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libmultiscale/src/md/spatial_filter_atomic.cc
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spatial_filter_atomic.cc
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/**
* @file spatial_filter_atomic.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
*
* @date Wed Dec 04 12:14:29 2013
*
* @brief This class allows to perform spatial filtering of atomic fields
*
* @section LICENSE
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* LibMultiScale 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.
*
* LibMultiScale 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 LibMultiScale. If not, see <http://www.gnu.org/licenses/>.
*
*/
#define TIMER
/* -------------------------------------------------------------------------- */
#include "spatial_filter_atomic.hh"
#include "container_array.hh"
#include "lm_common.hh"
#include <fstream>
#include <sstream>
/* -------------------------------------------------------------------------- */
__BEGIN_LIBMULTISCALE__
void SpatialFilterAtomic::readKernelFromFile(const std::string &filename) {
std::ifstream fs(filename.c_str());
std::string line;
std::vector<double> x;
if (fs.is_open()) {
while (!fs.eof()) {
getline(fs, line);
if (line == "")
continue;
if (line[0] == '#')
continue;
DUMP("read line in kernel " << line, DBG_DETAIL);
std::stringstream ss;
ss << line;
Real j = 0;
ss >> j;
x.push_back(j);
Real k_value;
ss >> k_value;
memory_kernel.push_back(k_value);
}
fs.close();
DUMP("MEMORY KERNEL SIZE IS " << memory_kernel.size(), DBG_DETAIL);
} else
LM_FATAL(
"cannot open the file to read the memory kernel file: " << filename);
buildCSpline(x, memory_kernel);
}
/* -------------------------------------------------------------------------- */
void SpatialFilterAtomic::buildCSpline(std::vector<double> &x,
std::vector<double> &memory_kernel) {
kernel_length = memory_kernel.size();
// kernel_distance_first_neigh = x[1];
kernel_distance = x[kernel_length - 1];
kernel_distance_sq = kernel_distance * kernel_distance;
// Real r0 = 4.032*sqrt(2)/2;
// std::ofstream fout("spatial_filter_kernel.txt");
// for (UInt i = 0; i < kernel_length; ++i) {
// fout << std::scientific << x[i]/r0 << " " <<
// r0*r0*sqrt(3)/2*memory_kernel[i] << std::endl;
// }
// fout.close();
std::vector<double> x_, f_;
x_.reserve(x.size() - 1);
f_.reserve(x.size() - 1);
copy(x.begin() + 1, x.end(), back_inserter(x_));
copy(memory_kernel.begin() + 1, memory_kernel.end(), back_inserter(f_));
double spacing = ((x[kernel_length - 1]) - (x[kernel_length - 2]));
// build the spline coefficients
this->cSpline->buildSplineCoefficients(x_, f_, spacing);
DUMP("Maximum distance between two atoms for filtering "
<< kernel_distance << " square of distance " << kernel_distance_sq
<< " spacing " << spacing,
DBG_MESSAGE);
}
/* -------------------------------------------------------------------------- */
__END_LIBMULTISCALE__
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