Interface for load MED files. More...

#include "src/interfaces/MedInterface.hpp"

Inheritance diagram for MoFEM::MedInterface:

Collaboration diagram for MoFEM::MedInterface:

Classes
struct	FieldData

Public Member Functions
MoFEMErrorCode	query_interface (boost::typeindex::type_index type_index, UnknownInterface **iface) const

	MedInterface (const MoFEM::Core &core)

MoFEMErrorCode	getFileNameFromCommandLine (int verb=1)
	Get MED file name from command line.

PetscBool	getFlgFile () const
	Check if file name is given in command line.

MoFEMErrorCode	medGetFieldNames (const string &file, int verb=1)
	Get field names in MED file.

MoFEMErrorCode	medGetFieldNames (int verb=1)
	get field names in MED file

MoFEMErrorCode	readMed (const string &file, int verb=1)
	read MED file

MoFEMErrorCode	readMed (int verb=1)
	read MED file

MoFEMErrorCode	writeMed (boost::shared_ptr< Range > range_ptr=nullptr, int verb=1)
	write MED file

MoFEMErrorCode	getMeshsets (boost::shared_ptr< std::vector< const CubitMeshSets * > > &meshsets_ptr)

MoFEMErrorCode	writeMed (const string &file, boost::shared_ptr< std::vector< const CubitMeshSets * > > meshsets_ptr, boost::shared_ptr< Range > range_ptr=nullptr, int verb=1)
	write MED file

MoFEMErrorCode	readFields (const std::string &file_name, const std::string &field_name, const bool load_series=false, const int only_step=-1, int verb=1)

Public Member Functions inherited from MoFEM::UnknownInterface
template<class IFACE >
MoFEMErrorCode	registerInterface (bool error_if_registration_failed=true)
	Register interface.

template<class IFACE >
MoFEMErrorCode	getInterface (IFACE *&iface) const
	Get interface reference to pointer of interface.

template<class IFACE >
MoFEMErrorCode	getInterface (IFACE **const iface) const
	Get interface pointer to pointer of interface.

template<class IFACE , typename boost::enable_if< boost::is_pointer< IFACE >, int >::type = 0>
IFACE	getInterface () const
	Get interface pointer to pointer of interface.

template<class IFACE , typename boost::enable_if< boost::is_reference< IFACE >, int >::type = 0>
IFACE	getInterface () const
	Get reference to interface.

template<class IFACE >
IFACE *	getInterface () const
	Function returning pointer to interface.

virtual	~UnknownInterface ()=default

Public Attributes
std::vector< std::string >	meshNames
	list of meshes in MED file

std::vector< EntityHandle >	meshMeshsets
	meshset for each mesh

std::map< std::string, FieldData >	fieldNames

std::string	medFileName
	MED file name.

Private Member Functions
MoFEMErrorCode	readMesh (const string &file, const int index, std::map< int, Range > &family_elem_map, int verb=1)
	read mesh from MED file

MoFEMErrorCode	readFamily (const string &file, const int index, const std::map< int, Range > &family_elem_mapint, std::map< string, Range > &group_elem_map, int verb=1)
	read family and groups

MoFEMErrorCode	makeBlockSets (const std::map< string, Range > &group_elem_map, int verb=1)
	make from groups meshsets

Private Attributes
MoFEM::Core &	cOre
	core database

PetscBool	flgFile
	true if file name given in command line

CubitMeshSet_multiIndex	cubitMeshsets
	cubit meshsets

Additional Inherited Members
Static Public Member Functions inherited from MoFEM::UnknownInterface
static MoFEMErrorCode	getLibVersion (Version &version)
	Get library version.

static MoFEMErrorCode	getFileVersion (moab::Interface &moab, Version &version)
	Get database major version.

static MoFEMErrorCode	setFileVersion (moab::Interface &moab, Version version=Version(MoFEM_VERSION_MAJOR, MoFEM_VERSION_MINOR, MoFEM_VERSION_BUILD))
	Get database major version.

static MoFEMErrorCode	getInterfaceVersion (Version &version)
	Get database major version.

Detailed Description

Interface for load MED files.

Definition at line 23 of file MedInterface.hpp.

Constructor & Destructor Documentation

◆ MedInterface()

MoFEM::MedInterface::MedInterface ( const MoFEM::Core & core )

Definition at line 51 of file MedInterface.cpp.

    : cOre(const_cast<Core &>(core)), flgFile(PETSC_FALSE) {
 
  if (!LogManager::checkIfChannelExist("MEDWORLD")) {
    auto core_log = logging::core::get();
    core_log->add_sink(
        LogManager::createSink(LogManager::getStrmWorld(), "MEDWORLD"));
    LogManager::setLog("MEDWORLD");
    MOFEM_LOG_TAG("MEDWORLD", "MED");
  }
 
  MOFEM_LOG("MEDWORLD", Sev::noisy) << "Mashset manager created";
}

Member Function Documentation

◆ getFileNameFromCommandLine()

MoFEMErrorCode MoFEM::MedInterface::getFileNameFromCommandLine ( int verb = 1 )

Get MED file name from command line.

Parameters

verb	verbosity level

Returns: error code

Definition at line 65 of file MedInterface.cpp.

                                                                {
  Interface &m_field = cOre;
  char mesh_file_name[255];
  MoFEMFunctionBeginHot;
  PetscOptionsBegin(m_field.get_comm(), "", "MED Interface", "none");
  ierr = PetscOptionsString("-med_file", "med file name", "", "mesh.med",
                            mesh_file_name, 255, &flgFile);
  CHKERRG(ierr);
  PetscOptionsEnd();
  if (flgFile == PETSC_TRUE) {
    medFileName = std::string(mesh_file_name);
  } else {
    medFileName = std::string("mesh.med");
  }
  MoFEMFunctionReturnHot(0);
}

◆ getFlgFile()

PetscBool MoFEM::MedInterface::getFlgFile ( ) const

inline

Check if file name is given in command line.

Definition at line 39 of file MedInterface.hpp.

39{ return flgFile; }

◆ getMeshsets()

MoFEMErrorCode MoFEM::MedInterface::getMeshsets ( boost::shared_ptr< std::vector< const CubitMeshSets * > > & meshsets_ptr )

Retrieves the meshsets

Parameters

meshsets_ptr A pointer to a vector of const CubitMeshSets objects. If provided, the retrieved meshsets will be stored in this vector.

Returns: A MoFEMErrorCode indicating the success or failure of the operation.

Definition at line 660 of file MedInterface.cpp.

