#include <WriteSLAC.hpp>

Inheritance diagram for moab::WriteSLAC:

Classes
struct	DirichletSetData
struct	MaterialSetData
class	MeshInfo
	contains the general information about a mesh More...
struct	NeumannSetData
Public Member Functions
	WriteSLAC (Interface *impl)
	Constructor.
virtual	~WriteSLAC ()
	Destructor.
ErrorCode	write_file (const char file_name, const bool overwrite, const FileOptions &opts, const EntityHandle output_list, const int num_sets, const std::vector< std::string > &qa_list, const Tag *tag_list=NULL, int num_tags=0, int export_dimension=3)
	writes out a file
Static Public Member Functions
static WriterIface *	factory (Interface *)
Protected Member Functions
ErrorCode	open_file (const char *filename)
	number of dimensions in this file
Private Member Functions
ErrorCode	gather_mesh_information (MeshInfo &mesh_info, std::vector< MaterialSetData > &matset_info, std::vector< NeumannSetData > &neuset_info, std::vector< DirichletSetData > &dirset_info, std::vector< EntityHandle > &matsets, std::vector< EntityHandle > &neusets, std::vector< EntityHandle > &dirsets)
ErrorCode	initialize_file (MeshInfo &mesh_info)
ErrorCode	write_nodes (const int num_nodes, const Range &nodes, const int dimension)
ErrorCode	write_matsets (MeshInfo &mesh_info, std::vector< MaterialSetData > &matset_data, std::vector< NeumannSetData > &neuset_data)
ErrorCode	get_valid_sides (Range &elems, const int sense, WriteSLAC::NeumannSetData &sideset_data)
void	reset_matset (std::vector< MaterialSetData > &matset_info)
ErrorCode	get_neuset_elems (EntityHandle neuset, int current_sense, Range &forward_elems, Range &reverse_elems)
ErrorCode	gather_interior_exterior (MeshInfo &mesh_info, std::vector< MaterialSetData > &matset_data, std::vector< NeumannSetData > &neuset_data)
Private Attributes
Interface *	mbImpl
	interface instance
WriteUtilIface *	mWriteIface
std::string	fileName
	file name
int	ncFile
EntityHandle	mCurrentMeshHandle
	Meshset Handle for the mesh that is currently being read.
Tag	mMaterialSetTag
Tag	mDirichletSetTag
Tag	mNeumannSetTag
Tag	mGlobalIdTag
Tag	mMatSetIdTag
Tag	mEntityMark

Detailed Description

Definition at line 49 of file WriteSLAC.hpp.

Constructor & Destructor Documentation

moab::WriteSLAC::WriteSLAC ( Interface * impl )

Constructor.

get and cache predefined tag handles

Definition at line 69 of file WriteSLAC.cpp.

    : mbImpl(impl), ncFile(0), mCurrentMeshHandle(0)
{
  assert(impl != NULL);

  impl->query_interface( mWriteIface );

  // initialize in case tag_get_handle fails below
  int negone = -1, zero = 0;
  impl->tag_get_handle(MATERIAL_SET_TAG_NAME, 1, MB_TYPE_INTEGER,
                       mMaterialSetTag, MB_TAG_SPARSE|MB_TAG_CREAT, &negone);

  impl->tag_get_handle(DIRICHLET_SET_TAG_NAME, 1, MB_TYPE_INTEGER,
                       mDirichletSetTag, MB_TAG_SPARSE|MB_TAG_CREAT, &negone);

  impl->tag_get_handle(NEUMANN_SET_TAG_NAME, 1, MB_TYPE_INTEGER,
                       mNeumannSetTag, MB_TAG_SPARSE|MB_TAG_CREAT, &negone);

  impl->tag_get_handle(GLOBAL_ID_TAG_NAME, 1, MB_TYPE_INTEGER,
                       mGlobalIdTag, MB_TAG_SPARSE|MB_TAG_CREAT, &zero);
  
  int dum_val = -1;
  impl->tag_get_handle("__matSetIdTag", 1, MB_TYPE_INTEGER, mMatSetIdTag,
                       MB_TAG_DENSE|MB_TAG_CREAT, &dum_val);

  impl->tag_get_handle("WriteSLAC element mark", 1, MB_TYPE_BIT, mEntityMark, MB_TAG_CREAT);

}

moab::WriteSLAC::~WriteSLAC ( ) [virtual]

Destructor.

Definition at line 99 of file WriteSLAC.cpp.

{
  mbImpl->release_interface(mWriteIface);

  mbImpl->tag_delete(mEntityMark);
}

Member Function Documentation

WriterIface * moab::WriteSLAC::factory ( Interface * iface ) [static]

Definition at line 66 of file WriteSLAC.cpp.

  { return new WriteSLAC( iface ); }

ErrorCode moab::WriteSLAC::gather_interior_exterior	(	MeshInfo &	mesh_info,
		std::vector< MaterialSetData > &	matset_data,
		std::vector< NeumannSetData > &	neuset_data
	)		`[private]`

Definition at line 622 of file WriteSLAC.cpp.

