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950 | // *****************************************************************************
/*!
\file src/IO/ExodusIIMeshReader.cpp
\copyright 2012-2015 J. Bakosi,
2016-2018 Los Alamos National Security, LLC.,
2019-2021 Triad National Security, LLC.
All rights reserved. See the LICENSE file for details.
\brief ExodusII mesh reader
\details ExodusII mesh reader class definition.
*/
// *****************************************************************************
#include <numeric>
#include "NoWarning/exodusII.hpp"
#include "ExodusIIMeshReader.hpp"
#include "ContainerUtil.hpp"
#include "Exception.hpp"
#include "UnsMesh.hpp"
#include "Reorder.hpp"
using tk::ExodusIIMeshReader;
ExodusIIMeshReader::ExodusIIMeshReader( const std::string& filename,
int cpuwordsize,
int iowordsize ) :
m_filename( filename ),
m_cpuwordsize( cpuwordsize ),
m_iowordsize( iowordsize ),
m_inFile( 0 ),
m_nnode( 0 ),
m_neblk( 0 ),
m_neset( 0 ),
m_from( 0 ),
m_till( 0 ),
m_blockid(),
m_blockid_by_type( ExoNnpe.size() ),
m_nel( ExoNnpe.size() ),
m_elemblocks(),
m_tri()
// *****************************************************************************
// Constructor: open Exodus II file
//! \param[in] filename File to open as ExodusII file
//! \param[in] cpuwordsize Set CPU word size, see ExodusII documentation
//! \param[in] iowordsize Set I/O word size, see ExodusII documentation
// *****************************************************************************
{
// Increase verbosity from ExodusII library in debug mode
#ifndef NDEBUG
ex_opts( EX_DEBUG | EX_VERBOSE );
#endif
float version;
m_inFile = ex_open( filename.c_str(), EX_READ, &cpuwordsize, &iowordsize,
&version );
ErrChk( m_inFile > 0, "Failed to open ExodusII file: " + filename );
}
ExodusIIMeshReader::~ExodusIIMeshReader() noexcept
// *****************************************************************************
// Destructor
// *****************************************************************************
{
if ( ex_close(m_inFile) < 0 )
printf( ">>> WARNING: Failed to close ExodusII file: %s\n",
m_filename.c_str() );
}
void
ExodusIIMeshReader::readMesh( UnsMesh& mesh )
// *****************************************************************************
// Read ExodusII mesh file
//! \param[in] mesh Unstructured mesh object
// *****************************************************************************
{
readHeader( mesh );
readAllElements( mesh );
readAllNodes( mesh );
readSidesetFaces( mesh.bface(), mesh.faceid() );
readTimeValues( mesh.vartimes() );
readNodeVarNames( mesh.nodevarnames() );
readNodeScalars( mesh.vartimes().size(),
mesh.nodevarnames().size(),
mesh.nodevars() );
}
void
ExodusIIMeshReader::readGraph( UnsMesh& mesh )
// *****************************************************************************
// Read only connectivity graph from file
//! \param[in] mesh Unstructured mesh object
// *****************************************************************************
{
readHeader( mesh );
readAllElements( mesh );
}
void
ExodusIIMeshReader::readMeshPart(
std::vector< std::size_t >& ginpoel,
std::vector< std::size_t >& inpoel,
std::vector< std::size_t >& triinp,
std::unordered_map< std::size_t, std::size_t >& lid,
tk::UnsMesh::Coords& coord,
int numpes, int mype )
// *****************************************************************************
// Read a part of the mesh (graph and coordinates) from ExodusII file
//! \param[in,out] ginpoel Container to store element connectivity of this PE's
//! chunk of the mesh (global ids)
//! \param[in,out] inpoel Container to store element connectivity with local
//! node IDs of this PE's mesh chunk
//! \param[in,out] triinp Container to store triangle element connectivity
//! (if exists in file) with global node indices
//! \param[in,out] lid Container to store global->local node IDs of elements of
//! this PE's mesh chunk
//! \param[in,out] coord Container to store coordinates of mesh nodes of this
//! PE's mesh chunk
//! \param[in] numpes Total number of PEs (default n = 1, for a single-CPU read)
//! \param[in] mype This PE (default m = 0, for a single-CPU read)
