NEM::MSH::EXOMesh::exoMesh Class Reference

A complete I/O class for EXODUS II file format. More...

Detailed Description

Methods for definition, addition, removal, and modification of the elements, nodes, element blocks, node sets, and side sets are implemented. The implementation relies on standard EXODUS II library provided in system repository.

Definition at line 172 of file exoMesh.H.

Public Member Functions
	exoMesh ()
	exoMesh (std::string ifname)
	Construct exoMesh with initial file name. More...
	exoMesh (const exoMesh &)=default
	exoMesh (exoMesh &&)=default
exoMesh &	operator= (const exoMesh &)=default
exoMesh &	operator= (exoMesh &&)=default
	~exoMesh ()
bool	isCompatible () const
int	getNumberOfNodes () const
	Returns total number of nodes. More...
int	getNumberOfElements () const
	Returns total number of elements. More...
int	getNumberOfElementBlocks () const
	Returns total number of element blocks. More...
int	getNumberOfNodeSets () const
	Returns total number of node sets. More...
int	getNumberOfSideSets () const
	Returns total number of side sets. More...
const std::string &	getElmBlkName (int idx) const
	Returns the name the element block for given index. More...
const std::string	getElmBlkNameById (int id) const
	Returns the name the element block for given element block ID. More...
const std::string &	getNdeSetName (int idx) const
	Returns the name the nodeset for given index. More...
std::string	getNdeSetNameById (int id) const
	Returns the name the nodeset for given nodeset id. More...
const std::string &	getSdeSetName (int idx) const
	Returns the name the sideset for given index. More...
int	getElmBlkIndex (int id) const
	Returns the index for the element block for given id. More...
int	getElmBlkIndex (const std::string name) const
	Returns the index for the element block for given name. More...
int	getElmBlkId (int idx) const
	Returns the id for the element block for given index. More...
int	getElmBlkId (std::string ebName) const
	Returns the id for the element block from element block name. More...
int	getNdeSetId (int idx) const
	Returns the id for the nodeset for given index. More...
int	getNdeSetId (const std::string &nsName) const
	Returns the id for the nodeset for nodeset name. More...
int	getNdeSetIndex (const std::string &nsName) const
	Returns the index for the nodeset for nodeset name. More...
int	getSdeSetId (int idx) const
	Returns the id for the sideset for given index. More...
int	getSdeSetId (const std::string &ssName) const
	Returns the id for the sideset for sideset name. More...
int	getSdeSetIndex (const std::string &ssName) const
	Returns the index of the sideset for sideset name. More...
elementType	getElmBlkType (int idx) const
	Returns the element type for the block. More...
elementType	getElmBlkTypeById (int id) const
	Returns the element type for the block. More...
elementType	getElmBlkType (const std::string &ebName) const
	Returns the element type for the block. More...
int	getNumElmsInBlk (int idx) const
	Returns the number of elements for the block. More...
int	getNumElmsInBlk (const std::string &ebName) const
	Returns the number of elements for the block. More...
int	getNumElmsInBlkById (int id) const
	Returns the number of elements for the block. More...
int	getNumNdesInNdeSet (int idx) const
	Returns the number of nodes for the nodeset. More...
int	getNumNdesInNdeSet (const std::string &nsName) const
	Returns the number of nodes for the nodeset. More...
int	getNumNdesInNdeSetById (int id) const
	Returns the number of nodes for the nodeset. More...
int	getNumSdesInSdeSet (int idx) const
	Returns the number of sides for the sideset. More...
int	getNumSdesInSdeSet (const std::string &ssName) const
	Returns the number of sides for the sideset. More...
int	getNumSdesInSdeSetById (int id) const
	Returns the number of sides for the sideset. More...
const std::vector< int > &	getElmBlkIds () const
	Returns the IDs of registered element blocks. More...
const std::vector< std::string > &	getElmBlkNames () const
	Returns the names of registered element blocks. More...
const std::vector< std::string > &	getNdeSetNames () const
	Returns the names of registered node sets. More...
const std::vector< std::string > &	getSdeSetNames () const
	Returns the names of registered side sets. More...
int	getDimension () const
	Returns problem dimension. More...
void	setBlockName (int idx, const std::string &name)
	Sets/changes block name. More...
void	setBlockName (const std::string &name, const std::string &newName)
	Sets/changes block name. More...
void	setSdeSetName (int idx, const std::string &name)
	Sets/changes sideset name. More...
void	setSdeSetName (const std::string &name, const std::string &newName)
	Sets/changes sideset name. More...
void	setNdeSetName (int idx, const std::string &name)
	Sets/changes nodeset name. More...
void	setNdeSetName (const std::string &name, const std::string &newName)
	Sets/changes nodeset name. More...
void	setDimension (int dim)
	Sets/changes the problem dimensionality. More...
void	addNde (double x, double y, double z)
	Add nodes to the database. More...
void	addNde (const std::vector< double > &xyz)
	Add nodes to the database. More...
void	addElmBlk (const elmBlkType &eb)
	Add element block to the database. More...
void	addNdeSet (const ndeSetType &ns)
	Add node set to the database. More...
void	addSdeSet (const sdeSetType &ss)
	Add side set to the database. More...
void	removeElmBlkByName (const std::string &blkName)
	Remove an element block by name. More...
void	removeElmBlkById (int id)
	Remove an element block by ID. More...
int	findElmBlkIdxByElmId (int elmId) const
	Finds index of the first block containing element. More...
int	findElmBlkIdxByElmIdLst (const std::vector< int > &elmIds) const
	Finds index of the block containing most or all of the list (slower) More...
std::vector< int >	lstElmInBlk (int blkIdx, const std::vector< int > &elmIds, bool &allIn) const
	Finds all elements that are within the block and generates a list of them. More...
void	combineElmBlks (const std::vector< int > &blkIdLst, const std::string &newName)
	Combines element blocks into one block. More...
void	updateSidesets (const std::map< int, int > &old2NewElmIds)
	Updates sidesets from combining blocks. More...
void	removeByElmIdLst (int blkIdx, const std::vector< int > &idLst)
	Removes a list of elements from an element block. More...
void	addElmBlkByElmIdLst (const std::string &name, std::vector< int > &idLst)
	Creates a new element block and augments previous owners. More...
void	addNdeSetByNdeIdLst (const std::string &name, const std::vector< int > &idLst)
	Creates a new node set and augments previous ones if needed. More...
void	snapNdeCrdsZero (double tol=1e-5)
	Filter nodal coordinates and snap to zero. More...
void	mergeNodes (double tol=1e-15)
	Merges duplicated and nodes within given proximity. More...
void	scaleNodes (double sc=1.0)
	scales the nodal coordinates More...
void	stitch (const exoMesh &otherMesh)
	Stitch another mesh into the current. More...
void	setFileName (const std::string &fName)
	Change the file name. More...
void	write ()
	Write to file name specified at construction or using setFileName method. More...
void	read (const std::string &ifname=std::string())
	Resets the class and reads from file name provided. More...
void	reset ()
	Resets the EXODUS database. More...
void	report () const
	Print out a report of the current EXODUS database. More...
void	togVrb ()
	Toggle verbosity. More...

Private Member Functions
void	exoPopulate (bool updElmLst=false)
template<typename T >
std::map< T, int >	findDuplicates (const std::vector< T > &vecOfElements)

Private Attributes
int	_numDim
int	_numNdes
std::vector< double >	_xCrds
std::vector< double >	_yCrds
std::vector< double >	_zCrds
int	_numElms
elmBlks	_elmBlks
std::vector< std::string >	_elmBlkNames
std::vector< int >	_elmBlkIds
ndeSets	_ndeSets
std::vector< std::string >	_ndeSetNames
sdeSets	_sdeSets
std::vector< std::string >	_sdeSetNames
int	_fid
float	_api_v
float	_dbs_v
int	_exErr
std::string	_ifname
bool	_isSupported
bool	_isPopulated
bool	_isOpen
bool	_isVerbose
bool	_reindexBlks {true}
std::vector< std::vector< int > >	glbConn

Constructor & Destructor Documentation

exoMesh() [1/4]

NEM::MSH::EXOMesh::exoMesh::exoMesh

(

)

Definition at line 171 of file exoMesh.C.

    : _numDim(2),
      _numNdes(0),
      _numElms(0),
      _fid(-1),
      _api_v(0.0),
      _dbs_v(0.0),
      _exErr(0),
      _isSupported(true),
      _isPopulated(false),
      _isOpen(false),
      _isVerbose(false) {}

exoMesh() [2/4]

NEM::MSH::EXOMesh::exoMesh::exoMesh ( std::string  ifname )

explicit

Parameters

ifname

file name

Definition at line 184 of file exoMesh.C.

    : _numDim(2),
      _numNdes(0),
      _numElms(0),
      _fid(-1),
      _api_v(0.0),
      _dbs_v(0.0),
      _exErr(0),
      _ifname(std::move(ifname)),
      _isSupported(true),
      _isPopulated(false),
      _isOpen(false),
      _isVerbose(false) {}

exoMesh() [3/4]

NEM::MSH::EXOMesh::exoMesh::exoMesh ( const exoMesh &  )

default

exoMesh() [4/4]

NEM::MSH::EXOMesh::exoMesh::exoMesh ( exoMesh &&  )

default

~exoMesh()

NEM::MSH::EXOMesh::exoMesh::~exoMesh

(

)

Definition at line 198 of file exoMesh.C.

References _fid, and _isOpen.

                  {
  if (_isOpen) ex_close(_fid);
}

Member Function Documentation

addElmBlk()

void NEM::MSH::EXOMesh::exoMesh::addElmBlk ( const elmBlkType &  eb )

inline

Parameters

eb	EXODUS element block

Definition at line 504 of file exoMesh.H.

Referenced by addElmBlkByElmIdLst(), NEM::DRV::ConversionDriver::genExo(), and stitch().

                                       {
    _elmBlks.emplace_back(eb);
    _isPopulated = false;
  }

addElmBlkByElmIdLst()

void NEM::MSH::EXOMesh::exoMesh::addElmBlkByElmIdLst	(	const std::string &	name,
		std::vector< int > &	idLst
	)

Parameters

name	new element block name
idLst	vector of element ids

Definition at line 807 of file exoMesh.C.

References _elmBlks, _isPopulated, addElmBlk(), NEM::MSH::EXOMesh::elmBlkType::conn, NEM::MSH::EXOMesh::elmBlkType::elmIds, NEM::MSH::EXOMesh::elmBlkType::eTpe, exoPopulate(), findElmBlkIdxByElmIdLst(), getElmBlkType(), glbConn, NEM::MSH::EXOMesh::elmBlkType::id, lstElmInBlk(), NEM::MSH::EXOMesh::elmBlkType::name, NEM::MSH::EXOMesh::elmBlkType::ndeIdOffset, NEM::MSH::EXOMesh::elmBlkType::ndePerElm, NEM::MSH::EXOMesh::elmBlkType::nElm, removeByElmIdLst(), and NEM::MSH::EXOMesh::wrnErrMsg().

Referenced by NEM::DRV::ConversionDriver::procExo().