{
    // need to assign a tag with the matset id
  Tag matset_id_tag;
  unsigned int i;
  int dum = -1;
  ErrorCode result = mbImpl->tag_get_handle("__matset_id", 4, MB_TYPE_INTEGER, matset_id_tag, MB_TAG_DENSE|MB_TAG_CREAT, &dum);
  if (MB_SUCCESS != result) return result;

  Range::iterator rit;
  mesh_info.num_int_hexes = mesh_info.num_int_tets = 0;
  
  for(i=0; i< matset_data.size(); i++)
  {
    WriteSLAC::MaterialSetData matset = matset_data[i];
    if (matset.moab_type == MBHEX)
      mesh_info.num_int_hexes += matset.elements->size();
    
    else if (matset.moab_type == MBTET)
      mesh_info.num_int_tets += matset.elements->size();
    else {
      std::cout << "WriteSLAC doesn't support elements of type " 
                << CN::EntityTypeName(matset.moab_type) << std::endl;
      continue;
    }
    
    for (rit = matset.elements->begin(); rit != matset.elements->end(); rit++) {
      result = mbImpl->tag_set_data(mMatSetIdTag, &(*rit), 1, &(matset.id));
      if (MB_SUCCESS != result) return result;
    }
  }

    // now go through the neumann sets, pulling out the hexes with faces on the 
    // boundary
  std::vector<EntityHandle>::iterator vit;
  for(i=0; i< neuset_data.size(); i++)
  {
    WriteSLAC::NeumannSetData neuset = neuset_data[i];
    for (vit = neuset.elements.begin(); vit != neuset.elements.end(); vit++) {
      if (TYPE_FROM_HANDLE(*vit) == MBHEX) mesh_info.bdy_hexes.insert(*vit);
      else if (TYPE_FROM_HANDLE(*vit) == MBTET) mesh_info.bdy_tets.insert(*vit);
    }
  }

    // now we have the number of bdy hexes and tets, we know how many interior ones
    // there are too
  mesh_info.num_int_hexes -= mesh_info.bdy_hexes.size();
  mesh_info.num_int_tets -= mesh_info.bdy_tets.size();

  return MB_SUCCESS;
}

ErrorCode moab::WriteSLAC::gather_mesh_information	(	MeshInfo &	mesh_info,
		std::vector< MaterialSetData > &	matset_info,
		std::vector< NeumannSetData > &	neuset_info,
		std::vector< DirichletSetData > &	dirset_info,
		std::vector< EntityHandle > &	matsets,
		std::vector< EntityHandle > &	neusets,
		std::vector< EntityHandle > &	dirsets
	)		`[private]`

Definition at line 216 of file WriteSLAC.cpp.

{

  std::vector<EntityHandle>::iterator vector_iter, end_vector_iter;

  mesh_info.num_nodes = 0;
  mesh_info.num_elements = 0;
  mesh_info.num_matsets = 0;
  
  int id = 0;

  vector_iter= matsets.begin();
  end_vector_iter = matsets.end();

  mesh_info.num_matsets = matsets.size();

  std::vector<EntityHandle> parent_meshsets;

  // clean out the bits for the element mark
  mbImpl->tag_delete(mEntityMark);
  mbImpl->tag_get_handle("WriteSLAC element mark", 1, MB_TYPE_BIT, mEntityMark, MB_TAG_CREAT);

  int highest_dimension_of_element_matsets = 0;

  for(vector_iter = matsets.begin(); vector_iter != matsets.end(); vector_iter++)
  {
       
    WriteSLAC::MaterialSetData matset_data;
    matset_data.elements = new Range;

    //for the purpose of qa records, get the parents of these matsets 
    if( mbImpl->get_parent_meshsets( *vector_iter, parent_meshsets ) != MB_SUCCESS )
      return MB_FAILURE;

    // get all Entity Handles in the mesh set
    Range dummy_range;
    mbImpl->get_entities_by_handle(*vector_iter, dummy_range, true );



    // wait a minute, we are doing some filtering here that doesn't make sense at this level  CJS

      // find the dimension of the last entity in this range
    Range::iterator entity_iter = dummy_range.end();
    entity_iter = dummy_range.end();
    entity_iter--;
    int this_dim = CN::Dimension(TYPE_FROM_HANDLE(*entity_iter));
    entity_iter = dummy_range.begin();
    while (entity_iter != dummy_range.end() &&
           CN::Dimension(TYPE_FROM_HANDLE(*entity_iter)) != this_dim)
      entity_iter++;
    
    if (entity_iter != dummy_range.end())
      std::copy(entity_iter, dummy_range.end(), range_inserter(*(matset_data.elements)));

    assert(matset_data.elements->begin() == matset_data.elements->end() ||
           CN::Dimension(TYPE_FROM_HANDLE(*(matset_data.elements->begin()))) == this_dim);
    
    // get the matset's id
    if(mbImpl->tag_get_data(mMaterialSetTag, &(*vector_iter), 1, &id) != MB_SUCCESS ) {
      mWriteIface->report_error("Couldn't get matset id from a tag for an element matset.");
      return MB_FAILURE;
    }
    
    matset_data.id = id; 
    matset_data.number_attributes = 0;
 
     // iterate through all the elements in the meshset
    Range::iterator elem_range_iter, end_elem_range_iter;
    elem_range_iter = matset_data.elements->begin();
    end_elem_range_iter = matset_data.elements->end();