                                                                     {
  Interface &m_field = cOre;
  MoFEMFunctionBegin;
 
  auto &meshsets_idx =
      m_field.getInterface<MeshsetsManager>()->getMeshsetsMultindex();
  std::vector<const CubitMeshSets *> meshsets;
 
  for (auto &m : meshsets_idx) {
    meshsets.push_back(&m);
  }
  // Sort meshsets based on meshsetId
  std::sort(meshsets.begin(), meshsets.end(),
            [](const CubitMeshSets *a, const CubitMeshSets *b) {
              return a->getMeshsetId() < b->getMeshsetId();
            });
 
  meshsets_ptr =
      boost::make_shared<std::vector<const CubitMeshSets *>>(meshsets);
  MoFEMFunctionReturn(0);
}

◆ makeBlockSets()

MoFEMErrorCode MoFEM::MedInterface::makeBlockSets	(	const std::map< string, Range > &	group_elem_map,
		int	verb = 1 )

private

make from groups meshsets

Parameters

group_elem_map	map of groups and elements
verb	verbosity level

Returns: error code

Definition at line 615 of file MedInterface.cpp.

                                      {
 
  Interface &m_field = cOre;
  MoFEMFunctionBegin;
  MeshsetsManager *meshsets_manager_ptr;
  CHKERR m_field.getInterface(meshsets_manager_ptr);
 
  int max_id = 0;
  for (_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(m_field, BLOCKSET, cit)) {
    max_id = (max_id < cit->getMeshsetId()) ? cit->getMeshsetId() : max_id;
  }
  max_id++;
 
  for (std::map<string, Range>::const_iterator git = group_elem_map.begin();
       git != group_elem_map.end(); git++) {
    CHKERR meshsets_manager_ptr->addMeshset(BLOCKSET, max_id, git->first);
    CubitMeshSet_multiIndex::index<
        Composite_Cubit_msId_And_MeshsetType_mi_tag>::type::iterator cit;
    cit =
        meshsets_manager_ptr->getMeshsetsMultindex()
            .get<Composite_Cubit_msId_And_MeshsetType_mi_tag>()
            .find(boost::make_tuple(max_id, CubitBCType(BLOCKSET).to_ulong()));
    EntityHandle meshsets = cit->getMeshset();
    if (!git->second.empty()) {
      CHKERR m_field.get_moab().add_entities(meshsets, git->second);
    }
    max_id++;
  }
 
  for (_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(m_field, BLOCKSET, cit))
    MOFEM_LOG("MEDWORLD", Sev::verbose) << *cit;
 
  MoFEMFunctionReturn(0);
}

◆ medGetFieldNames() [1/2]

MoFEMErrorCode MoFEM::MedInterface::medGetFieldNames	(	const string &	file,
		int	verb = 1 )

Get field names in MED file.

Parameters

file	file name
verb	verbosity level

Returns: error code

Definition at line 82 of file MedInterface.cpp.

                                                                          {
  Interface &m_field = cOre;
  MoFEMFunctionBegin;
  med_idt fid = MEDfileOpen(file.c_str(), MED_ACC_RDONLY);
  if (fid < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
             "Unable to open file '%s'", file.c_str());
  }
  med_int num_fields = MEDnField(fid);
  for (int index = 0; index < num_fields; index++) {
 
    med_int num_comp = MEDfieldnComponent(fid, index + 1);
    if (num_comp <= 0) {
      SETERRQ(m_field.get_comm(), MOFEM_IMPOSSIBLE_CASE,
              "Could not get number of components for MED field");
    }
 
    char name[MED_NAME_SIZE + 1], mesh_name[MED_NAME_SIZE + 1];
    char dt_unit[MED_SNAME_SIZE + 1];
    std::vector<char> comp_name(num_comp * MED_SNAME_SIZE + 1);
    std::vector<char> comp_unit(num_comp * MED_SNAME_SIZE + 1);
    med_int num_steps = 0;
    med_type_champ type;
    med_bool local_mesh;
    if (MEDfieldInfo(fid, index + 1, name, mesh_name, &local_mesh, &type,
                     &comp_name[0], &comp_unit[0], dt_unit, &num_steps) < 0) {
      SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
              "Could not get MED field info");
    }
 
    std::string field_name = std::string(name);
    fieldNames[field_name] = FieldData();
    fieldNames[field_name].fieldName = field_name;
    fieldNames[field_name].meshName = std::string(mesh_name);
    fieldNames[field_name].localMesh = (local_mesh == MED_TRUE);
    for (int ff = 0; ff != num_comp; ff++) {
      fieldNames[field_name].componentNames.push_back(
          std::string(&comp_name[ff * MED_SNAME_SIZE], MED_SNAME_SIZE));
      fieldNames[field_name].componentUnits.push_back(
          std::string(&comp_unit[ff * MED_SNAME_SIZE], MED_SNAME_SIZE));
    }
    fieldNames[field_name].dtUnit = std::string(&dt_unit[0]);
    fieldNames[field_name].ncSteps = num_steps;
 
    if (verb > 0)
      MOFEM_LOG("MEDWORLD", Sev::inform) << fieldNames[name];
  }
  if (MEDfileClose(fid) < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
             "Unable to close file '%s'", file.c_str());
  }
  MoFEMFunctionReturn(0);
}

◆ medGetFieldNames() [2/2]

MoFEMErrorCode MoFEM::MedInterface::medGetFieldNames ( int verb = 1 )

get field names in MED file

File name is get form command line

Parameters

verb	verbosity level

Returns: error code

Definition at line 136 of file MedInterface.cpp.

                                                      {
  MoFEMFunctionBegin;
  if (medFileName.empty()) {
    CHKERR getFileNameFromCommandLine(verb);
  }
  CHKERR medGetFieldNames(medFileName, verb);
  MoFEMFunctionReturn(0);
}

◆ query_interface()

MoFEMErrorCode MoFEM::MedInterface::query_interface	(	boost::typeindex::type_index	type_index,
		UnknownInterface **	iface ) const

virtual

Implements MoFEM::UnknownInterface.

Definition at line 45 of file MedInterface.cpp.

                                                              {
  *iface = const_cast<MedInterface *>(this);
  return 0;
}

◆ readFamily()

MoFEMErrorCode MoFEM::MedInterface::readFamily	(	const string &	file,
		const int	index,
		const std::map< int, Range > &	family_elem_mapint,
		std::map< string, Range > &	group_elem_map,
		int	verb = 1 )

private

read family and groups

Parameters

file	file name
index	mesh index
family_elem_mapint	map of families and elements
group_elem_map	map of groups and elements
verb	verbosity level

Returns: error code

Definition at line 523 of file MedInterface.cpp.

