to_lower(bc_value);

if (bc_value.empty() || bc_value == "transmit" ||

bc_value == "transmission") {

// set to transmission by default (nullptr)

} else if (bc_value == "vacuum") {

s->bc_ = make_unique<VacuumBC>();

} else if (bc_value == "reflective" || bc_value == "reflect" ||

bc_value == "reflecting") {

s->bc_ = make_unique<ReflectiveBC>();

} else if (bc_value == "periodic") {

fatal_error("Periodic boundary condition not supported in DAGMC.");

} else {

fatal_error(fmt::format("Unknown boundary condition \"{}\" specified "

"on surface {}",

bc_value, s->id_));

}

// graveyard check

moab::Range parent_vols;

rval = dagmc_instance_->moab_instance()->get_parent_meshsets(

surf_handle, parent_vols);

MB_CHK_ERR_CONT(rval);

// if this surface belongs to the graveyard

if (graveyard && parent_vols.find(graveyard) != parent_vols.end()) {

// set graveyard surface BC's to vacuum

s->bc_ = make_unique<VacuumBC>();

}

// add to global array and map

auto in_map = model::surface_map.find(s->id_);

if (in_map == model::surface_map.end()) {

model::surface_map[s->id_] = model::surfaces.size();

} else {

warning(fmt::format("DAGMC Surface IDs: {}", dagmc_ids_for_dim(2)));

fatal_error(fmt::format("Surface ID {} exists in both Universe {} "

"and the CSG geometry.",

s->id_, this->id_));

}

model::surfaces.emplace_back(std::move(s));

} // end surface loop

}

int32_t DAGUniverse::cell_index(moab::EntityHandle vol) const

{

// return the index of the volume in the DAGMC instance and then

// adjust by the offset into the model cells for this DAGMC universe

return dagmc_ptr()->index_by_handle(vol) + cell_idx_offset_;

}

int32_t DAGUniverse::surface_index(moab::EntityHandle surf) const

{

// return the index of the surface in the DAGMC instance and then

// adjust by the offset into the model cells for this DAGMC universe

return dagmc_ptr()->index_by_handle(surf) + surf_idx_offset_;

}

std::string DAGUniverse::dagmc_ids_for_dim(int dim) const

{

// generate a vector of ids

std::vector<int> id_vec;

int n_ents = dagmc_instance_->num_entities(dim);

for (int i = 1; i <= n_ents; i++) {

id_vec.push_back(dagmc_instance_->id_by_index(dim, i));

}

// sort the vector of ids

std::sort(id_vec.begin(), id_vec.end());

// generate a string representation of the ID range(s)

std::stringstream out;

int i = 0;

int start_id = id_vec[0]; // initialize with first ID

int stop_id;

// loop over all cells in the universe

while (i < n_ents) {

stop_id = id_vec[i];

// if the next ID is not in this contiguous set of IDS,

// figure out how to write the string representing this set

if (id_vec[i + 1] > stop_id + 1) {

if (start_id != stop_id) {

// there are several IDs in a row, print condensed version (i.e. 1-10,

// 12-20)

out << start_id << "-" << stop_id;

} else {

// only one ID in this contiguous block (i.e. 3, 5, 7, 9)

out << start_id;

}

// insert a comma as long as we aren't in the last ID set

if (i < n_ents - 1) {

out << ", ";

}

// if we are at the end of a set, set the start ID to the first value

// in the next set.

start_id = id_vec[++i];

}

i++;

}

return out.str();

}

int32_t DAGUniverse::implicit_complement_idx() const

{

moab::EntityHandle ic;

moab::ErrorCode rval =

dagmc_instance_->geom_tool()->get_implicit_complement(ic);

MB_CHK_SET_ERR_CONT(rval, "Failed to get implicit complement");

// off-by-one: DAGMC indices start at one

return cell_idx_offset_ + dagmc_instance_->index_by_handle(ic) - 1;

}

bool DAGUniverse::find_cell(GeometryState& p) const

{

// if the particle isn't in any of the other DagMC

// cells, place it in the implicit complement

bool found = Universe::find_cell(p);

if (!found && model::universe_map[this->id_] != model::root_universe) {

p.lowest_coord().cell() = implicit_complement_idx();

found = true;

}

return found;

}

void DAGUniverse::to_hdf5(hid_t universes_group) const

{

// Create a group for this universe.

