ATC version 2.0, date: Aug7
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10561 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
rjones
217
lib/atc/MeshReader.cpp
Normal file
217
lib/atc/MeshReader.cpp
Normal file
@ -0,0 +1,217 @@
|
||||
#include "MeshReader.h"
|
||||
#include "LammpsInterface.h"
|
||||
#include "Utility.h"
|
||||
#ifdef HAS_EXODUS
|
||||
//#include <stdio.h>
|
||||
//#include "netcdf.h"
|
||||
#include "exodusII.h"
|
||||
#endif
|
||||
|
||||
namespace ATC {
|
||||
using ATC_Utility::to_string;
|
||||
/** constructor, takes a filename */
|
||||
MeshReader::MeshReader(string filename,
|
||||
Array<bool> periodicity,
|
||||
double tol)
|
||||
: meshfile_(filename),
|
||||
periodicity_(periodicity),
|
||||
nNodes_(0),
|
||||
nElements_(0),
|
||||
coordTol_(tol)
|
||||
{
|
||||
conn_ = new Array2D<int>();
|
||||
nodeCoords_ = new DENS_MAT;
|
||||
nodeSets_ = new Array< pair< string,set<int> > >();
|
||||
|
||||
size_t idx = filename.rfind('.');
|
||||
if (idx == string::npos) {
|
||||
throw ATC_Error("Given mesh file is of unknown type.");
|
||||
}
|
||||
|
||||
string ext = filename.substr(idx+1);
|
||||
|
||||
if (ext == "mesh"){ read_mesh_file(); }
|
||||
else { throw ATC_Error("mesh file is of unknown type."); }
|
||||
}
|
||||
|
||||
/** destructor */
|
||||
MeshReader::~MeshReader()
|
||||
{
|
||||
}
|
||||
|
||||
/** creates handle to new mesh object */
|
||||
FE_Mesh* MeshReader::create_mesh()
|
||||
{
|
||||
return new FE_3DMesh(elementType_,
|
||||
nNodes_, nElements_,
|
||||
conn_, nodeCoords_,
|
||||
periodicity_,
|
||||
nodeSets_);
|
||||
}
|
||||
|
||||
/** reads .mesh format file */
|
||||
void MeshReader::read_mesh_file() {
|
||||
ifstream in;
|
||||
in.open(meshfile_.c_str(), ifstream::in);
|
||||
string header;
|
||||
while (getline(in,header)) {
|
||||
istringstream words(header);
|
||||
string section;
|
||||
words >> section;
|
||||
if (section == "Coordinates") {
|
||||
words >> nNodes_;
|
||||
nodeCoords_->reset(3, nNodes_, false);
|
||||
string line;
|
||||
for (int i = 0; i < nNodes_; ++i) {
|
||||
getline(in,line);
|
||||
istringstream coords(line);
|
||||
coords >> (*nodeCoords_)(0, i);
|
||||
coords >> (*nodeCoords_)(1, i);
|
||||
coords >> (*nodeCoords_)(2, i);
|
||||
}
|
||||
stringstream ss;
|
||||
ss << "read " << nNodes_ << " nodes";
|
||||
ATC::LammpsInterface::instance()->print_msg_once(ss.str());
|
||||
}
|
||||
else if (section == "Elements") {
|
||||
words >> nElements_;
|
||||
words >> elementType_;
|
||||
int nVerts = int_from_str(elementType_);
|
||||
conn_->reset(nVerts, nElements_);
|
||||
string line;
|
||||
for (int i = 0; i < nElements_; ++i) {
|
||||
getline(in,line);
|
||||
istringstream verts(line);
|
||||
for (int j = 0; j < nVerts; ++j ) {
|
||||
int node;
|
||||
verts >> node;
|
||||
(*conn_)(j,i) = node-1;
|
||||
}
|
||||
}
|
||||
stringstream ss;
|
||||
ss << "read " << nElements_ << " " << elementType_ << " elements";
|
||||
ATC::LammpsInterface::instance()->print_msg_once(ss.str());
|
||||
}
|
||||
else if (section == "Nodesets") {
|
||||
words >> nNodeSets_;
|
||||
nodeSets_->reset(nNodeSets_);
|
||||
string infoline;
|
||||
string setName;
|
||||
int nNodes;
|
||||
string line;
|
||||
for (int i = 0; i < nNodeSets_; ++i) {
|
||||
getline(in,infoline);
|
||||
istringstream info(infoline);
|
||||
info >> setName;
|
||||
info >> nNodes;
|
||||
(*nodeSets_)(i).first = setName;
|
||||
getline(in,line);
|
||||
istringstream nodes(line);
|
||||
for (int j = 0; j < nNodes; ++j ) {
|
||||
int node;
|
||||
nodes >> node;
|
||||
(*nodeSets_)(i).second.insert(node-1);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
in.close();
|
||||
if (nodeCoords_->size() == 0) {
|
||||