                                                                          {
  Interface &m_field = cOre;
  MoFEMFunctionBegin;
 
  med_idt fid = MEDfileOpen(file.c_str(), MED_ACC_RDONLY);
  if (fid < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
             "Unable to open file '%s'", file.c_str());
  }
  med_int v[3], vf[3];
  MEDlibraryNumVersion(&v[0], &v[1], &v[2]);
  MEDfileNumVersionRd(fid, &vf[0], &vf[1], &vf[2]);
 
  if (verb > 1) {
    MOFEM_LOG_C("MEDWORLD", Sev::noisy,
                "Reading MED file V%d.%d.%d using MED library V%d.%d.%d", vf[0],
                vf[1], vf[2], v[0], v[1], v[2]);
  }
  if (vf[0] < 2 || (vf[0] == 2 && vf[1] < 2)) {
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
            "Cannot read MED file older than V2.2");
  }
 
  // clear groups
  group_elem_map.clear();
 
  med_int num_families = MEDnFamily(fid, meshNames[index].c_str());
  if (num_families < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
            "Could not read MED families");
  }
  for (int i = 0; i < num_families; i++) {
    med_int num_attrib =
        (vf[0] == 2)
            ? MEDnFamily23Attribute(fid, meshNames[index].c_str(), i + 1)
            : 0;
    med_int num_groups = MEDnFamilyGroup(fid, meshNames[index].c_str(), i + 1);
    if (num_attrib < 0 || num_groups < 0) {
      SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
              "Could not read MED groups or attributes");
    }
 
    std::vector<med_int> attribId(num_attrib + 1);
    std::vector<med_int> attrib_val(num_attrib + 1);
    std::vector<char> attrib_des(MED_COMMENT_SIZE * num_attrib + 1);
    std::vector<char> group_names(MED_LNAME_SIZE * num_groups + 1);
    char family_name[MED_NAME_SIZE + 1];
    med_int family_num;
 
    if (vf[0] == 2) { // MED2 file
      if (MEDfamily23Info(fid, meshNames[index].c_str(), i + 1, family_name,
                          &attribId[0], &attrib_val[0], &attrib_des[0],
                          &family_num, &group_names[0]) < 0) {
        SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                 "Could not read info for MED2 family %d", i + 1);
      }
    } else {
      if (MEDfamilyInfo(fid, meshNames[index].c_str(), i + 1, family_name,
                        &family_num, &group_names[0]) < 0) {
        SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                 "Could not read info for MED3 family %d", i + 1);
      }
    }
 
    for (int g = 0; g != num_groups; g++) {
      std::string name =
          std::string(&group_names[MED_LNAME_SIZE * g], MED_LNAME_SIZE - 1);
      name.resize(NAME_TAG_SIZE - 1);
      if (family_elem_map.find(family_num) == family_elem_map.end()) {
        MOFEM_LOG_C(
            "MEDWORLD", Sev::warning,
            "Family %d not read, likely type of element is not added "
            "to moab database. Currently only triangle, quad, tetrahedral and "
            "hexahedral elements are read to moab database",
            family_num);
      } else {
        group_elem_map[name].merge(family_elem_map.at(family_num));
      }
    }
  }
 
  if (MEDfileClose(fid) < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
             "Unable to close file '%s'", file.c_str());
  }
 
  MoFEMFunctionReturn(0);
}

◆ readFields()

MoFEMErrorCode MoFEM::MedInterface::readFields	(	const std::string &	file_name,
		const std::string &	field_name,
		const bool	load_series = false,
		const int	only_step = -1,
		int	verb = 1 )

Read fields

Parameters

file_name	file name
file_index	mesh index
loadSeries	load field into series
onlyStep	read only one step

Returns: error code

Definition at line 1008 of file MedInterface.cpp.

                                                                       {
 
  Interface &m_field = cOre;
  MoFEMFunctionBeginHot;
  med_idt fid = MEDfileOpen((char *)file_name.c_str(), MED_LECTURE);
  if (fid < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
             "Unable to open file '%s'", file_name.c_str());
  }
 
  med_int num_comp = MEDfieldnComponentByName(fid, field_name.c_str());
  if (num_comp <= 0) {
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
            "Could not get number of components for MED field");
  }
 
  char meshName[MED_NAME_SIZE + 1];
  char dtUnit[MED_SNAME_SIZE + 1];
  std::vector<char> compName(num_comp * MED_SNAME_SIZE + 1);
  std::vector<char> compUnit(num_comp * MED_SNAME_SIZE + 1);
  med_int numSteps = 0;
  med_type_champ type;
  med_bool localMesh;
  if (MEDfieldInfoByName(fid, field_name.c_str(), meshName, &localMesh, &type,
                         &compName[0], &compUnit[0], dtUnit, &numSteps) < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
            "Could not get MED field info");
  }
 
  // Get meshset
  MeshsetsManager *meshsets_manager_ptr;
  CHKERR m_field.getInterface(meshsets_manager_ptr);
  const CubitMeshSets *cubit_meshset_ptr;
  CHKERR meshsets_manager_ptr->getCubitMeshsetPtr(meshName, &cubit_meshset_ptr);
  EntityHandle meshset = cubit_meshset_ptr->getMeshset();
 
  // Paraview can only plot field which have 1, 3, or 9 components. If field has
  // more that 9 comonents, it is stored on MOAB mesh but not viable in
  // ParaView.
  int num_comp_msh = (num_comp <= 1)   ? 1
                     : (num_comp <= 3) ? 3
                     : (num_comp <= 9) ? 9
                                       : num_comp;
 
  // Create tag to store nodal or cell values read form med file. Note that tag
  // has prefix MED to avoid collision with other tags.
  Tag th;
  std::string tag_name = "MED_" + field_name;
  {
    std::vector<double> def_val(num_comp_msh, 0);
    CHKERR m_field.get_moab().tag_get_handle(
        tag_name.c_str(), num_comp_msh, MB_TYPE_DOUBLE, th,
        MB_TAG_CREAT | MB_TAG_SPARSE, &def_val[0]);
  }
 
  // Warning! The ordering of the elements in the last two lists is
  // important: it should match the ordering of the MSH element types
  // (when elements are saved without tags, this governs the order
  // with which we implicitly index them in GModel::readMED)
  const med_entity_type entType[] = {MED_NODE, MED_CELL, MED_NODE_ELEMENT};
  const med_geometrie_element eleType[] = {
      MED_NONE,   MED_SEG2,   MED_TRIA3, MED_QUAD4,  MED_TETRA4,  MED_HEXA8,
      MED_PENTA6, MED_PYRA5,  MED_SEG3,  MED_TRIA6,  MED_QUAD9,   MED_TETRA10,
      MED_HEXA27, MED_POINT1, MED_QUAD8, MED_HEXA20, MED_PENTA15, MED_PYRA13};
  // const int nodesPerEle[] = {0, 2, 3, 4, 4, 8, 6, 5, 3, 6, 9, 10, 27, 1, 8,
  // 20, 15, 13};
 
  std::vector<std::pair<int, int>> pairs;
  for (unsigned int i = 0; i < sizeof(entType) / sizeof(entType[0]); i++) {
    for (unsigned int j = 0; j < sizeof(eleType) / sizeof(eleType[0]); j++) {
      if ((!i && !j) || j) {
        med_int n = numSteps;
        if (n > 0) {
          pairs.push_back(std::pair<int, int>(i, j));
          numSteps = std::max(numSteps, n);
        }
        if (!i && !j)
          break; // MED_NOEUD does not care about eleType
      }
    }
  }
 
  if (numSteps < 1 || pairs.empty()) {
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
            "Nothing to import from MED file");
  }
 
  if (load_series) {
    SETERRQ(m_field.get_comm(), MOFEM_NOT_IMPLEMENTED, "Not yet implemented");
  }
 
  if (numSteps == 1 && only_step > 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
            "Field has only one step. Cannot load step with -med_time_step, "
            "remove from command line.");
  } else if (numSteps == only_step) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
            "Cannot load final step %d. -med_time_step should be %d.",
            only_step, only_step - 1);
  }
 
  for (int step = (only_step == -1) ? 0 : only_step; step < numSteps; step++) {
    MOFEM_LOG_C("MEDWORLD", Sev::inform, "Loading step %d of field %s", step + 1,
                field_name.c_str());
    if (!load_series && only_step != step)
      continue;
 
