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dumper_lammps.hh
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Mon, Nov 11, 15:12

dumper_lammps.hh
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/**
* @file dumper_lammps.hh
*
* @author Till Junge <till.junge@epfl.ch>
*
* @date creation: Thu Nov 25 2010
* @date last modification: Tue Jun 04 2013
*
* @brief header for 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __IOHELPER_DUMPER_LAMMPS_H__
#define __IOHELPER_DUMPER_LAMMPS_H__
/* -------------------------------------------------------------------------- */
#include "dumper.hh"
#include <fstream>
/* -------------------------------------------------------------------------- */
__BEGIN_IOHELPER__
enum LammpsAtomStyle {atomic, bond}; //please extend ad libidum
template<LammpsAtomStyle style>
class DumperLammps: public Dumper, public Visitor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperLammps(Real * bounds = nullptr, const std::string & prefix = "./");
~DumperLammps() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
//! dump to file
void dump(const std::string & basename = std::string(),
UInt count = UInt(-1)) override;
void dumpHead(Real * bounds = nullptr);
template<typename T>
void visitField(T & cont);
void dumpFinalize();
//! set mode for file creation : TEXT, BASE64, COMPRESSED
void setMode(int mode) override { Dumper::setMode(mode); }
void dumpAdd(int grain_id = 1);
void setEmbeddedValue(__attribute__((unused)) const std::string & name,
__attribute__((unused)) int value){}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
//position of where the number of atoms is printed;
std::streampos nb_atom_position;
//current number of atoms printed to the file
unsigned long int curr_nb_atom;
std::fstream lammps_dump_file;
Real * bounds;
//! flag to produce zipped files
bool flag_compressed;
//! current values
int grain_id;
};
/* -------------------------------------------------------------------------- */
template<>
template <typename T>
void DumperLammps<bond>::visitField(T & visited) {
typename T::iterator it = visited.begin();
typename T::iterator end = visited.end();
UInt dim = visited.getDim();
for (; it != end ; ++it) {
this->lammps_dump_file << this->curr_nb_atom + 1 << " "
<< this->grain_id + 2 << " 1 ";
for (UInt i = 0 ; i < dim ; ++i) {
this->lammps_dump_file << (*it)[i] << " ";
}
this->lammps_dump_file << std::endl;
++this->curr_nb_atom;
}
}
/* -------------------------------------------------------------------------- */
template<>
template <typename T>
void DumperLammps<atomic>::visitField(T & visited) {
typename T::iterator it = visited.begin();
typename T::iterator end = visited.end();
UInt dim = visited.getDim();
for (; it != end ; ++it) {
this->lammps_dump_file << this->curr_nb_atom + 1 << " 1 ";
for (UInt i = 0 ; i < dim ; ++i) {
this->lammps_dump_file << (*it)[i] << " ";
}
this->lammps_dump_file << std::endl;
++this->curr_nb_atom;
}
}
/* -------------------------------------------------------------------------- */
__END_IOHELPER__
/* -------------------------------------------------------------------------- */
#include "field_inline_impl.cc"
/* -------------------------------------------------------------------------- */
#endif /* __IOHELPER_DUMPER_LAMMPS_H__ */

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