                                                       {
  if (lst.empty()) {
    std::cerr << "WARNING: Attempting to add element block " << name
              << " with no elements." << std::endl;
    return;
  }

  // preparing database
  if (!_isPopulated) exoPopulate(false);

  _isPopulated = false;
  // create element block
  // Assumption here: All elements in the provided list are in the same element
  // block
  elmBlkType neb;
  neb.id = _elmBlks.size() + 1;
  neb.name = name;
  neb.ndeIdOffset = 0;

  // int blkIdx = findElmBlkIdxByElmId(lst[0]); // faster but less accurate
  int blkIdx = findElmBlkIdxByElmIdLst(lst);  // slower, more accurate
  if (blkIdx == -1) wrnErrMsg(-1, "Elements ids are not registered.");
  // std::cout << "Block Indx = " << blkIdx << std::endl;

  // now adjust the list and remove elements that are not owned by this block
  std::vector<int> owndLst;
  bool allIn = false;
  owndLst = lstElmInBlk(blkIdx, lst, allIn);
  if (!allIn) {
    std::cout << owndLst.size() << " Elements are in the block.\n";
    std::cout << "Some of the elements in the list are outside the block.\n";
    lst = owndLst;
  }

  neb.elmIds = lst;
  neb.nElm = lst.size();
  neb.eTpe = getElmBlkType(blkIdx);
  neb.ndePerElm = _elmBlks[blkIdx].ndePerElm;
  for (const auto &eid : lst)
    for (int idx = 0; idx < neb.ndePerElm; ++idx)
      neb.conn.emplace_back(glbConn[eid][idx]);

  // updating the old element block and adding a new one
  removeByElmIdLst(blkIdx, lst);
  addElmBlk(neb);

  exoPopulate(false);
}

addNde() [1/2]

void NEM::MSH::EXOMesh::exoMesh::addNde ( double  x, double  y, double  z  )

inline

Parameters

x
y
z

Definition at line 487 of file exoMesh.H.

Referenced by NEM::DRV::ConversionDriver::genExo().

                                            {
    _xCrds.emplace_back(x);
    _yCrds.emplace_back(y);
    _zCrds.emplace_back(z);
    ++_numNdes;
  }

addNde() [2/2]

void NEM::MSH::EXOMesh::exoMesh::addNde ( const std::vector< double > &  xyz )

inline

Parameters

xyz	3-vector of form (x, y, z)

Definition at line 497 of file exoMesh.H.

                                            {
    addNde(xyz[0], xyz[1], xyz[2]);
  }

addNdeSet()

void NEM::MSH::EXOMesh::exoMesh::addNdeSet ( const ndeSetType &  ns )

inline

Parameters

ns	EXODUS node set

Definition at line 512 of file exoMesh.H.

Referenced by addNdeSetByNdeIdLst(), NEM::DRV::GmshToExoConversionDriver::execute(), NEM::DRV::ConversionDriver::genExo(), and stitch().

                                       {
    _ndeSets.emplace_back(ns);
    _isPopulated = false;
  }

addNdeSetByNdeIdLst()

void NEM::MSH::EXOMesh::exoMesh::addNdeSetByNdeIdLst	(	const std::string &	name,
		const std::vector< int > &	idLst
	)

Parameters

name	new node set name
idLst	vector of node ids

Definition at line 857 of file exoMesh.C.

References _isPopulated, _ndeSets, addNdeSet(), exoPopulate(), NEM::MSH::EXOMesh::ndeSetType::id, NEM::MSH::EXOMesh::ndeSetType::name, NEM::MSH::EXOMesh::ndeSetType::ndeIdOffset, NEM::MSH::EXOMesh::ndeSetType::ndeIds, and NEM::MSH::EXOMesh::ndeSetType::nNde.

Referenced by NEM::DRV::ConversionDriver::procExo().

                                                               {
  // preparing database
  if (!_isPopulated) exoPopulate(false);

  _isPopulated = false;
  // create and add new node set
  ndeSetType nns;
  nns.id = _ndeSets.size() + 1;  // 1-indexed
  nns.nNde = idLst.size();
  nns.name = name;
  nns.ndeIdOffset = 0;
  nns.ndeIds = idLst;
  addNdeSet(nns);

  // update exodus information
  exoPopulate(false);
}

addSdeSet()

void NEM::MSH::EXOMesh::exoMesh::addSdeSet ( const sdeSetType &  ss )

inline

Parameters

ss	EXODUS side set

Definition at line 520 of file exoMesh.H.

Referenced by NEM::DRV::ConversionDriver::freeSurfaceSideSet(), NEM::DRV::ConversionDriver::genExo(), and stitch().

                                       {
    _sdeSets.emplace_back(ss);
    _isPopulated = false;
  }

combineElmBlks()

void NEM::MSH::EXOMesh::exoMesh::combineElmBlks	(	const std::vector< int > &	blkIdLst,
		const std::string &	newName
	)

Note

automatically augments sidesets between combined blocks

Parameters

blkIdLst

vector of element block IDs

Definition at line 448 of file exoMesh.C.

References _elmBlkIds, _elmBlks, _numNdes, _reindexBlks, _sdeSets, _xCrds, _yCrds, _zCrds, nemAux::Timer::elapsed(), findDuplicates(), getElmBlkIndex(), getElmBlkTypeById(), getNumberOfElements(), glbConn, HEX, id, QUAD, removeElmBlkById(), nemAux::Timer::start(), nemAux::Timer::stop(), TETRA, TRIANGLE, updateSidesets(), and WEDGE.

                                                       {
  nemAux::Timer T;
  T.start();
  // Check for duplicate entries in blkIdLst
  if (findDuplicates(blkIdLst).size() != 0) {
    std::cerr << "Error: Duplicate block IDs defined." << std::endl;
    throw;
  }
  // Check there is more than one id in list
  if (blkIdLst.size() < 2) {
    std::cerr << "Error: More than one block ID is needed." << std::endl;
    throw;
  }
  // Check that block ID exists
  elementType elmtype;
  std::vector<elementType> eType_vec;
  for (auto &id : blkIdLst) {
    auto it = std::find(_elmBlkIds.begin(), _elmBlkIds.end(), id);
    if (it == _elmBlkIds.end()) {
      std::cerr << "Error: Block ID " << id << " does not exist." << std::endl;
      throw;
    }
    // Check element types for each ID
    elmtype = getElmBlkTypeById(id);
    eType_vec.push_back(elmtype);
  }
  // Check that element type in each block is the same
  for (int i = 0; i < eType_vec.size(); ++i) {
    elementType e;
    if (i == 0)
      e = eType_vec[i];
    else if (eType_vec[i] != e) {
      std::cerr << "Error: Block element types are not the same. Cannot "
                   "combine blocks."
                << std::endl;
      throw;
    }
  }

  // Loop through registered blocks and make vector list
  std::vector<int> blkIds;
  for (auto &blk : _elmBlks) {
    blkIds.push_back(blk.id);
  }

  std::vector<int> arrange_list;
  // Get the first id in combine block list
  int first = blkIdLst[0];
  // Loop through blkIds and insert into new vector
  arrange_list.push_back(blkIds[0]);
  for (int &id : blkIds) {
    if (id != first) {
      // Check if id is already in arrange_list,
      // if so, don't insert
      auto it = std::find(arrange_list.begin(), arrange_list.end(), id);
      if (it == arrange_list.end()) arrange_list.push_back(id);
    } else {
      // Check if each combine list item is in arrange_list
      // if so, remove from arrange_list
      for (const int &comId : blkIdLst) {
        for (int i = 0; i < arrange_list.size(); ++i) {
          if (comId == arrange_list[i]) {
            arrange_list.erase(arrange_list.begin() + i);
          }
        }
      }
      // Insert entire combine list into arrange_list
      for (const int &j : blkIdLst) {
        arrange_list.push_back(j);
      }
    }
  }

  // Populate old to new element ids map
  std::map<int, int> old2NewElmIds;
  int i = 0;
  int numElms = getNumberOfElements();
  for (int &id : arrange_list) {
    for (auto &elmBlk : _elmBlks) {
      if (id == elmBlk.id) {
        for (auto &eid : elmBlk.elmIds) {
          i++;
          old2NewElmIds.insert(std::pair<int, int>(eid, i));
        }
      }
    }
  }

  //**************************************************************//
  // Any part of a side set that is between the blocks being
  // combined should be deleted. Therefore, delete these parts
  // before combining the blocks by:
  //
  // Find all node IDs common between combining blocks (blkIdLst).
  // Build combining blocks point kdTree.
  // Go block by block and insert points into tree.
  // Find elements that have these common node IDs.
  // Find those elements in the side sets and compare common nodes
  // to the face nodes.
  //**************************************************************//
  std::cout << "\nModifying sidesets..." << std::flush;
  // Get the number nodes in block to be combined
  int numNodes = 0;
  for (auto &id : blkIdLst) {
    int idx = getElmBlkIndex(id);
    numNodes += _elmBlks[idx].ndeCoords.size();
  }

  // Build kdtree from node coords in each block
  // This will create duplicate nodes in the kdtree
  // which is desired to find common nodes b/w blocks
  int nDim = 3;
  std::map<int, int> tree_ndeId_map;
  ANNpointArray pntCrd;
  pntCrd = annAllocPts(numNodes, nDim);
  int ipts = 0;
  for (auto &id : blkIdLst) {
    int idx = getElmBlkIndex(id);
    auto it = _elmBlks[idx].ndeCoords.begin();
    while (it != _elmBlks[idx].ndeCoords.end()) {
      pntCrd[ipts][0] = it->second[0];
      pntCrd[ipts][1] = it->second[1];
      pntCrd[ipts][2] = it->second[2];
      tree_ndeId_map[ipts] = it->first;
      ipts++;
      it++;
    }
  }
  ANNkd_tree *kdTree = new ANNkd_tree(pntCrd, numNodes, nDim);

  // Finding duplicate node ids
  std::set<int> commonNodes;
  int nNib = 2;
  ANNpoint qryPnt;
  ANNidxArray nnIdx = new ANNidx[nNib];
  ANNdistArray dists = new ANNdist[nNib];
  qryPnt = annAllocPt(nDim);

  for (int iNde = 0; iNde < _numNdes; iNde++) {
    qryPnt[0] = _xCrds[iNde];
    qryPnt[1] = _yCrds[iNde];
    qryPnt[2] = _zCrds[iNde];
    kdTree->annkSearch(qryPnt, nNib, nnIdx, dists);

    if (dists[1] <= 1e-12) {
      int id1 = tree_ndeId_map[nnIdx[0]];
      int id2 = tree_ndeId_map[nnIdx[1]];
      commonNodes.insert(id1);
      commonNodes.insert(id2);
    }
  }
  delete kdTree;

  // Find all elements that have commonNodes
  std::set<int> commonElms;
  int idx, num_nodes_per_elem, ndeID, c;
  numElms = 0;
  for (auto &id : blkIdLst) {
    idx = getElmBlkIndex(id);
    numElms = _elmBlks[idx].nElm;
    num_nodes_per_elem = _elmBlks[idx].ndePerElm;
    c = 0;
    for (int el = 0; el < numElms; ++el) {
      for (int n = 0; n < num_nodes_per_elem; ++n) {
        c = el * num_nodes_per_elem + n;
        ndeID = _elmBlks[idx].conn[c];
        auto pos = commonNodes.find(ndeID);
        if (pos != commonNodes.end())
          commonElms.insert(_elmBlks[idx].elmIds[el]);
      }
    }
  }

