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dumper_lammps.cc
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Mon, Nov 11, 03:23

dumper_lammps.cc
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/**
* @file dumper_lammps.cc
*
* @author Till Junge <till.junge@epfl.ch>
*
* @date creation: Thu Nov 25 2010
* @date last modification: Mon Jun 10 2013
*
* @brief implementation of lammps dumper
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sstream>
#include "iohelper_common.hh"
#include "dumper_lammps.hh"
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
/// remark #981: operands are evaluated in unspecified order
#pragma warning ( disable : 981 )
#endif //defined(__INTEL_COMPILER)
__BEGIN_IOHELPER__
template<LammpsAtomStyle style>
DumperLammps<style>::DumperLammps(Real * bounds, const std::string & prefix)
:Dumper(prefix), bounds(bounds) {
this->registerDumpOptions("lammps","","", _df_proc_id);
}
/* -------------------------------------------------------------------------- */
template<LammpsAtomStyle style>
void DumperLammps<style>::dump(const std::string & current_name, const UInt count) {
Dumper::dump(current_name, count);
std::string filename = this->getAbsoluteFilePath(this->getBaseName(), "lammps");
std::ios_base::openmode mode = std::fstream::in | std::fstream::out | std::fstream::trunc;
this->lammps_dump_file.open(filename.c_str(), mode);
this->dumpHead(this->bounds);
this->dumpAdd();
this->dumpFinalize();
this->incDumpStep();
}
/* -------------------------------------------------------------------------- */
template<LammpsAtomStyle style>
void DumperLammps<style>::dumpHead(Real * bounds) {
this->curr_nb_atom = 0;
if (!this->lammps_dump_file.good()) {
std::cerr << "hach" << std::endl;
if (this->lammps_dump_file.rdstate() & std::fstream::eofbit) std::cerr << " 1 " << std::endl;
if (this->lammps_dump_file.rdstate() & std::fstream::failbit) std::cerr << " 2 " << std::endl;
if (this->lammps_dump_file.rdstate() & std::fstream::badbit) std::cerr << " 3 " << std::endl;
if (this->lammps_dump_file.rdstate() & std::fstream::goodbit) std::cerr << " 4 " << std::endl;
exit(-1);
}
this->lammps_dump_file << "LAMMPS data file" << std::endl << std::endl << std::endl;
this->nb_atom_position = lammps_dump_file.tellp();
//dump whitespaces to later fill in nb_atoms
this->lammps_dump_file << " " << std::endl;
this->lammps_dump_file << "0 bonds" << std::endl
<< "1 atom types" << std::endl
<< "0 bond types" << std::endl;
if (bounds != NULL) {
this->lammps_dump_file << std::endl;
this->lammps_dump_file << bounds[0] << " " << bounds[1] <<" xlo xhi" << std::endl;
this->lammps_dump_file << bounds[2] << " " << bounds[3] <<" ylo yhi" << std::endl;
this->lammps_dump_file << bounds[4] << " " << bounds[5] <<" zlo zhi" << std::endl;
this->lammps_dump_file << std::endl;
}
this->lammps_dump_file << "Atoms" << std::endl << std::endl;
this->lammps_dump_file.setf(std::ios::scientific, std::ios::floatfield);
this->lammps_dump_file.precision(16);
}
/* -------------------------------------------------------------------------- */
template<LammpsAtomStyle style>
void DumperLammps<style>::dumpAdd(int _grain_id) {
this->grain_id = _grain_id;
per_node_data[std::string("positions")]->accept(*this);
// ContainerArray<Real> cont(_points,_dimension,_nb);
// Field<ContainerArray<Real> > field(cont,"temporary");
// // set temporary values
// field.accept(*this);//this brings me to visit
}
/* -------------------------------------------------------------------------- */
template<LammpsAtomStyle style>
void DumperLammps<style>::dumpFinalize(){
this->lammps_dump_file.seekp(this->nb_atom_position);
this->lammps_dump_file << curr_nb_atom << " atoms";
this->lammps_dump_file.close();
}
/* -------------------------------------------------------------------------- */
template class DumperLammps<atomic>;
template class DumperLammps<bond>;
__END_IOHELPER__

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