      // get the entity type for this matset, verifying that it's the same for all elements
      // THIS ASSUMES HANDLES SORT BY TYPE!!!
    EntityType entity_type = TYPE_FROM_HANDLE(*elem_range_iter);
    end_elem_range_iter--;
    if (entity_type != TYPE_FROM_HANDLE(*(end_elem_range_iter++))) {
      mWriteIface->report_error("Entities in matset %i not of common type", id);
      return MB_FAILURE;
    }

    int dimension = -1;
    if(entity_type == MBQUAD || entity_type == MBTRI)
      dimension = 3;   // output shells by default
    else if(entity_type == MBEDGE)
      dimension = 2;
    else
      dimension = CN::Dimension(entity_type);

    if( dimension > highest_dimension_of_element_matsets )
      highest_dimension_of_element_matsets = dimension;

    matset_data.moab_type = mbImpl->type_from_handle(*(matset_data.elements->begin()));
    if (MBMAXTYPE == matset_data.moab_type) return MB_FAILURE;
    
    std::vector<EntityHandle> tmp_conn;
    mbImpl->get_connectivity(&(*(matset_data.elements->begin())), 1, tmp_conn);
    matset_data.element_type = 
      ExoIIUtil::get_element_type_from_num_verts(tmp_conn.size(), entity_type, dimension);
    
    if (matset_data.element_type == EXOII_MAX_ELEM_TYPE) {
      mWriteIface->report_error("Element type in matset %i didn't get set correctly", id);
      return MB_FAILURE;
    }
    
    matset_data.number_nodes_per_element = ExoIIUtil::VerticesPerElement[matset_data.element_type];

    // number of nodes for this matset
    matset_data.number_elements = matset_data.elements->size();

    // total number of elements
    mesh_info.num_elements += matset_data.number_elements;

    // get the nodes for the elements
    mWriteIface->gather_nodes_from_elements(*matset_data.elements, mEntityMark, mesh_info.nodes);

    if(!neusets.empty())
    {
      // if there are neusets, keep track of which elements are being written out
      for(Range::iterator iter = matset_data.elements->begin(); 
          iter != matset_data.elements->end(); ++iter)
      {
        unsigned char bit = 0x1;
        mbImpl->tag_set_data(mEntityMark, &(*iter), 1, &bit);
      }
    }

    matset_info.push_back( matset_data );
  
  }
 

  //if user hasn't entered dimension, we figure it out
  if( mesh_info.num_dim == 0 )
  {
    //never want 1 or zero dimensions
    if( highest_dimension_of_element_matsets < 2 )
      mesh_info.num_dim = 3;
    else
      mesh_info.num_dim = highest_dimension_of_element_matsets;
  }

  Range::iterator range_iter, end_range_iter;
  range_iter = mesh_info.nodes.begin();
  end_range_iter = mesh_info.nodes.end();

  mesh_info.num_nodes = mesh_info.nodes.size(); 

  //------dirsets--------
  
  vector_iter= dirsets.begin();
  end_vector_iter = dirsets.end();

  for(; vector_iter != end_vector_iter; vector_iter++)
  {
    
    WriteSLAC::DirichletSetData dirset_data;
    dirset_data.id = 0;
    dirset_data.number_nodes = 0;

    // get the dirset's id
    if(mbImpl->tag_get_data(mDirichletSetTag,&(*vector_iter), 1,&id) != MB_SUCCESS) {
      mWriteIface->report_error("Couldn't get id tag for dirset %i", id);
      return MB_FAILURE;
    }
    
    dirset_data.id = id; 

    std::vector<EntityHandle> node_vector;
    //get the nodes of the dirset that are in mesh_info.nodes
    if( mbImpl->get_entities_by_handle(*vector_iter, node_vector, true) != MB_SUCCESS ) {
      mWriteIface->report_error("Couldn't get nodes in dirset %i", id);
      return MB_FAILURE;
    }

    std::vector<EntityHandle>::iterator iter, end_iter;
    iter = node_vector.begin();
    end_iter= node_vector.end();
 
    int j=0; 
    unsigned char node_marked = 0;
    ErrorCode result;
    for(; iter != end_iter; iter++)
    {
      if (TYPE_FROM_HANDLE(*iter) != MBVERTEX) continue;
      result = mbImpl->tag_get_data(mEntityMark, &(*iter), 1, &node_marked);
      if (MB_SUCCESS != result) {
        mWriteIface->report_error("Couldn't get mark data.");
        return result;
      }
      
      if(node_marked == 0x1) dirset_data.nodes.push_back( *iter );    
      j++;
    } 
    
    dirset_data.number_nodes = dirset_data.nodes.size(); 
    dirset_info.push_back( dirset_data );
  }

  //------neusets--------
  vector_iter= neusets.begin();
  end_vector_iter = neusets.end();

  for(; vector_iter != end_vector_iter; vector_iter++)
  {
    WriteSLAC::NeumannSetData neuset_data;

    // get the neuset's id
    if(mbImpl->tag_get_data(mNeumannSetTag,&(*vector_iter), 1,&id) != MB_SUCCESS)
      return MB_FAILURE;

    neuset_data.id = id; 
    neuset_data.mesh_set_handle = *vector_iter; 
 
    //get the sides in two lists, one forward the other reverse; starts with forward sense
      // by convention
    Range forward_elems, reverse_elems;
    if(get_neuset_elems(*vector_iter, 0, forward_elems, reverse_elems) == MB_FAILURE)
      return MB_FAILURE;

    ErrorCode result = get_valid_sides(forward_elems, 1, neuset_data);
    if (MB_SUCCESS != result) {
      mWriteIface->report_error("Couldn't get valid sides data.");
      return result;
    }
    result = get_valid_sides(reverse_elems, -1, neuset_data);
    if (MB_SUCCESS != result) {
      mWriteIface->report_error("Couldn't get valid sides data.");
      return result;
    }
    
    neuset_data.number_elements = neuset_data.elements.size(); 
    neuset_info.push_back( neuset_data );
  }

    // get information about interior/exterior tets/hexes, and mark matset ids
  return gather_interior_exterior(mesh_info, matset_info, neuset_info);
}

ErrorCode moab::WriteSLAC::get_neuset_elems	(	EntityHandle	neuset,
		int	current_sense,
		Range &	forward_elems,
		Range &	reverse_elems
	)		`[private]`

Definition at line 1020 of file WriteSLAC.cpp.

