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GModelIO_MSH2.cpp
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Christophe Geuzaine authoredThis reverts commit 07cc55d9
Christophe Geuzaine authoredThis reverts commit 07cc55d9
GModelIO_MSH2.cpp 38.68 KiB
// Gmsh - Copyright (C) 1997-2019 C. Geuzaine, J.-F. Remacle
//
// See the LICENSE.txt file for license information. Please report all
// issues on https://gitlab.onelab.info/gmsh/gmsh/issues.
#include <stdlib.h>
#include <string.h>
#include <map>
#include <string>
#include <sstream>
#include <cassert>
#include <iomanip>
#include "GModel.h"
#include "OS.h"
#include "GmshDefines.h"
#include "MPoint.h"
#include "MLine.h"
#include "MTriangle.h"
#include "MQuadrangle.h"
#include "MTetrahedron.h"
#include "MHexahedron.h"
#include "MPrism.h"
#include "MPyramid.h"
#include "MElementCut.h"
#include "StringUtils.h"
#include "GmshMessage.h"
#include "Context.h"
#include "OS.h"
// periodic nodes and entities backported from MSH3 format
extern void writeMSHPeriodicNodes(FILE *fp, std::vector<GEntity *> &entities,
bool renumber, bool saveAll);
extern void readMSHPeriodicNodes(FILE *fp, GModel *gm);
extern void writeMSHEntities(FILE *fp, GModel *gm);
static bool getMeshVertices(int num, int *indices,
std::map<int, MVertex *> &map,
std::vector<MVertex *> &vertices)
{
for(int i = 0; i < num; i++) {
if(!map.count(indices[i])) {
Msg::Error("Wrong vertex index %d", indices[i]);
return false;
}
else
vertices.push_back(map[indices[i]]);
}
return true;
}
static bool getMeshVertices(int num, int *indices, std::vector<MVertex *> &vec,
std::vector<MVertex *> &vertices, int minVertex = 0)
{
for(int i = 0; i < num; i++) {
if(indices[i] < minVertex ||
indices[i] > (int)(vec.size() - 1 + minVertex)) {
Msg::Error("Wrong vertex index %d", indices[i]);
return false;
}
else
vertices.push_back(vec[indices[i]]);
}
return true;
}
static MElement *
createElementMSH2(GModel *m, int num, int typeMSH, int physical, int reg,
unsigned int part, std::vector<MVertex *> &v,
std::map<int, std::vector<MElement *> > elements[10],
std::map<int, std::map<int, std::string> > physicals[4], bool owner = false, MElement *parent = 0, MElement *d1 = 0,
MElement *d2 = 0)
{
if(CTX::instance()->mesh.switchElementTags) {
int tmp = reg;
reg = physical;
physical = tmp;
}
MElementFactory factory;
MElement *e = factory.create(typeMSH, v, num, part, owner, 0, parent, d1, d2);
if(!e) {
Msg::Error("Unknown type of element %d", typeMSH);
return NULL;
}
int dim = e->getDim();
if(physical &&
(!physicals[dim].count(reg) || !physicals[dim][reg].count(physical)))
physicals[dim][reg][physical] = "unnamed";
if(part > m->getNumPartitions()) m->setNumPartitions(part);
return e;
}
int GModel::_readMSH2(const std::string &name)
{
FILE *fp = Fopen(name.c_str(), "rb");
if(!fp) {
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
char str[256] = "XXX";
double version = 1.0;
bool binary = false, swap = false, postpro = false;
std::map<int, std::vector<MElement *> > elements[10];
std::map<int, std::map<int, std::string> > physicals[4];
std::map<int, MVertex *> vertexMap;
std::vector<MVertex *> vertexVector;
int minVertex = 0;
while(1) {
while(str[0] != '$') {
if(!fgets(str, sizeof(str), fp) || feof(fp)) break;
}
if(feof(fp)) break;
if(!strncmp(&str[1], "MeshFormat", 10)) {
if(!fgets(str, sizeof(str), fp)) {
fclose(fp);
return 0;
}
int format, size;
if(sscanf(str, "%lf %d %d", &version, &format, &size) != 3) {
fclose(fp);
return 0;
}
if(format) {
binary = true;
Msg::Debug("Mesh is in binary format");
int one;
if(fread(&one, sizeof(int), 1, fp) != 1) {
fclose(fp);
return 0;
}
if(one != 1) {
swap = true; Msg::Debug("Swapping bytes from binary file");
}
}
}
else if(!strncmp(&str[1], "PhysicalNames", 13)) {
if(!fgets(str, sizeof(str), fp)) {
fclose(fp);
return 0;
}
int numNames;