  // Face to local element connectivity maps
  std::map<int, std::vector<int>> tri_face_conn_map = {
      {1, {1, 2}}, {2, {2, 3}}, {3, {3, 1}}};
  std::map<int, std::vector<int>> quad_face_conn_map = {
      {1, {1, 2}}, {2, {2, 3}}, {3, {3, 4}}, {4, {4, 1}}};
  std::map<int, std::vector<int>> tet_face_conn_map = {
      {1, {1, 2, 4}}, {2, {2, 3, 4}}, {3, {1, 4, 3}}, {4, {1, 3, 2}}};
  std::map<int, std::vector<int>> hex_face_conn_map = {
      {1, {1, 2, 6, 5}}, {2, {2, 3, 7, 6}}, {3, {3, 4, 8, 7}},
      {4, {1, 5, 8, 4}}, {5, {1, 4, 3, 2}}, {6, {5, 6, 7, 8}}};
  std::map<int, std::vector<int>> wedge_face_conn_map = {{1, {1, 2, 5, 4}},
                                                         {2, {2, 3, 6, 5}},
                                                         {3, {3, 1, 4, 6}},
                                                         {4, {1, 2, 3}},
                                                         {5, {4, 5, 6}}};

  int numCommon = 0;
  // Find commonElms in sides sets
  for (auto &sdeSet : _sdeSets) {
    // Iterators for face id vector
    auto itf = sdeSet.sdeIds.begin();
    int loc = 0;
    int elmID = 0;
    for (auto ite = sdeSet.elmIds.begin(); ite != sdeSet.elmIds.end();) {
      loc = ite - sdeSet.elmIds.begin();
      elmID = sdeSet.elmIds[loc];
      auto pos = commonElms.find(elmID);
      if (pos != commonElms.end()) {
        int faceID = sdeSet.sdeIds[loc];

        // Use the elmID to get the connectivity
        std::vector<int> elmConn = glbConn[elmID - 1];
        std::vector<int> faceConn;
        // With the faceID get the local connectivity (map)
        if (elmtype == elementType::TETRA)
          faceConn = tet_face_conn_map[faceID];
        else if (elmtype == elementType::HEX)
          faceConn = hex_face_conn_map[faceID];
        else if (elmtype == elementType::WEDGE)
          faceConn = wedge_face_conn_map[faceID];
        else if (elmtype == elementType::TRIANGLE)
          faceConn = tri_face_conn_map[faceID];
        else if (elmtype == elementType::QUAD)
          faceConn = quad_face_conn_map[faceID];
        else {
          std::cerr << "Error: Mesh element type not supported." << std::endl;
          throw;
        }

        // Compare the local(face) nodes with commonNodes
        bool allCommon = false;
        for (int i = 0; i < faceConn.size(); ++i) {
          // This is the node ID on the face
          int ndeID = elmConn[faceConn[i] - 1];
          auto pos = commonNodes.find(ndeID);
          if (pos == commonNodes.end()) {
            // If a commonNode is not found, break
            allCommon = false;
            break;
          } else
            allCommon = true;
        }
        if (allCommon) {
          ite = sdeSet.elmIds.erase(ite);
          itf = sdeSet.sdeIds.erase(itf);
          sdeSet.nSde--;
          numCommon++;
        } else {
          ++ite;
          ++itf;
        }
      } else {
        ++ite;
        ++itf;
      }
    }
  }
  std::cout << "done." << std::endl;

  //**************************************************************//
  // Combine the blocks
  //**************************************************************//
  std::cout << "Combining blocks..." << std::flush;
  int firstBlk = getElmBlkIndex(blkIdLst[0]);
  // Combine the blocks
  for (int i = 0; i < blkIdLst.size(); ++i) {
    if (i > 0) {
      int idx = getElmBlkIndex(blkIdLst[i]);
      int ei = -1;
      for (const auto &eid : _elmBlks[idx].elmIds) {
        ei++;
        _elmBlks[firstBlk].elmIds.emplace_back(eid);
        _elmBlks[firstBlk].nElm++;

        for (int ni = ei * _elmBlks[idx].ndePerElm;
             ni < (ei + 1) * _elmBlks[idx].ndePerElm; ni++) {
          _elmBlks[firstBlk].conn.emplace_back(_elmBlks[idx].conn[ni]);
        }
      }
      // Set new block name, if given
      if (newName != "") _elmBlks[firstBlk].name = newName;
    }
  }
  std::cout << "done." << std::endl;
  std::cout << "Updating sideset element IDs..." << std::flush;
  // Update sides sets
  updateSidesets(old2NewElmIds);
  std::cout << "done." << std::endl;

  // Remove blocks, don't reindex blocks
  _reindexBlks = false;
  for (int i = 0; i < blkIdLst.size(); ++i) {
    if (i > 0) removeElmBlkById(blkIdLst[i]);
  }
  T.stop();

  std::cout << "Combined blocks and updated sidesets in "
            << T.elapsed() / 1000.0 << " seconds.\n"
            << std::endl;
}

exoPopulate()

void NEM::MSH::EXOMesh::exoMesh::exoPopulate ( bool  updElmLst = false )

private

Definition at line 309 of file exoMesh.C.

References _elmBlkNames, _elmBlks, _isPopulated, _isVerbose, _ndeSetNames, _ndeSets, _numElms, _reindexBlks, _sdeSetNames, _sdeSets, glbConn, and report().

Referenced by addElmBlkByElmIdLst(), addNdeSetByNdeIdLst(), mergeNodes(), removeElmBlkById(), removeElmBlkByName(), stitch(), and write().

                                        {
  _numElms = 0;
  _elmBlkNames.clear();
  if (updElmLst) {
    for (auto &&ieb : _elmBlks) ieb.elmIds.clear();
    glbConn.clear();
  }
  _ndeSetNames.clear();
  _sdeSetNames.clear();

  // removing empty element blocks
  std::vector<elmBlkType> nebs;
  for (auto &&ieb : _elmBlks)
    if (ieb.nElm > 0) nebs.emplace_back(std::move(ieb));
  _elmBlks = nebs;

  // removing empty node sets
  std::vector<ndeSetType> nnss;
  for (auto &&ins : _ndeSets)
    if (ins.nNde > 0) nnss.emplace_back(std::move(ins));
  _ndeSets = nnss;

  // removing empty side sets
  std::vector<sdeSetType> nsss;
  for (auto &&iss : _sdeSets)
    if (iss.nSde > 0) nsss.emplace_back(std::move(iss));
  _sdeSets = nsss;

  // updating element blocks
  int blkId = 0;  // Reindex the blocks.
  for (auto &&ieb : _elmBlks) {
    if (_reindexBlks) ieb.id = ++blkId;
    _elmBlkNames.emplace_back(ieb.name);

    // offsetting element connectivities
    if (ieb.ndeIdOffset != 0) {
      for (auto &&conn : ieb.conn) conn += ieb.ndeIdOffset;
      ieb.ndeIdOffset = 0;
    }

    // updating global connectivity
    if (updElmLst) {
      ieb.elmIds.clear();
      int nn = ieb.ndePerElm;
      for (int elmIdx = 0; elmIdx < ieb.nElm; ++elmIdx) {
        std::vector<int> elmConn;
        for (int idx = elmIdx * nn; idx < (elmIdx + 1) * nn; ++idx)
          elmConn.emplace_back(ieb.conn[idx]);
        ieb.elmIds.emplace_back(_numElms + elmIdx + 1);
        glbConn.emplace_back(elmConn);
      }

      // sanity check
      if (ieb.nElm != ieb.elmIds.size())
        std::cerr << "WARNING: Malformed element block " << ieb.name << ".\n";
    }

    // sanity check
    if (ieb.nElm * ieb.ndePerElm != ieb.conn.size())
      std::cerr << "WARNING: Malformed element block " << ieb.name << ".\n";

    _numElms += ieb.nElm;
  }

  // updating node sets
  int nsetId = 0;  // Reindex the node sets.
  for (auto &&ins : _ndeSets) {
    ins.id = ++nsetId;
    _ndeSetNames.emplace_back(ins.name);

    // offsetting node ids
    if (ins.ndeIdOffset != 0) {
      for (auto &&it2 : ins.ndeIds) it2 += ins.ndeIdOffset;
      ins.ndeIdOffset = 0;
    }

    // sanity check
    if (ins.nNde != ins.ndeIds.size())
      std::cerr << "WARNING: Malformed node set " << ins.name << ".\n";
  }

  // updating side sets
  int ssetId = 0;  // Reindex the side sets.
  for (auto &&iss : _sdeSets) {
    iss.id = ++ssetId;
    _sdeSetNames.emplace_back(iss.name);

    // offsetting element ids
    if (iss.elmIdOffset != 0) {
      for (auto &&elm : iss.elmIds) elm += iss.elmIdOffset;
      iss.elmIdOffset = 0;
    }

    // sanity check
    if (iss.nSde != iss.sdeIds.size() || iss.nSde != iss.elmIds.size())
      std::cerr << "WARNING: Malformed side set " << iss.name << ".\n";
  }

  if (_isVerbose) report();

  _isPopulated = true;
}

findDuplicates()

template<typename T >

std::map<T, int> NEM::MSH::EXOMesh::exoMesh::findDuplicates ( const std::vector< T > &  vecOfElements )

inlineprivate

Definition at line 680 of file exoMesh.H.

Referenced by combineElmBlks().

                                                                   {
    std::map<T, int> countMap;
    // Iterate over the vector and store the frequency of each element in map
    for (auto &elem : vecOfElements) {
      auto result = countMap.insert(std::pair<T, int>(elem, 1));
      if (result.second == false) result.first->second++;
    }

    // Remove the elements from Map which has 1 frequency count
    for (auto it = countMap.begin(); it != countMap.end();) {
      if (it->second == 1)
        it = countMap.erase(it);
      else
        it++;
    }
    return countMap;
  }

findElmBlkIdxByElmId()

int NEM::MSH::EXOMesh::exoMesh::findElmBlkIdxByElmId

(

int

elmId

)

const

Parameters

elmId

element id

Returns

element block index

Definition at line 927 of file exoMesh.C.

References _elmBlks.

                                                 {
  int blkIdx = 0;
  for (const auto &ieb : _elmBlks) {
    for (const auto &eid : ieb.elmIds)
      if (eid == elmId) return blkIdx;

    blkIdx++;
  }
  return -1;
}

findElmBlkIdxByElmIdLst()

int NEM::MSH::EXOMesh::exoMesh::findElmBlkIdxByElmIdLst

(

const std::vector< int > &

elmIds

)

const

Note

returns -1 if not found

Parameters

elmIds

vector of element ids

Returns

element block index

Definition at line 938 of file exoMesh.C.

References _elmBlks, and lstElmInBlk().

Referenced by addElmBlkByElmIdLst().

                                                                       {
  if (elmIds.empty()) return -1;

  int blkIdx = -1;
  int intfCnt = 0;

  bool allIn = false;
  for (int ieb = 0; ieb < _elmBlks.size(); ++ieb) {
    std::vector<int> intfLst;
    intfLst = lstElmInBlk(ieb, elmIds, allIn);

    if (allIn) {
      return ieb;
    } else if (intfLst.size() > intfCnt) {
      intfCnt = intfLst.size();
      blkIdx = ieb;
    }
  }

  if (!allIn)
    std::cerr << "WARNING: Elements in list are not all in one element block. "
                 "Only block containing largest amount of elements is "
                 "processed. This might indicate selected elements overlap or "
                 "are different element types (e.g., HEX and TETRA)."
              << std::endl;

  return blkIdx;
}

getDimension()

int NEM::MSH::EXOMesh::exoMesh::getDimension ( ) const

inline

Definition at line 412 of file exoMesh.H.

Referenced by NEM::DRV::ConversionDriver::freeSurfaceSideSet().

{ return _numDim; }

getElmBlkId() [1/2]

int NEM::MSH::EXOMesh::exoMesh::getElmBlkId ( int  idx ) const

inline

Parameters

idx	index of block

Definition at line 267 of file exoMesh.H.

{ return _elmBlks[idx].id; }

getElmBlkId() [2/2]

int NEM::MSH::EXOMesh::exoMesh::getElmBlkId

(

std::string

ebName

)

const

Parameters

ebName

name of block

Definition at line 1484 of file exoMesh.C.

References _elmBlks.