// *****************************************************************************
{
Assert( mype < numpes, "Invalid input: PE id must be lower than NumPEs" );
Assert( ginpoel.empty() && inpoel.empty() && lid.empty() &&
coord[0].empty() && coord[1].empty() && coord[2].empty(),
"Containers to store mesh must be empty" );
// Read info on element blocks from ExodusII file
readElemBlockIDs();
// Get number of number of tetrahedron elements in file
auto nel = nelem( tk::ExoElemType::TET );
// Compute extents of element IDs of this PE's mesh chunk to read
auto npes = static_cast< std::size_t >( numpes );
auto pe = static_cast< std::size_t >( mype );
auto chunk = nel / npes;
m_from = pe * chunk;
m_till = m_from + chunk;
if (pe == npes-1) m_till += nel % npes;
// Read tetrahedron connectivity between from and till
readElements( {{m_from, m_till-1}}, tk::ExoElemType::TET, ginpoel );
// Compute local data from global mesh connectivity
std::vector< std::size_t > gid;
std::tie( inpoel, gid, lid ) = tk::global2local( ginpoel );
// Read this PE's chunk of the mesh node coordinates from file
coord = readCoords( gid );
// Generate set of unique faces
tk::UnsMesh::FaceSet faces;
for (std::size_t e=0; e<ginpoel.size()/4; ++e)
for (std::size_t f=0; f<4; ++f) {
const auto& tri = tk::expofa[f];
faces.insert( {{{ ginpoel[ e*4+tri[0] ],
ginpoel[ e*4+tri[1] ],
ginpoel[ e*4+tri[2] ] }}} );
}
// Read triangle element connectivity (all triangle blocks in file)
auto ntri = nelem( tk::ExoElemType::TRI );
if ( ntri !=0 ) readElements( {{0,ntri-1}}, tk::ExoElemType::TRI, triinp );
// Keep triangles shared in (partially-read) tetrahedron mesh
std::vector< std::size_t > triinp_own;
std::size_t ltrid = 0; // local triangle id
for (std::size_t e=0; e<triinp.size()/3; ++e) {
auto i = faces.find( {{ triinp[e*3+0], triinp[e*3+1], triinp[e*3+2] }} );
if (i != end(faces)) {
m_tri[e] = ltrid++; // generate global->local triangle ids
triinp_own.push_back( triinp[e*3+0] );
triinp_own.push_back( triinp[e*3+1] );
triinp_own.push_back( triinp[e*3+2] );
}
}
triinp = std::move(triinp_own);
}
std::array< std::vector< tk::real >, 3 >
ExodusIIMeshReader::readCoords( const std::vector< std::size_t >& gid ) const
// *****************************************************************************
// Read coordinates of a number of mesh nodes from ExodusII file
//! \param[in] gid Global node IDs whose coordinates to read
//! \return Vector of node coordinates read from file
// *****************************************************************************
{
// Read node coordinates from file with global node IDs given in gid
return readNodes( gid );
}
std::size_t
ExodusIIMeshReader::readHeader()
// *****************************************************************************
// Read ExodusII header without setting mesh size
//! \return Number of nodes in mesh
// *****************************************************************************
{
char title[MAX_LINE_LENGTH+1];
int ndim, n, nnodeset, nelemset, nnode, neblk;
ErrChk(
ex_get_init( m_inFile, title, &ndim, &nnode, &n, &neblk, &nnodeset,
&nelemset ) == 0,
"Failed to read header from ExodusII file: " + m_filename );
ErrChk( nnode > 0,
"Number of nodes read from ExodusII file must be larger than zero" );
ErrChk( neblk > 0,
"Number of element blocks read from ExodusII file must be larger "
"than zero" );
ErrChk( ndim == 3, "Need a 3D mesh from ExodusII file " + m_filename );
m_neblk = static_cast< std::size_t >( neblk );
m_neset = static_cast< std::size_t >( nelemset );
return static_cast< std::size_t >( nnode );
}
void
ExodusIIMeshReader::readHeader( UnsMesh& mesh )
// *****************************************************************************
// Read ExodusII header with setting mesh size
//! \param[in] mesh Unstructured mesh object
// *****************************************************************************
{
// Read ExodusII file header and set mesh graph size
mesh.size() = m_nnode = static_cast< std::size_t >( readHeader() );
}
void
ExodusIIMeshReader::readAllNodes( UnsMesh& mesh ) const
// *****************************************************************************
// Read all node coordinates from ExodusII file
