diff --git a/src/mesh/GmshReader.cpp b/src/mesh/GmshReader.cpp
index 01ad632cf2fbfd013d0da8bc7e39b7b63f7c4129..cda9cb9b5f60c9f1ca74d2346120e4198e958d52 100644
--- a/src/mesh/GmshReader.cpp
+++ b/src/mesh/GmshReader.cpp
@@ -39,7 +39,8 @@ GmshConnectivityBuilder<1>::GmshConnectivityBuilder(const GmshReader::GmshData&
Array<int> cell_number_vector(nb_cells);
Array<unsigned int> cell_to_node_row(nb_cells + 1);
- parallel_for(cell_to_node_row.size(), PUGS_LAMBDA(const CellId cell_id) { cell_to_node_row[cell_id] = 2 * cell_id; });
+ parallel_for(
+ cell_to_node_row.size(), PUGS_LAMBDA(const CellId cell_id) { cell_to_node_row[cell_id] = 2 * cell_id; });
Array<unsigned int> cell_to_node_list(cell_to_node_row[cell_to_node_row.size() - 1]);
for (CellId cell_id = 0; cell_id < nb_cells; ++cell_id) {
@@ -949,6 +950,10 @@ struct physical_section : seq<TAO_PEGTL_STRING("$PhysicalNames"), until<TAO_PEGT
{
};
+struct entities_section : seq<TAO_PEGTL_STRING("$Entities"), until<TAO_PEGTL_STRING("$EndEntities")>, ignored>
+{
+};
+
struct nodes_section : seq<TAO_PEGTL_STRING("$Nodes"), until<TAO_PEGTL_STRING("$EndNodes")>, ignored>
{
};
@@ -981,6 +986,7 @@ struct interpolation_scheme_section
struct data_section
: sor<physical_section,
+ entities_section,
nodes_section,
elements_section,
periodic_section,
@@ -1039,7 +1045,8 @@ inline auto remove_embedding_spaces = [](std::string_view line) -> std::string_v
inline constexpr int number_of_gmsh_entities = 93;
-inline constexpr auto primitive_number_of_nodes = []() constexpr {
+inline constexpr auto primitive_number_of_nodes = []() constexpr
+{
std::array<short, number_of_gmsh_entities> number_of_nodes;
number_of_nodes.fill(-1);
@@ -1078,9 +1085,11 @@ inline constexpr auto primitive_number_of_nodes = []() constexpr {
number_of_nodes[92] = 125; // 125-node fourth order hexahedron
return number_of_nodes;
-}();
+}
+();
-inline constexpr auto entity_name = []() constexpr {
+inline constexpr auto entity_name = []() constexpr
+{
std::array<std::string_view, number_of_gmsh_entities> name;
name.fill("unknown");
name[0] = "edges";
@@ -1118,9 +1127,11 @@ inline constexpr auto entity_name = []() constexpr {
name[92] = "125-node fourth order hexahedron";
return name;
-}();
+}
+();
-inline constexpr auto supported_entity = []() constexpr {
+inline constexpr auto supported_entity = []() constexpr
+{
std::array<bool, number_of_gmsh_entities> supported;
supported.fill(false);
supported[0] = true; // edge
@@ -1133,7 +1144,8 @@ inline constexpr auto supported_entity = []() constexpr {
supported[14] = true; // point
return supported;
-}();
+}
+();
inline auto tokenize = [](std::string_view& line, auto& tokens) {
size_t token_idx = 0;
@@ -1181,6 +1193,7 @@ inline auto tokenize_variable = [](std::string_view& line, std::vector<std::stri
struct State
{
bool has_physiscal_section = false;
+ bool has_entities_section = false;
bool has_nodes_section = false;
bool has_elements_section = false;
bool has_periodic_section = false;
@@ -1231,7 +1244,7 @@ struct actions<meshformat>
}
std::cout << "- Reading Gmsh format " << gmsh_data.format.version << '\n';
- const std::set<double> supported_versions = {2.2};
+ const std::set<double> supported_versions = {2.2, 4.1};
if (not supported_versions.contains(gmsh_data.format.version)) {
std::stringstream error_msg;
@@ -1270,32 +1283,139 @@ struct actions<physical_section>
state.has_physiscal_section = true;
}
+ if ((gmsh_data.format.version == 2.2) or (gmsh_data.format.version == 4.1)) {
+ std::string_view body = in.string_view();
+
+ auto pos = body.find('\n');
+
+ if (pos == std::string_view::npos) {
+ throw NormalError("malformed Gmsh file, $PhysicalNames section is empty");
+ }
+ body = body.substr(pos + 1);
+
+ size_t number_of_physical_names;
+ try {
+ number_of_physical_names = parse_int(remove_embedding_spaces(get_next_line(body)));
+ }
+ catch (std::runtime_error& e) {
+ std::stringstream error_msg;
+ error_msg << "reading " << in.position().source << ':' << in.position().line + 1 << ": " << e.what();
+ throw NormalError(error_msg.str());
+ }
+
+ size_t i_physical_name = 0;
+ try {
