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Commit 9026059c authored by Christophe Geuzaine's avatar Christophe Geuzaine
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MED3 support, step 1: mesh I/O

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Geo/GModelIO_MED.cpp
+ 202
− 44
View file @ 9026059c
......@@ -29,6 +29,28 @@ extern "C" {
#include <med.h>
}
#if (MED_MAJOR_NUM == 3)
// To avoid to many ifdef's below we use defines for the bits of the
// API that did not change to much between MED2 and MED3. If we remove
// MED2 support at some point, please remove these defines and replace
// the symbols accordingly.
#define med_geometrie_element med_geometry_type
#define med_maillage med_mesh_type
#define MED_TAILLE_NOM MED_NAME_SIZE
#define MED_TAILLE_LNOM MED_LNAME_SIZE
#define MED_TAILLE_DESC MED_COMMENT_SIZE
#define MED_NON_STRUCTURE MED_UNSTRUCTURED_MESH
#define MED_LECTURE MED_ACC_RDONLY
#define MED_CREATION MED_ACC_CREAT
#define MEDouvrir MEDfileOpen
#define MEDversionDonner MEDlibraryNumVersion
#define MEDversionLire MEDfileNumVersionRd
#define MEDnMaa MEDnMesh
#define MEDfermer MEDfileClose
#define MEDnFam MEDnFamily
#define MEDfichDesEcr MEDfileCommentWr
#endif
med_geometrie_element msh2medElementType(int msh)
{
switch(msh) {
......@@ -47,6 +69,10 @@ med_geometrie_element msh2medElementType(int msh)
case MSH_HEX_20: return MED_HEXA20;
case MSH_PRI_15: return MED_PENTA15;
case MSH_PYR_13: return MED_PYRA13;
#if (MED_MAJOR_NUM == 3)
case MSH_QUA_9: return MED_QUAD9;
case MSH_HEX_27: return MED_HEXA27;
#endif
default: return MED_NONE;
}
}
......@@ -69,6 +95,10 @@ int med2mshElementType(med_geometrie_element med)
case MED_HEXA20: return MSH_HEX_20;
case MED_PENTA15: return MSH_PRI_15;
case MED_PYRA13: return MSH_PYR_13;
#if (MED_MAJOR_NUM == 3)
case MED_QUAD9: return MSH_QUA_9;
case MED_HEXA27: return MSH_HEX_27;
#endif
default: return 0;
}
}
......@@ -83,6 +113,9 @@ int med2mshNodeIndex(med_geometrie_element med, int k)
case MED_TRIA6:
case MED_QUAD4:
case MED_QUAD8:
#if (MED_MAJOR_NUM == 3)
case MED_QUAD9:
#endif
{
// same node numbering as in Gmsh
return k;
......@@ -104,6 +137,12 @@ int med2mshNodeIndex(med_geometrie_element med, int k)
10, 19, 9, 18, 17, 15, 12, 14, 13};
return map[k];
}
#if (MED_MAJOR_NUM == 3)
case MED_HEXA27: {
Msg::Error("FIXME HEX27 not implemented for MED3");
return k;
}
#endif
case MED_PENTA6: {
static const int map[6] = {0, 2, 1, 3, 5, 4};
return map[k];
......@@ -147,9 +186,19 @@ int GModel::readMED(const std::string &name)
std::vector<std::string> meshNames;
for(int i = 0; i < MEDnMaa(fid); i++){
char meshName[MED_TAILLE_NOM + 1], meshDesc[MED_TAILLE_DESC + 1];
med_int meshDim;
med_int spaceDim;
med_maillage meshType;
if(MEDmaaInfo(fid, i + 1, meshName, &meshDim, &meshType, meshDesc) < 0){
#if (MED_MAJOR_NUM == 3)
med_int meshDim, nStep;
char dtUnit[ MED_SNAME_SIZE + 1];
char axisName[3 * MED_SNAME_SIZE + 1], axisUnit[3 * MED_SNAME_SIZE + 1];
med_sorting_type sortingType;
med_axis_type axisType;
if(MEDmeshInfo(fid, i + 1, meshName, &spaceDim, &meshDim, &meshType, meshDesc,
dtUnit, &sortingType, &nStep, &axisType, axisName, axisUnit) < 0){
#else
if(MEDmaaInfo(fid, i + 1, meshName, &spaceDim, &meshType, meshDesc) < 0){
#endif
Msg::Error("Unable to read mesh information");
return 0;
}
......@@ -180,7 +229,7 @@ int GModel::readMED(const std::string &name)