if(sscanf(str, "%d", &numNames) != 1) {
fclose(fp);
return 0;
}
for(int i = 0; i < numNames; i++) {
int dim = -1, num;
if(version > 2.0) {
if(fscanf(fp, "%d", &dim) != 1) {
fclose(fp);
return 0;
}
}
if(fscanf(fp, "%d", &num) != 1) {
fclose(fp);
return 0;
}
if(!fgets(str, sizeof(str), fp)) {
fclose(fp);
return 0;
}
std::string name = ExtractDoubleQuotedString(str, 256);
if(name.size()) setPhysicalName(name, dim, num);
}
}
else if(!strncmp(&str[1], "NO", 2) || !strncmp(&str[1], "Nodes", 5) ||
!strncmp(&str[1], "ParametricNodes", 15)) {
const bool parametric = !strncmp(&str[1], "ParametricNodes", 15);
if(!fgets(str, sizeof(str), fp)) {
fclose(fp);
return 0;
}
int numVertices = -1;
if(sscanf(str, "%d", &numVertices) != 1) {
fclose(fp);
return 0;
}
Msg::Info("%d vertices", numVertices);
Msg::ResetProgressMeter();
vertexVector.clear();
vertexMap.clear();
minVertex = numVertices + 1;
int maxVertex = -1;
for(int i = 0; i < numVertices; i++) {
int num;
double xyz[3], uv[2];
MVertex *newVertex = 0;
if(!parametric) {
if(!binary) {
if(fscanf(fp, "%d %lf %lf %lf", &num, &xyz[0], &xyz[1], &xyz[2]) !=
4) {
fclose(fp);
return 0;
}
}
else {
if(fread(&num, sizeof(int), 1, fp) != 1) {
fclose(fp);
return 0;
}
if(swap) SwapBytes((char *)&num, sizeof(int), 1); if(fread(xyz, sizeof(double), 3, fp) != 3) {
fclose(fp);
return 0;
}
if(swap) SwapBytes((char *)xyz, sizeof(double), 3);
}
newVertex = new MVertex(xyz[0], xyz[1], xyz[2], 0, num);
}
else {
int iClasDim, iClasTag;
if(!binary) {
if(fscanf(fp, "%d %lf %lf %lf %d %d", &num, &xyz[0], &xyz[1],
&xyz[2], &iClasDim, &iClasTag) != 6) {
fclose(fp);
return 0;
}
}
else {
if(fread(&num, sizeof(int), 1, fp) != 1) {
fclose(fp);
return 0;
}
if(swap) SwapBytes((char *)&num, sizeof(int), 1);
if(fread(xyz, sizeof(double), 3, fp) != 3) {
fclose(fp);
return 0;
}
if(swap) SwapBytes((char *)xyz, sizeof(double), 3);
if(fread(&iClasDim, sizeof(int), 1, fp) != 1) {
fclose(fp);
return 0;
}
if(swap) SwapBytes((char *)&iClasDim, sizeof(int), 1);
if(fread(&iClasTag, sizeof(int), 1, fp) != 1) {
fclose(fp);
return 0;
}
if(swap) SwapBytes((char *)&iClasTag, sizeof(int), 1);
}
if(iClasDim == 0) {
GVertex *gv = getVertexByTag(iClasTag);
if(gv) gv->mesh_vertices.clear();
newVertex = new MVertex(xyz[0], xyz[1], xyz[2], gv, num);
}
else if(iClasDim == 1) {
GEdge *ge = getEdgeByTag(iClasTag);
if(!binary) {
if(fscanf(fp, "%lf", &uv[0]) != 1) {
fclose(fp);
return 0;
}
}
else {
if(fread(uv, sizeof(double), 1, fp) != 1) {
fclose(fp);
return 0;
}
if(swap) SwapBytes((char *)uv, sizeof(double), 1);
}
newVertex = new MEdgeVertex(xyz[0], xyz[1], xyz[2], ge, uv[0], num);
}
else if(iClasDim == 2) {
GFace *gf = getFaceByTag(iClasTag);
if(!binary) {
if(fscanf(fp, "%lf %lf", &uv[0], &uv[1]) != 2) {
fclose(fp);
return 0;
}
}
else { if(fread(uv, sizeof(double), 2, fp) != 2) {
fclose(fp);
return 0;
}
if(swap) SwapBytes((char *)uv, sizeof(double), 2);
}
newVertex =
new MFaceVertex(xyz[0], xyz[1], xyz[2], gf, uv[0], uv[1], num);
}
else if(iClasDim == 3) {
GRegion *gr = getRegionByTag(iClasTag);
newVertex = new MVertex(xyz[0], xyz[1], xyz[2], gr, num);
}
}
minVertex = std::min(minVertex, num);
maxVertex = std::max(maxVertex, num);
if(vertexMap.count(num))
Msg::Warning("Skipping duplicate vertex %d", num);
vertexMap[num] = newVertex;
if(numVertices > 100000)
Msg::ProgressMeter(i + 1, numVertices, true, "Reading nodes");
}
// If the vertex numbering is dense, transfer the map into a
// vector to speed up element creation
if((int)vertexMap.size() == numVertices &&
((minVertex == 1 && maxVertex == numVertices) ||
(minVertex == 0 && maxVertex == numVertices - 1))) {
Msg::Debug("Vertex numbering is dense");
vertexVector.resize(vertexMap.size() + 1);
if(minVertex == 1)
vertexVector[0] = 0;
else
vertexVector[numVertices] = 0;
std::map<int, MVertex *>::const_iterator it = vertexMap.begin();