{
  Range ss_elems, ss_meshsets;

    // get the sense tag; don't need to check return, might be an error if the tag
    // hasn't been created yet
  Tag sense_tag = 0;
  mbImpl->tag_get_handle("SENSE", 1, MB_TYPE_INTEGER, sense_tag);

    // get the entities in this set
  ErrorCode result = mbImpl->get_entities_by_handle(neuset, ss_elems, true);
  if (MB_FAILURE == result) return result;
  
    // now remove the meshsets into the ss_meshsets; first find the first meshset,
  Range::iterator range_iter = ss_elems.begin();
  while (TYPE_FROM_HANDLE(*range_iter) != MBENTITYSET && range_iter != ss_elems.end())
    range_iter++;
  
    // then, if there are some, copy them into ss_meshsets and erase from ss_elems
  if (range_iter != ss_elems.end()) {
    std::copy(range_iter, ss_elems.end(), range_inserter(ss_meshsets));
    ss_elems.erase(range_iter, ss_elems.end());
  }
  

    // ok, for the elements, check the sense of this set and copy into the right range
    // (if the sense is 0, copy into both ranges)

    // need to step forward on list until we reach the right dimension
  Range::iterator dum_it = ss_elems.end();
  dum_it--;
  int target_dim = CN::Dimension(TYPE_FROM_HANDLE(*dum_it));
  dum_it = ss_elems.begin();
  while (target_dim != CN::Dimension(TYPE_FROM_HANDLE(*dum_it)) &&
         dum_it != ss_elems.end()) 
    dum_it++;

  if (current_sense == 1 || current_sense == 0)
    std::copy(dum_it, ss_elems.end(), range_inserter(forward_elems));
  if (current_sense == -1 || current_sense == 0)
    std::copy(dum_it, ss_elems.end(), range_inserter(reverse_elems));
  
    // now loop over the contained meshsets, getting the sense of those and calling this
    // function recursively
  for (range_iter = ss_meshsets.begin(); range_iter != ss_meshsets.end(); range_iter++) {

      // first get the sense; if it's not there, by convention it's forward
    int this_sense;
    if (0 == sense_tag ||
        MB_FAILURE == mbImpl->tag_get_data(sense_tag, &(*range_iter), 1, &this_sense))
      this_sense = 1;
      
      // now get all the entities on this meshset, with the proper (possibly reversed) sense
    get_neuset_elems(*range_iter, this_sense*current_sense,
                      forward_elems, reverse_elems);
  }
  
  return result;
}

ErrorCode moab::WriteSLAC::get_valid_sides	(	Range &	elems,
		const int	sense,
		WriteSLAC::NeumannSetData &	sideset_data
	)		`[private]`

Definition at line 461 of file WriteSLAC.cpp.

{
    // this is where we see if underlying element of side set element is included in output 

  unsigned char element_marked = 0;
  ErrorCode result;
  for(Range::iterator iter = elems.begin(); iter != elems.end(); iter++)
  {
      // should insert here if "side" is a quad/tri on a quad/tri mesh
    result = mbImpl->tag_get_data(mEntityMark, &(*iter), 1, &element_marked);
    if (MB_SUCCESS != result) {
      mWriteIface->report_error("Couldn't get mark data.");
      return result;
    }
    
    if(element_marked == 0x1)
    {
      neuset_data.elements.push_back( *iter );

        // TJT TODO: the sense should really be # edges + 1or2
      neuset_data.side_numbers.push_back((sense == 1 ? 1 : 2));
    }
    else //then "side" is probably a quad/tri on a hex/tet mesh
    {
      std::vector<EntityHandle> parents;
      int dimension = CN::Dimension( TYPE_FROM_HANDLE(*iter));

        //get the adjacent parent element of "side"
      if( mbImpl->get_adjacencies( &(*iter), 1, dimension+1, false, parents) != MB_SUCCESS ) {
        mWriteIface->report_error("Couldn't get adjacencies for neuset.");
        return MB_FAILURE;
      }
       
      if(!parents.empty())     
      {
          //make sure the adjacent parent element will be output
        for(unsigned int k=0; k<parents.size(); k++)
        {
          result = mbImpl->tag_get_data(mEntityMark, &(parents[k]), 1, &element_marked);
          if (MB_SUCCESS != result) {
            mWriteIface->report_error("Couldn't get mark data.");
            return result;
          }
        
          int side_no, this_sense, this_offset;
          if(element_marked == 0x1 &&
             mbImpl->side_number(parents[k], *iter, side_no, 
                                  this_sense, this_offset) == MB_SUCCESS &&
             this_sense == sense) {
            neuset_data.elements.push_back(parents[k]);
            neuset_data.side_numbers.push_back(side_no+1);
            break;
          }
        }
      }
      else
      {
        mWriteIface->report_error("No parent element exists for element in neuset %i", neuset_data.id);
        return MB_FAILURE;
      }
    }
  }

  return MB_SUCCESS;
}

ErrorCode moab::WriteSLAC::initialize_file ( MeshInfo & mesh_info ) [private]

Definition at line 874 of file WriteSLAC.cpp.