                                               {
  auto eb = _elmBlks.begin();
  for (; eb != _elmBlks.end(); eb++)
    if (eb->name == ebName) return (eb->id);

  // warning if the element block name is not registered
  if (eb == _elmBlks.end())
    std::cerr << "Warning: There is no element block with name " << ebName
              << std::endl;

  return -1;
}

getElmBlkIds()

const std::vector<int>& NEM::MSH::EXOMesh::exoMesh::getElmBlkIds ( ) const

inline

Definition at line 386 of file exoMesh.H.

{ return _elmBlkIds; };

getElmBlkIndex() [1/2]

int NEM::MSH::EXOMesh::exoMesh::getElmBlkIndex

(

int

id

)

const

Parameters

id	Id of block

Definition at line 1468 of file exoMesh.C.

References _elmBlks, and getNumberOfElementBlocks().

Referenced by combineElmBlks().

                                        {
  int numElmBlks = getNumberOfElementBlocks();
  for (int i = 0; i < numElmBlks; ++i) {
    if (_elmBlks[i].id == id) return i;
  }
  return -1;
}

getElmBlkIndex() [2/2]

int NEM::MSH::EXOMesh::exoMesh::getElmBlkIndex

(

const std::string

name

)

const

Parameters

id	Id of block

Definition at line 1476 of file exoMesh.C.

References _elmBlks, and getNumberOfElementBlocks().

                                                {
  int numElmBlks = getNumberOfElementBlocks();
  for (int i = 0; i < numElmBlks; ++i) {
    if (_elmBlks[i].name == name) return i;
  }
  return -1;
}

getElmBlkName()

const std::string& NEM::MSH::EXOMesh::exoMesh::getElmBlkName ( int  idx ) const

inline

Parameters

idx	index of block

Definition at line 223 of file exoMesh.H.

{ return _elmBlks[idx].name; }

getElmBlkNameById()

const std::string NEM::MSH::EXOMesh::exoMesh::getElmBlkNameById

(

int

id

)

const

Parameters

id	ID of block

Definition at line 1455 of file exoMesh.C.

References _elmBlks.

                                                       {
  auto eb = _elmBlks.begin();
  for (; eb != _elmBlks.end(); eb++)
    if (eb->id == id) return (eb->name);

  // warning if the element block name is not registered
  if (eb == _elmBlks.end())
    std::cerr << "Warning: There is no element block with ID " << id
              << std::endl;

  return "";
}

getElmBlkNames()

const std::vector<std::string>& NEM::MSH::EXOMesh::exoMesh::getElmBlkNames ( ) const

inline

Definition at line 391 of file exoMesh.H.

Referenced by NEM::DRV::ConversionDriver::procExo().

                                                     {
    return _elmBlkNames;
  };

getElmBlkType() [1/2]

elementType NEM::MSH::EXOMesh::exoMesh::getElmBlkType ( int  idx ) const

inline

Parameters

idx	index of block

Definition at line 315 of file exoMesh.H.

Referenced by addElmBlkByElmIdLst().

{ return _elmBlks[idx].eTpe; };

getElmBlkType() [2/2]

elementType NEM::MSH::EXOMesh::exoMesh::getElmBlkType

(

const std::string &

ebName

)

const

Parameters

ebName

name of the element block

Definition at line 1416 of file exoMesh.C.

References _elmBlks.

                                                                {
  auto eb = _elmBlks.begin();
  for (; eb != _elmBlks.end(); eb++)
    if (eb->name == ebName) return (eb->eTpe);

  // warning if the element block name is not registered
  if (eb == _elmBlks.end())
    std::cerr << "Warning: There is no element block with name " << ebName
              << std::endl;

  return (NEM::MSH::EXOMesh::elementType::OTHER);
}

getElmBlkTypeById()

elementType NEM::MSH::EXOMesh::exoMesh::getElmBlkTypeById

(

int

id

)

const

Parameters

id	ID of block

Definition at line 1403 of file exoMesh.C.

References _elmBlks.

Referenced by combineElmBlks().

                                                   {
  auto eb = _elmBlks.begin();
  for (; eb != _elmBlks.end(); eb++)
    if (eb->id == id) return (eb->eTpe);

  // warning if the element block id is not registered
  if (eb == _elmBlks.end())
    std::cerr << "Warning: There is no element block with id " << id
              << std::endl;

  return (NEM::MSH::EXOMesh::elementType::OTHER);
}

getNdeSetId() [1/2]

int NEM::MSH::EXOMesh::exoMesh::getNdeSetId ( int  idx ) const

inline

Parameters

idx	index of block

Definition at line 279 of file exoMesh.H.

{ return _ndeSets[idx].id; }

getNdeSetId() [2/2]

int NEM::MSH::EXOMesh::exoMesh::getNdeSetId

(

const std::string &

nsName

)

const

Parameters

nsName

name of nodeset

Definition at line 1534 of file exoMesh.C.

References _ndeSets.

                                                      {
  auto ns = _ndeSets.begin();
  for (; ns != _ndeSets.end(); ns++)
    if (ns->name == nsName) return (ns->id);

  // warning if the element block name is not registered
  if (ns == _ndeSets.end())
    std::cerr << "Warning: There is no nodeset with name " << nsName
              << std::endl;

  return -1;
}

getNdeSetIndex()

int NEM::MSH::EXOMesh::exoMesh::getNdeSetIndex

(

const std::string &

nsName

)

const

Parameters

nsName

name of nodeset

Definition at line 1547 of file exoMesh.C.

References _ndeSets.

                                                         {
  auto ns = _ndeSets.begin();
  for (; ns != _ndeSets.end(); ns++)
    if (ns->name == nsName) return ns - _ndeSets.begin();

  // warning if the element block name is not registered
  if (ns == _ndeSets.end())
    std::cerr << "Warning: There is no nodeset with name " << nsName
              << std::endl;

  return -1;
}

getNdeSetName()

const std::string& NEM::MSH::EXOMesh::exoMesh::getNdeSetName ( int  idx ) const

inline

Parameters

idx	index of block

Returns

string The name of nodeset

Definition at line 236 of file exoMesh.H.

{ return _ndeSets[idx].name; }

getNdeSetNameById()

std::string NEM::MSH::EXOMesh::exoMesh::getNdeSetNameById

(

int

id

)

const

Parameters

id	ID of nodeset

Returns

string The name of nodeset

Definition at line 1497 of file exoMesh.C.

References _ndeSets.

                                                 {
  auto ns = _ndeSets.begin();
  for (; ns != _ndeSets.end(); ns++)
    if (ns->id == id) return (ns->name);

  // warning if the element block name is not registered
  if (ns == _ndeSets.end())
    std::cerr << "Warning: There is no nodeset with ID " << id << std::endl;

  return "";
}

getNdeSetNames()

const std::vector<std::string>& NEM::MSH::EXOMesh::exoMesh::getNdeSetNames ( ) const

inline

Definition at line 398 of file exoMesh.H.

                                                     {
    return _ndeSetNames;
  };

getNumberOfElementBlocks()

int NEM::MSH::EXOMesh::exoMesh::getNumberOfElementBlocks ( ) const

inline

Definition at line 207 of file exoMesh.H.

Referenced by NEM::DRV::GmshToExoConversionDriver::execute(), getElmBlkIndex(), removeByElmIdLst(), and report().

{ return _elmBlks.size(); }

getNumberOfElements()

int NEM::MSH::EXOMesh::exoMesh::getNumberOfElements ( ) const

inline

Definition at line 202 of file exoMesh.H.

Referenced by combineElmBlks(), and NEM::DRV::GmshToExoConversionDriver::execute().

{ return _numElms; }

getNumberOfNodes()

int NEM::MSH::EXOMesh::exoMesh::getNumberOfNodes ( ) const

inline

Definition at line 197 of file exoMesh.H.

Referenced by NEM::DRV::GmshToExoConversionDriver::execute().

{ return _numNdes; }

getNumberOfNodeSets()

int NEM::MSH::EXOMesh::exoMesh::getNumberOfNodeSets ( ) const

inline

Definition at line 212 of file exoMesh.H.

Referenced by NEM::DRV::GmshToExoConversionDriver::execute(), and report().

{ return _ndeSets.size(); }

getNumberOfSideSets()

int NEM::MSH::EXOMesh::exoMesh::getNumberOfSideSets ( ) const

inline

Definition at line 217 of file exoMesh.H.

Referenced by NEM::DRV::GmshToExoConversionDriver::execute(), and report().

{ return _sdeSets.size(); }

getNumElmsInBlk() [1/2]

int NEM::MSH::EXOMesh::exoMesh::getNumElmsInBlk ( int  idx ) const

inline

Parameters

idx	index of block

Definition at line 333 of file exoMesh.H.

{ return _elmBlks[idx].nElm; };

getNumElmsInBlk() [2/2]

int NEM::MSH::EXOMesh::exoMesh::getNumElmsInBlk

(

const std::string &

ebName

)

const

Parameters

ebName

name of the element block

Definition at line 1429 of file exoMesh.C.

References _elmBlks.

                                                          {
  auto eb = _elmBlks.begin();
  for (; eb != _elmBlks.end(); eb++)
    if (eb->name == ebName) return (eb->nElm);

  // warning if the element block name is not registered
  if (eb == _elmBlks.end())
    std::cerr << "Warning: There is no element block with name " << ebName
              << std::endl;

  return -1;
}

getNumElmsInBlkById()

int NEM::MSH::EXOMesh::exoMesh::getNumElmsInBlkById

(

int

id

)

const

Parameters

id	ID of the element block

Definition at line 1442 of file exoMesh.C.

References _elmBlks.

                                             {
  auto eb = _elmBlks.begin();
  for (; eb != _elmBlks.end(); eb++)
    if (eb->id == id) return (eb->nElm);

  // warning if the element block name is not registered
  if (eb == _elmBlks.end())
    std::cerr << "Warning: There is no element block with ID " << id
              << std::endl;

  return -1;
}

getNumNdesInNdeSet() [1/2]

int NEM::MSH::EXOMesh::exoMesh::getNumNdesInNdeSet ( int  idx ) const

inline

Parameters

idx	index of nodeset

Definition at line 351 of file exoMesh.H.

{ return _ndeSets[idx].nNde; };

getNumNdesInNdeSet() [2/2]

int NEM::MSH::EXOMesh::exoMesh::getNumNdesInNdeSet

(

const std::string &

nsName

)

const

Parameters

nsName

name of nodeset

Definition at line 1509 of file exoMesh.C.

References _ndeSets.

                                                             {
  auto ns = _ndeSets.begin();
  for (; ns != _ndeSets.end(); ns++)
    if (ns->name == nsName) return (ns->nNde);

  // warning if the element block name is not registered
  if (ns == _ndeSets.end())
    std::cerr << "Warning: There is no nodeset with name " << nsName
              << std::endl;

  return -1;
}

getNumNdesInNdeSetById()

int NEM::MSH::EXOMesh::exoMesh::getNumNdesInNdeSetById

(

int

id

)

const

Parameters

id	ID of nodeset

Definition at line 1522 of file exoMesh.C.

References _ndeSets.

                                                {
  auto ns = _ndeSets.begin();
  for (; ns != _ndeSets.end(); ns++)
    if (ns->id == id) return (ns->nNde);

  // warning if the element block name is not registered
  if (ns == _ndeSets.end())
    std::cerr << "Warning: There is no nodeset with ID " << id << std::endl;

  return -1;
}

getNumSdesInSdeSet() [1/2]

int NEM::MSH::EXOMesh::exoMesh::getNumSdesInSdeSet ( int  idx ) const

inline

Parameters

idx	index of sideset

Definition at line 369 of file exoMesh.H.