for(; it != vertexMap.end(); ++it) vertexVector[it->first] = it->second;
vertexMap.clear();
}
}
else if(!strncmp(&str[1], "ELM", 3) || !strncmp(&str[1], "Elements", 8)) {
if(!fgets(str, sizeof(str), fp)) {
fclose(fp);
return 0;
}
int numElements;
std::map<int, MElement *> elems;
std::map<int, MElement *> parents;
std::map<int, MElement *> domains;
std::map<int, int> elemreg;
std::map<int, int> elemphy;
std::set<MElement *> parentsOwned;
sscanf(str, "%d", &numElements);
Msg::Info("%d elements", numElements);
Msg::ResetProgressMeter();
if(!binary) {
for(int i = 0; i < numElements; i++) {
int num, type, physical = 0, elementary = 0, partition = 0,
parent = 0;
int dom1 = 0, dom2 = 0, numVertices;
std::vector<short> ghosts;
if(version <= 1.0) {
if(fscanf(fp, "%d %d %d %d %d", &num, &type, &physical, &elementary,
&numVertices) != 5) {
fclose(fp);
return 0;
}
if(numVertices != (int)MElement::getInfoMSH(type)) {
fclose(fp);
return 0; }
}
else {
int numTags;
if(fscanf(fp, "%d %d %d", &num, &type, &numTags) != 3) {
fclose(fp);
return 0;
}
int numPartitions = 0;
for(int j = 0; j < numTags; j++) {
int tag;
if(fscanf(fp, "%d", &tag) != 1) {
fclose(fp);
return 0;
}
if(j == 0)
physical = tag;
else if(j == 1)
elementary = tag;
else if(version < 2.2 && j == 2)
partition = tag;
else if(version >= 2.2 && j == 2 && numTags > 3)
numPartitions = tag;
else if(version >= 2.2 && j == 3)
partition = tag;
else if(j >= 4 && j < 4 + numPartitions - 1)
ghosts.push_back(-tag);
else if(j == 3 + numPartitions && (numTags == 4 + numPartitions))
parent = tag;
else if(j == 3 + numPartitions &&
(numTags == 5 + numPartitions)) {
dom1 = tag;
j++;
if(fscanf(fp, "%d", &dom2) != 1) {
fclose(fp);
return 0;
}
}
}
if(!(numVertices = MElement::getInfoMSH(type))) {
if(type != MSH_POLYG_ && type != MSH_POLYH_ &&
type != MSH_POLYG_B) {
fclose(fp);
return 0;
}
if(fscanf(fp, "%d", &numVertices) != 1) {
fclose(fp);
return 0;
}
}
}
int *indices = new int[numVertices];
for(int j = 0; j < numVertices; j++) {
if(fscanf(fp, "%d", &indices[j]) != 1) {
delete[] indices;
fclose(fp);
return 0;
}
}
std::vector<MVertex *> vertices;
if(vertexVector.size()) {
if(!getMeshVertices(numVertices, indices, vertexVector, vertices,
minVertex)) {
delete[] indices;
fclose(fp);
return 0;
}
}
else {
if(!getMeshVertices(numVertices, indices, vertexMap, vertices)) { delete[] indices;
fclose(fp);
return 0;
}
}
MElement *p = NULL;
bool own = false;
// search parent element
if(parent != 0) {
std::map<int, MElement *>::iterator ite = elems.find(parent);
if(ite == elems.end())
Msg::Error(
"Parent element (ascii) %d not found for element %d of type %d",
parent, num, type);
else {
p = ite->second;
parents[parent] = p;
}
std::set<MElement *>::iterator itpo = parentsOwned.find(p);
if(itpo == parentsOwned.end()) {
own = true;
parentsOwned.insert(p);
}
assert(p != NULL);
}
// search domains
MElement *doms[2] = {NULL, NULL};
if(dom1) {
std::map<int, MElement *>::iterator ite = elems.find(dom1);
if(ite == elems.end())
Msg::Error("Domain element %d not found for element %d", dom1,
num);
else
doms[0] = ite->second;
ite = elems.find(dom2);
if(ite != elems.end()) doms[1] = ite->second;
if(!doms[0])
Msg::Error("Domain element %d not found for element %d", dom1,
num);
if(dom2 && !doms[1])
Msg::Error("Domain element %d not found for element %d", dom2,
num);
}
delete[] indices;
if(elementary < 0) continue;
MElement *e = createElementMSH2(this, num, type, physical, elementary,
partition, vertices, elements,
physicals, own, p, doms[0], doms[1]);
elems[num] = e;
elemreg[num] = elementary;
elemphy[num] = physical;
for(std::size_t j = 0; j < ghosts.size(); j++)
_ghostCells.insert(std::pair<MElement *, short>(e, ghosts[j]));
if(numElements > 100000)
Msg::ProgressMeter(i + 1, numElements, true, "Reading elements");
}
}
else {
int numElementsPartial = 0;