//! \param[in] mesh Unstructured mesh object
// *****************************************************************************
{
mesh.x().resize( m_nnode );
mesh.y().resize( m_nnode );
mesh.z().resize( m_nnode );
ErrChk( ex_get_coord( m_inFile, mesh.x().data(), mesh.y().data(),
mesh.z().data() ) == 0,
"Failed to read coordinates from ExodusII file: " + m_filename );
}
void
ExodusIIMeshReader::readNode( std::size_t fid,
std::size_t mid,
std::vector< tk::real >& x,
std::vector< tk::real >& y,
std::vector< tk::real >& z ) const
// *****************************************************************************
// Read coordinates of a single mesh node from ExodusII file
//! \param[in] fid Node id in file whose coordinates to read
//! \param[in] mid Node id in memory to which to put new cordinates
//! \param[in,out] x Vector of x coordinates to push to
//! \param[in,out] y Vector of y coordinates to push to
//! \param[in,out] z Vector of z coordinates to push to
// *****************************************************************************
{
Assert( x.size() == y.size() && x.size() == z.size(), "Size mismatch" );
Assert( mid < x.size() && mid < y.size() && mid < z.size(),
"Indexing out of bounds" );
readNode( fid, x[mid], y[mid], z[mid] );
}
void
ExodusIIMeshReader::readNode( std::size_t id,
std::array< tk::real, 3 >& coord ) const
// *****************************************************************************
// Read coordinates of a single mesh node from ExodusII file
//! \param[in] id Node id whose coordinates to read
//! \param[in,out] coord Array of x, y, and z coordinates
// *****************************************************************************
{
readNode( id, coord[0], coord[1], coord[2] );
}
void
ExodusIIMeshReader::readNode( std::size_t id,
tk::real& x,
tk::real& y,
tk::real& z ) const
// *****************************************************************************
// Read coordinates of a single mesh node from file
//! \param[in] id Node id whose coordinates to read
//! \param[in,out] x X coordinate to write to
//! \param[in,out] y Y coordinate to write to
//! \param[in,out] z Z coordinate to write to
// *****************************************************************************
{
ErrChk(
ex_get_partial_coord( m_inFile, static_cast<int64_t>(id)+1, 1,
&x, &y, &z ) == 0,
"Failed to read coordinates of node " + std::to_string(id) +
" from ExodusII file: " + m_filename );
}
std::array< std::vector< tk::real >, 3 >
ExodusIIMeshReader::readNodes( const std::vector< std::size_t >& gid ) const
// *****************************************************************************
// Read coordinates of a number of mesh nodes from ExodusII file
//! \param[in] gid Node IDs whose coordinates to read
//! \return Mesh node coordinates
// *****************************************************************************
{
std::vector< tk::real > px( gid.size() ), py( gid.size() ), pz( gid.size() );
std::size_t i=0;
for (auto g : gid) readNode( g, i++, px, py, pz );
return {{ std::move(px), std::move(py), std::move(pz) }};
}
std::size_t
ExodusIIMeshReader::readElemBlockIDs()
// *****************************************************************************
// Read element block IDs from ExodusII file
//! \return Total number of nodes in mesh
// *****************************************************************************
{
// Read ExodusII file header
auto nnode = readHeader();<--- Variable 'nnode' is assigned a value that is never used.
std::vector< int > bid( m_neblk );
// Read element block ids
ErrChk( ex_get_ids( m_inFile, EX_ELEM_BLOCK, bid.data()) == 0,
"Failed to read element block ids from ExodusII file: " +
m_filename );
m_elemblocks.clear();
m_nel.clear();
m_nel.resize( ExoNnpe.size() );
m_blockid_by_type.clear();
m_blockid_by_type.resize( ExoNnpe.size() );
// Fill element block ID vector
for (auto id : bid) {
char eltype[MAX_STR_LENGTH+1];
int n, nnpe, nattr;
// Read element block information
ErrChk( ex_get_block( m_inFile, EX_ELEM_BLOCK, id, eltype, &n, &nnpe,
&nattr, nullptr, nullptr ) == 0,
"Failed to read element block information from ExodusII file: " +
m_filename );
// Store ExodusII element block ID