{
    // perform the initializations

  int coord_size = -1, ncoords = -1;
    // initialization to avoid warnings on linux
  int hexinterior = -1, hexinteriorsize, hexexterior = -1, hexexteriorsize = -1;
  int tetinterior = -1, tetinteriorsize, tetexterior = -1, tetexteriorsize = -1;
  
  if (nc_def_dim(ncFile, "coord_size", (size_t)mesh_info.num_dim, &coord_size) != NC_NOERR)
  {
    mWriteIface->report_error("WriteSLAC: failed to define number of dimensions");
    return (MB_FAILURE);
  }

  if (nc_def_dim(ncFile, "ncoords", (size_t)mesh_info.num_nodes, &ncoords) != NC_NOERR)
  {
    mWriteIface->report_error("WriteSLAC: failed to define number of nodes");
    return (MB_FAILURE);
  }

  if (0 != mesh_info.num_int_hexes &&
      nc_def_dim(ncFile, "hexinterior", (size_t)mesh_info.num_int_hexes, &hexinterior) != NC_NOERR)
  {
    mWriteIface->report_error("WriteSLAC: failed to define number of interior hex elements");
    return (MB_FAILURE);
  }

  if (nc_def_dim(ncFile, "hexinteriorsize", (size_t)9, &hexinteriorsize) != NC_NOERR)
  {
    mWriteIface->report_error("WriteSLAC: failed to define interior hex element size");
    return (MB_FAILURE);
  }

  if (0 != mesh_info.bdy_hexes.size() &&
      nc_def_dim(ncFile, "hexexterior", (size_t)mesh_info.bdy_hexes.size(), &hexexterior) != NC_NOERR)
  {
    mWriteIface->report_error("WriteSLAC: failed to define number of exterior hex elements");
    return (MB_FAILURE);
  }

  if (nc_def_dim(ncFile, "hexexteriorsize", (size_t)15, &hexexteriorsize) != NC_NOERR)
  {
    mWriteIface->report_error("WriteSLAC: failed to define exterior hex element size");
    return (MB_FAILURE);
  }

  if (0 != mesh_info.num_int_tets &&
      nc_def_dim(ncFile, "tetinterior", (size_t)mesh_info.num_int_tets, &tetinterior) != NC_NOERR)
  {
    mWriteIface->report_error("WriteSLAC: failed to define number of interior tet elements");
    return (MB_FAILURE);
  }

  if (nc_def_dim(ncFile, "tetinteriorsize", (size_t)5, &tetinteriorsize) != NC_NOERR)
  {
    mWriteIface->report_error("WriteSLAC: failed to define interior tet element size");
    return (MB_FAILURE);
  }

  if (0 != mesh_info.bdy_tets.size() &&
      nc_def_dim(ncFile, "tetexterior", (size_t)mesh_info.bdy_tets.size(), &tetexterior) != NC_NOERR)
  {
    mWriteIface->report_error("WriteSLAC: failed to define number of exterior tet elements");
    return (MB_FAILURE);
  }

  if (nc_def_dim(ncFile, "tetexteriorsize", (size_t)9, &tetexteriorsize) != NC_NOERR)
  {
    mWriteIface->report_error("WriteSLAC: failed to define exterior tet element size");
    return (MB_FAILURE);
  }

/* ...and some variables */

  int dims[2];
  dims[0] = hexinterior;
  dims[1] = hexinteriorsize;
  int dum_var;
  if (0 != mesh_info.num_int_hexes &&
      NC_NOERR != nc_def_var(ncFile, "hexahedron_interior", NC_LONG, 2, dims, &dum_var))
  {
    mWriteIface->report_error("WriteSLAC: failed to create connectivity array for interior hexes.");
    return (MB_FAILURE);
  }

  dims[0] = hexexterior;
  dims[1] = hexexteriorsize;
  if (0 != mesh_info.bdy_hexes.size() &&
      NC_NOERR != nc_def_var(ncFile, "hexahedron_exterior", NC_LONG, 2, dims, &dum_var))
  {
    mWriteIface->report_error("WriteSLAC: failed to create connectivity array for exterior hexes.");
    return (MB_FAILURE);
  }

  dims[0] = tetinterior;
  dims[1] = tetinteriorsize;
  if (0 != mesh_info.num_int_tets &&
      NC_NOERR != nc_def_var(ncFile, "tetrahedron_exterior", NC_LONG, 2, dims, &dum_var))
  {
    mWriteIface->report_error("WriteSLAC: failed to create connectivity array for interior tets.");
    return (MB_FAILURE);
  }

  dims[0] = tetexterior;
  dims[1] = tetexteriorsize;
  if (0 != mesh_info.bdy_tets.size() &&
      NC_NOERR != nc_def_var(ncFile, "tetrahedron_exterior", NC_LONG, 2, dims, &dum_var))
  {
    mWriteIface->report_error("WriteSLAC: failed to create connectivity array for exterior tets.");
    return (MB_FAILURE);
  }

/* node coordinate arrays: */

  dims[0] = ncoords;
  dims[1] = coord_size;
  if (NC_NOERR != nc_def_var(ncFile, "coords", NC_DOUBLE, 2, dims, &dum_var))
   {
     mWriteIface->report_error("WriteSLAC: failed to define node coordinate array");
     return (MB_FAILURE);
   }

   return MB_SUCCESS;
}

ErrorCode moab::WriteSLAC::open_file ( const char * filename ) [protected]

number of dimensions in this file

open a file for writing

Definition at line 1001 of file WriteSLAC.cpp.