int GModel::readMED(const std::string &name, int meshIndex)
{
med_idt fid = MEDouvrir((char*)name.c_str(), MED_LECTURE);
if(fid < 0) {
if(fid < 0){
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
......@@ -193,24 +242,43 @@ int GModel::readMED(const std::string &name, int meshIndex)
// read mesh info
char meshName[MED_TAILLE_NOM + 1], meshDesc[MED_TAILLE_DESC + 1];
med_int meshDim;
med_int spaceDim;
med_maillage meshType;
if(MEDmaaInfo(fid, meshIndex + 1, meshName, &meshDim, &meshType, meshDesc) < 0){
#if (MED_MAJOR_NUM == 3)
med_int meshDim, nStep;
char dtUnit[MED_SNAME_SIZE + 1];
char axisName[3 * MED_SNAME_SIZE + 1], axisUnit[3 * MED_SNAME_SIZE + 1];
med_sorting_type sortingType;
med_axis_type axisType;
if(MEDmeshInfo(fid, meshIndex + 1, meshName, &spaceDim, &meshDim, &meshType, meshDesc,
dtUnit, &sortingType, &nStep, &axisType, axisName, axisUnit) < 0){
#else
if(MEDmaaInfo(fid, meshIndex + 1, meshName, &spaceDim, &meshType, meshDesc) < 0){
#endif
Msg::Error("Unable to read mesh information");
return 0;
}
setName(meshName);
if(meshType == MED_NON_STRUCTURE){
Msg::Info("Reading %d-D unstructured mesh <<%s>>", meshDim, meshName);
Msg::Info("Reading %d-D unstructured mesh <<%s>>", spaceDim, meshName);
}
else{
Msg::Error("Cannot read structured mesh");
return 0;
}
med_int vf[3];
MEDversionLire(fid, &vf[0], &vf[1], &vf[2]);
// read nodes
#if (MED_MAJOR_NUM == 3)
med_bool changeOfCoord, geoTransform;
med_int numNodes = MEDmeshnEntity(fid, meshName, MED_NO_DT, MED_NO_IT, MED_NODE,
MED_NO_GEOTYPE, MED_COORDINATE, MED_NO_CMODE,
&changeOfCoord, &geoTransform);
#else
med_int numNodes = MEDnEntMaa(fid, meshName, MED_COOR, MED_NOEUD, MED_NONE,
MED_NOD);
#endif
if(numNodes < 0){
Msg::Error("Could not read number of MED nodes");
return 0;
......@@ -220,44 +288,79 @@ int GModel::readMED(const std::string &name, int meshIndex)
return 0;
}
std::vector<MVertex*> verts(numNodes);
std::vector<med_float> coord(meshDim * numNodes);
std::vector<char> coordName(meshDim * MED_TAILLE_PNOM + 1);
std::vector<char> coordUnit(meshDim * MED_TAILLE_PNOM + 1);
std::vector<med_float> coord(spaceDim * numNodes);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshNodeCoordinateRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_FULL_INTERLACE,
&coord[0]) < 0){
#else
std::vector<char> coordName(spaceDim * MED_TAILLE_PNOM + 1);
std::vector<char> coordUnit(spaceDim * MED_TAILLE_PNOM + 1);
med_repere rep;
if(MEDcoordLire(fid, meshName, meshDim, &coord[0], MED_FULL_INTERLACE,
if(MEDcoordLire(fid, meshName, spaceDim, &coord[0], MED_FULL_INTERLACE,
MED_ALL, 0, 0, &rep, &coordName[0], &coordUnit[0]) < 0){
#endif
Msg::Error("Could not read MED node coordinates");
return 0;
}
std::vector<med_int> nodeTags(numNodes);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshEntityNumberRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_NODE,
MED_NO_GEOTYPE, &nodeTags[0]) < 0)
#else
if(MEDnumLire(fid, meshName, &nodeTags[0], numNodes, MED_NOEUD, MED_NONE) < 0)
#endif
nodeTags.clear();
for(int i = 0; i < numNodes; i++)
verts[i] = new MVertex(coord[meshDim * i],
(meshDim > 1) ? coord[meshDim * i + 1] : 0.,
(meshDim > 2) ? coord[meshDim * i + 2] : 0.,
verts[i] = new MVertex(coord[spaceDim * i],
(spaceDim > 1) ? coord[spaceDim * i + 1] : 0.,
(spaceDim > 2) ? coord[spaceDim * i + 2] : 0.,
0, nodeTags.empty() ? 0 : nodeTags[i]);
// read elements (loop over all possible MSH element types)
