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md_builder.cc
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/**
* @file md_builder.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
*
* @date Fri Jan 10 23:04:26 2014
*
* @brief This class constructs the 1D atomic chains
*
* @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 "md_builder.hh"
#include "lm_parser.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_LIBMULTISCALE__
/* -------------------------------------------------------------------------- */
void ZoneMDBuilder::buildMD1D(const Cube & b, const Real & r0,
const Real & mass, const Real & shift,
bool periodic_flag,
std::vector<DOF> & atoms) {
Real range = b.getXmax()[0]-b.getXmin()[0];
int nb_atoms = (int)(range/r0);
Real center = b.getCenter(0)+shift;
// this->buildMD1D(nb_atoms,b.getCenter(0)+shift,r0,mass,periodic_flag,atoms);
int center_index=0;
if (periodic_flag){
--nb_atoms;
center_index = nb_atoms/2;
}
else center_index = (nb_atoms-1)/2;
DUMP("Requesting build of a md zone of size " << (nb_atoms-1)*r0
<< " center index = " << center_index,DBG_INFO_STARTUP);
atoms.resize(nb_atoms);
//higher than center part
for (int i = center_index; i < nb_atoms; ++i) {
atoms[i].p = center + (i-center_index)*r0;
atoms[i].p0 = center + (i-center_index)*r0;
DUMP("creation of atom " << i << " at position " << atoms[i].p0,DBG_DETAIL);
atoms[i].v = 0.0f;
LM_ASSERT(mass != 0,"used mass cannot be 0 -> have you used MASS keyword ?");
atoms[i].m = mass;
atoms[i].a = 0.0f;
atoms[i].f = 0.0f;
atoms[i].alpha = 1.0;
atoms[i].pe = 0.0;
}
//lower than center part
for (int i=center_index-1; i > -1; --i) {
atoms[i].p = center + (i-center_index)*r0;
atoms[i].p0 = center + (i-center_index)*r0;
DUMP("creation of atom " << i << " at position " << atoms[i].p0,DBG_DETAIL);
atoms[i].v = 0.0f;
LM_ASSERT(mass != 0,"used mass cannot be 0 -> have you used MASS keyword ?");
atoms[i].m = mass;
atoms[i].a = 0.0f;
atoms[i].f = 0.0f;
atoms[i].alpha = 1.0;
atoms[i].pe = 0.0;
}
DUMP("Number of generated atoms " << atoms.size(),DBG_MESSAGE);
}
/* -------------------------------------------------------------------------- */
void ZoneMDBuilder::readMD1D(const std::string & filename,
const Cube & b, const Real & r0,
const Real & mass,
std::vector<DOF> & atoms) {
std::ifstream f;
f.open(filename.c_str());
if (!f.is_open()){
LM_FATAL("could not open config file " << filename);
}
UInt line_count = 0;
while (f.good()){
std::string buffer;
std::getline(f,buffer);
++line_count;
unsigned long found = buffer.find_first_of("#");
std::string buffer_comment_free = buffer.substr(0,found-1);
buffer = buffer_comment_free;
// if it is a comment, then do nothing
if (buffer[0] == '#' || buffer == ""){
continue;
}
std::stringstream line(buffer);
Real x;
try {
Parser::parse(x,line);
}
catch (LibMultiScaleException & e) {
LM_THROW(filename << ":" << line_count << ":" <<
" unable to read coordinate: " << buffer);
}
DOF _d;
_d.p = x;
_d.p0 = x;
_d.v = 0.;
_d.a = 0.;
_d.m = mass;
_d.f = 0.;
_d.alpha = 1.;
_d.T = 0.;
_d.charge = 1.;
atoms.push_back(_d);
}
DUMP("Number of generated atoms " << atoms.size(),DBG_MESSAGE);
}
/* -------------------------------------------------------------------------- */
__END_LIBMULTISCALE__

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