{
   // not a valid filname
   if(strlen((const char*)filename) == 0)
   {
     mWriteIface->report_error("Output filename not specified");
      return MB_FAILURE;
   }

   int fail = nc_create(filename, NC_CLOBBER, &ncFile);
   // file couldn't be opened
   if(NC_NOERR != fail) 
   {
     mWriteIface->report_error("Cannot open %s", filename);
     return MB_FAILURE;
   }
   return MB_SUCCESS;
}

void moab::WriteSLAC::reset_matset ( std::vector< MaterialSetData > & matset_info ) [private]

Definition at line 106 of file WriteSLAC.cpp.

{
  std::vector<WriteSLAC::MaterialSetData>::iterator iter;
  
  for (iter = matset_info.begin(); iter != matset_info.end(); iter++)
  {
    delete (*iter).elements;
  }
}

ErrorCode moab::WriteSLAC::write_file	(	const char *	file_name,
		const bool	overwrite,
		const FileOptions &	opts,
		const EntityHandle *	output_list,
		const int	num_sets,
		const std::vector< std::string > &	qa_list,
		const Tag *	tag_list = `NULL`,
		int	num_tags = `0`,
		int	export_dimension = `3`
	)		`[virtual]`

writes out a file

Implements moab::WriterIface.

Definition at line 116 of file WriteSLAC.cpp.

{
  assert(0 != mMaterialSetTag &&
         0 != mNeumannSetTag &&
         0 != mDirichletSetTag);

    // check the file name
  if (NULL == strstr(file_name, ".ncdf"))
    return MB_FAILURE;

  std::vector<EntityHandle> matsets, dirsets, neusets, entities;

  fileName = file_name;
  
    // separate into material sets, dirichlet sets, neumann sets

  if (num_sets == 0) {
      // default to all defined sets
    Range this_range;
    mbImpl->get_entities_by_type_and_tag(0, MBENTITYSET, &mMaterialSetTag, NULL, 1, this_range);
    std::copy(this_range.begin(), this_range.end(), std::back_inserter(matsets));
    this_range.clear();
    mbImpl->get_entities_by_type_and_tag(0, MBENTITYSET, &mDirichletSetTag, NULL, 1, this_range);
    std::copy(this_range.begin(), this_range.end(), std::back_inserter(dirsets));
    this_range.clear();
    mbImpl->get_entities_by_type_and_tag(0, MBENTITYSET, &mNeumannSetTag, NULL, 1, this_range);
    std::copy(this_range.begin(), this_range.end(), std::back_inserter(neusets));
  }
  else {
    int dummy;
    for (const EntityHandle *iter = ent_handles; iter < ent_handles+num_sets; iter++) 
    {
      if (MB_SUCCESS == mbImpl->tag_get_data(mMaterialSetTag, &(*iter), 1, &dummy))
        matsets.push_back(*iter);
      else if (MB_SUCCESS == mbImpl->tag_get_data(mDirichletSetTag, &(*iter), 1, &dummy))
        dirsets.push_back(*iter);
      else if (MB_SUCCESS == mbImpl->tag_get_data(mNeumannSetTag, &(*iter), 1, &dummy))
        neusets.push_back(*iter);
    }
  }
  
    // if there is nothing to write just return.
  if (matsets.empty() && dirsets.empty() && neusets.empty())
    return MB_FILE_WRITE_ERROR;

  std::vector<WriteSLAC::MaterialSetData> matset_info;
  std::vector<WriteSLAC::DirichletSetData> dirset_info;
  std::vector<WriteSLAC::NeumannSetData> neuset_info;

  MeshInfo mesh_info;
  
  matset_info.clear();
  if(gather_mesh_information(mesh_info, matset_info, neuset_info, dirset_info,
                             matsets, neusets, dirsets) != MB_SUCCESS)
  {
    reset_matset(matset_info);
    return MB_FAILURE;
  }


  // try to open the file after gather mesh info succeeds
  int fail = nc_create(file_name, overwrite ? NC_CLOBBER : NC_NOCLOBBER, &ncFile);
  if (NC_NOERR != fail) {
    reset_matset(matset_info);
    return MB_FAILURE;
  }

  if( initialize_file(mesh_info) != MB_SUCCESS)
  {
    reset_matset(matset_info);
    return MB_FAILURE;
  }

  if( write_nodes(mesh_info.num_nodes, mesh_info.nodes, mesh_info.num_dim) != MB_SUCCESS )
  {
    reset_matset(matset_info);
    return MB_FAILURE;
  }

  if( write_matsets(mesh_info, matset_info, neuset_info) )
  {
    reset_matset(matset_info);
    return MB_FAILURE;
  }

  fail = nc_close(ncFile);
  if (NC_NOERR != fail) 
    return MB_FAILURE;
  
  return MB_SUCCESS;
}

ErrorCode moab::WriteSLAC::write_matsets	(	MeshInfo &	mesh_info,
		std::vector< MaterialSetData > &	matset_data,
		std::vector< NeumannSetData > &	neuset_data
	)		`[private]`

Definition at line 677 of file WriteSLAC.cpp.