while(numElementsPartial < numElements) {
int header[3];
if(fread(header, sizeof(int), 3, fp) != 3) {
fclose(fp);
return 0;
} if(swap) SwapBytes((char *)header, sizeof(int), 3);
int type = header[0];
int numElms = header[1];
int numTags = header[2];
int numVertices = MElement::getInfoMSH(type);
unsigned int n = 1 + numTags + numVertices;
int *data = new int[n];
for(int i = 0; i < numElms; i++) {
if(fread(data, sizeof(int), n, fp) != n) {
delete[] data;
fclose(fp);
return 0;
}
if(swap) SwapBytes((char *)data, sizeof(int), n);
int num = data[0];
int physical = (numTags > 0) ? data[1] : 0;
int elementary = (numTags > 1) ? data[2] : 0;
int numPartitions = (version >= 2.2 && numTags > 3) ? data[3] : 0;
int partition = (version < 2.2 && numTags > 2) ?
data[3] :
(version >= 2.2 && numTags > 3) ? data[4] : 0;
int parent = (version < 2.2 && numTags > 3) ||
(version >= 2.2 && numPartitions &&
numTags > 3 + numPartitions) ||
(version >= 2.2 && !numPartitions && numTags > 2) ?
data[numTags] :
0;
int *indices = &data[numTags + 1];
std::vector<MVertex *> vertices;
if(vertexVector.size()) {
if(!getMeshVertices(numVertices, indices, vertexVector, vertices,
minVertex)) {
delete[] data;
fclose(fp);
return 0;
}
}
else {
if(!getMeshVertices(numVertices, indices, vertexMap, vertices)) {
delete[] data;
fclose(fp);
return 0;
}
}
MElement *p = NULL;
bool own = false;
if(parent) {
std::map<int, MElement *>::iterator ite = elems.find(parent);
if(ite == elems.end())
Msg::Error(
"Parent (binary) element %d not found for element %d", parent,
num);
else {
p = ite->second;
parents[parent] = p;
}
std::set<MElement *>::iterator itpo = parentsOwned.find(p);
if(itpo == parentsOwned.end()) {
own = true;
parentsOwned.insert(p);
}
assert(p != NULL);
}
MElement *e = createElementMSH2(this, num, type, physical,
elementary, partition, vertices,
elements, physicals, own, p);
elems[num] = e;
elemreg[num] = elementary;
elemphy[num] = physical;
if(numPartitions > 1) for(int j = 0; j < numPartitions - 1; j++)
_ghostCells.insert(
std::pair<MElement *, short>(e, -data[5 + j]));
if(numElements > 100000)
Msg::ProgressMeter(numElementsPartial + i + 1, numElements, true,
"Reading elements");
}
delete[] data;
numElementsPartial += numElms;
}
}
for(int i = 0; i < 10; i++) elements[i].clear();
std::map<int, MElement *>::iterator ite;
for(ite = elems.begin(); ite != elems.end(); ite++) {
int num = ite->first;
MElement *e = ite->second;
if(parents.find(num) == parents.end()) {
int reg;
if(CTX::instance()->mesh.switchElementTags) {
reg = elemphy[num];
}
else {
reg = elemreg[num];
}
switch(e->getType()) {
case TYPE_PNT: elements[0][reg].push_back(e); break;
case TYPE_LIN: elements[1][reg].push_back(e); break;
case TYPE_TRI: elements[2][reg].push_back(e); break;
case TYPE_QUA: elements[3][reg].push_back(e); break;
case TYPE_TET: elements[4][reg].push_back(e); break;
case TYPE_HEX: elements[5][reg].push_back(e); break;
case TYPE_PRI: elements[6][reg].push_back(e); break;
case TYPE_PYR: elements[7][reg].push_back(e); break;
case TYPE_POLYG: elements[8][reg].push_back(e); break;
case TYPE_POLYH: elements[9][reg].push_back(e); break;
default:
Msg::Error("Wrong type of element");
fclose(fp);
return 0;
}
}
}
}
else if(!strncmp(&str[1], "NodeData", 8)) {
// there's some nodal post-processing data to read later on, so
// cache the vertex indexing data
if(vertexVector.size())
_vertexVectorCache = vertexVector;
else
_vertexMapCache = vertexMap;
postpro = true;
break;
}
else if(!strncmp(&str[1], "ElementData", 11) ||
!strncmp(&str[1], "ElementNodeData", 15)) {
// there's some element post-processing data to read later on
postpro = true;
break;
}
do {
if(!fgets(str, sizeof(str), fp) || feof(fp)) break;
} while(str[0] != '$');
}
// store the elements in their associated elementary entity. If the
// entity does not exist, create a new (discrete) one.