    // FIXME: in MED3 we might want to loop over all profiles instead
    // of relying of the default one
 
    // FIXME: MED3 allows to store multi-step meshes; we should
 
    for (unsigned int pair = 0; pair < pairs.size(); pair++) {
 
      // get step info
      med_entite_maillage ent = entType[pairs[pair].first];
      med_geometrie_element ele = eleType[pairs[pair].second];
      med_int numdt, numit, ngauss;
      med_float dt;
      if (MEDfieldComputingStepInfo(fid, field_name.c_str(), step + 1, &numdt,
                                    &numit, &dt) < 0) {
        SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                "Could not read step info");
      }
 
      char locName[MED_NAME_SIZE + 1], profileName[MED_NAME_SIZE + 1];
 
      // get number of values in the field (numVal takes the number of
      // Gauss points or the number of nodes per element into account,
      // but not the number of components)
      med_int profileSize;
      med_int numVal = MEDfieldnValueWithProfile(
          fid, field_name.c_str(), numdt, numit, ent, ele, 1,
          MED_COMPACT_STMODE, profileName, &profileSize, locName, &ngauss);
      numVal *= ngauss;
 
      if (numVal <= 0)
        continue;
 
      // read field data
      std::vector<double> val(numVal * num_comp);
      if (MEDfieldValueWithProfileRd(fid, field_name.c_str(), numdt, numit, ent,
                                     ele, MED_COMPACT_STMODE, profileName,
                                     MED_FULL_INTERLACE, MED_ALL_CONSTITUENT,
                                     (unsigned char *)&val[0]) < 0) {
        SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                "Could not read field values");
      }
 
      switch (ent) {
      case MED_CELL: {
        EntityType ent_type = MBMAXTYPE;
        switch (ele) {
        case MED_TETRA4:
        case MED_TETRA10:
          ent_type = MBTET;
          break;
        case MED_HEXA8:
        case MED_HEXA20:
          ent_type = MBHEX;
          break;
        default:
          MOFEM_LOG_C("MEDWORLD", Sev::warning,
                      "Not yet implemented for this cell %d", ele);
        }
        if (ent_type != MBMAXTYPE) {
          if (ngauss == 1) {
            Range ents;
            CHKERR m_field.get_moab().get_entities_by_type(meshset, ent_type,
                                                           ents, true);
            double e_vals[num_comp_msh];
            bzero(e_vals, sizeof(double) * num_comp_msh);
            std::vector<double>::iterator vit = val.begin();
            for (Range::iterator eit = ents.begin(); eit != ents.end(); eit++) {
              for (int ii = 0; ii != num_comp; ii++, vit++) {
                e_vals[ii] = *vit;
              }
              CHKERR m_field.get_moab().tag_set_data(th, &*eit, 1, e_vals);
            }
          } else {
            Range ents;
            CHKERR m_field.get_moab().get_entities_by_type(meshset, ent_type,
                                                           ents, true);
            if (ents.size() * ngauss * num_comp != val.size()) {
              SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
                      "data inconsistency");
            }
            // FIXME simply average gauss values, far from perfect need fix
            double e_vals[num_comp_msh];
            std::vector<double>::iterator vit = val.begin();
            for (Range::iterator eit = ents.begin(); eit != ents.end(); eit++) {
              bzero(e_vals, sizeof(double) * num_comp_msh);
              for (int gg = 0; gg != ngauss; gg++) {
                for (int ii = 0; ii != num_comp; ii++, vit++) {
                  e_vals[ii] += *vit / ngauss;
                }
              }
              CHKERR m_field.get_moab().tag_set_data(th, &*eit, 1, e_vals);
            }
          }
        }
      } break;
      case MED_NODE:
      case MED_NODE_ELEMENT: {
        EntityType ent_type = MBVERTEX;
        Range ents;
        CHKERR m_field.get_moab().get_entities_by_type(meshset, ent_type, ents,
                                                       true);
        double e_vals[num_comp_msh];
        bzero(e_vals, sizeof(double) * num_comp_msh);
        std::vector<double>::iterator vit = val.begin();
        for (Range::iterator eit = ents.begin(); eit != ents.end(); eit++) {
          for (int ii = 0; ii != num_comp; ii++, vit++) {
            e_vals[ii] = *vit;
          }
          CHKERR m_field.get_moab().tag_set_data(th, &*eit, 1, e_vals);
        }
      } break;
      default:
        MOFEM_LOG_C("MEDWORLD", Sev::inform, "Entity type %d not implemented",
                    ent);
      }
    }
  }
 
  MoFEMFunctionReturnHot(0);
}

◆ readMed() [1/2]

MoFEMErrorCode MoFEM::MedInterface::readMed	(	const string &	file,
		int	verb = 1 )

read MED file

Parameters

file	field name
verb	verbosity level

Returns: error code

Definition at line 145 of file MedInterface.cpp.

                                                                 {
  Interface &m_field = cOre;
  MoFEMFunctionBegin;
 
  med_idt fid = MEDfileOpen(file.c_str(), MED_ACC_RDONLY);
  if (fid < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
             "Unable to open file '%s'", file.c_str());
  }
 
  med_int v[3], vf[3];
  MEDlibraryNumVersion(&v[0], &v[1], &v[2]);
  MEDfileNumVersionRd(fid, &vf[0], &vf[1], &vf[2]);
 
  if (verb > 0)
    MOFEM_LOG_C("MEDWORLD", Sev::inform,
                "Reading MED file V%d.%d.%d using MED library V%d.%d.%d", vf[0],
                vf[1], vf[2], v[0], v[1], v[2]);
 
  if (vf[0] < 2 || (vf[0] == 2 && vf[1] < 2)) {
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
            "Cannot read MED file older than V2.2");
  }
 