{

  unsigned int i;
  std::vector<int> connect;
  const EntityHandle *connecth;
  int num_connecth;
  ErrorCode result;
  
    // first write the interior hexes
  int hex_conn = -1;
  std::vector<int> dims;
  if (mesh_info.bdy_hexes.size() != 0 || mesh_info.num_int_hexes != 0) {
    GET_VAR("hexahedron_interior", hex_conn, dims);
    if (-1 == hex_conn) return MB_FAILURE;
  }
  connect.reserve(13);
  Range::iterator rit;

  int elem_num = 0;
  WriteSLAC::MaterialSetData matset;
  size_t start[2] = {0, 0}, count[2] = {1, 1};
  int fail;
  for (i = 0; i < matset_data.size(); i++) {
    matset = matset_data[i];
    if (matset.moab_type != MBHEX) continue;
    
    int id = matset.id;
    connect[0] = id;

    for (rit = matset.elements->begin(); rit != matset.elements->end(); rit++) {
        // skip if it's on the bdy
      if (mesh_info.bdy_hexes.find(*rit) != mesh_info.bdy_hexes.end()) continue;
      
        // get the connectivity of this element
      result = mbImpl->get_connectivity(*rit, connecth, num_connecth);
      if (MB_SUCCESS != result) return result;
      
        // get the vertex ids
      result = mbImpl->tag_get_data(mGlobalIdTag, connecth, num_connecth, &connect[1]);
      if (MB_SUCCESS != result) return result;
      
        // put the variable at the right position
      start[0] = elem_num++;
      count[1] = 9;
      
        // write the data
      fail = nc_put_vara_int(ncFile, hex_conn, start, count, &connect[0]);
      if(NC_NOERR != fail)
        return MB_FAILURE;
    }
  }

  int tet_conn = -1;
  if (mesh_info.bdy_tets.size() != 0 || mesh_info.num_int_tets != 0) {
    GET_VAR("tetrahedron_interior", tet_conn, dims);
    if (-1 == tet_conn) return MB_FAILURE;
  }

    // now the interior tets
  elem_num = 0;
  for (i = 0; i < matset_data.size(); i++) {
    matset = matset_data[i];
    if (matset.moab_type != MBTET) continue;
    
    int id = matset.id;
    connect[0] = id;
    elem_num = 0;
    for (rit = matset.elements->begin(); rit != matset.elements->end(); rit++) {
        // skip if it's on the bdy
      if (mesh_info.bdy_tets.find(*rit) != mesh_info.bdy_tets.end()) continue;
      
        // get the connectivity of this element
      result = mbImpl->get_connectivity(*rit, connecth, num_connecth);
      if (MB_SUCCESS != result) return result;
      
        // get the vertex ids
      result = mbImpl->tag_get_data(mGlobalIdTag, connecth, num_connecth, &connect[1]);
      if (MB_SUCCESS != result) return result;
      
        // put the variable at the right position
      start[0] = elem_num++;
      count[1] = 5;
      fail = nc_put_vara_int(ncFile, tet_conn, start, count, &connect[0]);
        // write the data
      if(NC_NOERR != fail)
        return MB_FAILURE;
    }
  }
  
    // now the exterior hexes
  if (mesh_info.bdy_hexes.size() != 0) {
    hex_conn = -1;
    GET_VAR("hexahedron_exterior", hex_conn, dims);
    if (-1 == hex_conn) return MB_FAILURE;

    connect.reserve(15);
    elem_num = 0;

      // write the elements
    for (rit = mesh_info.bdy_hexes.begin(); rit != mesh_info.bdy_hexes.end(); rit++) {
      
        // get the material set for this hex
        result = mbImpl->tag_get_data(mMatSetIdTag, &(*rit), 1, &connect[0]);
        if (MB_SUCCESS != result) return result;

          // get the connectivity of this element
        result = mbImpl->get_connectivity(*rit, connecth, num_connecth);
        if (MB_SUCCESS != result) return result;
      
          // get the vertex ids
        result = mbImpl->tag_get_data(mGlobalIdTag, connecth, num_connecth, &connect[1]);
        if (MB_SUCCESS != result) return result;

          // preset side numbers
        for (i = 9; i < 15; i++)
          connect[i] = -1;

          // now write the side numbers
        for (i = 0; i < neuset_data.size(); i++) {
          std::vector<EntityHandle>::iterator vit = 
            std::find(neuset_data[i].elements.begin(), neuset_data[i].elements.end(), *rit);
          while (vit != neuset_data[i].elements.end()) {
              // have a side - get the side # and put in connect array
            int side_no = neuset_data[i].side_numbers[vit-neuset_data[i].elements.begin()];
            connect[9+side_no] = neuset_data[i].id;
            vit++;
            vit = std::find(vit, neuset_data[i].elements.end(), *rit);
          }
        }
      
          // put the variable at the right position
        start[0] = elem_num++;
        count[1] = 15;
        fail = nc_put_vara_int(ncFile, hex_conn, start, count, &connect[0]);
          // write the data
        if(NC_NOERR != fail)
          return MB_FAILURE;
    }
  }

