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dumper_paraview_mesh.cc
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dumper_paraview_mesh.cc
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/**
* @file dumper_paraview_mesh.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
*
* @date Tue Jul 22 14:47:56 2014
*
* @brief This dumper allows to generate paraview files for vizualization
*
* @section LICENSE
*
* Copyright INRIA and CEA
*
* The LibMultiScale is a C++ parallel framework for the multiscale
* coupling methods dedicated to material simulations. This framework
* provides an API which makes it possible to program coupled simulations
* and integration of already existing codes.
*
* This Project was initiated in a collaboration between INRIA Futurs Bordeaux
* within ScAlApplix team and CEA/DPTA Ile de France.
* The project is now continued at the Ecole Polytechnique Fédérale de Lausanne
* within the LSMS/ENAC laboratory.
*
* This software is governed by the CeCILL-C license under French law and
* abiding by the rules of distribution of free software. You can use,
* modify and/ or redistribute the software under the terms of the CeCILL-C
* license as circulated by CEA, CNRS and INRIA at the following URL
* "http://www.cecill.info".
*
* As a counterpart to the access to the source code and rights to copy,
* modify and redistribute granted by the license, users are provided only
* with a limited warranty and the software's author, the holder of the
* economic rights, and the successive licensors have only limited
* liability.
*
* In this respect, the user's attention is drawn to the risks associated
* with loading, using, modifying and/or developing or reproducing the
* software by the user in light of its specific status of free software,
* that may mean that it is complicated to manipulate, and that also
* therefore means that it is reserved for developers and experienced
* professionals having in-depth computer knowledge. Users are therefore
* encouraged to load and test the software's suitability as regards their
* requirements in conditions enabling the security of their systems and/or
* data to be ensured and, more generally, to use and operate it in the
* same conditions as regards security.
*
* The fact that you are presently reading this means that you have had
* knowledge of the CeCILL-C license and that you accept its terms.
*
*/
#include "lm_common.hh"
#include "lib_continuum.hh"
#include "dumper_paraview.hh"
#include "compute.hh"
#include "filter.hh"
#include "filter_manager.hh"
#include "communicator.hh"
#include "units_converter.hh"
/* -------------------------------------------------------------------------- */
#include <sys/stat.h>
#include <sys/types.h>
/* -------------------------------------------------------------------------- */
__BEGIN_LIBMULTISCALE__
template <typename Cont>
void DumperParaview<Cont>::dump(Cont & cont){
static const UInt Dim = Cont::Dim;
Communicator & comm = Communicator::getCommunicator();
CommGroup group = cont.getCommGroup();
UInt my_rank = comm.groupRank(lm_my_proc_id,group);
UInt group_size = comm.getNBprocsOnGroup(group);
if (my_rank == 0){
openPVTU();
file.printf("<VTKFile type=\"PUnstructuredGrid\" version=\"0.1\" ");
// #ifdef BIG_ENDIAN
// file.printf("byte_order=\"BigEndian\">\n");
// #else
file.printf("byte_order=\"LittleEndian\">\n");
// #endif
file.printf("<PUnstructuredGrid GhostLevel=\"1\">\n");
file.printf("<PPointData>\n");
if (dep_serie)
paraHelper.PDataArray("displacements",3);
if (p0_serie)
paraHelper.PDataArray("P0",3);
if (vel_serie)
paraHelper.PDataArray("velocities",3);
if (force_serie)
paraHelper.PDataArray("force",3);
if (applied_force_serie)
paraHelper.PDataArray("applied_force",3);