{ return _sdeSets[idx].nSde; };

getNumSdesInSdeSet() [2/2]

int NEM::MSH::EXOMesh::exoMesh::getNumSdesInSdeSet

(

const std::string &

ssName

)

const

Parameters

ssName

name of sideset

Definition at line 1586 of file exoMesh.C.

References _sdeSets.

                                                             {
  auto ss = _sdeSets.begin();
  for (; ss != _sdeSets.end(); ss++)
    if (ss->name == ssName) return (ss->nSde);

  // warning if the element block name is not registered
  if (ss == _sdeSets.end())
    std::cerr << "Warning: There is no sideset with name " << ssName
              << std::endl;

  return -1;
}

getNumSdesInSdeSetById()

int NEM::MSH::EXOMesh::exoMesh::getNumSdesInSdeSetById

(

int

id

)

const

Parameters

id	ID of sideset

Definition at line 1599 of file exoMesh.C.

References _sdeSets.

                                                {
  auto ss = _sdeSets.begin();
  for (; ss != _sdeSets.end(); ss++)
    if (ss->id == id) return (ss->nSde);

  // warning if the element block name is not registered
  if (ss == _sdeSets.end())
    std::cerr << "Warning: There is no sideset with ID " << id << std::endl;

  return -1;
}

getSdeSetId() [1/2]

int NEM::MSH::EXOMesh::exoMesh::getSdeSetId ( int  idx ) const

inline

Parameters

idx	index of block

Definition at line 297 of file exoMesh.H.

{ return _sdeSets[idx].id; }

getSdeSetId() [2/2]

int NEM::MSH::EXOMesh::exoMesh::getSdeSetId

(

const std::string &

ssName

)

const

Parameters

ssName

name of sideset

Definition at line 1560 of file exoMesh.C.

References _sdeSets.

                                                      {
  auto ss = _sdeSets.begin();
  for (; ss != _sdeSets.end(); ss++)
    if (ss->name == ssName) return (ss->id);

  // warning if the sideset name is not registered
  if (ss == _sdeSets.end())
    std::cerr << "Warning: There is no sideset with name " << ssName
              << std::endl;

  return -1;
}

getSdeSetIndex()

int NEM::MSH::EXOMesh::exoMesh::getSdeSetIndex

(

const std::string &

ssName

)

const

Parameters

ssName

name of sideset

Definition at line 1573 of file exoMesh.C.

References _sdeSets.

                                                         {
  auto ss = _sdeSets.begin();
  for (; ss != _sdeSets.end(); ss++)
    if (ss->name == ssName) return ss - _sdeSets.begin();

  // warning if the sideset name is not registered
  if (ss == _sdeSets.end())
    std::cerr << "Warning: There is no sideset with name " << ssName
              << std::endl;

  return -1;
}

getSdeSetName()

const std::string& NEM::MSH::EXOMesh::exoMesh::getSdeSetName ( int  idx ) const

inline

Parameters

idx	index of block

Definition at line 249 of file exoMesh.H.

{ return _sdeSets[idx].name; }

getSdeSetNames()

const std::vector<std::string>& NEM::MSH::EXOMesh::exoMesh::getSdeSetNames ( ) const

inline

Definition at line 405 of file exoMesh.H.

                                                     {
    return _sdeSetNames;
  };

isCompatible()

bool NEM::MSH::EXOMesh::exoMesh::isCompatible ( ) const

inline

Definition at line 192 of file exoMesh.H.

{ return _isSupported; }

lstElmInBlk()

std::vector< int > NEM::MSH::EXOMesh::exoMesh::lstElmInBlk	(	int	blkIdx,
		const std::vector< int > &	elmIds,
		bool &	allIn
	)		const

Parameters

blkIdx	element block index
elmIds	vector of element ids
allIn	true if all elements are in given element block

Returns

subset of given element ids in given element block

Definition at line 967 of file exoMesh.C.

References _elmBlks.

Referenced by addElmBlkByElmIdLst(), findElmBlkIdxByElmIdLst(), and NEM::DRV::ConversionDriver::procExo().

                                                         {
  std::vector<int> out;
  allIn = true;

  // compare elmIds with list of the elements within block
  std::set<int> current;
  for (const auto &elmId : _elmBlks[blkIdx].elmIds) current.insert(elmId);
  for (const auto &elmId : elmIds)
    if (!current.insert(elmId).second)
      out.emplace_back(elmId);
    else
      allIn = false;

  return out;
}

mergeNodes()

void NEM::MSH::EXOMesh::exoMesh::mergeNodes

(

double

tol = 1e-15

)

Parameters

tol	tolerance used in determining if a line intersects a surface

Definition at line 1232 of file exoMesh.C.

References _elmBlks, _ndeSets, _numNdes, _xCrds, _yCrds, _zCrds, and exoPopulate().

Referenced by NEM::DRV::ConversionDriver::procExo().

                                   {
  // build all point kdTree
  int nDim = 3;
  ANNpointArray pntCrd;
  pntCrd = annAllocPts(_numNdes, nDim);
  for (int iPnt = 0; iPnt < _numNdes; iPnt++) {
    pntCrd[iPnt][0] = _xCrds[iPnt];
    pntCrd[iPnt][1] = _yCrds[iPnt];
    pntCrd[iPnt][2] = _zCrds[iPnt];
  }
  ANNkd_tree *kdTree = new ANNkd_tree(pntCrd, _numNdes, nDim);

  // finding duplicate node ids
  std::map<int, int> dupNdeMap;  // exoMesh is one-indexed
  int nNib = 2;
  ANNpoint qryPnt;
  ANNidxArray nnIdx = new ANNidx[nNib];
  ANNdistArray dists = new ANNdist[nNib];
  qryPnt = annAllocPt(nDim);
  for (int iNde = 0; iNde < _numNdes; iNde++) {
    qryPnt[0] = _xCrds[iNde];
    qryPnt[1] = _yCrds[iNde];
    qryPnt[2] = _zCrds[iNde];
    kdTree->annkSearch(qryPnt, nNib, nnIdx, dists);
    if (dists[1] <= tol) dupNdeMap[nnIdx[0] + 1] = nnIdx[1] + 1;
  }
  std::cout << "Found " << dupNdeMap.size() << " duplicate nodes.\n";

  // removing duplicated nodal coordinates
  std::vector<double> xn, yn, zn;
  std::map<int, int> old2NewNde;
  for (int iNde = 0; iNde < _numNdes; iNde++) {
    if (dupNdeMap.find(iNde + 1) == dupNdeMap.end()) {
      xn.push_back(_xCrds[iNde]);
      yn.push_back(_yCrds[iNde]);
      zn.push_back(_zCrds[iNde]);
    }
  }

  delete kdTree;

  // mapping
  for (int iPnt = 0; iPnt < xn.size(); iPnt++) {
    pntCrd[iPnt][0] = xn[iPnt];
    pntCrd[iPnt][1] = yn[iPnt];
    pntCrd[iPnt][2] = zn[iPnt];
  }
  kdTree = new ANNkd_tree(pntCrd, xn.size(), nDim);

  // creating map from old ids to new ids
  for (int iNde = 0; iNde < _numNdes; iNde++) {
    qryPnt[0] = _xCrds[iNde];
    qryPnt[1] = _yCrds[iNde];
    qryPnt[2] = _zCrds[iNde];
    kdTree->annkSearch(qryPnt, 1, nnIdx, dists);
    if (dists[0] <= tol) {
      old2NewNde[iNde + 1] = nnIdx[0] + 1;
    } else {
      std::cerr << "ERROR: Found a node in database not properly copied.\n";
      exit(1);
    }
  }

  // sanity check
  int max = 0;
  int min = std::numeric_limits<int>::max();
  for (const auto &im : old2NewNde) {
    max = std::max(max, im.second);
    min = std::min(min, im.second);
  }
  std::cout << "Max new node id = " << max << "\n";
  std::cout << "Min new node id = " << min << "\n";

  // update node coordinates
  _xCrds.clear();
  _yCrds.clear();
  _zCrds.clear();
  _xCrds.assign(xn.begin(), xn.end());
  _yCrds.assign(yn.begin(), yn.end());
  _zCrds.assign(zn.begin(), zn.end());
  std::cout << "Number of nodes changed from " << _numNdes << " to "
            << xn.size() << "\n";
  _numNdes = xn.size();

  // update element block connectivities
  max = 0;
  min = std::numeric_limits<int>::max();
  for (auto &&ieb : _elmBlks) {
    for (auto &&icn : ieb.conn) {
      int nid = icn;
      icn = old2NewNde[nid];
      max = std::max(max, icn);
      min = std::min(min, icn);
    }
  }
  std::cout << "Max conn = " << max << "\n";
  std::cout << "Min conn = " << min << "\n";

  // update node set ids
  for (auto &&ins : _ndeSets) {
    // updating node indices, removing duplicates
    std::set<int> newNSNdeIds;  // set must have unique entries

    for (const auto &nid : ins.ndeIds) newNSNdeIds.insert(old2NewNde[nid]);

    ins.ndeIds.clear();
    ins.ndeIds.assign(newNSNdeIds.begin(), newNSNdeIds.end());
    std::cout << "Original node set with " << ins.nNde
              << " nodes after cleaning becomes " << ins.ndeIds.size() << "\n";

    // updating the nodeset data structure
    ins.nNde = ins.ndeIds.size();
  }

  // side sets do not need to be updated since they contain only element ids

  // deleting KDTree
  delete kdTree;
  delete[] nnIdx;
  delete[] dists;

  // Need to update the element list.
  exoPopulate(true);
}

operator=() [1/2]

exoMesh& NEM::MSH::EXOMesh::exoMesh::operator= ( const exoMesh &  )

default

operator=() [2/2]

exoMesh& NEM::MSH::EXOMesh::exoMesh::operator= ( exoMesh &&  )

default

read()

void NEM::MSH::EXOMesh::exoMesh::read

(

const std::string &

ifname = std::string()

)

Definition at line 1003 of file exoMesh.C.

References _api_v, _dbs_v, _elmBlkIds, _elmBlkNames, _elmBlks, _exErr, _fid, _ifname, _isOpen, _isPopulated, _ndeSetNames, _ndeSets, _numDim, _numElms, _numNdes, _sdeSetNames, _sdeSets, _xCrds, _yCrds, _zCrds, NEM::MSH::EXOMesh::elmBlkType::conn, NEM::MSH::EXOMesh::sdeSetType::elmIdOffset, NEM::MSH::EXOMesh::elmBlkType::elmIds, NEM::MSH::EXOMesh::sdeSetType::elmIds, NEM::MSH::EXOMesh::elmTypeNum(), NEM::MSH::EXOMesh::elmBlkType::eTpe, glbConn, NEM::MSH::EXOMesh::ndeSetType::id, NEM::MSH::EXOMesh::elmBlkType::id, NEM::MSH::EXOMesh::sdeSetType::id, NEM::MSH::EXOMesh::ndeSetType::name, NEM::MSH::EXOMesh::elmBlkType::name, NEM::MSH::EXOMesh::sdeSetType::name, NEM::MSH::EXOMesh::elmBlkType::ndeCoords, NEM::MSH::EXOMesh::ndeSetType::ndeIdOffset, NEM::MSH::EXOMesh::elmBlkType::ndeIdOffset, NEM::MSH::EXOMesh::ndeSetType::ndeIds, NEM::MSH::EXOMesh::elmBlkType::ndePerElm, NEM::MSH::EXOMesh::elmBlkType::nElm, NEM::MSH::EXOMesh::ndeSetType::nNde, NEM::MSH::EXOMesh::sdeSetType::nSde, report(), reset(), NEM::MSH::EXOMesh::sdeSetType::sdeIds, and NEM::MSH::EXOMesh::wrnErrMsg().

Referenced by NEM::DRV::GmshToExoConversionDriver::execute().