for(int mshType = 0; mshType < MSH_NUM_TYPE; mshType++){
med_geometrie_element type = msh2medElementType(mshType);
if(type == MED_NONE) continue;
#if (MED_MAJOR_NUM == 3)
med_bool changeOfCoord;
med_bool geoTransform;
med_int numEle = MEDmeshnEntity(fid, meshName, MED_NO_DT, MED_NO_IT, MED_CELL,
type, MED_CONNECTIVITY, MED_NODAL, &changeOfCoord,
&geoTransform);
#else
med_int numEle = MEDnEntMaa(fid, meshName, MED_CONN, MED_MAILLE, type, MED_NOD);
#endif
if(numEle <= 0) continue;
int numNodPerEle = type % 100;
std::vector<med_int> conn(numEle * numNodPerEle);
if(MEDconnLire(fid, meshName, meshDim, &conn[0], MED_FULL_INTERLACE, 0, MED_ALL,
MED_MAILLE, type, MED_NOD) < 0) {
#if (MED_MAJOR_NUM == 3)
if(MEDmeshElementConnectivityRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_CELL,
type, MED_NODAL, MED_FULL_INTERLACE, &conn[0]) < 0){
#else
if(MEDconnLire(fid, meshName, spaceDim, &conn[0], MED_FULL_INTERLACE, 0, MED_ALL,
MED_MAILLE, type, MED_NOD) < 0){
#endif
Msg::Error("Could not read MED elements");
return 0;
}
std::vector<med_int> fam(numEle);
if(MEDfamLire(fid, meshName, &fam[0], numEle, MED_MAILLE, type) < 0) {
#if (MED_MAJOR_NUM == 3)
if(MEDmeshEntityFamilyNumberRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_CELL,
type, &fam[0]) < 0){
#else
if(MEDfamLire(fid, meshName, &fam[0], numEle, MED_MAILLE, type) < 0){
#endif
Msg::Error("Could not read MED families");
return 0;
}
std::vector<med_int> eleTags(numEle);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshEntityNumberRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_CELL,
type, &eleTags[0]) < 0)
#else
if(MEDnumLire(fid, meshName, &eleTags[0], numEle, MED_MAILLE, type) < 0)
#endif
eleTags.clear();
std::map<int, std::vector<MElement*> > elements;
MElementFactory factory;
......@@ -275,13 +378,18 @@ int GModel::readMED(const std::string &name, int meshIndex)
// read family info
med_int numFamilies = MEDnFam(fid, meshName);
if(numFamilies < 0) {
if(numFamilies < 0){
Msg::Error("Could not read MED families");
return 0;
}
for(int i = 0; i < numFamilies; i++) {
for(int i = 0; i < numFamilies; i++){
#if (MED_MAJOR_NUM == 3)
med_int numAttrib = (vf[0] == 3) ? 0 : MEDnFamily23Attribute(fid, meshName, i + 1);
med_int numGroups = MEDnFamilyGroup(fid, meshName, i + 1);
#else
med_int numAttrib = MEDnAttribut(fid, meshName, i + 1);
med_int numGroups = MEDnGroupe(fid, meshName, i + 1);
#endif
if(numAttrib < 0 || numGroups < 0){
Msg::Error("Could not read MED groups or attributes");
return 0;
......@@ -292,35 +400,55 @@ int GModel::readMED(const std::string &name, int meshIndex)
std::vector<char> groupNames(MED_TAILLE_LNOM * numGroups + 1);
char familyName[MED_TAILLE_NOM + 1];
med_int familyNum;
#if (MED_MAJOR_NUM == 3)
if(vf[0] == 3){ // MED3 file
if(MEDfamilyInfo(fid, meshName, i + 1, familyName, &familyNum, &groupNames[0]) < 0){
Msg::Error("Could not read info for MED3 family %d", i + 1);
continue;
}
}
else{
if(MEDfamily23Info(fid, meshName, i + 1, familyName, &attribId[0],
&attribVal[0], &attribDes[0], &familyNum, &groupNames[0]) < 0){
Msg::Error("Could not read info for MED2 family %d", i + 1);
continue;
}
}
#else
if(MEDfamInfo(fid, meshName, i + 1, familyName, &familyNum, &attribId[0],
&attribVal[0], &attribDes[0], &numAttrib, &groupNames[0],
&numGroups) < 0) {
&numGroups) < 0){
Msg::Error("Could not read info for MED family %d", i + 1);
continue;
}
else{