m_blockid.push_back( id );
auto nel = static_cast< std::size_t >( n );
// Store info on ExodusII element blocks
if (nnpe == 4) { // tetrahedra
m_elemblocks.push_back( { ExoElemType::TET, nel } );
auto e = static_cast< std::size_t >( ExoElemType::TET );
m_blockid_by_type[ e ].push_back( id );
m_nel[ e ].push_back( nel );
Assert( m_blockid_by_type[e].size() == m_nel[e].size(), "Size mismatch" );
} else if (nnpe == 3) { // triangles
m_elemblocks.push_back( { ExoElemType::TRI, nel } );
auto e = static_cast< std::size_t >( ExoElemType::TRI );
m_blockid_by_type[ e ].push_back( id );
m_nel[ e ].push_back( nel );
Assert( m_blockid_by_type[e].size() == m_nel[e].size(), "Size mismatch" );
}
}
return nnode;
}
void
ExodusIIMeshReader::readAllElements( UnsMesh& mesh )
// *****************************************************************************
// Read all element blocks and mesh connectivity from ExodusII file
//! \param[inout] mesh Unstructured mesh object to store mesh in
// *****************************************************************************
{
// Read element block ids
readElemBlockIDs();
for (auto id : m_blockid) {
char eltype[MAX_STR_LENGTH+1];
int nel, nnpe, nattr;
// Read element block information
ErrChk( ex_get_block( m_inFile, EX_ELEM_BLOCK, id, eltype, &nel, &nnpe,
&nattr, nullptr, nullptr ) == 0,
"Failed to read element block information from ExodusII file: " +
m_filename );
// Read element connectivity
auto connectsize = static_cast< std::size_t >( nel*nnpe );
if (nnpe == 4) { // tetrahedra
std::vector< int > inpoel( connectsize );
ErrChk( ex_get_conn( m_inFile, EX_ELEM_BLOCK, id, inpoel.data(),
nullptr, nullptr ) == 0,
"Failed to read " + std::string(eltype) + " element connectivity from "
"ExodusII file: " + m_filename );
for (auto n : inpoel)
mesh.tetinpoel().push_back( static_cast< std::size_t >( n ) );
} else if (nnpe == 3) { // triangles
std::vector< int > inpoel( connectsize );
ErrChk( ex_get_conn( m_inFile, EX_ELEM_BLOCK, id, inpoel.data(),
nullptr, nullptr ) == 0,
"Failed to read " + std::string(eltype) + " element connectivity from "
"ExodusII file: " + m_filename );
for (auto n : inpoel)
mesh.triinpoel().push_back( static_cast< std::size_t >( n ) );
}
}
// Shift node IDs to start from zero
shiftToZero( mesh.triinpoel() );
shiftToZero( mesh.tetinpoel() );
}
void
ExodusIIMeshReader::readElements( const std::array< std::size_t, 2 >& ext,
tk::ExoElemType elemtype,
std::vector< std::size_t >& conn ) const
// *****************************************************************************
// Read element connectivity of a number of mesh cells from ExodusII file
//! \param[in] ext Extents of element IDs whose connectivity to read:
//! [from...till), using zero-based element IDs, where 'from' >=0, inclusive
//! and 'till < 'maxelements', where 'maxelements' is the total number of
//! elements of all element blocks in the file of the requested cell type.
//! Note that 'maxelements' can be queried by nelem().
//! \param[in] elemtype Element type
//! \param[inout] conn Connectivity vector to push to
//! \note Must be preceded by a call to readElemBlockIDs()
//! \details This function takes the extents of element IDs in a zero-based
//! fashion. These input extents can be thought of "absolute" extents that
//! denote lowest and the largest-1 element IDs to be read from file.
// *****************************************************************************
{
Assert( tk::sumsize(m_blockid_by_type) > 0,
"A call to this function must be preceded by a call to "
"ExodusIIMeshReader::readElemBlockIDs()" );
Assert( ext[0] <= ext[1] &&
ext[0] < nelem(elemtype) &&
ext[1] < nelem(elemtype),
"Invalid element ID extents. Of the requested extents [from...till), "
"'from' must be lower than or equal to 'till', and they must be in "
"the range [0...maxelements), where 'maxelements' is the total "
"number of elements of all element blocks in the file of the "
"requested cell type. Requested element ID extents: ["
+ std::to_string(ext[0]) + "..." + std::to_string(ext[1])
+ "), 'maxelements' of cell type with "
+ std::to_string( ExoNnpe[ static_cast<std::size_t>(elemtype) ] )
+ " nodes per cell in file '" + m_filename + "': "
