c6891a465204bb20e5234a8a890cfbb9f9339b0e to adda73c65f316d80a7a1317908b4e338c653718b · code / pugs

CMakeLists.txt

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@@ -98,7 +98,7 @@ endif()

#------------------------------------------------------

#------------------------------------------------------

# Checks if compiler version is compatible with Pugs sources

# Checks if compiler version is compatible with Pugs sources

set(GNU_CXX_MIN_VERSION "10.0.0")

set(GNU_CXX_MIN_VERSION "11.0.0")

set(CLANG_CXX_MIN_VERSION "14.0.0")

set(CLANG_CXX_MIN_VERSION "14.0.0")

#------------------------------------------------------

#------------------------------------------------------

src/mesh/GmshReader.cpp

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@@ -39,7 +39,8 @@ GmshConnectivityBuilder<1>::GmshConnectivityBuilder(const GmshReader::GmshData&

  Array<int> cell_number_vector(nb_cells);

  Array<int> cell_number_vector(nb_cells);

  Array<unsigned int> cell_to_node_row(nb_cells + 1);

  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]);

  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) {

  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>

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

struct data_section

  : sor<physical_section,

  : sor<physical_section,

        entities_section,

        nodes_section,

        nodes_section,

        elements_section,

        elements_section,

        periodic_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 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;

  std::array<short, number_of_gmsh_entities> number_of_nodes;

  number_of_nodes.fill(-1);

  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

  number_of_nodes[92] = 125;   // 125-node fourth order hexahedron

  return number_of_nodes;

  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;

  std::array<std::string_view, number_of_gmsh_entities> name;

  name.fill("unknown");

  name.fill("unknown");

  name[0]  = "edges";

  name[0]  = "edges";

@@ -1118,9 +1127,11 @@ inline constexpr auto entity_name = []() constexpr {

  name[92] = "125-node fourth order hexahedron";

  name[92] = "125-node fourth order hexahedron";

  return name;

  return name;

}();

}

();

inline constexpr auto supported_entity = []() constexpr {

inline constexpr auto supported_entity = []() constexpr

{

  std::array<bool, number_of_gmsh_entities> supported;

  std::array<bool, number_of_gmsh_entities> supported;

  supported.fill(false);

  supported.fill(false);

  supported[0]  = true;   // edge

  supported[0]  = true;   // edge

@@ -1133,7 +1144,8 @@ inline constexpr auto supported_entity = []() constexpr {

  supported[14] = true;   // point

  supported[14] = true;   // point

  return supported;

  return supported;

}();

}

();

inline auto tokenize = [](std::string_view& line, auto& tokens) {

inline auto tokenize = [](std::string_view& line, auto& tokens) {

  size_t token_idx = 0;

  size_t token_idx = 0;

@@ -1181,6 +1193,7 @@ inline auto tokenize_variable = [](std::string_view& line, std::vector<std::stri

struct State

struct State

{

{

  bool has_physiscal_section            = false;

  bool has_physiscal_section            = false;

  bool has_entities_section             = false;

  bool has_nodes_section                = false;

  bool has_nodes_section                = false;

  bool has_elements_section             = false;

  bool has_elements_section             = false;

  bool has_periodic_section             = false;

  bool has_periodic_section             = false;

@@ -1231,7 +1244,7 @@ struct actions<meshformat>

      }

      }

      std::cout << "- Reading Gmsh format " << gmsh_data.format.version << '\n';

      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)) {

      if (not supported_versions.contains(gmsh_data.format.version)) {

        std::stringstream error_msg;

        std::stringstream error_msg;

@@ -1270,6 +1283,7 @@ struct actions<physical_section>

      state.has_physiscal_section = true;

      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();

      std::string_view body = in.string_view();

      auto pos = body.find('\n');

      auto pos = body.find('\n');

@@ -1340,22 +1354,34 @@ struct actions<physical_section>

                  << e.what();

                  << e.what();

        throw NormalError(error_msg.str());

        throw NormalError(error_msg.str());

      }

      }

    } else {

      throw UnexpectedError("invalid file format version: " + std::to_string(gmsh_data.format.version));

    }

  }

  }

};

};

template <>

template <>

struct actions<nodes_section>

struct actions<entities_section>

{

{

  template <typename Input>

  template <typename Input>

  static void

  static void

  apply(const Input& in, State& state, GmshReader::GmshData& gmsh_data)

  apply([[maybe_unused]] const Input& in, State& state, [[maybe_unused]] GmshReader::GmshData& gmsh_data)

  {

  {

    if (state.has_nodes_section) {

    if (state.has_entities_section) {

      throw NormalError("malformed Gmsh file, $Nodes section should appear only once");

      throw NormalError("malformed Gmsh file, $Entities section should appear only once");

    } else {

    } else {

      state.has_nodes_section = true;

      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();

    std::string_view body = in.string_view();

    auto pos = body.find('\n');

    auto pos = body.find('\n');

@@ -1422,6 +1448,111 @@ struct actions<nodes_section>

    gmsh_data.node_number     = vertex_number_list;

    gmsh_data.node_number     = vertex_number_list;

    gmsh_data.node_coordinate = vertex_list;

    gmsh_data.node_coordinate = vertex_list;

  }

  }

  template <typename Input>

  static void

  apply_4_1(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, $Nodes section is empty");

    }

    body = body.substr(pos + 1);

    int nb_nodes;

    try {

      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;

      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';

    Array<int> vertex_number_list{number_of_nodes};

    Array<TinyVector<3>> vertex_list{number_of_nodes};

    size_t i_node = 0;

    try {

      for (; i_node < number_of_nodes; ++i_node) {

        if (body.empty()) {

          std::stringstream error_msg;

          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));

        if (line.empty()) {

          throw std::runtime_error("empty entry");

        }

        std::array<std::string_view, 4> tokens{};

        size_t token_number = tokenize(line, tokens);

        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());

        }

        vertex_number_list[i_node] = parse_int(tokens[0]);

        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_node + 2 << ": " << e.what();

      throw NormalError(error_msg.str());

    }

    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 <>

template <>

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CMakeLists.txt

src/mesh/GmshReader.cpp