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DRMSD.cpp
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DRMSD.cpp
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/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Copyright (c) 2013 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed-code.org for more information.
This file is part of plumed, version 2.0.
plumed 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.
plumed 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 plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "DRMSD.h"
#include "PDB.h"
#include "Pbc.h"
#include <cmath>
using namespace std;
namespace PLMD{
void DRMSD::setFromPDB(const PDB&pdb, double lbound, double ubound){
setReference(pdb.getPositions(), lbound, ubound);
}
void DRMSD::clear(){
targets.clear();
}
void DRMSD::setReference(const vector<Vector> & reference, double lbound, double ubound)
{
natoms = reference.size();
for(unsigned i=0;i<natoms-1;++i){
for(unsigned j=i+1;j<natoms;++j){
double distance = delta(reference[i],reference[j]).modulo();
if(distance > lbound && distance < ubound){
targets[make_pair(i,j)] = distance;
}
}
}
}
double DRMSD::calculate(const std::vector<Vector> & positions,
std::vector<Vector> &derivatives, Tensor& virial) const {
Pbc fake_pbc;
return DRMSD::calculate(positions,fake_pbc,derivatives,virial,false);
}
double DRMSD::calculate(const std::vector<Vector> & positions, const Pbc& pbc,
std::vector<Vector> &derivatives, Tensor& virial, bool do_pbc) const {
plumed_assert(positions.size()==natoms && derivatives.size()==natoms );
Vector distance;
double drmsd=0.; virial.zero();
for(unsigned i=0;i<derivatives.size();++i) derivatives[i].zero();
for(map< pair <unsigned,unsigned> , double>::const_iterator it=targets.begin();it!=targets.end();++it){
unsigned i=it->first.first;
unsigned j=it->first.second;
if(do_pbc){distance=pbc.distance( positions[i] , positions[j] );}
else{distance=delta( positions[i] , positions[j] );}
double len = distance.modulo();
double diff = len - it->second;
drmsd += diff * diff;
derivatives[i] += -( diff / len ) * distance;
derivatives[j] += ( diff / len ) * distance;
virial -= ( diff / len ) * Tensor(distance,distance);
}
double npairs = static_cast<double>(targets.size());
drmsd=sqrt( drmsd / npairs );
double idrmsd=1.0/( drmsd * npairs );
virial *= idrmsd;
for(unsigned i=0;i<natoms;++i){derivatives[i] *= idrmsd;}
return drmsd;
}
}