for(int i = 0; i < (int)(sizeof(elements) / sizeof(elements[0])); i++)
_storeElementsInEntities(elements[i]);
// associate the correct geometrical entity with each mesh vertex
_associateEntityWithMeshVertices();
// store the vertices in their associated geometrical entity
if(vertexVector.size())
_storeVerticesInEntities(vertexVector);
else
_storeVerticesInEntities(vertexMap);
// store the physical tags
for(int i = 0; i < 4; i++) _storePhysicalTagsInEntities(i, physicals[i]);
// copying periodic information from the mesh
if(!CTX::instance()->mesh.ignorePeriodicity) {
rewind(fp);
while(1) {
while(str[0] != '$') {
if(!fgets(str, sizeof(str), fp) || feof(fp)) break;
}
if(feof(fp)) break;
if(!strncmp(&str[1], "Periodic", 8) &&
strncmp(&str[1], "PeriodicNodes", 13)) {
readMSHPeriodicNodes(fp, this);
break;
}
do {
if(!fgets(str, sizeof(str), fp) || feof(fp)) break;
} while(str[0] != '$');
}
}
fclose(fp);
if(!CTX::instance()->mesh.ignorePeriodicity) alignPeriodicBoundaries();
return postpro ? 2 : 1;
}
template <class T>
static void writeElementMSH(FILE *fp, GModel *model, GEntity *ge, T *ele,
bool saveAll, double version, bool binary, int &num,
int elementary, std::vector<int> &physicals,
int parentNum = 0, int dom1Num = 0, int dom2Num = 0)
{
if(CTX::instance()->mesh.partitionOldStyleMsh2 && ge->getParentEntity()
&& ge->getParentEntity()->dim() > ge->dim())
return; // ignore partition boundaries
std::vector<short> ghosts;
if(model->getGhostCells().size()) {
std::pair<std::multimap<MElement *, short>::iterator,
std::multimap<MElement *, short>::iterator>
itp = model->getGhostCells().equal_range(ele);
for(std::multimap<MElement *, short>::iterator it = itp.first;
it != itp.second; it++)
ghosts.push_back(it->second);
}
if(saveAll)
ele->writeMSH2(fp, version, binary, ++num, elementary, 0, parentNum,
dom1Num, dom2Num, &ghosts);
else {
if(parentNum) parentNum = parentNum - physicals.size() + 1;
for(std::size_t j = 0; j < physicals.size(); j++) {
ele->writeMSH2(fp, version, binary, ++num, elementary, physicals[j],
parentNum, dom1Num, dom2Num, &ghosts); if(parentNum) parentNum++;
}
}
model->setMeshElementIndex(ele, num); // should really be a multimap...