  for (int i = 0; i < MEDnMesh(fid); i++) {
    char mesh_name[MED_NAME_SIZE + 1], mesh_desc[MED_COMMENT_SIZE + 1];
    bzero(mesh_name, MED_NAME_SIZE);
    bzero(mesh_desc, MED_COMMENT_SIZE);
    med_int space_dim;
    med_mesh_type mesh_type;
    med_int mesh_dim, n_step;
    char dt_unit[MED_SNAME_SIZE + 1];
    char axis_name[3 * MED_SNAME_SIZE + 1], axis_unit[3 * MED_SNAME_SIZE + 1];
    med_sorting_type sorting_type;
    med_axis_type axis_type;
    if (MEDmeshInfo(fid, i + 1, mesh_name, &space_dim, &mesh_dim, &mesh_type,
                    mesh_desc, dt_unit, &sorting_type, &n_step, &axis_type,
                    axis_name, axis_unit) < 0) {
      SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
              "Unable to read mesh information");
    }
    meshNames.push_back(std::string(mesh_name));
    if (verb > 0) {
      MOFEM_LOG_C("MEDWORLD", Sev::inform, "Check mesh %s nsteps %d", mesh_name,
                  n_step);
    }
  }
 
  std::map<int, Range> family_elem_map;
  std::map<string, Range> group_elem_map;
 
  for (unsigned int ii = 0; ii != meshNames.size(); ii++) {
    CHKERR readMesh(file, ii, family_elem_map, verb);
    CHKERR readFamily(file, ii, family_elem_map, group_elem_map, verb);
    CHKERR makeBlockSets(group_elem_map, verb);
  }
 
  if (MEDfileClose(fid) < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
             "Unable to close file '%s'", file.c_str());
  }
 
  MoFEMFunctionReturn(0);
}

◆ readMed() [2/2]

MoFEMErrorCode MoFEM::MedInterface::readMed ( int verb = 1 )

read MED file

File name is form command line ////

Parameters

verb	verbosity level

Returns: error code

Definition at line 651 of file MedInterface.cpp.

                                             {
  MoFEMFunctionBegin;
  if (medFileName.empty()) {
    CHKERR getFileNameFromCommandLine(verb);
  }
  CHKERR readMed(medFileName, verb);
  MoFEMFunctionReturn(0);
}

◆ readMesh()

MoFEMErrorCode MoFEM::MedInterface::readMesh	(	const string &	file,
		const int	index,
		std::map< int, Range > &	family_elem_map,
		int	verb = 1 )

private

read mesh from MED file

Parameters

file	file name
index	index of mesh
family_elem_map	map of families and elements
verb	verbosity level

Returns: error code

Definition at line 253 of file MedInterface.cpp.

                                                {
 
  Interface &m_field = cOre;
  MoFEMFunctionBegin;
 
  med_idt fid = MEDfileOpen(file.c_str(), MED_ACC_RDONLY);
  if (fid < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
             "Unable to open file '%s'", file.c_str());
  }
  med_int v[3], vf[3];
  MEDlibraryNumVersion(&v[0], &v[1], &v[2]);
  MEDfileNumVersionRd(fid, &vf[0], &vf[1], &vf[2]);
  if (verb > 1)
    MOFEM_LOG_C("MEDWORLD", Sev::noisy,
                "Reading MED file V%d.%d.%d using MED library V%d.%d.%d", vf[0],
                vf[1], vf[2], v[0], v[1], v[2]);
 
  if (vf[0] < 2 || (vf[0] == 2 && vf[1] < 2)) {
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
            "Cannot read MED file older than V2.2");
  }
 
  char mesh_name[MED_NAME_SIZE + 1], mesh_desc[MED_COMMENT_SIZE + 1];
  bzero(mesh_name, MED_NAME_SIZE + 1);
  bzero(mesh_desc, MED_COMMENT_SIZE + 1);
  med_int space_dim;
  med_mesh_type mesh_type;
  med_int mesh_dim, n_step;
  char dt_unit[MED_SNAME_SIZE + 1];
  char axis_name[3 * MED_SNAME_SIZE + 1], axis_unit[3 * MED_SNAME_SIZE + 1];
  med_sorting_type sorting_type;
  med_axis_type axis_type;
  if (MEDmeshInfo(fid, index + 1, mesh_name, &space_dim, &mesh_dim, &mesh_type,
                  mesh_desc, dt_unit, &sorting_type, &n_step, &axis_type,
                  axis_name, axis_unit) < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
            "Unable to read mesh information");
  }
  if (verb > 0)
    MOFEM_LOG_C("MEDWORLD", Sev::inform, "Reading mesh %s nsteps %d", mesh_name,
                n_step);
 
  switch (axis_type) {
  case MED_CARTESIAN:
    break;
  case MED_SPHERICAL:
  case MED_CYLINDRICAL:
  default:
    SETERRQ(m_field.get_comm(), MOFEM_NOT_IMPLEMENTED,
            "Curvilinear coordinate system implemented");
  }
  if (space_dim < 2) {
    SETERRQ(m_field.get_comm(), MOFEM_NOT_IMPLEMENTED,
             "Not implemented for space dim %d", space_dim);
  }
 
  EntityHandle mesh_meshset;
  {
    MeshsetsManager *meshsets_manager_ptr;
    CHKERR m_field.getInterface(meshsets_manager_ptr);
    int max_id = 0;
    for (_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(m_field, BLOCKSET, cit)) {
      max_id = (max_id < cit->getMeshsetId()) ? cit->getMeshsetId() : max_id;
    }
    max_id++;
    CHKERR meshsets_manager_ptr->addMeshset(BLOCKSET, max_id,
                                            std::string(mesh_name));
    CubitMeshSet_multiIndex::index<
        Composite_Cubit_msId_And_MeshsetType_mi_tag>::type::iterator cit;
    cit =
        meshsets_manager_ptr->getMeshsetsMultindex()
            .get<Composite_Cubit_msId_And_MeshsetType_mi_tag>()
            .find(boost::make_tuple(max_id, CubitBCType(BLOCKSET).to_ulong()));
    max_id++;
    mesh_meshset = cit->getMeshset();
    meshMeshsets.push_back(mesh_meshset);
  }
 
  med_bool change_of_coord, geo_transform;
  med_int num_nodes = MEDmeshnEntity(
      fid, mesh_name, MED_NO_DT, MED_NO_IT, MED_NODE, MED_NO_GEOTYPE,
      MED_COORDINATE, MED_NO_CMODE, &change_of_coord, &geo_transform);
  if (num_nodes < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
            "Could not read number of MED nodes");
  }
  if (num_nodes == 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
            "No nodes in MED mesh");
  }
  if (verb > 0)
    MOFEM_LOG_C("MEDWORLD", Sev::inform, "Read number of nodes %d", num_nodes);
 
  std::vector<med_float> coord_med(space_dim * num_nodes);
  if (MEDmeshNodeCoordinateRd(fid, mesh_name, MED_NO_DT, MED_NO_IT,
                              MED_NO_INTERLACE, &coord_med[0]) < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
            "Could not read MED node coordinates");
  }
 