                                          {
  if (!ifname.empty()) _ifname = ifname;

  // before reading all internal data base will be reset
  reset();

  int CPU_word_size = sizeof(double);
  int IO_word_size = 0;
  float version;
  _exErr = 0;

  /* open EXODUS II files */
  _fid = ex_open(_ifname.c_str(), EX_READ, &CPU_word_size, &IO_word_size,
                 &version);
  _isOpen = true;
  wrnErrMsg(_fid > 0 ? 0 : -1, "Problem opening file " + _ifname + "\n");

  int numElmBlks;
  int numNdeSets;
  int numSdeSets;

  // parameter inquiry from Exodus file
  int idum;
  float fdum;
  char cdum;

  _exErr = ex_inquire(_fid, EX_INQ_API_VERS, &idum, &fdum, &cdum);
  wrnErrMsg(_exErr, "Problem reading file contents.\n");
  std::cout << "Exodus II API version is " << fdum << std::endl;
  _api_v = fdum;

  _exErr = ex_inquire(_fid, EX_INQ_DB_VERS, &idum, &fdum, &cdum);
  wrnErrMsg(_exErr, "Problem reading file contents.\n");
  std::cout << "Exodus II Database version is " << fdum << std::endl;
  _dbs_v = fdum;

  _exErr = ex_inquire(_fid, EX_INQ_DIM, &idum, &fdum, &cdum);
  wrnErrMsg(_exErr, "Problem reading file contents.\n");
  _numDim = idum;
  std::cout << "Number of coordinate dimensions is " << idum << std::endl;

  _exErr = ex_inquire(_fid, EX_INQ_NODES, &idum, &fdum, &cdum);
  wrnErrMsg(_exErr, "Problem reading file contents.\n");
  std::cout << "Number of points " << idum << std::endl;
  _numNdes = idum;

  _exErr = ex_inquire(_fid, EX_INQ_ELEM, &idum, &fdum, &cdum);
  wrnErrMsg(_exErr, "Problem reading file contents.\n");
  std::cout << "Number of elements " << idum << std::endl;
  _numElms = idum;

  _exErr = ex_inquire(_fid, EX_INQ_ELEM_BLK, &idum, &fdum, &cdum);
  wrnErrMsg(_exErr, "Problem reading file contents.\n");
  std::cout << "Number of element blocks " << idum << std::endl;
  numElmBlks = idum;

  _exErr = ex_inquire(_fid, EX_INQ_NODE_SETS, &idum, &fdum, &cdum);
  wrnErrMsg(_exErr, "Problem reading file contents.\n");
  std::cout << "Number of node sets " << idum << std::endl;
  numNdeSets = idum;

  _exErr = ex_inquire(_fid, EX_INQ_SIDE_SETS, &idum, &fdum, &cdum);
  wrnErrMsg(_exErr, "Problem reading file contents.\n");
  std::cout << "Number of side sets " << idum << std::endl;
  numSdeSets = idum;

  // nodal coordinates
  _xCrds.resize(_numNdes, 0.0);
  _yCrds.resize(_numNdes, 0.0);
  _zCrds.resize(_numNdes, 0.0);
  _exErr = ex_get_coord(_fid, _xCrds.data(), _yCrds.data(), _zCrds.data());
  wrnErrMsg(_exErr, "Problem reading nodal coordinates.\n");

  // ids
  std::vector<int> elmBlkIds(numElmBlks, 0);
  if (numElmBlks > 0) {
    _exErr = ex_get_elem_blk_ids(_fid, elmBlkIds.data());
    wrnErrMsg(_exErr, "Problem reading element block ids.\n");

    for (int i = 0; i < numElmBlks; ++i) {
      _elmBlkIds.push_back(elmBlkIds[i]);
    }
  }

  std::vector<int> ndeSetIds(numNdeSets, 0);
  if (numNdeSets > 0) {
    _exErr = ex_get_node_set_ids(_fid, ndeSetIds.data());
    wrnErrMsg(_exErr, "Problem reading node set ids.\n");
  }

  std::vector<int> sdeSetIds(numSdeSets, 0);
  if (numSdeSets > 0) {
    _exErr = ex_get_side_set_ids(_fid, sdeSetIds.data());
    wrnErrMsg(_exErr, "Problem reading side set ids.\n");
  }

  // element block names
  std::string blk_name;
  for (int iEB = 0; iEB < numElmBlks; ++iEB) {
    blk_name.clear();
    blk_name.resize(MAX_STR_LENGTH);
    int blk_id = elmBlkIds[iEB];
    _exErr = ex_get_name(_fid, EX_ELEM_BLOCK, blk_id, &blk_name[0]);
    wrnErrMsg(_exErr, "Problem reading element block names.\n");
    blk_name.erase(std::remove(blk_name.begin(), blk_name.end(), '\0'),
                   blk_name.end());
    // std::cout << "debugging" << std::endl;
    // std::cout << blk_id << " " << blk_name << std::endl;
    _elmBlkNames.push_back(blk_name);
  }

  // node set names
  for (int iNS = 0; iNS < numNdeSets; ++iNS) {
    blk_name.clear();
    blk_name.resize(MAX_STR_LENGTH);
    int blk_id = ndeSetIds[iNS];
    _exErr = ex_get_name(_fid, EX_NODE_SET, blk_id, &blk_name[0]);
    wrnErrMsg(_exErr, "Problem reading node set names.\n");
    blk_name.erase(std::remove(blk_name.begin(), blk_name.end(), '\0'),
                   blk_name.end());
    // std::cout << blk_id << " " << blk_name << std::endl;
    _ndeSetNames.push_back(blk_name);
  }

  // side set names
  for (int iSS = 0; iSS < numSdeSets; ++iSS) {
    blk_name.clear();
    blk_name.resize(MAX_STR_LENGTH);
    int blk_id = sdeSetIds[iSS];
    _exErr = ex_get_name(_fid, EX_SIDE_SET, blk_id, &blk_name[0]);
    wrnErrMsg(_exErr, "Problem reading side set names.\n");
    blk_name.erase(std::remove(blk_name.begin(), blk_name.end(), '\0'),
                   blk_name.end());
    // std::cout << blk_id << " " << blk_name << std::endl;
    _sdeSetNames.push_back(blk_name);
  }

  // element blocks
  std::string elem_type;
  int elmId = 1;
  for (int iEB = 0; iEB < numElmBlks; ++iEB) {
    elem_type.clear();
    elem_type.resize(MAX_STR_LENGTH);
    elmBlkType eb;
    eb.id = elmBlkIds[iEB];
    int num_el_in_blk, num_nod_per_el, num_attr;
    _exErr = ex_get_elem_block(_fid, elmBlkIds[iEB], &elem_type[0],
                               &num_el_in_blk, &num_nod_per_el, &num_attr);
    wrnErrMsg(_exErr, "Problem reading element block parameters.\n");
    elem_type.erase(std::remove(elem_type.begin(), elem_type.end(), '\0'),
                    elem_type.end());
    eb.nElm = num_el_in_blk;
    eb.name = _elmBlkNames[iEB];
    eb.ndePerElm = num_nod_per_el;
    eb.eTpe = elmTypeNum(elem_type);

    eb.ndeIdOffset = 0;

    // read element connectivity
    eb.conn.clear();
    eb.conn.resize(num_el_in_blk * num_nod_per_el, 0);
    _exErr = ex_get_elem_conn(_fid, elmBlkIds[iEB], eb.conn.data());
    wrnErrMsg(_exErr, "Problem reading element block connectivities.\n");

    double x, y, z;
    // get node coords for each block
    for (int &ndeId : eb.conn) {
      x = _xCrds[ndeId];
      y = _yCrds[ndeId];
      z = _zCrds[ndeId];
      eb.ndeCoords.insert(
          std::pair<int, std::vector<double>>(ndeId, {x, y, z}));
    }

    // fill element ids
    eb.elmIds.clear();
    eb.elmIds.resize(num_el_in_blk);
    std::iota(eb.elmIds.begin(), eb.elmIds.end(), elmId);
    elmId += num_el_in_blk;

    // global connectivity
    int nn = eb.ndePerElm;
    for (int elmIdx = 0; elmIdx < eb.nElm; ++elmIdx) {
      std::vector<int> elmConn;
      for (int idx = elmIdx * nn; idx < (elmIdx + 1) * nn; ++idx)
        elmConn.emplace_back(eb.conn[idx]);
      glbConn.emplace_back(elmConn);
    }

    _elmBlks.push_back(eb);
  }

  // node sets
  for (int iNS = 0; iNS < numNdeSets; ++iNS) {
    ndeSetType ns;
    ns.id = ndeSetIds[iNS];
    _exErr = ex_get_node_set_param(_fid, ns.id, &ns.nNde, &idum);
    wrnErrMsg(_exErr, "Problem reading node set parameters.\n");
    ns.name = _ndeSetNames[iNS];

    ns.ndeIdOffset = 0;
    ns.ndeIds.resize(ns.nNde, 0);
    _exErr = ex_get_node_set(_fid, ns.id, ns.ndeIds.data());
    wrnErrMsg(_exErr, "Problem reading node set node ids.\n");
    _ndeSets.push_back(ns);
  }

  // side sets
  for (int iSS = 0; iSS < numSdeSets; ++iSS) {
    sdeSetType ss;
    ss.id = sdeSetIds[iSS];
    _exErr = ex_get_side_set_param(_fid, ss.id, &ss.nSde, &idum);
    wrnErrMsg(_exErr, "Problem reading side set parameters.\n");
    ss.name = _sdeSetNames[iSS];

    ss.elmIdOffset = 0;
    ss.sdeIds.resize(ss.nSde, 0);
    ss.elmIds.resize(ss.nSde, 0);
    _exErr = ex_get_side_set(_fid, ss.id, ss.elmIds.data(), ss.sdeIds.data());
    wrnErrMsg(_exErr, "Problem reading side set element and side ids.\n");
    _sdeSets.push_back(ss);
  }

  report();

  // since all data structures are manually populated from the file
  _isPopulated = true;
}

removeByElmIdLst()

void NEM::MSH::EXOMesh::exoMesh::removeByElmIdLst	(	int	blkIdx,
		const std::vector< int > &	idLst
	)

Parameters

blkIdx	element block index
idLst	vector of element ids

Definition at line 758 of file exoMesh.C.

References _elmBlks, _isPopulated, NEM::MSH::EXOMesh::elmBlkType::conn, NEM::MSH::EXOMesh::elmBlkType::elmIds, NEM::MSH::EXOMesh::elmBlkType::eTpe, getNumberOfElementBlocks(), NEM::MSH::EXOMesh::elmBlkType::id, NEM::MSH::EXOMesh::elmBlkType::name, NEM::MSH::EXOMesh::elmBlkType::ndeIdOffset, NEM::MSH::EXOMesh::elmBlkType::ndePerElm, NEM::MSH::EXOMesh::elmBlkType::nElm, and NEM::MSH::EXOMesh::wrnErrMsg().

Referenced by addElmBlkByElmIdLst().