if(CTX::instance()->mesh.saveTri && ele->getNumChildren())
num += ele->getNumChildren() - 1;
}
template <class T>
static void writeElementsMSH(FILE *fp, GModel *model, GEntity *ge,
std::vector<T *> &ele,
bool saveAll, int saveSinglePartition,
double version, bool binary, int &num,
int elementary, std::vector<int> &physicals)
{
if(CTX::instance()->mesh.partitionOldStyleMsh2 && ge->getParentEntity()
&& ge->getParentEntity()->dim() > ge->dim())
return; // ignore partition boundaries
// Hack to save each partition as a separate physical entity
if(saveSinglePartition < 0) {
if(ele.empty()) return;
int offset = -saveSinglePartition;
int maxPhysical = model->getMaxPhysicalNumber(ele[0]->getDim());
for(std::size_t i = 0; i < ele.size(); i++) {
std::vector<int> newPhysicals;
int newElementary = elementary;
if(elementary > 0) { // classical entity
newElementary = elementary * offset + ele[i]->getPartition();
for(std::size_t j = 0; j < physicals.size(); j++)
newPhysicals.push_back(physicals[j] * offset +
ele[i]->getPartition());
}
else if(elementary < 0) { // partition boundary
newPhysicals.push_back((maxPhysical - elementary) * offset);
}
ele[i]->setPartition(0);
writeElementMSH(fp, model, ge, ele[i], saveAll, version, binary, num,
newElementary, newPhysicals);
}
return;
}
for(std::size_t i = 0; i < ele.size(); i++) {
if(saveSinglePartition && ele[i]->getPartition() != saveSinglePartition)
continue;
if(ele[i]->getDomain(0)) continue;
int parentNum = 0;
MElement *parent = ele[i]->getParent();
if(parent) parentNum = model->getMeshElementIndex(parent);
writeElementMSH(fp, model, ge, ele[i], saveAll, version, binary, num,
elementary, physicals, parentNum);
}
}
static int getNumElementsMSH(GEntity *ge, bool saveAll, int saveSinglePartition)
{
if(CTX::instance()->mesh.partitionOldStyleMsh2 && ge->getParentEntity()
&& ge->getParentEntity()->dim() > ge->dim())
return 0; // ignore partition boundaries
int n = 0, p = saveAll ? 1 : ge->physicals.size();
if(saveSinglePartition < 0 && ge->tag() < 0) p = 1; // partition boundary
if(saveSinglePartition <= 0)
n = p * ge->getNumMeshElements();
else for(std::size_t i = 0; i < ge->getNumMeshElements(); i++)
if(ge->getMeshElement(i)->getPartition() == saveSinglePartition) n += p;
return n;
}
static int getNumElementsMSH(GModel *m, bool saveAll, int saveSinglePartition)
{
int n = 0;
for(GModel::viter it = m->firstVertex(); it != m->lastVertex(); ++it) {
n += getNumElementsMSH(*it, saveAll, saveSinglePartition);
if(!CTX::instance()->mesh.saveTri) {
for(std::size_t i = 0; i < (*it)->points.size(); i++)
if((*it)->points[i]->ownsParent())
n += (saveAll ? 1 : (*it)->physicals.size());
}
}
for(GModel::eiter it = m->firstEdge(); it != m->lastEdge(); ++it) {
n += getNumElementsMSH(*it, saveAll, saveSinglePartition);
if(!CTX::instance()->mesh.saveTri) {
for(std::size_t i = 0; i < (*it)->lines.size(); i++)
if((*it)->lines[i]->ownsParent())
n += (saveAll ? 1 : (*it)->physicals.size());
}
}
for(GModel::fiter it = m->firstFace(); it != m->lastFace(); ++it) {
n += getNumElementsMSH(*it, saveAll, saveSinglePartition);
if(CTX::instance()->mesh.saveTri) {
for(std::size_t i = 0; i < (*it)->polygons.size(); i++) {
int nbC = (*it)->polygons[i]->getNumChildren() - 1;
n += (saveAll ? nbC : nbC * (*it)->physicals.size());
}
}
else {
for(std::size_t i = 0; i < (*it)->triangles.size(); i++)
if((*it)->triangles[i]->ownsParent())
n += (saveAll ? 1 : (*it)->physicals.size());
for(std::size_t i = 0; i < (*it)->polygons.size(); i++)
if((*it)->polygons[i]->ownsParent())
n += (saveAll ? 1 : (*it)->physicals.size());
}
}
for(GModel::riter it = m->firstRegion(); it != m->lastRegion(); ++it) {
n += getNumElementsMSH(*it, saveAll, saveSinglePartition);
if(CTX::instance()->mesh.saveTri) {
for(std::size_t i = 0; i < (*it)->polyhedra.size(); i++) {
int nbC = (*it)->polyhedra[i]->getNumChildren() - 1;
n += (saveAll ? nbC : nbC * (*it)->physicals.size());
}
}
else {
for(std::size_t i = 0; i < (*it)->tetrahedra.size(); i++)
if((*it)->tetrahedra[i]->ownsParent())
n += (saveAll ? 1 : (*it)->physicals.size());
for(std::size_t i = 0; i < (*it)->polyhedra.size(); i++)
if((*it)->polyhedra[i]->ownsParent())
n += (saveAll ? 1 : (*it)->physicals.size());
}
n -= (*it)->trihedra.size();
}
return n;
}
static int _getElementary(GEntity *ge)
{