auto group = create_group(universes_group, fmt::format("universe {}", id_));

// Write the geometry representation type.

write_string(group, "geom_type", "dagmc", false);

// Write other properties of the DAGMC Universe

write_string(group, "filename", filename_, false);

write_attribute(

group, "auto_geom_ids", static_cast<int>(adjust_geometry_ids_));

write_attribute(

group, "auto_mat_ids", static_cast<int>(adjust_material_ids_));

write_attribute(group, "length_multiplier", length_multiplier_);

close_group(group);

}

bool DAGUniverse::uses_uwuw() const

{

#ifdef OPENMC_UWUW_ENABLED

return uwuw_ && !uwuw_->material_library.empty();

#else

return false;

#endif // OPENMC_UWUW_ENABLED

}

std::string DAGUniverse::get_uwuw_materials_xml() const

{

#ifdef OPENMC_UWUW_ENABLED

if (!uses_uwuw()) {

throw std::runtime_error("This DAGMC Universe does not use UWUW materials");

}

std::stringstream ss;

// write header

ss << "<?xml version=\"1.0\"?>\n";

ss << "<materials>\n";

const auto& mat_lib = uwuw_->material_library;

// write materials

for (auto mat : mat_lib) {

ss << mat.second->openmc("atom");

}

// write footer

ss << "</materials>";

return ss.str();

#else

fatal_error("DAGMC was not configured with UWUW.");

#endif // OPENMC_UWUW_ENABLED

}

void DAGUniverse::write_uwuw_materials_xml(const std::string& outfile) const

{

#ifdef OPENMC_UWUW_ENABLED

if (!uses_uwuw()) {

throw std::runtime_error(

"This DAGMC universe does not use UWUW materials.");

}

std::string xml_str = get_uwuw_materials_xml();

// if there is a material library in the file

std::ofstream mats_xml(outfile);

mats_xml << xml_str;

mats_xml.close();

#else

fatal_error("DAGMC was not configured with UWUW.");

#endif // OPENMC_UWUW_ENABLED

}

void DAGUniverse::legacy_assign_material(

std::string mat_string, std::unique_ptr<DAGCell>& c) const

{

bool mat_found_by_name = false;

// attempt to find a material with a matching name

to_lower(mat_string);

for (const auto& m : model::materials) {

std::string m_name = m->name();

to_lower(m_name);

if (mat_string == m_name) {

// assign the material with that name

if (!mat_found_by_name) {

mat_found_by_name = true;

c->material_.push_back(m->id_);

// report error if more than one material is found

} else {

fatal_error(fmt::format(

"More than one material found with name '{}'. Please ensure "

"materials "

"have unique names if using this property to assign materials.",

mat_string));

}

}

}

// if no material was set using a name, assign by id

if (!mat_found_by_name) {

bool found_by_id = true;

try {

auto id = std::stoi(mat_string);

if (model::material_map.find(id) == model::material_map.end())

found_by_id = false;

c->material_.emplace_back(id);

} catch (const std::invalid_argument&) {

found_by_id = false;

}

// report failure for failed int conversion or missing material

if (!found_by_id)

fatal_error(

fmt::format("Material with name/ID '{}' not found for volume (cell) {}",

mat_string, c->id_));

}

if (settings::verbosity >= 10) {

const auto& m = model::materials[model::material_map.at(c->material_[0])];

std::stringstream msg;

msg << "DAGMC material " << mat_string << " was assigned";

if (mat_found_by_name) {

msg << " using material name: " << m->name_;

} else {

msg << " using material id: " << m->id_;

}

write_message(msg.str(), 10);

}

}

void DAGUniverse::read_uwuw_materials()

{

#ifdef OPENMC_UWUW_ENABLED

// If no filename was provided, don't read UWUW materials

if (filename_ == "")

return;

uwuw_ = std::make_shared<UWUW>(filename_.c_str());

if (!uses_uwuw())

return;

// Notify user if UWUW materials are going to be used

write_message("Found UWUW Materials in the DAGMC geometry file.", 6);

// if we're using automatic IDs, update the UWUW material metadata

if (adjust_material_ids_) {

int32_t next_material_id = 0;

for (const auto& m : model::materials) {

next_material_id = std::max(m->id_, next_material_id);

}

next_material_id++;

for (auto& mat : uwuw_->material_library) {

mat.second->metadata["mat_number"] = next_material_id++;