  // Add vertices to moab
  ReadUtilIface *iface;
  vector<double *> arrays_coord;
  EntityHandle startv;
  CHKERR m_field.get_moab().query_interface(iface);
  CHKERR iface->get_node_coords(3, num_nodes, 0, startv, arrays_coord);
  Range verts(startv, startv + num_nodes - 1);
  std::copy(&coord_med[0 * num_nodes], &coord_med[1 * num_nodes],
            arrays_coord[0]);
  std::copy(&coord_med[1 * num_nodes], &coord_med[2 * num_nodes],
            arrays_coord[1]);
  if (space_dim == 2) {
    std::fill(arrays_coord[2], &arrays_coord[2][num_nodes], 0.);
  } else {
    std::copy(&coord_med[2 * num_nodes], &coord_med[3 * num_nodes],
              arrays_coord[2]);
  }
  CHKERR m_field.get_moab().add_entities(mesh_meshset, verts);
  family_elem_map.clear();
 
  // get family for vertices
  {
    std::vector<med_int> nodes_tags(num_nodes, 0);
    if (MEDmeshEntityFamilyNumberRd(fid, mesh_name, MED_NO_DT, MED_NO_IT,
                                    MED_NODE, MED_NO_GEOTYPE,
                                    &nodes_tags[0]) < 0) {
      nodes_tags.clear();
    }
    for (int i = 0; i < num_nodes; i++) {
      family_elem_map[nodes_tags.empty() ? i : nodes_tags[i]].insert(verts[i]);
    }
  }
 
  // read elements (loop over all possible MSH element types)
  for (EntityType ent_type = MBVERTEX; ent_type < MBMAXTYPE; ent_type++) {
 
    auto types = moab2med_element_type(ent_type);
 
    for (auto type : types) {
 
      // get number of cells
      med_bool change_of_coord;
      med_bool geo_transform;
      med_int num_ele = MEDmeshnEntity(
          fid, mesh_name, MED_NO_DT, MED_NO_IT, MED_CELL, type,
          MED_CONNECTIVITY, MED_NODAL, &change_of_coord, &geo_transform);
 
      // get connectivity
      if (num_ele <= 0)
        continue;
 
      int num_nod_per_ele = type % 100;
      if (verb > 0)
        MOFEM_LOG("MEDWORLD", Sev::inform)
            << "Reading elements " << num_ele << " of type "
            << moab::CN::EntityTypeName(ent_type) << " number of nodes "
            << num_nod_per_ele;
 
      std::vector<med_int> conn_med(num_ele * num_nod_per_ele);
      if (MEDmeshElementConnectivityRd(fid, mesh_name, MED_NO_DT, MED_NO_IT,
                                       MED_CELL, type, MED_NODAL,
                                       MED_FULL_INTERLACE, &conn_med[0]) < 0) {
        SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                "Could not read MED elements");
      }
 
      Range ents;
 
      if (ent_type != MBVERTEX) {
        EntityHandle *conn_moab;
        EntityHandle starte;
        CHKERR iface->get_element_connect(num_ele, num_nod_per_ele, ent_type, 0,
                                          starte, conn_moab);
        switch (ent_type) {
        // FIXME: Some connectivity could not work, need to run and test
        case MBTET: {
          int ii = 0;
          for (int ee = 0; ee != num_ele; ee++) {
            std::vector<EntityHandle> n(num_nod_per_ele);
            for (int nn = 0; nn != num_nod_per_ele; nn++) {
              n[nn] = verts[conn_med[ii + nn] - 1];
            }
 
            std::array<int, 10> nodes_map{
 
                1, 0, 2, 3,
 
                4, 6, 5, 8,
                7, 9
 
            };
 
            for (int nn = 0; nn != num_nod_per_ele; nn++, ii++) {
              conn_moab[ii] = n[nodes_map[nn]];
            }
          }
        }
        case MBHEX: {
          int ii = 0;
          for (int ee = 0; ee != num_ele; ee++) {
            std::vector<EntityHandle> n(num_nod_per_ele);
            for (int nn = 0; nn != num_nod_per_ele; nn++) {
              n[nn] = verts[conn_med[ii + nn] - 1];
            }
 
            std::array<int, 20> nodes_map{
                0,  3,  2,  1,  4, 7, 6, 5, // corner nodes
                11, 10, 9,  8,              // edges on bottom face
                16, 19, 18, 17,             // vertical edges
                15, 14, 13, 12              // edges on top face
 
            };
 
            for (int nn = 0; nn != num_nod_per_ele; nn++, ii++) {
              conn_moab[ii] = n[nodes_map[nn]];
            }
          }
        } break;
        default: {
          int ii = 0;
          for (int ee = 0; ee != num_ele; ee++) {
            for (int nn = 0; nn != num_nod_per_ele; nn++, ii++) {
              conn_moab[ii] = verts[conn_med[ii] - 1];
            }
          }
        }
        }
        CHKERR iface->update_adjacencies(starte, num_ele, num_nod_per_ele,
                                         conn_moab);
        ents = Range(starte, starte + num_ele - 1);
      } else {
        // This is special case when in med vertices are defined as elements
        int ii = 0;
        std::vector<EntityHandle> conn_moab(num_ele * num_nod_per_ele);
        for (int ee = 0; ee != num_ele; ++ee)
          for (int nn = 0; nn != num_nod_per_ele; ++nn, ++ii)
            conn_moab[ii] = verts[conn_med[ii] - 1];
        ents.insert_list(conn_moab.begin(), conn_moab.end());
      }
 
      // Add elements to family meshset
      CHKERR m_field.get_moab().add_entities(mesh_meshset, ents);
 
      // get family for cells
      {
        std::vector<med_int> fam(num_ele, 0);
        if (MEDmeshEntityFamilyNumberRd(fid, mesh_name, MED_NO_DT, MED_NO_IT,
                                        MED_CELL, type, &fam[0]) < 0) {
            MOFEM_LOG("MEDWORLD", Sev::warning) <<
                  "No family number for elements: using 0 as default family number";
        }
        for (int j = 0; j < num_ele; j++) {
          family_elem_map[fam[j]].insert(ents[j]);
        }
      }
    }
  }
 
  if (MEDfileClose(fid) < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
             "Unable to close file '%s'", file.c_str());
  }
 
  MoFEMFunctionReturn(0);
}

◆ writeMed() [1/2]

MoFEMErrorCode MoFEM::MedInterface::writeMed	(	boost::shared_ptr< Range >	range_ptr = nullptr,
		int	verb = 1 )

write MED file

File name is form command line

Parameters

verb	verbosity level

Returns: error code

Definition at line 683 of file MedInterface.cpp.