if (temperature_serie)
paraHelper.PDataArray("temperature",1);
if (temperatureVar_serie)
paraHelper.PDataArray("temperatureVariation",1);
if (heatCapacity_serie)
paraHelper.PDataArray("heatCapacity",1);
if (heatRate_serie)
paraHelper.PDataArray("heatRate",1);
if (external_heatRate_serie)
paraHelper.PDataArray("externalHeatRate",1);
if (id_serie)
paraHelper.PDataArray("id",1);
if (mass_serie)
paraHelper.PDataArray("mass",1);
if (flag_boundary)
paraHelper.PDataArray("blocked_dof",3);
if (barycenters_serie)
paraHelper.PDataArray("barycenters",3);
if (proc_serie)
paraHelper.PDataArray("procs",1);
if (alpha_serie)
paraHelper.PDataArray("alpha",1);
for (UInt i = 0; i < additional_fields.size(); ++i) {
FilterID additional_field = additional_fields[i];
if (additional_field != invalidFilter){
ComputeInterface * ptr =
dynamic_cast<ComputeInterface *>(FilterManager::getManager().getObject(additional_field));
if (ptr) {
ptr->build();
paraHelper.PDataArray(additional_field,ptr->getDim());
}
}
}
file.printf("</PPointData>");
if (stress_serie || strain_serie){
file.printf("<PCellData>\n");
}
if (stress_serie && Dim == 3) paraHelper.PDataArray("stress",6);
if (strain_serie && Dim == 3) paraHelper.PDataArray("strain",6);
if (stress_serie && Dim == 2) paraHelper.PDataArray("stress",3);
if (strain_serie && Dim == 2) paraHelper.PDataArray("strain",3);
if (stress_serie || strain_serie){
file.printf("</PCellData>\n");
}
file.printf("<PPoints><PDataArray type=\"Float64\" NumberOfComponents=\"3\" format=\"ascii\"/></PPoints>");
if (group_size > 1)
for (UInt l=0 ; l < group_size; ++l){
file.printf("<Piece Source=\"%s-VTUs/%s_pvf%.4d.proc%.4d.vtu\"/>\n",
this->getID().c_str(),this->getID().c_str(),this->action_step,l);
}
else
file.printf("<Piece Source=\"%s-VTUs/%s_pvf%.4d.proc%.4d.vtu\"/>\n",
this->getID().c_str(),this->getID().c_str(),this->action_step,lm_my_proc_id);
file.printf("</PUnstructuredGrid></VTKFile>");
file.close();
}
openVTU();
typename Cont::ContainerElems & contElems = cont.getContainerElems();
typename Cont::ContainerNodes & contNodes = cont.getContainerNodes();
UInt nb = contNodes.nbElem(dt_all);
UInt nbElems = contElems.nbElem();
std::vector<UInt > nodes;
UInt compteur;
/* start */
paraHelper.write_header(nb,nbElems);
UnitsConverter unit;
unit.setInUnits(code_unit_system);
unit.setOutUnits(this->dump_unit_system);
unit.computeConversions();
paraHelper.startDofList();
typedef typename Cont::ContainerNodes::Ref RefNd;
typedef typename Cont::ContainerElems::Ref RefElt;
typename Cont::ContainerNodes::iterator itNodes = contNodes.getIterator(dt_all);
typename Cont::ContainerElems::iterator itElems = contElems.getIterator();
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext()) {
Real X[Dim];
n.getPositions0(X);
for (UInt i = 0; i < Dim; ++i)
paraHelper.pushReal(X[i] * unit.getConversion<Length>());
for (UInt i = Dim; i < 3; ++i) paraHelper.pushReal(0.0);
}
paraHelper.endDofList();
paraHelper.startCellsConnectivityList();
for (RefElt el = itElems.getFirst();!itElems.end();el = itElems.getNext())
{
if (el.isAltered()) nodes = el.getAlteredConnectivity();
else el.localIndexes(nodes);
UInt nd_sz = nodes.size();
if (nd_sz == 10) nd_sz = 4;
for (UInt j=0;j < nd_sz;++j)
{
paraHelper.pushInteger(nodes[j]);
}
}
paraHelper.endCellsConnectivityList();
paraHelper.startCellsoffsetsList();
compteur = 0;
for (RefElt el = itElems.getFirst();!itElems.end();el = itElems.getNext())
{
el.localIndexes(nodes);
if (nodes.size() == 10)
compteur += 4;
else
compteur += nodes.size();
paraHelper.pushInteger(compteur);
}
paraHelper.endCellsoffsetsList();
paraHelper.startCellstypesList();
UInt code_type= UINT_MAX;
for (RefElt el = itElems.getFirst();!itElems.end();el = itElems.getNext())