// family tags are unique (for all dimensions)
GEntity *ge;
if((ge = getRegionByTag(-familyNum))){}
else if((ge = getFaceByTag(-familyNum))){}
else if((ge = getEdgeByTag(-familyNum))){}
else ge = getVertexByTag(-familyNum);
if(ge){
elementaryNames[std::pair<int, int>(ge->dim(), -familyNum)] = familyName;
if(numGroups > 0){
for(int j = 0; j < numGroups; j++) {
char tmp[MED_TAILLE_LNOM + 1];
strncpy(tmp, &groupNames[j * MED_TAILLE_LNOM], MED_TAILLE_LNOM);
tmp[MED_TAILLE_LNOM] = '\0';
ge->physicals.push_back(setPhysicalName(tmp, ge->dim()));
}
#endif
// family tags are unique (for all dimensions)
GEntity *ge;
if((ge = getRegionByTag(-familyNum))){}
else if((ge = getFaceByTag(-familyNum))){}
else if((ge = getEdgeByTag(-familyNum))){}
else ge = getVertexByTag(-familyNum);
if(ge){
elementaryNames[std::pair<int, int>(ge->dim(), -familyNum)] = familyName;
if(numGroups > 0){
for(int j = 0; j < numGroups; j++){
char tmp[MED_TAILLE_LNOM + 1];
strncpy(tmp, &groupNames[j * MED_TAILLE_LNOM], MED_TAILLE_LNOM);
tmp[MED_TAILLE_LNOM] = '\0';
ge->physicals.push_back(setPhysicalName(tmp, ge->dim()));
}
}
}
}
// check if we need to read some post-processing data later
#if (MED_MAJOR_NUM == 3)
bool postpro = (MEDnField(fid) > 0) ? true : false;
#else
bool postpro = (MEDnChamp(fid, 0) > 0) ? true : false;
#endif
if(MEDfermer(fid) < 0){
Msg::Error("Unable to close file '%s'", (char*)name.c_str());
return 0;
......@@ -353,30 +481,45 @@ static void writeElementsMED(med_idt &fid, char *meshName, std::vector<med_int>
std::vector<med_int> &fam, med_geometrie_element type)
{
if(fam.empty()) return;
#if (MED_MAJOR_NUM == 3)
if(MEDmeshElementWr(fid, meshName, MED_NO_DT, MED_NO_IT, 0., MED_CELL, type,
MED_NODAL, MED_FULL_INTERLACE, (med_int)fam.size(),
&conn[0], MED_FALSE, 0, MED_FALSE, 0, MED_TRUE, &fam[0]) < 0)
#else
if(MEDelementsEcr(fid, meshName, (med_int)3, &conn[0], MED_FULL_INTERLACE,
0, MED_FAUX, 0, MED_FAUX, &fam[0], (med_int)fam.size(),
MED_MAILLE, type, MED_NOD) < 0)
#endif
Msg::Error("Could not write elements");
}
int GModel::writeMED(const std::string &name, bool saveAll, double scalingFactor)
{
med_idt fid = MEDouvrir((char*)name.c_str(), MED_CREATION);
if(fid < 0) {
if(fid < 0){
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
// write header
if(MEDfichDesEcr(fid, (char*)"MED file generated by Gmsh") < 0) {
if(MEDfichDesEcr(fid, (char*)"MED file generated by Gmsh") < 0){
Msg::Error("Unable to write MED descriptor");
return 0;
}
char *meshName = (char*)getName().c_str();
// Gmsh always writes 3D unstructured meshes
if(MEDmaaCr(fid, meshName, 3, MED_NON_STRUCTURE, (char*)"gmsh") < 0){
#if (MED_MAJOR_NUM == 3)
char dtUnit[MED_SNAME_SIZE + 1] = "";
char axisName[3 * MED_SNAME_SIZE + 1] = "";
char axisUnit[3 * MED_SNAME_SIZE + 1] = "";
if(MEDmeshCr(fid, meshName, 3, 3, MED_UNSTRUCTURED_MESH, "Mesh created with Gmsh",
dtUnit, MED_SORT_DTIT, MED_CARTESIAN, axisName, axisUnit) < 0){
#else
if(MEDmaaCr(fid, meshName, 3, MED_NON_STRUCTURE,
(char*)"Mesh created with Gmsh") < 0){
#endif
Msg::Error("Could not create MED mesh");
return 0;
}
......@@ -395,11 +538,14 @@ int GModel::writeMED(const std::string &name, bool saveAll, double scalingFactor
getEntities(entities);
std::map<GEntity*, int> families;
// write the families
{
// always create a "0" family, with no groups or attributes
#if (MED_MAJOR_NUM == 3)
if(MEDfamilyCr(fid, meshName, "F_0", 0, 0, "") < 0)
#else