+ std::to_string( nelem( elemtype ) ) );
auto e = static_cast< std::size_t >( elemtype );
// List of number of elements of all blocks of element type requested
const auto& nel = m_nel[e];
// List of element block IDs for element type requested
const auto& bid = m_blockid_by_type[e];
// Compute lower and upper element block ids to read from based on extents
std::size_t lo_bid = 0, hi_bid = 0, offset = 0;
for (std::size_t b=0; b<nel.size(); ++b) {
std::size_t lo = offset; // lo (min) elem ID in block
std::size_t hi = offset + nel[b] - 1; // hi (max) elem ID in block
if (ext[0] >= lo && ext[0] <= hi) lo_bid = b;
if (ext[1] >= lo && ext[1] <= hi) hi_bid = b;
offset += nel[b];
}
Assert( lo_bid < nel.size() && lo_bid < bid.size(),
"Invalid start block ID" );
Assert( hi_bid < nel.size() && hi_bid < bid.size(),
"Invalid end block ID" );
// Compute relative extents based on absolute ones for each block to read from
std::vector< std::array< std::size_t, 2 > > rext;
offset = 0;
for (std::size_t b=0; b<lo_bid; ++b) offset += nel[b];
for (std::size_t b=lo_bid; b<=hi_bid; ++b) {
std::size_t lo = offset;
std::size_t hi = offset + nel[b] - 1;
std::size_t le = 1, he = nel[b];
if (ext[0] >= lo && ext[0] <= hi) le = ext[0] - lo + 1;
if (ext[1] >= lo && ext[1] <= hi) he = ext[1] - lo + 1;
Assert( le >= 1 && le <= nel[b] && he >= 1 && he <= nel[b],
"Relative index out of block" );
rext.push_back( {{ le, he }} );
offset += nel[b];
}
Assert( std::accumulate(
std::next(rext.cbegin()), rext.cend(), rext[0][1]-rext[0][0]+1,
[]( std::size_t n, const std::array< std::size_t, 2 >& r )
{ return n + r[1] - r[0] + 1; }
) == ext[1]-ext[0]+1,
"Total number of elements to read incorrect, requested extents: " +
std::to_string(ext[0]) + " ... " + std::to_string(ext[1]) );
std::vector< int > inpoel;
// Read element connectivity from file
std::size_t B = 0;
for (auto b=lo_bid; b<=hi_bid; ++b, ++B) {
const auto& r = rext[B];
std::vector< int > c( (r[1]-r[0]+1) * ExoNnpe[e] );
ErrChk( ex_get_partial_conn( m_inFile,
EX_ELEM_BLOCK,
bid[b],
static_cast< int64_t >( r[0] ),
static_cast< int64_t >( r[1]-r[0]+1 ),
c.data(),
nullptr,
nullptr ) == 0,
"Failed to read element connectivity of elements [" +
std::to_string(r[0]) + "..." + std::to_string(r[1]) +
"] from element block " + std::to_string(bid[b]) + " in ExodusII "
"file: " + m_filename );
inpoel.reserve( inpoel.size() + c.size() );
std::move( begin(c), end(c), std::back_inserter(inpoel) );
}
Assert( inpoel.size() == (ext[1]-ext[0]+1)*ExoNnpe[e],
"Failed to read element connectivity of elements [" +
std::to_string(ext[0]) + "..." + std::to_string(ext[1]) + ") from "
"ExodusII file: " + m_filename );
// Put in element connectivity using zero-based node indexing
for (auto& i : inpoel) --i;
conn.reserve( conn.size() + inpoel.size() );
std::move( begin(inpoel), end(inpoel), std::back_inserter(conn) );
}
void
ExodusIIMeshReader::readFaces( std::vector< std::size_t >& conn ) const
// *****************************************************************************
// Read face connectivity of a number of boundary faces from ExodusII file
//! \param[inout] conn Connectivity vector to push to
//! \details This function reads in the total number of boundary faces,
//! also called triangle-elements in the EXO2 file, and their connectivity.
// *****************************************************************************
{
// Return quietly if no triangle elements in file
if (nelem(tk::ExoElemType::TRI) == 0) return;
// Read triangle boundary-face connectivity (all the triangle element block)
readElements( {{0,nelem(tk::ExoElemType::TRI)-1}}, tk::ExoElemType::TRI,
conn );
}
std::vector< std::size_t >
ExodusIIMeshReader::readNodemap()
// *****************************************************************************
// Read local to global node-ID map from ExodusII file
//! \return node_map Vector mapping the local Exodus node-IDs to global node-IDs
//! \details The node-map is required to get the "Exodus-global" node-IDs from
//! the "Exodus-internal" node-IDs, which are returned from the exodus APIs.
//! The node-IDs in the exodus file are referred to as the "Exodus-global"
//! node-IDs or "fileIDs" in Quinoa.