                                                                      {
  // TODO: Does NOT update side sets properly!
  // range check
  if (blkIdx > getNumberOfElementBlocks() || blkIdx < 0)
    wrnErrMsg(-1, "Block Id is out of the range.");

  // the idLst should not eliminate the old block
  // at least one element should remain
  // if (idLst.size() >= _elmBlock[blkIdx].elmIds.size())
  //{
  //    std::cout << idLst.size() << " " << _elmBlock[blkIdx].elmIds.size() <<
  //    std::endl; wrnErrMsg(-1, "Can not remove the entire block!.");
  //}

  // now updating the old block
  _isPopulated = false;

  elmBlkType oeb = _elmBlks[blkIdx];
  elmBlkType neb;
  neb.id = oeb.id;
  neb.name = oeb.name;
  neb.eTpe = oeb.eTpe;
  neb.ndePerElm = oeb.ndePerElm;
  neb.ndeIdOffset = 0;
  neb.nElm = 0;

  // elmIds and connectivities
  int oei = -1;
  for (const auto &eid : oeb.elmIds) {
    oei++;

    bool stays = true;
    for (const auto &id : idLst)
      if (id == eid) {
        stays = false;
        break;
      }
    if (!stays) continue;

    neb.nElm++;
    neb.elmIds.emplace_back(eid);
    for (int ni = oei * oeb.ndePerElm; ni < (oei + 1) * oeb.ndePerElm; ni++)
      neb.conn.emplace_back(oeb.conn[ni]);
  }
  std::cout << "Removed " << oeb.elmIds.size() - neb.elmIds.size()
            << " elements from original" << std::endl;
  _elmBlks[blkIdx] = neb;
}

removeElmBlkById()

void NEM::MSH::EXOMesh::exoMesh::removeElmBlkById

(

int

id

)

Note

Calls exoPopulate but does not reindex blocks

Parameters

id	element block ID

Definition at line 915 of file exoMesh.C.

References _elmBlks, _isPopulated, and exoPopulate().

Referenced by combineElmBlks().

                                     {
  std::vector<elmBlkType> nebs;
  for (const auto &ieb : _elmBlks)
    if (ieb.id != id)
      nebs.emplace_back(ieb);
    else
      _isPopulated = false;
  _elmBlks = nebs;

  exoPopulate(true);
}

removeElmBlkByName()

void NEM::MSH::EXOMesh::exoMesh::removeElmBlkByName

(

const std::string &

blkName

)

Note

Calls exoPopulate.

Parameters

blkName

element block name

Definition at line 901 of file exoMesh.C.

References _elmBlks, _isPopulated, and exoPopulate().

Referenced by NEM::DRV::ConversionDriver::procExo().

                                                         {
  if (blkName.empty()) return;

  std::vector<elmBlkType> nebs;
  for (const auto &ieb : _elmBlks)
    if (ieb.name != blkName)
      nebs.emplace_back(ieb);
    else
      _isPopulated = false;
  _elmBlks = nebs;

  exoPopulate(true);
}

report()

void NEM::MSH::EXOMesh::exoMesh::report

(

)

const

Definition at line 412 of file exoMesh.C.

References _elmBlks, _ifname, _ndeSets, _numDim, _numElms, _numNdes, _sdeSets, NEM::MSH::EXOMesh::elmTypeStr(), getNumberOfElementBlocks(), getNumberOfNodeSets(), and getNumberOfSideSets().

Referenced by exoPopulate(), and read().

                           {
  std::cout << " ----- Exodus II Database Report ----- \n";
  std::cout << "Database: " << _ifname << "\n";
  std::cout << "Dimension: " << _numDim << "\n";
  std::cout << "Nodes: " << _numNdes << "\n";
  std::cout << "Elements: " << _numElms << "\n";
  std::cout << "Element blocks: " << getNumberOfElementBlocks() << "\n";
  std::cout << "Node sets: " << getNumberOfNodeSets() << "\n";
  std::cout << "Side sets: " << getNumberOfSideSets() << "\n";
  if (getNumberOfElementBlocks() > 0) {
    std::cout << "  Blk      nElm     eType               Name\n";
    std::cout << "  ---      ----     -----              ------\n";
    for (const auto &ieb : _elmBlks)
      std::cout << std::setw(5) << ieb.id << std::setw(10) << ieb.nElm
                << std::setw(10) << elmTypeStr(ieb.eTpe) << std::setw(20)
                << ieb.name << "\n";
  }
  if (getNumberOfNodeSets() > 0) {
    std::cout << "  Nde      nNde               Name\n";
    std::cout << "  ---      ----              ------\n";
    for (const auto &ins : _ndeSets)
      std::cout << std::setw(5) << ins.id << std::setw(10) << ins.nNde
                << std::setw(20) << ins.name << "\n";
  }
  if (getNumberOfSideSets() > 0) {
    std::cout << "  Sde      nSde               Name\n";
    std::cout << "  ---      ----              ------\n";
    for (const auto &iss : _sdeSets)
      std::cout << std::setw(5) << iss.id << std::setw(10) << iss.nSde
                << std::setw(20) << iss.name << "\n";
  }
  std::cout << std::flush;
}

reset()

void NEM::MSH::EXOMesh::exoMesh::reset

(

)

Clears nodes, element blocks, node sets, side sets.

Definition at line 985 of file exoMesh.C.

References _elmBlkNames, _elmBlks, _fid, _isPopulated, _ndeSetNames, _ndeSets, _numDim, _numElms, _numNdes, _sdeSetNames, _sdeSets, _xCrds, _yCrds, _zCrds, and glbConn.

Referenced by read().

                    {
  _isPopulated = false;
  _ndeSets.clear();
  _elmBlks.clear();
  _sdeSets.clear();
  _fid = 0;
  _numDim = 2;
  _numNdes = 0;
  _numElms = 0;
  _xCrds.clear();
  _yCrds.clear();
  _zCrds.clear();
  glbConn.clear();
  _ndeSetNames.clear();
  _elmBlkNames.clear();
  _sdeSetNames.clear();
}

scaleNodes()

void NEM::MSH::EXOMesh::exoMesh::scaleNodes

(

double

sc = 1.0

)

Parameters

sc	scale factor

Definition at line 1357 of file exoMesh.C.

References _xCrds, _yCrds, and _zCrds.

Referenced by NEM::DRV::ConversionDriver::procExo().

                                  {
  using nemAux::operator*;  // for vector multiplication.
  _xCrds = sc * _xCrds;
  _yCrds = sc * _yCrds;
  _zCrds = sc * _zCrds;
}

setBlockName() [1/2]

void NEM::MSH::EXOMesh::exoMesh::setBlockName ( int  idx, const std::string &  name  )

inline

Parameters

idx	index of block
name	name of the block

Definition at line 421 of file exoMesh.H.

Referenced by NEM::DRV::GmshToExoConversionDriver::execute().

                                                    {
    _elmBlks[idx].name = name;
  }

setBlockName() [2/2]

void NEM::MSH::EXOMesh::exoMesh::setBlockName ( const std::string &  name, const std::string &  newName  )

inline

Parameters

name	of block
newName	new name of the block

Definition at line 430 of file exoMesh.H.

                                                                     {
    int idx = getElmBlkIndex(name);
    _elmBlks[idx].name = newName;
  }

setDimension()

void NEM::MSH::EXOMesh::exoMesh::setDimension ( int  dim )

inline

Parameters

dim	dimension of problem 2D/3D

Definition at line 477 of file exoMesh.H.

Referenced by NEM::DRV::ConversionDriver::genExo().

{ _numDim = dim; }

setFileName()

void NEM::MSH::EXOMesh::exoMesh::setFileName ( const std::string &  fName )

inline

Affects calls to the write method.

Parameters

fName

file name

Definition at line 643 of file exoMesh.H.

{ _ifname = fName; }

setNdeSetName() [1/2]

void NEM::MSH::EXOMesh::exoMesh::setNdeSetName ( int  idx, const std::string &  name  )

inline

Parameters

idx	index of nodeset
name	name of the nodeset

Definition at line 459 of file exoMesh.H.

                                                     {
    _ndeSets[idx].name = name;
  }

setNdeSetName() [2/2]

void NEM::MSH::EXOMesh::exoMesh::setNdeSetName ( const std::string &  name, const std::string &  newName  )

inline

Parameters

name	name of nodeset
newName	new name of the nodeset

Definition at line 468 of file exoMesh.H.

                                                                      {
    int idx = getNdeSetIndex(name);
    _ndeSets[idx].name = newName;
  }

setSdeSetName() [1/2]

void NEM::MSH::EXOMesh::exoMesh::setSdeSetName ( int  idx, const std::string &  name  )

inline

Parameters

idx	index of sideset
name	name of the sideset

Definition at line 440 of file exoMesh.H.

                                                     {
    _sdeSets[idx].name = name;
  }

setSdeSetName() [2/2]

void NEM::MSH::EXOMesh::exoMesh::setSdeSetName ( const std::string &  name, const std::string &  newName  )

inline

Parameters

name	name of sideset
newName	new name of the sideset

Definition at line 449 of file exoMesh.H.

                                                                      {
    int idx = getSdeSetIndex(name);
    _sdeSets[idx].name = newName;
  }

snapNdeCrdsZero()

void NEM::MSH::EXOMesh::exoMesh::snapNdeCrdsZero

(

double

tol = 1e-5

)

Parameters

tol	tolerance used to determine if zero

Definition at line 876 of file exoMesh.C.

References _numNdes, _xCrds, _yCrds, and _zCrds.

Referenced by NEM::DRV::ConversionDriver::procExo().

                                        {
  int nPnt = 0;

  // loop through nodes
  bool chk;
  for (auto i = 0; i < _numNdes; ++i) {
    chk = false;
    if (std::abs(_xCrds[i]) <= tol) {
      _xCrds[i] = 0.0;
      chk = true;
    }
    if (std::abs(_yCrds[i]) <= tol) {
      _yCrds[i] = 0.0;
      chk = true;
    }
    if (std::abs(_zCrds[i]) <= tol) {
      _zCrds[i] = 0.0;
      chk = true;
    }
    if (chk) nPnt++;
  }

  std::cout << "Number of points snapped : " << nPnt << std::endl;
}

stitch()

void NEM::MSH::EXOMesh::exoMesh::stitch

(

const exoMesh &

otherMesh

)

The stitching appends nodes, element blocks, node sets, and side sets to the end of the current exoMesh. The appended items will be re-indexed off the end of the current.

Parameters

otherMesh

Other mesh to stitch into current mesh.

Definition at line 1364 of file exoMesh.C.

References _elmBlks, _ndeSets, _numElms, _numNdes, _sdeSets, _xCrds, _yCrds, _zCrds, addElmBlk(), addNdeSet(), addSdeSet(), and exoPopulate().

                                             {
  // Append nodes.
  _xCrds.insert(_xCrds.end(), otherMesh._xCrds.begin(), otherMesh._xCrds.end());
  _yCrds.insert(_yCrds.end(), otherMesh._yCrds.begin(), otherMesh._yCrds.end());
  _zCrds.insert(_zCrds.end(), otherMesh._zCrds.begin(), otherMesh._zCrds.end());

  // Append all element blocks with extra offset.
  for (const auto &elmBlk : otherMesh._elmBlks) {
    // offset by number of nodes in current mesh.
    auto offElmBlk = elmBlk;
    offElmBlk.ndeIdOffset += _numNdes;

    addElmBlk(offElmBlk);
  }

  // Append all node sets.
  for (const auto &ndeSet : otherMesh._ndeSets) {
    auto offNdeSet = ndeSet;
    offNdeSet.ndeIdOffset += _numNdes;

    addNdeSet(offNdeSet);
  }

  // Append all side sets.
  for (const auto &sdeSet : otherMesh._sdeSets) {
    auto offSdeSet = sdeSet;
    offSdeSet.elmIdOffset += _numElms;

    addSdeSet(offSdeSet);
  }

  // Increase node count. This is delayed as the old value is needed for adding
  // offset to blocks and sets.
  _numNdes += otherMesh._numNdes;

  // Full update to the database. Also updates element count _numElms
  exoPopulate(true);
}

togVrb()

void NEM::MSH::EXOMesh::exoMesh::togVrb ( )

inline

Definition at line 668 of file exoMesh.H.