                                                {
  MoFEMFunctionBegin;
  if (medFileName.empty()) {
    CHKERR getFileNameFromCommandLine(verb);
  }
 
  // Get all meshsets
  boost::shared_ptr<std::vector<const CubitMeshSets *>> meshsets_ptr;
  getMeshsets(meshsets_ptr);
 
  CHKERR writeMed(medFileName, meshsets_ptr, range_ptr, verb);
  MoFEMFunctionReturn(0);
}

◆ writeMed() [2/2]

MoFEMErrorCode MoFEM::MedInterface::writeMed	(	const string &	file,
		boost::shared_ptr< std::vector< const CubitMeshSets * > >	meshsets_ptr,
		boost::shared_ptr< Range >	range_ptr = nullptr,
		int	verb = 1 )

write MED file

Parameters

file	file name
meshsets_ptr	meshsets
verb	verbosity level

Returns: error code

Definition at line 698 of file MedInterface.cpp.

                                                      {
  Interface &m_field = cOre;
  // Get the MOAB instance from the field
  moab::Interface &moab = m_field.get_moab();
 
  MoFEMFunctionBeginHot;
  MOFEM_LOG("MEDWORLD", Sev::warning)
      << "WRITE_MED IS EXPERIMENTAL, MAY CONTAIN BUGS, ALWAYS CHECK THE OUTPUT "
         "FILE";
  // Open a med file with the specified version
  med_idt fid =
      MEDfileVersionOpen((char *)file.c_str(), MED_ACC_CREAT, MED_MAJOR_NUM,
                         MED_MINOR_NUM, MED_RELEASE_NUM);
  // Throw an error if the file could not be opened
  if (fid < 0) {
    SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
            "Cannot create MED file");
    return 0;
  }
 
  // Write appropriate header
  CHKERR MEDfichDesEcr(fid, (char *)"MED file generated by MoFEM");
 
  // Generate empty mesh
  char dtUnit[MED_SNAME_SIZE + 1] = "";       // time unit
  char axisName[3 * MED_SNAME_SIZE + 1] = ""; // axis name
  char axisUnit[3 * MED_SNAME_SIZE + 1] = ""; // axis unit
 
  PetscBool is_cubit_meshset = PETSC_TRUE;
  int med_mesh_name_id = 0;
 
  // Create the mesh
  char mesh_name_char[255];
  std::string mesh_name = "Mesh";
 
  // Get mesh_name from command line
  PetscOptionsBegin(PETSC_COMM_WORLD, "", "MED mesh options", "");
  CHKERR PetscOptionsString("-med_mesh_name", "get med mesh name", "",
                            mesh_name.c_str(), mesh_name_char, 255, PETSC_NULLPTR);
  PetscOptionsEnd();
 
  mesh_name = mesh_name_char;
 
  // check if mesh_name is a meshset
  for (auto &m : *meshsets_ptr) {
    if (m->getName() == mesh_name) {
      med_mesh_name_id = m->getMeshsetId();
      is_cubit_meshset = PETSC_FALSE;
      break;
    }
  }
 
  // Get the maximum meshset id
  int max_id = 0;
  for (auto &m : *meshsets_ptr) {
    if (m->getMeshsetId() == med_mesh_name_id)
      mesh_name = m->getName();
    max_id = (max_id < m->getMeshsetId()) ? m->getMeshsetId() : max_id;
  }
 
  // Create a mesh
  CHKERR MEDmeshCr(fid, mesh_name.c_str(), 3, 3, MED_UNSTRUCTURED_MESH,
                   "Mesh created", dtUnit, MED_SORT_DTIT, MED_CARTESIAN,
                   axisName, axisUnit);
 
  // Create a map of meshset names to family ids and shared meshsets
  med_int family_id = 0;
  std::map<std::vector<std::string>, std::tuple<med_int, std::vector<int>>>
      shared_meshsets_map;
  std::map<EntityHandle, med_int> entityHandle_family_map;
 
  // initialise zero family id
  shared_meshsets_map[std::vector<string>()] =
      std::make_tuple(family_id, std::vector<int>());
 
  // function to get meshset names
  auto get_set_name = [&](const CubitMeshSets *iit) {
    std::string bc_type_name;
    if (iit->getBcTypeULong() & BLOCKSET) {
 
      bc_type_name = iit->getName();
      if (bc_type_name == "NoNameSet") {
        bc_type_name = "BLOCKSET_";
        bc_type_name += std::to_string(iit->getMeshsetId());
      }
      return bc_type_name;
    } else if (iit->getBcTypeULong() & SIDESET ||
               iit->getBcTypeULong() & NODESET) {
 
      CubitBCType cubitBcType(iit->getBcTypeULong());
 
      unsigned jj = 0;
      while (1 << jj != LASTSET_BC) {
        const CubitBCType jj_bc_type = 1 << jj;
        if ((iit->getBcType() & jj_bc_type).any()) {
 
          std::string temp_bc_type_name = string(CubitBCNames[jj + 1]);
          if (temp_bc_type_name.length() > 10) {
            temp_bc_type_name = temp_bc_type_name.substr(0, 4);
          }
          bc_type_name += temp_bc_type_name;
          bc_type_name += "_";
        }
        ++jj;
      }
      bc_type_name += std::to_string(iit->getMeshsetId());
    } else {
      bc_type_name = "UnknownSet";
    }
    return bc_type_name;
  };
 
  // loop over all entities in the write range
  // FIXME: This is a very slow implementation
  //        We should use a binary search tree
  //        instead of looping each entity in
  //        write_range_ptr to find shared meshsets
  for (auto &entity : *write_range_ptr) {
    // check if entity is shared with other meshsets
    std::vector<int> shared_meshsets;
    std::vector<string> shared_names;
 
    // function to add shared meshsets to vectors
    auto add_shared_meshset = [&](auto &other_meshset) {
      std::string other_name = get_set_name(other_meshset);
      if (std::find(shared_names.begin(), shared_names.end(), other_name) ==
          shared_names.end()) {
        shared_meshsets.push_back(other_meshset->getMeshsetId());
        shared_names.push_back(other_name);
      }
    };
 
    // loop over all meshsets provided
    for (auto &other_meshset : *meshsets_ptr) {
      // skip if meshset is the global meshset given by user
      if (med_mesh_name_id == other_meshset->getMeshsetId())
        continue;
 
      Range other_entities;
      EntityHandle other_set = other_meshset->getMeshset();
      moab.get_entities_by_handle(other_set, other_entities);
      if (other_entities.empty())
        continue;
 
      bool is_in_meshset = moab.contains_entities(other_set, &entity, 1);
      if (is_in_meshset) {
        // add shared meshset id to list
        add_shared_meshset(other_meshset);
      }
    }
 
    // check if shared meshset is already in map
    auto it = shared_meshsets_map.find(shared_names);
    if (it == shared_meshsets_map.end()) {
      // create new family id
      family_id++;
      // create and insert new tuple into the map
      it = shared_meshsets_map
               .insert(
                   {shared_names, std::make_tuple(family_id, shared_meshsets)})
               .first;
    }
    // assign family id to entity
    entityHandle_family_map[entity] = std::get<0>(it->second);
  }
 