// *****************************************************************************
{
// Read triangle boundary-face connectivity
auto nnode = readElemBlockIDs();
// Create array to store node-number map
std::vector< int > node_map( nnode );
// Read in the node number map to map the above nodes to the global node-IDs
ErrChk( ex_get_id_map( m_inFile, EX_NODE_MAP, node_map.data() ) == 0,
"Failed to read node map length from ExodusII file: " );
std::vector< std::size_t > node_map1( nnode );
for (std::size_t i=0; i<nnode; ++i)
{
node_map1[i] = static_cast< std::size_t >(node_map[i]-1);
}
return node_map1;
}
std::map< int, std::vector< std::size_t > >
ExodusIIMeshReader::readSidesetNodes()
// *****************************************************************************
// Read node list of all side sets from ExodusII file
//! \return Node lists mapped to side set ids
// *****************************************************************************
{
// Read ExodusII file header (fills m_neset)
readHeader();
// Node lists mapped to side set ids
std::map< int, std::vector< std::size_t > > side;
if (m_neset > 0) {
// Read all side set ids from file
std::vector< int > ids( m_neset );
ErrChk( ex_get_ids( m_inFile, EX_SIDE_SET, ids.data() ) == 0,
"Failed to read side set ids from ExodusII file: " + m_filename );
// Read in node list for all side sets
for (auto i : ids) {
int nface, nnode;
// Read number of faces and number of distribution factors in side set i
ErrChk( ex_get_set_param( m_inFile, EX_SIDE_SET, i, &nface, &nnode ) == 0,
"Failed to read side set " + std::to_string(i) + " parameters "
"from ExodusII file: " + m_filename );
// Read number of nodes in side set i (overwrite nnode)
ErrChk( ex_get_side_set_node_list_len( m_inFile, i, &nnode ) == 0,
"Failed to read side set " + std::to_string(i) + " node list "
"length from ExodusII file: " + m_filename );
Assert(nnode > 0, "Number of nodes = 0 in side set" + std::to_string(i));
std::vector< int > df( static_cast< std::size_t >( nface ) );
std::vector< int > nodes( static_cast< std::size_t >( nnode ) );
// Read in node list for side set i
ErrChk( ex_get_side_set_node_list( m_inFile, i, df.data(), nodes.data() )
== 0, "Failed to read node list of side set " +
std::to_string(i) + " from ExodusII file: " +
m_filename );
// Make node list unique
tk::unique( nodes );
// Store 0-based node ID list as std::size_t vector instead of ints
auto& list = side[ i ];
for (auto n : nodes) list.push_back( static_cast<std::size_t>(n-1) );<--- Consider using std::transform algorithm instead of a raw loop.
}
}
return side;
}
void
ExodusIIMeshReader::readSidesetFaces(
std::map< int, std::vector< std::size_t > >& bface,
std::map< int, std::vector< std::size_t > >& faces )
// *****************************************************************************
// Read side sets from ExodusII file
//! \param[in,out] bface Elem ids of side sets to read into
//! \param[in,out] faces Elem-relative face ids of tets of side sets
// *****************************************************************************
{
// Read element block ids
readElemBlockIDs();
if (m_neset > 0) {
// Read side set ids from file
std::vector< int > ids( m_neset );
ErrChk( ex_get_ids( m_inFile, EX_SIDE_SET, ids.data() ) == 0,
"Failed to read side set ids from ExodusII file: " + m_filename );
// Read all side sets from file
for (auto i : ids) {
int nface, nnode;
// Read number of faces in side set
ErrChk( ex_get_set_param( m_inFile, EX_SIDE_SET, i, &nface, &nnode ) == 0,
"Failed to read side set " + std::to_string(i) + " parameters "
"from ExodusII file: " + m_filename );
Assert(nface > 0, "Number of faces = 0 in side set" + std::to_string(i));
std::vector< int > exoelem( static_cast< std::size_t >( nface ) );
std::vector< int > exoface( static_cast< std::size_t >( nface ) );
// Read in file-internal element ids and relative face ids for side set
ErrChk( ex_get_set( m_inFile, EX_SIDE_SET, i, exoelem.data(),
exoface.data() ) == 0,
"Failed to read side set " + std::to_string(i) );
// Store file-internal element ids of side set
auto& elem = bface[i];
elem.resize( exoelem.size() );
std::size_t j = 0;
for (auto e : exoelem) elem[j++] = static_cast< std::size_t >( e-1 );
// Store zero-based relative face ids of side set
auto& face = faces[i];
face.resize( exoface.size() );
j = 0;
for (auto n : exoface) face[j++] = static_cast< std::size_t >( n-1 );
Assert( std::all_of( begin(face), end(face),
[](std::size_t f){ return f<4; } ),
"Relative face id of side set must be between 0 and 3" );
Assert( elem.size() == face.size(), "Size mismatch" );
}
}
}
std::pair< tk::ExoElemType, std::size_t >
ExodusIIMeshReader::blkRelElemId( std::size_t id ) const
// *****************************************************************************
// Compute element-block-relative element id and element type
//! \param[in] id (ExodusII) file-internal element id
//! \return Element type the internal id points to and element id relative to
//! cell-type
//! \details This function takes an internal element id, which in general can
//! point to any element block in the ExodusII file and thus we do not know
//! which element type a block contains. It then computes which cell type the
//! id points to and computes the relative index for the given cell type. This
//! is necessary because elements are read in from file by from potentially
//! multiple blocks by cell type.
