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libmultiscale/src/dumper/dumper_paraview_atom.cc
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dumper_paraview_atom.cc
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/**
* @file dumper_paraview_atom.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date Thu Sep 18 16:13:19 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 "dumper_paraview.hh"
#include "compute.hh"
#include "filter.hh"
#include "filter_manager.hh"
#include "lib_md.hh"
#include <iomanip>
#include "communicator.hh"
#include "ref_point_data.hh"
#include "units_converter.hh"
#include "container_mesh.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_LIBMULTISCALE__
template <typename Cont>
void DumperParaview<Cont>::dump(Cont & cont){
const UInt Dim = Cont::Dim;
typedef typename Cont::Ref RefAtom;
UInt nb = cont.nbElem();
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\" ");
file.printf("byte_order=\"LittleEndian\">\n");
file.printf("<PUnstructuredGrid GhostLevel=\"0\">\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 (stress_serie) paraHelper.PDataArray("stress",6);
if (barycenters_serie) paraHelper.PDataArray("barycenters",3);
if (proc_serie) paraHelper.PDataArray("procs",1);
if (id_serie) paraHelper.PDataArray("id",1);
if (mass_serie) paraHelper.PDataArray("mass",1);
if (epot_serie) paraHelper.PDataArray("epot",1);
if (charge_serie) paraHelper.PDataArray("charge",1);
if (alpha_serie) paraHelper.PDataArray("alpha",1);
if (tag_serie) paraHelper.PDataArray("tag",1);
if (e_density_serie) paraHelper.PDataArray("electronic_density",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>");
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,
comm.realRank(l, group));
}
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();
if(nb) paraHelper.write_header(nb,1);
else paraHelper.write_header(nb,0);
UnitsConverter unit;
unit.setInUnits(code_unit_system);
unit.setOutUnits(this->dump_unit_system);
unit.computeConversions();
paraHelper.startDofList();
typename Cont::iterator it = cont.getIterator();
for (RefAtom at = it.getFirst();!it.end();at = it.getNext()) {
Real X[Dim];
at.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 (UInt i=0;i < nb;++i)
{
paraHelper.pushInteger(i);
}
paraHelper.endCellsConnectivityList();
paraHelper.startCellsoffsetsList();
paraHelper.pushInteger(nb);
paraHelper.endCellsoffsetsList();
paraHelper.startCellstypesList();
if(nb){
paraHelper.pushInteger(2);
}
paraHelper.endCellstypesList();
paraHelper.startPointDataList();
if (dep_serie){
paraHelper.startData("displacements",3);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
Real u[3] = {0.,0.,0.};
for (UInt i = 0; i < Dim; ++i) {
u[i] = at.displacement(i);
//if (std::abs(u[i]) > 50.) LM_FATAL("biiiiip " << at);
}
for (UInt i = 0; i < 3; ++i) {
paraHelper.pushReal(u[i]*unit.getConversion<Length>());
}
}
paraHelper.endData();
}
if (p0_serie){
paraHelper.startData("P0",3);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
Real ux=0,uy=0,uz=0;
ux = at.position0(0);
if (Dim > 1)
uy = at.position0(1);
if (Dim == 3)
uz = at.position0(2);
ux *= unit.getConversion<Length>();
uy *= unit.getConversion<Length>();
uz *= unit.getConversion<Length>();
paraHelper.pushReal(ux);
paraHelper.pushReal(uy);
paraHelper.pushReal(uz);
}
paraHelper.endData();
}
if (vel_serie){
paraHelper.startData("velocities",3);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
Real vx=0,vy=0,vz=0;
vx = at.velocity(0);
if (Dim > 1)
vy = at.velocity(1);
if (Dim == 3)
vz = at.velocity(2);
paraHelper.pushReal(vx);
paraHelper.pushReal(vy);
paraHelper.pushReal(vz);
}
paraHelper.endData();
}
if (force_serie){
paraHelper.startData("force",3);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
Real fx=0,fy=0,fz=0;
fx = at.force(0);
if (Dim > 1)
fy = at.force(1);
if (Dim == 3)
fz = at.force(2);
paraHelper.pushReal(fx);
paraHelper.pushReal(fy);
paraHelper.pushReal(fz);
}
paraHelper.endData();
}
if (stress_serie){
paraHelper.startData("stress",6);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
LM_TOIMPLEMENT;
//1.60217653e-19 / 1e-30 / 1e9 = 1.60217653e2 is for conversion from eV/A^3 to GigaPascals
Real x = at.stress(0)*1.60217653e2;
Real y = at.stress(1)*1.60217653e2;
Real z = at.stress(2)*1.60217653e2;
paraHelper.pushReal(x);
paraHelper.pushReal(y);
paraHelper.pushReal(z);
x = at.stress(3)*1.60217653e2;
y = at.stress(4)*1.60217653e2;
z = at.stress(5)*1.60217653e2;
paraHelper.pushReal(x);
paraHelper.pushReal(y);
paraHelper.pushReal(z);
}
paraHelper.endData();
}
if (barycenters_serie){
paraHelper.startData("barycenters",3);
Real x=0,y=0,z=0;
UInt cpt = 0;
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
x += at.position(0);
y += at.position(1);
z += at.position(2);
++cpt;
}
x /= cpt;
y /= cpt;
z /= cpt;
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
paraHelper.pushReal(x);
paraHelper.pushReal(y);
paraHelper.pushReal(z);
}
paraHelper.endData();
}
if (proc_serie){
paraHelper.startData("procs",1);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
paraHelper.pushReal(lm_my_proc_id);
}
paraHelper.endData();
}
if (id_serie){
// UInt cpt=0;
paraHelper.startData("id",1);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
paraHelper.pushReal(at.id());
//paraHelper.pushReal(cpt);
//++cpt;
}
paraHelper.endData();
}
if (mass_serie){
paraHelper.startData("mass",1);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
paraHelper.pushReal(at.mass());
}
paraHelper.endData();
}
if (epot_serie){
paraHelper.startData("epot",1);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
paraHelper.pushReal(at.getEPot());
}
paraHelper.endData();
}
if (charge_serie){
paraHelper.startData("charge",1);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
paraHelper.pushReal(at.charge());
}
paraHelper.endData();
}
if (alpha_serie){
paraHelper.startData("alpha",1);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
paraHelper.pushReal(at.alpha());
}
paraHelper.endData();
}
if (e_density_serie){
paraHelper.startData("electronic_density",1);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
paraHelper.pushReal(at.electronic_density());
}
paraHelper.endData();
}
if (tag_serie){
paraHelper.startData("tag",1);
for (RefAtom at = it.getFirst();!it.end();at = it.getNext())
{
paraHelper.pushReal(at.tag());
}
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) {
ptr->build();
dumpField(additional_field,cont,*ptr,ptr->getDim());
}
}
}
paraHelper.endPointDataList();
paraHelper.write_conclusion();
file.close();
}
/* -------------------------------------------------------------------------- */
DECLARE_DUMPER_REF(DumperParaview,LIST_ATOM_MODEL);
DECLARE_DUMPER_REFPOINT(DumperParaview);
DECLARE_DUMPER_GENERIC_MESH(DumperParaview);
__END_LIBMULTISCALE__
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