{
el.localIndexes(nodes);
switch(nodes.size())
{
case 2 : code_type = 3;break;
case 3 : code_type = 5;break;
case 8 : code_type = 12;break;
case 4 : code_type = 10;break;
case 10 : code_type = 10;break;
default: LM_FATAL("unable to dump for VTK : " << nodes.size());
}
paraHelper.pushInteger(code_type);
}
paraHelper.endCellstypesList();
paraHelper.startPointDataList();
if (dep_serie){
paraHelper.startData("displacements",3);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
Real x = n.displacement(0)*unit.getConversion<Length>();
Real y = 0;
Real z = 0;
if (Dim > 1)
y = n.displacement(1)*unit.getConversion<Length>();
if (Dim > 2)
z = n.displacement(2)*unit.getConversion<Length>();
paraHelper.pushReal(x);
paraHelper.pushReal(y);
paraHelper.pushReal(z);
}
paraHelper.endData();
}
if (p0_serie){
paraHelper.startData("P0",3);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
Real x = n.position0(0)*unit.getConversion<Length>();
Real y = 0;
Real z = 0;
if (Dim > 1)
y = n.position0(1)*unit.getConversion<Length>();
if (Dim > 2)
z = n.position0(2)*unit.getConversion<Length>();
paraHelper.pushReal(x);
paraHelper.pushReal(y);
paraHelper.pushReal(z);
}
paraHelper.endData();
}
if (vel_serie){
paraHelper.startData("velocities",3);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
Real x = n.velocity(0);
Real y = 0;
Real z = 0;
if (Dim > 1)
y = n.velocity(1);
if (Dim > 2)
z = n.velocity(2);
paraHelper.pushReal(x);
paraHelper.pushReal(y);
paraHelper.pushReal(z);
}
paraHelper.endData();
}
if (force_serie){
paraHelper.startData("force",3);
UInt cpt=0;
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
Real x = n.force(0);
Real y = 0;
Real z = 0;
if (Dim > 1)
y = n.force(1);
if (Dim > 2)
z = n.force(2);
paraHelper.pushReal(x);
paraHelper.pushReal(y);
paraHelper.pushReal(z);
++cpt;
}
paraHelper.endData();
}
if (applied_force_serie){
paraHelper.startData("applied_force",3);
UInt cpt=0;
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
Real x = n.appliedForce(0);
Real y = 0;
Real z = 0;
if (Dim > 1)
y = n.appliedForce(1);
if (Dim > 2)
z = n.appliedForce(2);
paraHelper.pushReal(x);
paraHelper.pushReal(y);
paraHelper.pushReal(z);
++cpt;
}
paraHelper.endData();
}
if (temperature_serie){
paraHelper.startData("temperature",1);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
Real t = n.temperature();
paraHelper.pushReal(t);
}
paraHelper.endData();
}
if (temperatureVar_serie){
paraHelper.startData("temperatureVariation",1);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
Real t = n.temperatureVar();
paraHelper.pushReal(t);
}
paraHelper.endData();
}
if (heatCapacity_serie){
paraHelper.startData("heatCapacity",1);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext()){
Real t = n.capacity();
paraHelper.pushReal(t);
}
paraHelper.endData();
}
if (heatRate_serie){
paraHelper.startData("heatRate",1);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext()){
Real t = n.heatRate();
paraHelper.pushReal(t);
}
paraHelper.endData();
}
if (external_heatRate_serie){
paraHelper.startData("externalHeatRate",1);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext()){
Real t = n.externalHeatRate();
paraHelper.pushReal(t);
}
paraHelper.endData();
}
if (id_serie){
paraHelper.startData("id",1);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
paraHelper.pushReal(n.id());
}
paraHelper.endData();
}
if (mass_serie){
paraHelper.startData("mass",1);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
Real mass = n.mass()*unit.getConversion<Mass>();
paraHelper.pushReal(mass);
}
paraHelper.endData();
}
if (flag_boundary){
paraHelper.startData("blocked_dof", 3);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
for (UInt i = 0 ; i < Dim ; ++i) {
Real is_blocked = n.boundary(i);