//! \note Must be preceded by a call to readElemBlockIDs()
// *****************************************************************************
{
auto TRI = tk::ExoElemType::TRI;
auto TET = tk::ExoElemType::TET;
std::size_t e = 0; // counts elements (independent of cell type)
std::size_t ntri = 0; // counts triangle elements
std::size_t ntet = 0; // counts tetrahedron elements
for (const auto& b : m_elemblocks) { // walk all element blocks in order
e += b.second; // increment file-internal element id
if (e > id) { // found element block for internal id
if (b.first == TRI) { // if triangle block
return { TRI, id-ntet }; // return cell type and triangle id
} else if (b.first == TET) { // if tetrahedron block
return { TET, id-ntri }; // return cell type and tetrahedron id
}
}
// increment triangle and tetrahedron elements independently
if (b.first == TRI)
ntri += b.second;
else if (b.first == TET)
ntet += b.second;
}
Throw( " Exodus internal element id not found" );
}
std::vector< std::size_t >
ExodusIIMeshReader::triinpoel(
std::map< int, std::vector< std::size_t > >& belem,
const std::map< int, std::vector< std::size_t > >& faces,
const std::vector< std::size_t >& ginpoel,
const std::vector< std::size_t >& triinp ) const
// *****************************************************************************
// Generate triangle face connectivity for side sets
//! \param[in,out] belem File-internal elem ids of side sets
//! \param[in] faces Elem-relative face ids of side sets
//! \param[in] ginpoel Tetrahedron element connectivity with global nodes
//! \param[in] triinp Triangle element connectivity with global nodes
//! (if exists in file)
//! \return Triangle face connectivity with global node IDs of side sets
//! \details This function takes lists of file-internal element ids (in belem)
//! for side sets and does two things: (1) generates face connectivity (with
//! global node IDs) for side sets, and (2) converts the (ExodusII)
//! file-internal element IDs to face ids so that they can be used to index
//! into the face connectivity. The IDs in belem are modified and the face
//! connectivity (for boundary faces only) is returned.
//! \note Must be preceded by a call to readElemBlockIDs()
// *****************************************************************************
{
Assert( !(m_from == 0 && m_till == 0),
"Lower and upper tetrahedron id bounds must not both be zero" );
// This will contain one of our final results: face (triangle) connectivity
// for the side sets only. The difference between bnd_triinpoel and triinpoel
// is that triinpoel is a triangle element connectivity, independent of side
// sets, while bnd_triinpoel is a triangle connectivity only for side sets.
std::vector< std::size_t > bnd_triinpoel;
// Storage for boundary face lists for each side set on this PE
std::map< int, std::vector< std::size_t > > belem_own;
std::size_t f = 0; // counts all faces
for (auto& ss : belem) { // for all side sets
// insert side set id into new map
auto& b = belem_own[ ss.first ];
// get element-relative face ids for side set
const auto& face = tk::cref_find( faces, ss.first );
std::size_t s = 0; // counts side set faces
for (auto& i : ss.second) { // for all faces on side set
// compute element-block-relative element id and element type
auto r = blkRelElemId( i );
// extract boundary face connectivity based on element type
bool localface = false;
if (r.first == tk::ExoElemType::TRI) {
auto t = m_tri.find(r.second);
if (t != end(m_tri)) { // only if triangle id exists on this PE
Assert( t->second < triinp.size()/3,
"Indexing out of triangle connectivity" );
// generate triangle (face) connectivity using global node ids
bnd_triinpoel.push_back( triinp[ t->second*3 + 0 ] );
bnd_triinpoel.push_back( triinp[ t->second*3 + 1 ] );
bnd_triinpoel.push_back( triinp[ t->second*3 + 2 ] );
localface = true;
}
} else if (r.first == tk::ExoElemType::TET) {
if (r.second >= m_from && r.second < m_till) { // if tet is on this PE
auto t = r.second - m_from;
Assert( t < ginpoel.size()/4,
"Indexing out of tetrahedron connectivity" );
// get ExodusII face-node numbering for side sets, see ExodusII
// manual figure on "Sideset side Numbering"
const auto& tri = tk::expofa[ face[s] ];
// generate triangle (face) connectivity using global node ids, note