if(MEDfamCr(fid, meshName, (char*)"F_0", 0, 0, 0, 0, 0, 0, 0) < 0)
#endif
Msg::Error("Could not create MED family 0");
// create one family per elementary entity, with one group per
......@@ -422,16 +568,22 @@ int GModel::writeMED(const std::string &name, bool saveAll, double scalingFactor
}
else
groupName += tmp;
groupName.resize((j + 1) * 80, ' ');
groupName.resize((j + 1) * MED_TAILLE_LNOM, ' ');
}
#if (MED_MAJOR_NUM == 3)
if(MEDfamilyCr(fid, meshName, familyName.c_str(),
(med_int)num, (med_int)entities[i]->physicals.size(),
groupName.c_str()) < 0)
#else
if(MEDfamCr(fid, meshName, (char*)familyName.c_str(),
(med_int)num, 0, 0, 0, 0, (char*)groupName.c_str(),
(med_int)entities[i]->physicals.size()) < 0)
#endif
Msg::Error("Could not create MED family %d", num);
}
}
}
// write the nodes
{
std::vector<med_float> coord;
......@@ -451,6 +603,11 @@ int GModel::writeMED(const std::string &name, bool saveAll, double scalingFactor
Msg::Error("No nodes to write in MED mesh");
return 0;
}
#if (MED_MAJOR_NUM == 3)
if(MEDmeshNodeWr(fid, meshName, MED_NO_DT, MED_NO_IT, 0., MED_FULL_INTERLACE,
(med_int)fam.size(), &coord[0], MED_FALSE, "", MED_FALSE, 0,
MED_TRUE, &fam[0]) < 0)
#else
char coordName[3 * MED_TAILLE_PNOM + 1] =
"x y z ";
char coordUnit[3 * MED_TAILLE_PNOM + 1] =
......@@ -458,9 +615,10 @@ int GModel::writeMED(const std::string &name, bool saveAll, double scalingFactor
if(MEDnoeudsEcr(fid, meshName, (med_int)3, &coord[0], MED_FULL_INTERLACE,
MED_CART, coordName, coordUnit, 0, MED_FAUX, 0, MED_FAUX,
&fam[0], (med_int)fam.size()) < 0)
#endif
Msg::Error("Could not write nodes");
}
// write the elements
{
med_geometrie_element typ = MED_NONE;
......
Post/PViewDataGModelIO.cpp
+ 18
− 0
View file @ 9026059c
......@@ -276,6 +276,22 @@ extern "C" {
#include <med.h>
}
#if (MED_MAJOR_NUM == 3)
bool PViewDataGModel::readMED(std::string fileName, int fileIndex)
{
Msg::Error("FIXME reading MED3 fields is not implemented yet");
return false;
}
bool PViewDataGModel::writeMED(std::string fileName)
{
Msg::Error("FIXME writing MED3 fields is not implemented yet");
return false;
}
#else
extern int med2mshElementType(med_geometrie_element med);
extern int med2mshNodeIndex(med_geometrie_element med, int k);
......@@ -597,6 +613,8 @@ bool PViewDataGModel::writeMED(std::string fileName)
return true;
}
#endif
#else
bool PViewDataGModel::readMED(std::string fileName, int fileIndex)
......
Post/PViewIO.cpp
+ 13
− 1
View file @ 9026059c
......@@ -243,15 +243,27 @@ extern "C" {
bool PView::readMED(std::string fileName, int fileIndex)
{
#if (MED_MAJOR_NUM == 3)
med_idt fid = MEDfileOpen(fileName.c_str(), MED_ACC_RDONLY);
#else
med_idt fid = MEDouvrir((char*)fileName.c_str(), MED_LECTURE);
#endif
if(fid < 0) {
Msg::Error("Unable to open file '%s'", fileName.c_str());
return false;
}
#if (MED_MAJOR_NUM == 3)
med_int numFields = MEDnField(fid);
#else
med_int numFields = MEDnChamp(fid, 0);
#endif
#if (MED_MAJOR_NUM == 3)
if(MEDfileClose(fid) < 0){
#else
if(MEDfermer(fid) < 0){
#endif
Msg::Error("Unable to close file '%s'", fileName.c_str());
return false;
}
......@@ -280,7 +292,7 @@ bool PView::readMED(std::string fileName, int fileIndex)
bool PView::readMED(std::string fileName, int fileIndex)
{
Msg::Error("Gmsh must be compiled with MED support to read '%s'",
fileName.c_str());
fileName.c_str());
return false;
}
......
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