{ _isVerbose = !_isVerbose; };

updateSidesets()

void NEM::MSH::EXOMesh::exoMesh::updateSidesets

(

const std::map< int, int > &

old2NewElmIds

)

Parameters

old2NewElmIds

map containing old and new element ids

Definition at line 745 of file exoMesh.C.

References _sdeSets.

Referenced by combineElmBlks().

                                                                  {
  // Loop through side sets, update elem ids with map
  for (auto &sSet : _sdeSets) {
    for (auto &elmId : sSet.elmIds) {
      auto it = old2NewElmIds.find(elmId);
      if (it != old2NewElmIds.end())
        elmId = it->second;
      else
        std::cerr << "Error: element not found in sideset" << std::endl;
    }
  }
}

write()

void NEM::MSH::EXOMesh::exoMesh::write

(

)

Definition at line 213 of file exoMesh.C.

References _elmBlkNames, _elmBlks, _exErr, _fid, _ifname, _isOpen, _ndeSetNames, _ndeSets, _numDim, _numElms, _numNdes, _sdeSetNames, _sdeSets, _xCrds, _yCrds, _zCrds, NEM::MSH::EXOMesh::elmTypeStr(), exoPopulate(), and NEM::MSH::EXOMesh::wrnErrMsg().

                    {
  // preparing database
  // regardless we update it
  exoPopulate(true);

  // writing to file
  int comp_ws = 8;
  int io_ws = 8;
  _fid = ex_create(_ifname.c_str(), EX_CLOBBER, &comp_ws, &io_ws);
  _isOpen = true;

  // initializing exodus database
  _exErr =
      ex_put_init(_fid, "NEMoSys ExodusII database", _numDim, _numNdes,
                  _numElms, _elmBlks.size(), _ndeSets.size(), _sdeSets.size());
  wrnErrMsg(_exErr, "Problem initializing EXODUS II database");

  // writing node coordinates
  _exErr = ex_put_coord(_fid, _xCrds.data(), _yCrds.data(), _zCrds.data());
  wrnErrMsg(_exErr, "Problem writing node coordinates.");

  // writing element blocks
  for (const auto &ieb : _elmBlks) {
    _exErr = ex_put_elem_block(_fid, ieb.id, elmTypeStr(ieb.eTpe).c_str(),
                               ieb.nElm, ieb.ndePerElm, 0);
    wrnErrMsg(_exErr, "Problem writing element block parameters.");
    /*
    int elem_blk_id, num_elem_this_blk, num_nodes_per_elem, num_attr;
    std::string elem_type;
    elem_type.resize(MAX_STR_LENGTH, '\0');
    elem_blk_id = ieb + 1;
    ex_get_elem_block(_fid, elem_blk_id, &elem_type[0], &num_elem_this_blk,
                      &num_nodes_per_elem, &num_attr);
    std::cout << "elem_blk_id : " << elem_blk_id
              << "\nelem_type : " << std::string(elem_type)
              << "\nnum_elem_this_blk : " << num_elem_this_blk
              << "\nnum_nodes_per_elem : " << num_nodes_per_elem
              << "\nnum_attr : " << num_attr
              << std::endl;
    */
    _exErr = ex_put_elem_conn(_fid, ieb.id, ieb.conn.data());
    wrnErrMsg(_exErr, "Problem writing element block connectivities.");
    // write element attribute
    /*
    std::vector<double> elmAttrib;
    elmAttrib.resize(_elmBlock[ieb].nElm, 1);
    _exErr = ex_put_elem_attr(_fid, 1, elmAttrib.data());
    wrnErrMsg(_exErr, "Problem during writing elementBlock attributes.");
    */
  }

  // writing node sets
  for (const auto &ins : _ndeSets) {
    _exErr = ex_put_node_set_param(_fid, ins.id, ins.nNde, 0);
    wrnErrMsg(_exErr, "Problem writing node set parameters.");
    _exErr = ex_put_node_set(_fid, ins.id, ins.ndeIds.data());
    wrnErrMsg(_exErr, "Problem writing node set node ids.");
  }

  // writing side sets
  for (const auto &iss : _sdeSets) {
    _exErr = ex_put_side_set_param(_fid, iss.id, iss.nSde, 0);
    wrnErrMsg(_exErr, "Problem writing side set parameters.");
    _exErr =
        ex_put_side_set(_fid, iss.id, iss.elmIds.data(), iss.sdeIds.data());
    wrnErrMsg(_exErr, "Problem writing side set element and side ids.");
  }

  // writing names
  std::vector<char *> names;
  for (auto &&_elmBlkName : _elmBlkNames) names.push_back(&_elmBlkName[0]);
  if (!names.empty()) {
    _exErr = ex_put_names(_fid, EX_ELEM_BLOCK, names.data());
    wrnErrMsg(_exErr, "Problem writing element block names.");
  }

  names.clear();
  for (auto &&_ndeSetName : _ndeSetNames) names.push_back(&_ndeSetName[0]);
  if (!names.empty()) {
    _exErr = ex_put_names(_fid, EX_NODE_SET, names.data());
    wrnErrMsg(_exErr, "Problem writing node set names.");
  }

  names.clear();
  for (auto &&_sdeSetName : _sdeSetNames) names.push_back(&_sdeSetName[0]);
  if (!names.empty()) {
    _exErr = ex_put_names(_fid, EX_SIDE_SET, names.data());
    wrnErrMsg(_exErr, "Problem writing side set names.");
  }

  // closing the file
  _exErr = ex_close(_fid);
  wrnErrMsg(_exErr, "Problem closing the EXODUS II database.");
  _isOpen = false;
}

Member Data Documentation

_api_v

float NEM::MSH::EXOMesh::exoMesh::_api_v

private

Definition at line 725 of file exoMesh.H.

Referenced by read().

_dbs_v

float NEM::MSH::EXOMesh::exoMesh::_dbs_v

private

Definition at line 726 of file exoMesh.H.

Referenced by read().

_elmBlkIds

std::vector<int> NEM::MSH::EXOMesh::exoMesh::_elmBlkIds

private

Definition at line 713 of file exoMesh.H.

Referenced by combineElmBlks(), and read().

_elmBlkNames

std::vector<std::string> NEM::MSH::EXOMesh::exoMesh::_elmBlkNames

private

Definition at line 712 of file exoMesh.H.

Referenced by exoPopulate(), read(), reset(), and write().

_elmBlks

elmBlks NEM::MSH::EXOMesh::exoMesh::_elmBlks

private

Definition at line 711 of file exoMesh.H.

Referenced by addElmBlkByElmIdLst(), combineElmBlks(), exoPopulate(), findElmBlkIdxByElmId(), findElmBlkIdxByElmIdLst(), getElmBlkId(), getElmBlkIndex(), getElmBlkNameById(), getElmBlkType(), getElmBlkTypeById(), getNumElmsInBlk(), getNumElmsInBlkById(), lstElmInBlk(), mergeNodes(), read(), removeByElmIdLst(), removeElmBlkById(), removeElmBlkByName(), report(), reset(), stitch(), and write().

_exErr

int NEM::MSH::EXOMesh::exoMesh::_exErr

private

Definition at line 727 of file exoMesh.H.

Referenced by read(), and write().

_fid

int NEM::MSH::EXOMesh::exoMesh::_fid

private

Definition at line 724 of file exoMesh.H.

Referenced by read(), reset(), write(), and ~exoMesh().

_ifname

std::string NEM::MSH::EXOMesh::exoMesh::_ifname

private

Definition at line 731 of file exoMesh.H.

Referenced by read(), report(), and write().

_isOpen

bool NEM::MSH::EXOMesh::exoMesh::_isOpen

private

Definition at line 734 of file exoMesh.H.

Referenced by read(), write(), and ~exoMesh().

_isPopulated

bool NEM::MSH::EXOMesh::exoMesh::_isPopulated

private

Definition at line 733 of file exoMesh.H.

Referenced by addElmBlkByElmIdLst(), addNdeSetByNdeIdLst(), exoPopulate(), read(), removeByElmIdLst(), removeElmBlkById(), removeElmBlkByName(), and reset().

_isSupported

bool NEM::MSH::EXOMesh::exoMesh::_isSupported

private

Definition at line 732 of file exoMesh.H.

_isVerbose

bool NEM::MSH::EXOMesh::exoMesh::_isVerbose

private

Definition at line 735 of file exoMesh.H.

Referenced by exoPopulate().

_ndeSetNames

std::vector<std::string> NEM::MSH::EXOMesh::exoMesh::_ndeSetNames

private

Definition at line 717 of file exoMesh.H.

Referenced by exoPopulate(), read(), reset(), and write().

_ndeSets

ndeSets NEM::MSH::EXOMesh::exoMesh::_ndeSets

private

Definition at line 716 of file exoMesh.H.

Referenced by addNdeSetByNdeIdLst(), exoPopulate(), getNdeSetId(), getNdeSetIndex(), getNdeSetNameById(), getNumNdesInNdeSet(), getNumNdesInNdeSetById(), mergeNodes(), read(), report(), reset(), stitch(), and write().

_numDim

int NEM::MSH::EXOMesh::exoMesh::_numDim

private

Definition at line 701 of file exoMesh.H.

Referenced by read(), report(), reset(), and write().

_numElms

int NEM::MSH::EXOMesh::exoMesh::_numElms

private

Definition at line 710 of file exoMesh.H.

Referenced by exoPopulate(), read(), report(), reset(), stitch(), and write().

_numNdes

int NEM::MSH::EXOMesh::exoMesh::_numNdes

private

Definition at line 704 of file exoMesh.H.

Referenced by combineElmBlks(), mergeNodes(), read(), report(), reset(), snapNdeCrdsZero(), stitch(), and write().

_reindexBlks

bool NEM::MSH::EXOMesh::exoMesh::_reindexBlks {true}

private

Definition at line 736 of file exoMesh.H.

Referenced by combineElmBlks(), and exoPopulate().

_sdeSetNames

std::vector<std::string> NEM::MSH::EXOMesh::exoMesh::_sdeSetNames

private

Definition at line 721 of file exoMesh.H.

Referenced by exoPopulate(), read(), reset(), and write().

_sdeSets

sdeSets NEM::MSH::EXOMesh::exoMesh::_sdeSets

private

Definition at line 720 of file exoMesh.H.

Referenced by combineElmBlks(), exoPopulate(), getNumSdesInSdeSet(), getNumSdesInSdeSetById(), getSdeSetId(), getSdeSetIndex(), read(), report(), reset(), stitch(), updateSidesets(), and write().

_xCrds

std::vector<double> NEM::MSH::EXOMesh::exoMesh::_xCrds

private

Definition at line 705 of file exoMesh.H.

Referenced by combineElmBlks(), mergeNodes(), read(), reset(), scaleNodes(), snapNdeCrdsZero(), stitch(), and write().

_yCrds

std::vector<double> NEM::MSH::EXOMesh::exoMesh::_yCrds

private

Definition at line 706 of file exoMesh.H.

Referenced by combineElmBlks(), mergeNodes(), read(), reset(), scaleNodes(), snapNdeCrdsZero(), stitch(), and write().

_zCrds

std::vector<double> NEM::MSH::EXOMesh::exoMesh::_zCrds

private

Definition at line 707 of file exoMesh.H.

Referenced by combineElmBlks(), mergeNodes(), read(), reset(), scaleNodes(), snapNdeCrdsZero(), stitch(), and write().

glbConn

std::vector<std::vector<int> > NEM::MSH::EXOMesh::exoMesh::glbConn

private

Definition at line 737 of file exoMesh.H.

Referenced by addElmBlkByElmIdLst(), combineElmBlks(), exoPopulate(), read(), and reset().

---

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

• exoMesh.H
• exoMesh.C