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Fix GMSH format 2 loader to accept non-contiguous physical entities #401

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Fix GMSH format 2 loader to accept non-contiguous physical entities #401

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23 changes: 12 additions & 11 deletions src/Omega_h_gmsh.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -144,7 +144,7 @@ static void read(
}

static void read_internal_entities_section(Mesh& mesh, Real format,
std::vector<std::string>& physical_names, std::istream& stream,
std::unordered_map<int, std::string>& physical_names, std::istream& stream,
bool is_binary, bool needs_swapping) {
Int num_points, num_curves, num_surfaces, num_volumes;
read(stream, num_points, is_binary, needs_swapping);
Expand All @@ -171,8 +171,9 @@ static void read_internal_entities_section(Mesh& mesh, Real format,
read(stream, physical, is_binary, needs_swapping);
OMEGA_H_CHECK(physical != 0);
if (physical > 0) {
const auto& physicalname = physical_names[physical - 1];
mesh.class_sets[physicalname].emplace_back(0, tag);
const auto& physicalname = physical_names.find(physical);
OMEGA_H_CHECK(physicalname != physical_names.end());
mesh.class_sets[physicalname->second].emplace_back(0, tag);
}
}
}
Expand All @@ -198,8 +199,9 @@ static void read_internal_entities_section(Mesh& mesh, Real format,
read(stream, physical, is_binary, needs_swapping);
OMEGA_H_CHECK(physical != 0);
if (physical > 0) {
const auto& physical_name = physical_names[physical - 1];
mesh.class_sets[physical_name].emplace_back(dim, tag);
auto physical_name = physical_names.find(physical);
OMEGA_H_CHECK(physical_name != physical_names.end());
mesh.class_sets[physical_name->second].emplace_back(dim, tag);
}
}
Int num_bounding_points;
Expand Down Expand Up @@ -232,20 +234,18 @@ void read_internal(std::istream& stream, Mesh* mesh) {
}
}
OMEGA_H_CHECK(data_size == sizeof(Real));
std::vector<std::string> physical_names;
std::unordered_map<int, std::string> physical_names;
if (seek_optional_section(stream, "$PhysicalNames")) {
Int num_physicals;
read(stream, num_physicals, is_binary, needs_swapping);
physical_names.reserve(static_cast<std::size_t>(num_physicals));
eat_newlines(stream);
for (auto i = 0; i < num_physicals; ++i) {
Int dim, number;
read(stream, dim, is_binary, needs_swapping);
read(stream, number, is_binary, needs_swapping);
OMEGA_H_CHECK(number == i + 1);
std::string name;
stream >> name;
physical_names.push_back(name.substr(1, name.size() - 2));
physical_names.emplace(number, name.substr(1, name.size() - 2));
}
}
if (seek_optional_section(stream, "$Entities")) {
Expand Down Expand Up @@ -465,8 +465,9 @@ void read_internal(std::istream& stream, Mesh* mesh) {
const auto entity = pair.first;
const auto physical = pair.second;
std::string physical_name(std::to_string(physical));
if (physical <= static_cast<Int>(physical_names.size())) {
physical_name = physical_names[physical - 1];
auto physical_name_it = physical_names.find(physical);
if (physical_name_it != physical_names.end()) {
physical_name = physical_name_it->second;
}
mesh->class_sets[physical_name].emplace_back(dim, entity);
}
Expand Down
50 changes: 50 additions & 0 deletions src/unit_io.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,36 @@ Mesh 2;
)GMSH";
#endif

static const char* GMSH_PHYSICAL_ENTITIES_MSH2 = R"GMSH(
$MeshFormat
2.2 0 8
$EndMeshFormat
$PhysicalNames
4
2 13 "patch1"
2 14 "patchInBetween"
3 15 "comp1"
3 16 "comp2"
$EndPhysicalNames
$Nodes
6
1 0 0 0
2 1 0 0
3 0 1 0
4 0 0 1
5 -1 0 0
6 0 -1 0
$EndNodes
$Elements
5
1 2 2 14 2 1 4 2
2 2 2 13 4 1 5 3
3 4 2 15 1 2 4 3 1
4 4 2 15 1 5 3 4 1
5 4 2 16 2 1 2 4 6
$EndElements
)GMSH";

static const char* GMSH_SQUARE_MSH2 = R"GMSH(
$MeshFormat
2.2 0 8
Expand Down Expand Up @@ -1393,6 +1423,26 @@ static void test_gmsh(Library* lib) {
OMEGA_H_CHECK(mesh.class_sets.empty());
}
}
{
if (lib->world()->rank() == 0) {
{
std::ofstream oss("physical-entities.msh");
oss << GMSH_PHYSICAL_ENTITIES_MSH2;
}
lib->world()->barrier();
auto mesh = Omega_h::gmsh::read("physical-entities.msh", lib->world());
const auto num_class_sets = mesh.class_sets.size();
OMEGA_H_CHECK(num_class_sets == 4);
OMEGA_H_CHECK(mesh.class_sets["patch1"].size() == 1);
OMEGA_H_CHECK(mesh.class_sets["patch1"][0].id == 4);
OMEGA_H_CHECK(mesh.class_sets["patchInBetween"].size() == 1);
OMEGA_H_CHECK(mesh.class_sets["patchInBetween"][0].id == 2);
OMEGA_H_CHECK(mesh.class_sets["comp1"].size() == 1);
OMEGA_H_CHECK(mesh.class_sets["comp1"][0].id == 1);
OMEGA_H_CHECK(mesh.class_sets["comp2"].size() == 1);
OMEGA_H_CHECK(mesh.class_sets["comp2"][0].id == 2);
}
}
{
const std::vector<const char*> meshes{
GMSH_PHYSICAL_MSH2, GMSH_PHYSICAL_MSH40, GMSH_PHYSICAL_MSH41};
Expand Down