if(CTX::instance()->mesh.partitionOldStyleMsh2 && ge->getParentEntity()
&& ge->getParentEntity()->dim() == ge->dim()) {
// hack for backward compatibility of partitioned meshes in MSH2 format: use
// elementary tag of parent entity if they are of the same dimension
// (i.e. if they are not partition boundaries)
return ge->getParentEntity()->tag(); }
else {
return ge->tag();
}
}
int GModel::_writeMSH2(const std::string &name, double version, bool binary,
bool saveAll, bool saveParametric, double scalingFactor,
int elementStartNum, int saveSinglePartition,
bool append, bool renumberVertices)
{
FILE *fp;
if(append)
fp = Fopen(name.c_str(), binary ? "ab" : "a");
else
fp = Fopen(name.c_str(), binary ? "wb" : "w");
if(!fp) {
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
// binary format exists only in version 2
if(version > 1 || binary)
version = 2.2;
else
version = 1.0;
// if there are no physicals we save all the elements
if(noPhysicalGroups()) saveAll = true;
// get the number of vertices and index the vertices in a continuous
// sequence
int numVertices =
indexMeshVertices(saveAll, saveSinglePartition, renumberVertices);
// get the number of elements we need to save
int numElements = getNumElementsMSH(this, saveAll, saveSinglePartition);
if(version >= 2.0) {
fprintf(fp, "$MeshFormat\n");
fprintf(fp, "%g %d %d\n", version, binary ? 1 : 0, (int)sizeof(double));
if(binary) {
int one = 1;
fwrite(&one, sizeof(int), 1, fp);
fprintf(fp, "\n");
}
fprintf(fp, "$EndMeshFormat\n");
if(numPhysicalNames()) {
fprintf(fp, "$PhysicalNames\n");
fprintf(fp, "%d\n", numPhysicalNames());
for(piter it = firstPhysicalName(); it != lastPhysicalName(); it++) {
std::string name = it->second;
if(name.size() > 128) name.resize(128);
fprintf(fp, "%d %d \"%s\"\n", it->first.first, it->first.second,
name.c_str());
}
fprintf(fp, "$EndPhysicalNames\n");
}
if(CTX::instance()->mesh.saveTopology) writeMSHEntities(fp, this);
if(saveParametric)
fprintf(fp, "$ParametricNodes\n");
else
fprintf(fp, "$Nodes\n");
}
else
fprintf(fp, "$NOD\n");
fprintf(fp, "%d\n", numVertices);
std::vector<GEntity *> entities;
getEntities(entities);
for(std::size_t i = 0; i < entities.size(); i++)
for(std::size_t j = 0; j < entities[i]->mesh_vertices.size(); j++)
entities[i]->mesh_vertices[j]->writeMSH2(fp, binary, saveParametric,
scalingFactor);
if(binary) fprintf(fp, "\n");
if(version >= 2.0) {
if(saveParametric)
fprintf(fp, "$EndParametricNodes\n");
else
fprintf(fp, "$EndNodes\n");
fprintf(fp, "$Elements\n");
}
else {
fprintf(fp, "$ENDNOD\n");
fprintf(fp, "$ELM\n");
}
fprintf(fp, "%d\n", numElements);
int num = elementStartNum;
_elementIndexCache.clear();
// parents
if(!CTX::instance()->mesh.saveTri) {
for(viter it = firstVertex(); it != lastVertex(); ++it) {
for(std::size_t i = 0; i < (*it)->points.size(); i++)
if((*it)->points[i]->ownsParent())
writeElementMSH(fp, this, *it, (*it)->points[i]->getParent(), saveAll,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
for(eiter it = firstEdge(); it != lastEdge(); ++it) {
for(std::size_t i = 0; i < (*it)->lines.size(); i++)
if((*it)->lines[i]->ownsParent())
writeElementMSH(fp, this, *it, (*it)->lines[i]->getParent(), saveAll,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
for(fiter it = firstFace(); it != lastFace(); ++it) {
for(std::size_t i = 0; i < (*it)->triangles.size(); i++)
if((*it)->triangles[i]->ownsParent())
writeElementMSH(fp, this, *it, (*it)->triangles[i]->getParent(), saveAll,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
for(riter it = firstRegion(); it != lastRegion(); ++it) {
for(std::size_t i = 0; i < (*it)->tetrahedra.size(); i++)
if((*it)->tetrahedra[i]->ownsParent())
writeElementMSH(fp, this, *it, (*it)->tetrahedra[i]->getParent(), saveAll,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
for(fiter it = firstFace(); it != lastFace(); ++it) {
for(std::size_t i = 0; i < (*it)->polygons.size(); i++)
if((*it)->polygons[i]->ownsParent())
writeElementMSH(fp, this, *it, (*it)->polygons[i]->getParent(), saveAll,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
for(riter it = firstRegion(); it != lastRegion(); ++it) {
for(std::size_t i = 0; i < (*it)->polyhedra.size(); i++)
if((*it)->polyhedra[i]->ownsParent())
writeElementMSH(fp, this, *it, (*it)->polyhedra[i]->getParent(), saveAll, version, binary, num, _getElementary(*it),