throw ATC_Error("Could not find mesh file, or mesh file empty.");
|
||||
}
|
||||
}
|
||||
|
||||
/** reads .exo format file */
|
||||
void MeshReader::read_exo_file() {
|
||||
#ifndef HAS_EXODUS
|
||||
throw ATC_Error("Reading ExodusII .exo files not supported.");
|
||||
#else
|
||||
int CPU_word_size=0,IO_word_size=0;
|
||||
float version;
|
||||
int exoid = ex_open (meshfile_.c_str(), EX_READ,
|
||||
&CPU_word_size, &IO_word_size, &version);
|
||||
if (exoid < 0) { throw ATC_Error("couldn't open "+meshfile_); }
|
||||
int nsd,nelemblk,nfsets;
|
||||
char title[MAX_LINE_LENGTH+1];
|
||||
int error = ex_get_init (exoid, title,
|
||||
&nsd, &nNodes_, &nElements_, &nelemblk, &nNodeSets_, &nfsets);
|
||||
if (error > 0) { throw ATC_Error("problem with init "+meshfile_+" "+title); }
|
||||
// coordinates
|
||||
float x[nNodes_], y[nNodes_], z[nNodes_];
|
||||
error = ex_get_coord (exoid, x, y, z);
|
||||
if (error > 0) { throw ATC_Error("problem with getting coordinates "+meshfile_); }
|
||||
nodeCoords_->reset(nsd,nNodes_);
|
||||
DENS_MAT & nodes = *nodeCoords_;
|
||||
for (int i = 0; i < nNodes_; ++i) {
|
||||
nodes(0,i) = x[i]; // this is a float to double conversion
|
||||
nodes(1,i) = y[i]; // this is a float to double conversion
|
||||
nodes(2,i) = z[i]; // this is a float to double conversion
|
||||
}
|
||||
ATC::LammpsInterface::instance()->print_msg_once("read "+to_string(nNodes_)+
|
||||
" nodes");
|
||||
// elements
|
||||
int blkIds[nelemblk],nblkelem[nelemblk],nnpe[nelemblk],na[nelemblk];
|
||||
error = ex_get_elem_blk_ids(exoid, blkIds);
|
||||
char etype[MAX_STR_LENGTH+1];
|
||||
string lastType;
|
||||
for (int i=0; i<nelemblk; i++){
|
||||
error = ex_get_elem_block (exoid, blkIds[i], etype,
|
||||
&(nblkelem[i]), &(nnpe[i]), &(na[i]));
|
||||
elementType_ = etype;
|
||||
if (i > 0 && elementType_ != lastType )
|
||||
{ throw ATC_Error(meshfile_+" is composed of multiple types"); }
|
||||
lastType = etype;
|
||||
}
|
||||
int nVerts = int_from_str(elementType_);
|
||||
conn_->reset(nVerts, nElements_);
|
||||
int n = 0;
|
||||
for (int i=0; i<nelemblk; i++) {
|
||||
int bconn[nnpe[i]*nblkelem[i]];
|
||||
error = ex_get_elem_conn (exoid, blkIds[i], &bconn);
|
||||
for (int j=0; j<nblkelem[i]; j++) {
|
||||
for (int k=0; k<nnpe[i]; k++) {
|
||||
(*conn_)(k,n) = bconn[k+j*nnpe[i]]-1;
|
||||
}
|
||||
n++;
|
||||
}
|
||||
ATC::LammpsInterface::instance()->print_msg_once("read "+to_string(n)+" "+elementType_+" elements, block "+to_string(i+1)+"/"+to_string(nelemblk));
|
||||
}
|
||||
// nodesets
|
||||
int nsetIds[nNodeSets_];
|
||||
error = ex_get_node_set_ids (exoid, nsetIds);
|
||||
int nnodes,ndist;
|
||||
//nodeSets_ = new Array< pair< string,set<int> > >();
|
||||
nodeSets_->reset(nNodeSets_);
|
||||
for (int i=0; i<nNodeSets_; i++) {
|
||||
(*nodeSets_)(i).first = to_string(nsetIds[i]);
|
||||
error = ex_get_node_set_param (exoid, nsetIds[i], &nnodes, &ndist);
|
||||
int nodes[nnodes];
|
||||
error = ex_get_node_set (exoid, nsetIds[i], nodes);
|
||||
for (int j=0; j<nnodes; j++) {
|
||||
(*nodeSets_)(i).second.insert(nodes[j]-1);
|
||||
}
|
||||
}
|
||||
error = ex_close(exoid);
|
||||
if (error > 0) { throw ATC_Error("problem with closing "+meshfile_); }
|
||||
#endif
|
||||
}
|
||||
|
||||
int MeshReader::int_from_str(string str)
|
||||
{
|
||||
string temp;
|
||||
int number=0;
|
||||
|
||||
for (unsigned int i=0; i < str.size(); i++) {
|
||||
if (isdigit(str[i])) {
|
||||
for (unsigned int a=i; a<str.size(); a++) {
|
||||
temp += str[a];
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
istringstream(temp) >> number;
|
||||
return number;
|
||||
}
|
||||
|
||||
}; // end namespace ATC
|
||||
Reference in New Issue
Block a user