  // loop to create families based on shared meshsets map
  for (const auto &it : shared_meshsets_map) {
    // create family
    std::string family_name = "F_";
    const auto &[family_id, shared_meshsets] = it.second;
    family_name += std::to_string(family_id);
 
    const auto &shared_meshset_names = it.first;
    std::string group_name;
    for (const auto &name : shared_meshset_names) {
      // get meshset name
      std::string meshset_name = name;
      meshset_name.resize(MED_LNAME_SIZE, ' ');
      group_name += meshset_name;
    }
 
    // create family
    CHKERR MEDfamilyCr(fid, mesh_name.c_str(), family_name.c_str(), family_id,
                       shared_meshset_names.size(), group_name.c_str());
 
    MOFEM_LOG("MEDWORLD", Sev::inform)
        << "Creating family " << family_name << " with id " << family_id
        << " and " << shared_meshset_names.size() << " groups " << std::endl;
  }
 
  // write nodes from range
  Range verts;
  verts = write_range_ptr->subset_by_type(MBVERTEX);
 
  // Prepare arrays to hold the coordinates
  std::vector<med_float> coord_med(3 * verts.size());
  std::vector<med_int> fam;
  std::vector<med_int> tags;
  std::map<EntityHandle, med_int> entityHandle_tag_map;
  med_int med_node_num = 1;
 
  // For each vertex, get its coordinates
  for (Range::iterator it = verts.begin(); it != verts.end(); ++it) {
    double coords[3];
    moab.get_coords(&(*it), 1, coords);
    coord_med[3 * (it - verts.begin())] = coords[0];
    coord_med[3 * (it - verts.begin()) + 1] = coords[1];
    coord_med[3 * (it - verts.begin()) + 2] = coords[2];
    fam.push_back(entityHandle_family_map[*it]);
    tags.push_back(*it);
    // map entityHandle to new tag (node) number
    entityHandle_tag_map[*it] = med_node_num;
    med_node_num++;
  }
  // Write the coordinates to the MED file
  CHKERR MEDmeshNodeWr(fid, mesh_name.c_str(), MED_NO_DT, MED_NO_IT,
                       MED_UNDEF_DT, MED_FULL_INTERLACE, verts.size(),
                       &coord_med[0], MED_FALSE, "", MED_TRUE, &tags[0],
                       MED_TRUE, &fam[0]);
 
  // get last vertex id
  double last_tag = tags.back();
  // loop to write elements to families
  for (EntityType ent_type = MBVERTEX; ent_type < MBMAXTYPE; ent_type++) {
    // get all entities of type ent_type
    Range entities;
    moab.get_entities_by_type(0, ent_type, entities, true);
    Range ents_to_write;
    ents_to_write = intersect(entities, *write_range_ptr);
 
    if (ents_to_write.empty())
      continue;
 
    // vectors to write
    std::vector<med_int> tag_number;
    std::vector<med_int> family_number;
    std::vector<med_int> connectivity;
 
    // loop over all entities
    for (auto &entity : ents_to_write) {
      if (ent_type != MBVERTEX) {
        last_tag++;
        // get family id for entity
        family_number.push_back(entityHandle_family_map[entity]);
        // get tag number for entity
        tag_number.push_back(last_tag);
        // get connectivity for entity
        std::vector<EntityHandle> conn;
        moab.get_connectivity(&entity, 1, conn);
        // add connectivity to vector from map of entityHandle to new tag number
        for (auto &c : conn) {
          connectivity.push_back(entityHandle_tag_map[c]);
        }
      } else {
        continue;
      }
    }
 
    auto get_med_element_type = [](EntityType ent_type) {
      med_geometrie_element type;
      switch (ent_type) {
      case MBHEX:
        type = MED_HEXA8;
        break;
      case MBTET:
        type = MED_TETRA4;
        break;
      case MBQUAD:
        type = MED_QUAD4;
        break;
      case MBTRI:
        type = MED_TRIA3;
        break;
      case MBEDGE:
        type = MED_SEG2;
        break;
      case MBPRISM:
        type = MED_PENTA6;
        break;
      default:
        type = MED_POINT1;
        break;
      }
      return type;
    };
 
    med_geometrie_element med_type = get_med_element_type(ent_type);
    if (ent_type == MBENTITYSET) {
      continue;
    }
    CHKERR MEDmeshElementWr(fid, mesh_name.c_str(), MED_NO_DT, MED_NO_IT, 0.,
                            MED_CELL, med_type, MED_NODAL, MED_FULL_INTERLACE,
                            family_number.size(), &connectivity[0], MED_FALSE,
                            nullptr, MED_TRUE, &tag_number[0], MED_TRUE,
                            &family_number[0]);
 
    MOFEM_LOG_C("MEDWORLD", Sev::inform, "Writing %i elements of type %i (%s) ",
                family_number.size(), med_type,
                moab::CN::EntityTypeName(ent_type));
  }
 
  // Close the MED file
  CHKERR MEDfermer(fid);
  MoFEMFunctionReturnHot(0);
}

Member Data Documentation

◆ cOre

MoFEM::Core& MoFEM::MedInterface::cOre

private

core database

Definition at line 136 of file MedInterface.hpp.

◆ cubitMeshsets

CubitMeshSet_multiIndex MoFEM::MedInterface::cubitMeshsets

private

cubit meshsets

Definition at line 140 of file MedInterface.hpp.

◆ fieldNames

std::map<std::string, FieldData> MoFEM::MedInterface::fieldNames

Definition at line 132 of file MedInterface.hpp.

◆ flgFile

PetscBool MoFEM::MedInterface::flgFile

private

true if file name given in command line

Definition at line 138 of file MedInterface.hpp.

◆ medFileName

std::string MoFEM::MedInterface::medFileName

MED file name.

Definition at line 133 of file MedInterface.hpp.

◆ meshMeshsets

std::vector<EntityHandle> MoFEM::MedInterface::meshMeshsets

meshset for each mesh

Definition at line 131 of file MedInterface.hpp.

◆ meshNames

std::vector<std::string> MoFEM::MedInterface::meshNames

list of meshes in MED file

Definition at line 130 of file MedInterface.hpp.

The documentation for this struct was generated from the following files:

src/interfaces/MedInterface.hpp
src/interfaces/impl/MedInterface.cpp

Classes

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MedInterface()

Member Function Documentation

◆ getFileNameFromCommandLine()

◆ getFlgFile()

◆ getMeshsets()

◆ makeBlockSets()

◆ medGetFieldNames() [1/2]

◆ medGetFieldNames() [2/2]

◆ query_interface()

◆ readFamily()

◆ readFields()

◆ readMed() [1/2]

◆ readMed() [2/2]

◆ readMesh()

◆ writeMed() [1/2]

◆ writeMed() [2/2]

Member Data Documentation

◆ cOre

◆ cubitMeshsets

◆ fieldNames

◆ flgFile

◆ medFileName

◆ meshMeshsets

◆ meshNames