(*it)->physicals);
}
}
// points
for(viter it = firstVertex(); it != lastVertex(); ++it) {
writeElementsMSH(fp, this, *it, (*it)->points, saveAll, saveSinglePartition,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
// lines
for(eiter it = firstEdge(); it != lastEdge(); ++it) {
writeElementsMSH(fp, this, *it, (*it)->lines, saveAll, saveSinglePartition,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
// triangles
for(fiter it = firstFace(); it != lastFace(); ++it) {
writeElementsMSH(fp, this, *it, (*it)->triangles, saveAll, saveSinglePartition,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
// quads
for(fiter it = firstFace(); it != lastFace(); ++it) {
writeElementsMSH(fp, this, *it, (*it)->quadrangles, saveAll, saveSinglePartition,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
// polygons
for(fiter it = firstFace(); it != lastFace(); it++) {
writeElementsMSH(fp, this, *it, (*it)->polygons, saveAll, saveSinglePartition,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
// tets
for(riter it = firstRegion(); it != lastRegion(); ++it) {
writeElementsMSH(fp, this, *it, (*it)->tetrahedra, saveAll, saveSinglePartition,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
// hexas
for(riter it = firstRegion(); it != lastRegion(); ++it) {
writeElementsMSH(fp, this, *it, (*it)->hexahedra, saveAll, saveSinglePartition,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
// prisms
for(riter it = firstRegion(); it != lastRegion(); ++it) {
writeElementsMSH(fp, this, *it, (*it)->prisms, saveAll, saveSinglePartition,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
// pyramids
for(riter it = firstRegion(); it != lastRegion(); ++it) {
writeElementsMSH(fp, this, *it, (*it)->pyramids, saveAll, saveSinglePartition,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
// polyhedra
for(riter it = firstRegion(); it != lastRegion(); ++it) {
writeElementsMSH(fp, this, *it, (*it)->polyhedra, saveAll, saveSinglePartition,
version, binary, num, _getElementary(*it),
(*it)->physicals);
}
// level set faces
for(fiter it = firstFace(); it != lastFace(); ++it) {
for(std::size_t i = 0; i < (*it)->triangles.size(); i++) {
MTriangle *t = (*it)->triangles[i];
if(t->getDomain(0))
writeElementMSH(fp, this, *it, t, saveAll, version, binary, num, _getElementary(*it), (*it)->physicals, 0,
getMeshElementIndex(t->getDomain(0)),
getMeshElementIndex(t->getDomain(1)));
}
for(std::size_t i = 0; i < (*it)->polygons.size(); i++) {
MPolygon *p = (*it)->polygons[i];
if(p->getDomain(0))
writeElementMSH(fp, this, *it, p, saveAll, version, binary, num,
_getElementary(*it), (*it)->physicals, 0,
getMeshElementIndex(p->getDomain(0)),
getMeshElementIndex(p->getDomain(1)));
}
}
// level set lines
for(eiter it = firstEdge(); it != lastEdge(); ++it) {
for(std::size_t i = 0; i < (*it)->lines.size(); i++) {
MLine *l = (*it)->lines[i];
if(l->getDomain(0))
writeElementMSH(fp, this, *it, l, saveAll, version, binary, num,
_getElementary(*it), (*it)->physicals, 0,
getMeshElementIndex(l->getDomain(0)),
getMeshElementIndex(l->getDomain(1)));
}
}
if(binary) fprintf(fp, "\n");
if(version >= 2.0) {
fprintf(fp, "$EndElements\n");
}
else {
fprintf(fp, "$ENDELM\n");
}
writeMSHPeriodicNodes(fp, entities, renumberVertices, saveAll);
fclose(fp);
return 1;
}
int GModel::_writePartitionedMSH2(const std::string &baseName, bool binary,
bool saveAll, bool saveParametric,
double scalingFactor)
{
int numElements;
int startNum = 0;
for(std::size_t partition = 1; partition <= getNumPartitions();
partition++) {
std::ostringstream sstream;
sstream << baseName << "_" << partition << ".msh";
numElements = getNumElementsMSH(this, saveAll, partition);
Msg::Info("Writing partition %d in file '%s'", partition,
sstream.str().c_str());
_writeMSH2(sstream.str(), 2.2, binary, saveAll, saveParametric,
scalingFactor, startNum, partition, false,
false); // NO RENUMBERING!
startNum += numElements; // update for next iteration in the loop
}
#if 0
if(_ghostCells.size()){
Msg::Info("Writing ghost cells in debug file 'ghosts.pos'");
FILE *fp = Fopen("ghosts.pos", "w");
fprintf(fp, "View \"ghosts\"{\n");
for(std::multimap<MElement*, short>::iterator it = _ghostCells.begin();
it != _ghostCells.end(); it++)
it->first->writePOS(fp, false, true, false, false, false, false);
fprintf(fp, "};\n"); fclose(fp);
}
#endif
return 1;
}