    // now the exterior tets
  if (mesh_info.bdy_tets.size() != 0) {
    tet_conn = -1;
    GET_VAR("tetrahedron_exterior", tet_conn, dims);
    if (-1 == tet_conn) return MB_FAILURE;

    connect.reserve(9);
    elem_num = 0;

      // write the elements
    for (rit = mesh_info.bdy_tets.begin(); rit != mesh_info.bdy_tets.end(); rit++) {
      
        // get the material set for this tet
        result = mbImpl->tag_get_data(mMatSetIdTag, &(*rit), 1, &connect[0]);
        if (MB_SUCCESS != result) return result;

          // get the connectivity of this element
        result = mbImpl->get_connectivity(*rit, connecth, num_connecth);
        if (MB_SUCCESS != result) return result;
      
          // get the vertex ids
        result = mbImpl->tag_get_data(mGlobalIdTag, connecth, num_connecth, &connect[1]);
        if (MB_SUCCESS != result) return result;

          // preset side numbers
        for (i = 5; i < 9; i++)
          connect[i] = -1;

          // now write the side numbers
        for (i = 0; i < neuset_data.size(); i++) {
          std::vector<EntityHandle>::iterator vit = 
            std::find(neuset_data[i].elements.begin(), neuset_data[i].elements.end(), *rit);
          while (vit != neuset_data[i].elements.end()) {
              // have a side - get the side # and put in connect array
            int side_no = neuset_data[i].side_numbers[vit-neuset_data[i].elements.begin()];
            connect[5+side_no] = neuset_data[i].id;
            vit++;
            vit = std::find(vit, neuset_data[i].elements.end(), *rit);
          }
        }
      
          // put the variable at the right position
        start[0] = elem_num++;
        count[1] = 9;
        fail = nc_put_vara_int(ncFile, tet_conn, start, count, &connect[0]);
          // write the data
        if(NC_NOERR != fail)
          return MB_FAILURE;
    }
  }

  return MB_SUCCESS;
}

ErrorCode moab::WriteSLAC::write_nodes	(	const int	num_nodes,
		const Range &	nodes,
		const int	dimension
	)		`[private]`

Definition at line 528 of file WriteSLAC.cpp.

{
  //see if should transform coordinates
  ErrorCode result;
  Tag trans_tag;
  result = mbImpl->tag_get_handle( MESH_TRANSFORM_TAG_NAME, 16, MB_TYPE_DOUBLE, trans_tag);
  bool transform_needed = true;
  if( result == MB_TAG_NOT_FOUND )
    transform_needed = false;

  int num_coords_to_fill = transform_needed ? 3 : dimension;

  std::vector<double*> coord_arrays(3);
  coord_arrays[0] = new double[num_nodes];
  coord_arrays[1] = new double[num_nodes];
  coord_arrays[2] = NULL;

  if( num_coords_to_fill == 3 ) 
    coord_arrays[2] = new double[num_nodes];
 
  result = mWriteIface->get_node_coords(dimension, num_nodes, nodes, 
                                        mGlobalIdTag, 0, coord_arrays);
  if(result != MB_SUCCESS)
  {
    delete [] coord_arrays[0];
    delete [] coord_arrays[1];
    if(coord_arrays[2]) delete [] coord_arrays[2];
    return result;
  }

  if( transform_needed )
  {
    double trans_matrix[16]; 
    const EntityHandle mesh = 0;
    result = mbImpl->tag_get_data( trans_tag, &mesh, 1, trans_matrix ); 
    if (MB_SUCCESS != result) {
      mWriteIface->report_error("Couldn't get transform data.");
      return result;
    }
      
    for( int i=0; i<num_nodes; i++)
    {

      double vec1[3];
      double vec2[3];

      vec2[0] =  coord_arrays[0][i];
      vec2[1] =  coord_arrays[1][i];
      vec2[2] =  coord_arrays[2][i];

      for( int row=0; row<3; row++ )
      {
        vec1[row] = 0.0;
        for( int col = 0; col<3; col++ )
        {
          vec1[row] += ( trans_matrix[ (row*4)+col ] * vec2[col] );
        }
      }

      coord_arrays[0][i] = vec1[0];
      coord_arrays[1][i] = vec1[1];
      coord_arrays[2][i] = vec1[2];

    }
  }


  // write the nodes 
  int nc_var = -1;
  std::vector<int> dims;
  GET_VAR("coords", nc_var, dims);
  if (-1 == nc_var) return MB_FAILURE;
  size_t start[2] = {0, 0}, count[2] = {static_cast<size_t>(num_nodes), 1};
  int fail = nc_put_vara_double(ncFile, nc_var, start, count, coord_arrays[0]) != 0;
  if (NC_NOERR != fail) 
    return MB_FAILURE;
  start[1] = 1;
  fail = nc_put_vara_double(ncFile, nc_var, start, count, coord_arrays[1]) != 0;
  if (NC_NOERR != fail) 
    return MB_FAILURE;
  start[1] = 2;
  fail = nc_put_vara_double(ncFile, nc_var, start, count, coord_arrays[2]) != 0;
  if (NC_NOERR != fail) 
  
  delete [] coord_arrays[0];
  delete [] coord_arrays[1];
  if(coord_arrays[2]) 
    delete [] coord_arrays[2];

  return MB_SUCCESS;

}