}

}

std::string mat_xml_string = get_uwuw_materials_xml();

// create a pugi XML document from this string

pugi::xml_document doc;

auto result = doc.load_string(mat_xml_string.c_str());

if (!result) {

fatal_error("Error processing XML created using DAGMC UWUW materials.");

}

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

for (pugi::xml_node material_node : root.children("material")) {

model::materials.push_back(std::make_unique<Material>(material_node));

}

#else

fatal_error("DAGMC was not configured with UWUW.");

#endif // OPENMC_UWUW_ENABLED

}

void DAGUniverse::uwuw_assign_material(

moab::EntityHandle vol_handle, std::unique_ptr<DAGCell>& c) const

{

#ifdef OPENMC_UWUW_ENABLED

// lookup material in uwuw if present

std::string uwuw_mat = dmd_ptr->volume_material_property_data_eh[vol_handle];

if (uwuw_->material_library.count(uwuw_mat) != 0) {

// Note: material numbers are set by UWUW

int mat_number = uwuw_->material_library.get_material(uwuw_mat)

.metadata["mat_number"]

.asInt();

c->material_.push_back(mat_number);

} else {

fatal_error(fmt::format("Material with value '{}' not found in the "

"UWUW material library",

uwuw_mat));

}

#else

fatal_error("DAGMC was not configured with UWUW.");

#endif // OPENMC_UWUW_ENABLED

}

void DAGUniverse::override_assign_material(std::unique_ptr<DAGCell>& c,

const MaterialOverrides& material_overrides) const

{

// if Cell ID matches an override key, use it to override the material

// assignment else if UWUW is used, get the material assignment from the DAGMC

// metadata

// Notify User that an override is being applied on a DAGMCCell

write_message(fmt::format("Applying override for DAGMCCell {}", c->id_), 8);

const auto& mat_overrides = material_overrides.at(c->id_);

if (settings::verbosity >= 10) {

std::stringstream override_values;

for (size_t i = 0; i < mat_overrides.size(); ++i) {

if (i > 0) {

override_values << " ";

}

if (mat_overrides[i] == MATERIAL_VOID) {

override_values << "void";

} else {

override_values << mat_overrides[i];

}

}

auto msg = fmt::format("Overriding DAGMC cell {} property 'material' "

"with value(s): {}",

c->id_, override_values.str());

write_message(msg, 10);

}

// Override the material assignment for each cell instance using the legacy

// assignement

for (auto mat_id : mat_overrides) {

if (mat_id != MATERIAL_VOID &&

model::material_map.find(mat_id) == model::material_map.end()) {

fatal_error(fmt::format(

"Material with ID '{}' not found for DAGMC cell {}", mat_id, c->id_));

}

c->material_.push_back(mat_id);

}

}

//==============================================================================

// DAGMC Cell implementation

//==============================================================================

DAGCell::DAGCell(std::shared_ptr<moab::DagMC> dag_ptr, int32_t dag_idx)

: Cell {}, dagmc_ptr_(dag_ptr), dag_index_(dag_idx) {};

std::pair<double, int32_t> DAGCell::distance(

Position r, Direction u, int32_t on_surface, GeometryState* p) const

{

// if we've changed direction or we're not on a surface,

// reset the history and update last direction

if (u != p->last_dir()) {

p->last_dir() = u;

p->history().reset();

}

if (on_surface == SURFACE_NONE) {

p->history().reset();

}

const auto& univ = model::universes[p->lowest_coord().universe()];

DAGUniverse* dag_univ = static_cast<DAGUniverse*>(univ.get());

if (!dag_univ)

fatal_error("DAGMC call made for particle in a non-DAGMC universe");

// initialize to lost particle conditions

int surf_idx = -1;

double dist = INFINITY;

moab::EntityHandle vol = dagmc_ptr_->entity_by_index(3, dag_index_);

moab::EntityHandle hit_surf;

// create the ray

double pnt[3] = {r.x, r.y, r.z};

double dir[3] = {u.x, u.y, u.z};

MB_CHK_ERR_CONT(

dagmc_ptr_->ray_fire(vol, pnt, dir, hit_surf, dist, &p->history()));

if (hit_surf != 0) {

surf_idx =

dag_univ->surf_idx_offset_ + dagmc_ptr_->index_by_handle(hit_surf);

} else if (!dagmc_ptr_->is_implicit_complement(vol) ||

is_root_universe(dag_univ->id_)) {

// surface boundary conditions are ignored for projection plotting, meaning

// that the particle may move through the graveyard (bounding) volume and

// into the implicit complement on the other side where no intersection will

// be found. Treating this as a lost particle is problematic when plotting.