+ for (; i_physical_name < number_of_physical_names; ++i_physical_name) {
+ if (body.empty()) {
+ std::stringstream error_msg;
+ error_msg << "malformed Gmsh file, $PhysicalNames section contains " << i_physical_name
+ << " entries, expecting " << number_of_physical_names;
+ throw std::runtime_error(error_msg.str());
+ }
+ auto line = remove_embedding_spaces(get_next_line(body));
+
+ if (line.empty()) {
+ throw std::runtime_error("empty entry");
+ }
+
+ std::array<std::string_view, 3> tokens{};
+ size_t number_of_tokens = tokenize(line, tokens);
+
+ if (number_of_tokens != 3) {
+ throw std::runtime_error("expecting 3 entries");
+ }
+
+ if ((tokens[2][0] != '"') or (tokens[2][tokens[2].size() - 1] != '"')) {
+ throw std::runtime_error("physical name must be enclosed by double quotes");
+ }
+ if (tokens[2].size() == 2) {
+ throw std::runtime_error("physical name cannot be an empty string");
+ }
+
+ const size_t physical_dimension = parse_int(tokens[0]);
+ const size_t physical_number = parse_int(tokens[1]);
+ const std::string physical_name{tokens[2].substr(1, tokens[2].size() - 2)};
+
+ GmshReader::PhysicalRefId physical_ref_id(physical_dimension, RefId(physical_number, physical_name));
+
+ if (auto i_searched_physical_ref_id = gmsh_data.m_physical_ref_map.find(physical_number);
+ i_searched_physical_ref_id != gmsh_data.m_physical_ref_map.end()) {
+ std::stringstream os;
+ os << "Physical reference id '" << physical_ref_id << "' already defined as '"
+ << i_searched_physical_ref_id->second << "'!";
+ throw std::runtime_error(os.str());
+ }
+ gmsh_data.m_physical_ref_map[physical_number] = physical_ref_id;
+ }
+ }
+ catch (std::runtime_error& e) {
+ std::stringstream error_msg;
+ error_msg << "reading " << in.position().source << ':' << in.position().line + i_physical_name + 2 << ": "
+ << e.what();
+ throw NormalError(error_msg.str());
+ }
+ } else {
+ throw UnexpectedError("invalid file format version: " + std::to_string(gmsh_data.format.version));
+ }
+ }
+};
+
+template <>
+struct actions<entities_section>
+{
+ template <typename Input>
+ static void
+ apply([[maybe_unused]] const Input& in, State& state, [[maybe_unused]] GmshReader::GmshData& gmsh_data)
+ {
+ if (state.has_entities_section) {
+ throw NormalError("malformed Gmsh file, $Entities section should appear only once");
+ } else {
+ state.has_entities_section = true;
+ }
+ }
+};
+
+template <>
+struct actions<nodes_section>
+{
+ template <typename Input>
+ static void
+ apply_2_2(const Input& in, GmshReader::GmshData& gmsh_data)
+ {
std::string_view body = in.string_view();
auto pos = body.find('\n');
if (pos == std::string_view::npos) {
- throw NormalError("malformed Gmsh file, $PhysicalNames section is empty");
+ throw NormalError("malformed Gmsh file, $Nodes section is empty");
}
+
body = body.substr(pos + 1);
- size_t number_of_physical_names;
+ int nb_nodes;
try {
- number_of_physical_names = parse_int(remove_embedding_spaces(get_next_line(body)));
+ nb_nodes = parse_int(remove_embedding_spaces(get_next_line(body)));
+ if (nb_nodes < 0) {
+ throw std::runtime_error("number of vertices is negative");
+ }
}
catch (std::runtime_error& e) {
std::stringstream error_msg;
error_msg << "reading " << in.position().source << ':' << in.position().line + 1 << ": " << e.what();
throw NormalError(error_msg.str());
}
+ const size_t number_of_nodes = nb_nodes;
+ std::cout << "- Number Of Vertices: " << number_of_nodes << '\n';
- size_t i_physical_name = 0;
+ Array<int> vertex_number_list{number_of_nodes};
+ Array<TinyVector<3>> vertex_list{number_of_nodes};
+
+ size_t i_node = 0;
try {
- for (; i_physical_name < number_of_physical_names; ++i_physical_name) {
+ for (; i_node < number_of_nodes; ++i_node) {
if (body.empty()) {
std::stringstream error_msg;
- error_msg << "malformed Gmsh file, $PhysicalNames section contains " << i_physical_name
- << " entries, expecting " << number_of_physical_names;
+ error_msg << "$Nodes section contains " << i_node << " entries, expecting " << number_of_nodes;
throw std::runtime_error(error_msg.str());
}
auto line = remove_embedding_spaces(get_next_line(body));