paraHelper.pushReal(is_blocked);
}
}
paraHelper.endData();
}
if (barycenters_serie){
paraHelper.startData("barycenters",3);
Real x=0,y=0,z=0;
UInt cpt = 0;
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
x += n.position0(0);
y += n.position0(1);
z += n.position0(2);
++cpt;
}
x /= cpt;
y /= cpt;
z /= cpt;
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
paraHelper.pushReal(x);
paraHelper.pushReal(y);
paraHelper.pushReal(z);
}
paraHelper.endData();
}
if (proc_serie){
paraHelper.startData("procs",1);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
paraHelper.pushReal(lm_my_proc_id);
}
paraHelper.endData();
}
if (alpha_serie){
paraHelper.startData("alpha",1);
for (RefNd n = itNodes.getFirst();!itNodes.end();n = itNodes.getNext())
{
paraHelper.pushReal(n.alpha());
}
paraHelper.endData();
}
for (UInt i = 0; i < additional_fields.size(); ++i) {
FilterID additional_field = additional_fields[i];
if (additional_field != invalidFilter){
ComputeInterface * ptr =
dynamic_cast<ComputeInterface *>(FilterManager::getManager().getObject(additional_field));
if (ptr) {
dumpField(additional_field,cont,*ptr,ptr->getDim());
}
}
}
paraHelper.endPointDataList();
if (stress_serie || strain_serie) paraHelper.startCellDataList();
if (stress_serie){
if (Dim == 3) paraHelper.startData("stress",6);
if (Dim == 2) paraHelper.startData("stress",3);
for (RefElt el = itElems.getFirst();!itElems.end();el = itElems.getNext()){
// order of dimensions for paraview: xx, yy, zz, xy yz xz
// order of dimensions for libmultiscale : akantu COLmajor
paraHelper.pushReal(el.stress(0 + 0*Dim)*unit.getConversion<Pressure>());
if (Dim == 2) {
paraHelper.pushReal(el.stress(1 + 1*Dim)*unit.getConversion<Pressure>());
paraHelper.pushReal(el.stress(0 + 1*Dim)*unit.getConversion<Pressure>());
} else if(Dim == 3){
paraHelper.pushReal(el.stress(1 + 1*Dim)*unit.getConversion<Pressure>());
paraHelper.pushReal(el.stress(2 + 2*Dim)*unit.getConversion<Pressure>());
paraHelper.pushReal(el.stress(0 + 1*Dim)*unit.getConversion<Pressure>());
paraHelper.pushReal(el.stress(1 + 2*Dim)*unit.getConversion<Pressure>());
paraHelper.pushReal(el.stress(0 + 2*Dim)*unit.getConversion<Pressure>());
}
}
paraHelper.endData();
}
if (strain_serie){
if (Dim == 3) paraHelper.startData("strain",6);
if (Dim == 2) paraHelper.startData("strain",3);
for (RefElt el = itElems.getFirst();!itElems.end();el = itElems.getNext()){
// order of dimensions for paraview: xx, yy, zz, xy yz xz,
// order of dimensions for libmultiscale : akantu COLmajor
paraHelper.pushReal(el.strain(0 + 0*Dim));
if (Dim == 2) {
paraHelper.pushReal(el.strain(1 + 1*Dim));
paraHelper.pushReal(el.strain(0 + 1*Dim));
} else if(Dim == 3){
paraHelper.pushReal(el.strain(1 + 1*Dim));
paraHelper.pushReal(el.strain(2 + 2*Dim));
paraHelper.pushReal(el.strain(0 + 1*Dim));
paraHelper.pushReal(el.strain(1 + 2*Dim));
paraHelper.pushReal(el.strain(0 + 2*Dim));
}
}
paraHelper.endData();
}
if (stress_serie || strain_serie) paraHelper.endCellDataList();
// paraHelper.startData(file,"deformation",3);
// for (RefElt el = itNodes.GetFirstElem();!itNodes.endElem();el = itNodes.getNextElem()) {
// file.printf("%.15e",el.GetDeformations(0));
// if (Dim > 1)
// file.printf(" %.15e",el.GetDeformations(1));
// else
// file.printf(" %.15e",0.0);
// if (Dim > 2)
// file.printf(" %.15e",el.GetDeformations(2));
// else
// file.printf(" %.15e",0.0);
// file.printf("\n");
// }
// paraHelper.endData(file);
// paraHelper.endCellDataList(file);
paraHelper.write_conclusion();
file.close();
}
/* -------------------------------------------------------------------------- */
DECLARE_DUMPER_REF(DumperParaview,LIST_CONTINUUM_MODEL);
__END_LIBMULTISCALE__

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