// Instead, the infinite distance and invalid surface index are returned.

if (settings::run_mode == RunMode::PLOTTING)

return {INFTY, -1};

// the particle should be marked as lost immediately if an intersection

// isn't found in a volume that is not the implicit complement. In the case

// that the DAGMC model is the root universe of the geometry, even a missing

// intersection in the implicit complement should trigger this condition.

std::string material_id =

p->material() == MATERIAL_VOID

? "-1 (VOID)"

: std::to_string(model::materials[p->material()]->id());

p->mark_as_lost(fmt::format(

"No intersection found with DAGMC cell {}, filled with material {}", id_,

material_id));

}

return {dist, surf_idx};

}

bool DAGCell::contains(Position r, Direction u, int32_t on_surface) const

{

moab::ErrorCode rval;

moab::EntityHandle vol = dagmc_ptr_->entity_by_index(3, dag_index_);

int result = 0;

double pnt[3] = {r.x, r.y, r.z};

double dir[3] = {u.x, u.y, u.z};

rval = dagmc_ptr_->point_in_volume(vol, pnt, result, dir);

MB_CHK_ERR_CONT(rval);

return result;

}

moab::EntityHandle DAGCell::mesh_handle() const

{

return dagmc_ptr()->entity_by_index(3, dag_index());

}

void DAGCell::to_hdf5_inner(hid_t group_id) const

{

write_string(group_id, "geom_type", "dagmc", false);

}

BoundingBox DAGCell::bounding_box() const

{

moab::ErrorCode rval;

moab::EntityHandle vol = dagmc_ptr_->entity_by_index(3, dag_index_);

double min[3], max[3];

rval = dagmc_ptr_->getobb(vol, min, max);

MB_CHK_ERR_CONT(rval);

return {{min[0], min[1], min[2]}, {max[0], max[1], max[2]}};

}

//==============================================================================

// DAGSurface implementation

//==============================================================================

DAGSurface::DAGSurface(std::shared_ptr<moab::DagMC> dag_ptr, int32_t dag_idx)

: Surface {}, dagmc_ptr_(dag_ptr), dag_index_(dag_idx)

{} // empty constructor

moab::EntityHandle DAGSurface::mesh_handle() const

{

return dagmc_ptr()->entity_by_index(2, dag_index());

}

double DAGSurface::evaluate(Position r) const

{

return 0.0;

}

double DAGSurface::distance(Position r, Direction u, bool coincident) const

{

moab::ErrorCode rval;

moab::EntityHandle surf = dagmc_ptr_->entity_by_index(2, dag_index_);

moab::EntityHandle hit_surf;

double dist;

double pnt[3] = {r.x, r.y, r.z};

double dir[3] = {u.x, u.y, u.z};

rval = dagmc_ptr_->ray_fire(surf, pnt, dir, hit_surf, dist, NULL, 0, 0);

MB_CHK_ERR_CONT(rval);

if (dist < 0.0)

dist = INFTY;

return dist;

}

Direction DAGSurface::normal(Position r) const

{

moab::ErrorCode rval;

moab::EntityHandle surf = dagmc_ptr_->entity_by_index(2, dag_index_);

double pnt[3] = {r.x, r.y, r.z};

double dir[3];

rval = dagmc_ptr_->get_angle(surf, pnt, dir);

MB_CHK_ERR_CONT(rval);

return dir;

}

Direction DAGSurface::reflect(Position r, Direction u, GeometryState* p) const

{

assert(p);

double pnt[3] = {r.x, r.y, r.z};

double dir[3];

moab::ErrorCode rval =

dagmc_ptr_->get_angle(mesh_handle(), pnt, dir, &p->history());

MB_CHK_ERR_CONT(rval);

return u.reflect(dir);

}

//==============================================================================

// Non-member functions

//==============================================================================

void read_dagmc_universes(pugi::xml_node node)

{

for (pugi::xml_node dag_node : node.children("dagmc_universe")) {

model::universes.push_back(std::make_unique<DAGUniverse>(dag_node));

model::universe_map[model::universes.back()->id_] =

model::universes.size() - 1;

}

}