// the switched node order, 0,2,1, as lpofa is different from expofa
bnd_triinpoel.push_back( ginpoel[ t*4 + tri[0] ] );
bnd_triinpoel.push_back( ginpoel[ t*4 + tri[1] ] );
bnd_triinpoel.push_back( ginpoel[ t*4 + tri[2] ] );
localface = true;
}
}
++s;
// generate PE-local face id for side set (this is to be used to index
// into triinpoel)
if (localface) b.push_back( f++ );
}
// if no faces on this side set (on this PE), remove side set id
if (b.empty()) belem_own.erase( ss.first );
}
belem = std::move(belem_own);
return bnd_triinpoel;
}
void
ExodusIIMeshReader::readNodeVarNames( std::vector< std::string >& nv ) const
// *****************************************************************************
// Read the names of nodal output variables from ExodusII file
//! \param[in,out] nv Nodal variable names
// *****************************************************************************
{
#if defined(__clang__)
#pragma clang diagnostic push
#pragma clang diagnostic ignored "-Wvla"
#pragma clang diagnostic ignored "-Wvla-extension"
#elif defined(STRICT_GNUC)
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wvla"
#endif
int numvars = 0;
ErrChk(
ex_get_variable_param( m_inFile, EX_NODE_BLOCK, &numvars ) == 0,
"Failed to read nodal output variable parameters from ExodusII file: " +
m_filename );
if (numvars) {
char* names[ static_cast< std::size_t >( numvars ) ];
for (int i=0; i<numvars; ++i)
names[i] = static_cast<char*>( calloc((MAX_STR_LENGTH+1), sizeof(char)) );
ErrChk( ex_get_variable_names( m_inFile,
EX_NODAL,
numvars,
names ) == 0,
"Failed to read nodal variable names from ExodusII file: " +
m_filename );
nv.resize( static_cast< std::size_t >( numvars ) );
std::size_t i = 0;
for (auto& n : nv) n = names[ i++ ];<--- Consider using std::fill or std::generate algorithm instead of a raw loop.
}
#if defined(__clang__)
#pragma clang diagnostic pop
#elif defined(STRICT_GNUC)
#pragma GCC diagnostic pop
#endif
}
void
ExodusIIMeshReader::readTimeValues( std::vector< tk::real >& tv ) const
// *****************************************************************************
// Read time values from ExodusII file
//! \param[in] tv Vector of time values at which field data is saved
// *****************************************************************************
{
auto num_time_steps =
static_cast< std::size_t >( ex_inquire_int( m_inFile, EX_INQ_TIME ) );
if (num_time_steps) {
tv.resize( num_time_steps, 0.0 );
ErrChk( ex_get_all_times( m_inFile, tv.data() ) == 0,
"Failed to read time values from ExodusII file: " + m_filename );
}
}
void
ExodusIIMeshReader::readNodeScalars(
std::size_t ntime,
std::size_t nvar,
std::vector< std::vector< std::vector< tk::real > > >& var ) const
// *****************************************************************************
// Read node scalar fields from ExodusII file
//! \param[in] ntime Number of time steps to read
//! \param[in] nvar Number of variables to read
//! \param[in] var Vector of nodal variables to read to: inner vector: nodes,
//! middle vector: (physics) variable, outer vector: time step
// *****************************************************************************
{
var.resize( ntime );
for (auto& v : var) {
v.resize( nvar );
for (auto& n : v) n.resize( m_nnode );
}
for (std::size_t t=0; t<var.size(); ++t) {
for (std::size_t id=0; id<var[t].size(); ++id) {
ErrChk( ex_get_var( m_inFile,
static_cast< int >( t+1 ),
EX_NODAL,
static_cast< int >( id+1 ),
1,
static_cast< int64_t >( var[t][id].size() ),
var[t][id].data() ) == 0,
"Failed to read node scalar from ExodusII file: " + m_filename );
}
}
}
std::size_t
ExodusIIMeshReader::nelem( tk::ExoElemType elemtype ) const
// *****************************************************************************
// Return number of elements in all mesh blocks for a given elem type in file
//! \param[in] elemtype Element type
//! \return Number of elements in all blocks for the elem type
//! \note Must be preceded by a call to readElemBlockIDs()
// *****************************************************************************
{
auto e = static_cast< std::size_t >( elemtype );
return std::accumulate( m_nel[e].cbegin(), m_nel[e].cend(), 0u );
}
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