@@ -1304,58 +1424,35 @@ struct actions<physical_section>
throw std::runtime_error("empty entry");
}
- std::array<std::string_view, 3> tokens{};
- size_t number_of_tokens = tokenize(line, tokens);
-
- if (number_of_tokens != 3) {
- throw std::runtime_error("expecting 3 entries");
- }
+ std::array<std::string_view, 4> tokens{};
+ size_t token_number = tokenize(line, tokens);
- if ((tokens[2][0] != '"') or (tokens[2][tokens[2].size() - 1] != '"')) {
- throw std::runtime_error("physical name must be enclosed by double quotes");
- }
- if (tokens[2].size() == 2) {
- throw std::runtime_error("physical name cannot be an empty string");
+ if (token_number != 4) {
+ std::stringstream error_msg;
+ error_msg << "malformed Gmsh file, $Nodes section contains " << i_node << " entries, expecting "
+ << number_of_nodes;
+ throw std::runtime_error(error_msg.str());
}
- const size_t physical_dimension = parse_int(tokens[0]);
- const size_t physical_number = parse_int(tokens[1]);
- const std::string physical_name{tokens[2].substr(1, tokens[2].size() - 2)};
-
- GmshReader::PhysicalRefId physical_ref_id(physical_dimension, RefId(physical_number, physical_name));
+ vertex_number_list[i_node] = parse_int(tokens[0]);
- if (auto i_searched_physical_ref_id = gmsh_data.m_physical_ref_map.find(physical_number);
- i_searched_physical_ref_id != gmsh_data.m_physical_ref_map.end()) {
- std::stringstream os;
- os << "Physical reference id '" << physical_ref_id << "' already defined as '"
- << i_searched_physical_ref_id->second << "'!";
- throw std::runtime_error(os.str());
- }
- gmsh_data.m_physical_ref_map[physical_number] = physical_ref_id;
+ vertex_list[i_node] = TinyVector<3>{parse_double(tokens[1]), parse_double(tokens[2]), parse_double(tokens[3])};
}
}
catch (std::runtime_error& e) {
std::stringstream error_msg;
- error_msg << "reading " << in.position().source << ':' << in.position().line + i_physical_name + 2 << ": "
- << e.what();
+ error_msg << "reading " << in.position().source << ':' << in.position().line + i_node + 2 << ": " << e.what();
throw NormalError(error_msg.str());
}
+
+ gmsh_data.node_number = vertex_number_list;
+ gmsh_data.node_coordinate = vertex_list;
}
-};
-template <>
-struct actions<nodes_section>
-{
template <typename Input>
static void
- apply(const Input& in, State& state, GmshReader::GmshData& gmsh_data)
+ apply_4_1(const Input& in, GmshReader::GmshData& gmsh_data)
{
- if (state.has_nodes_section) {
- throw NormalError("malformed Gmsh file, $Nodes section should appear only once");
- } else {
- state.has_nodes_section = true;
- }
-
std::string_view body = in.string_view();
auto pos = body.find('\n');
@@ -1368,10 +1465,25 @@ struct actions<nodes_section>
int nb_nodes;
try {
- nb_nodes = parse_int(remove_embedding_spaces(get_next_line(body)));
+ auto line = remove_embedding_spaces(get_next_line(body));
+
+ std::array<std::string_view, 4> tokens{};
+ size_t token_number = tokenize(line, tokens);
+
+ if (token_number != 4) {
+ throw std::runtime_error("malformed $Nodes descriptor expecting 4 values");
+ }
+
+ // size_t nb_entity_blocks =
+ parse_int(tokens[0]);
+ nb_nodes = parse_int(tokens[1]);
if (nb_nodes < 0) {
throw std::runtime_error("number of vertices is negative");
}
+ // size_t min_node_tag =
+ parse_int(tokens[2]);
+ // size_t max_node_tag =
+ parse_int(tokens[3]);
}
catch (std::runtime_error& e) {
std::stringstream error_msg;
@@ -1422,6 +1534,25 @@ struct actions<nodes_section>
gmsh_data.node_number = vertex_number_list;
gmsh_data.node_coordinate = vertex_list;
}
+
+ template <typename Input>
+ static void
+ apply(const Input& in, State& state, GmshReader::GmshData& gmsh_data)
+ {
+ if (state.has_nodes_section) {
+ throw NormalError("malformed Gmsh file, $Nodes section should appear only once");
+ } else {
+ state.has_nodes_section = true;
+ }
+
+ if (gmsh_data.format.version == 2.2) {
+ apply_2_2(in, gmsh_data);
+ } else if (gmsh_data.format.version == 4.1) {
+ apply_4_1(in, gmsh_data);
+ } else {
+ throw UnexpectedError("invalid file format " + std::to_string(gmsh_data.format.version));
+ }
+ }
};
template <>