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// $Id: BondStretch.cpp 1528 2010-09-26 17:04:37Z glandrum $
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "BondStretch.h"
#include "Params.h"
#include <math.h>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
namespace ForceFields {
namespace UFF {
namespace Utils {
double calcBondRestLength(double bondOrder,
const AtomicParams *end1Params,
const AtomicParams *end2Params){
PRECONDITION(bondOrder>0,"bad bond order");
PRECONDITION(end1Params,"bad params pointer");
PRECONDITION(end2Params,"bad params pointer");
double ri=end1Params->r1,rj=end2Params->r1;
// this is the pauling correction:
double rBO = -Params::lambda * (ri + rj) * log(bondOrder);
// O'Keefe and Breese electronegativity correction:
double Xi=end1Params->GMP_Xi,Xj=end2Params->GMP_Xi;
double rEN = ri*rj*(sqrt(Xi)-sqrt(Xj))*(sqrt(Xi)-sqrt(Xj)) /
(Xi*ri + Xj*rj);
double res = ri + rj + rBO + rEN;
return res;
}
double calcBondForceConstant(double restLength,
const AtomicParams *end1Params,
const AtomicParams *end2Params){
double res = 2.0 * Params::G * end1Params->Z1 * end2Params->Z1 / pow(restLength,3.0);
return res;
}
} // end of namespace Utils
BondStretchContrib::BondStretchContrib(ForceField *owner,
unsigned int idx1,unsigned int idx2,
double bondOrder,
const AtomicParams *end1Params,
const AtomicParams *end2Params){
PRECONDITION(owner,"bad owner");
PRECONDITION(end1Params,"bad params pointer");
PRECONDITION(end2Params,"bad params pointer");
RANGE_CHECK(0,idx1,owner->positions().size()-1);
RANGE_CHECK(0,idx2,owner->positions().size()-1);
dp_forceField = owner;
d_end1Idx = idx1;
d_end2Idx = idx2;
this->d_restLen = Utils::calcBondRestLength(bondOrder,
end1Params,end2Params);
this->d_forceConstant = Utils::calcBondForceConstant(this->d_restLen,
end1Params,end2Params);
}
double BondStretchContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField,"no owner");
PRECONDITION(pos,"bad vector");
double distTerm=this->dp_forceField->distance(this->d_end1Idx,this->d_end2Idx,pos) -
this->d_restLen;
double res = 0.5*this->d_forceConstant*distTerm*distTerm;
return res;
}
void BondStretchContrib::getGrad(double *pos,double *grad) const {
PRECONDITION(dp_forceField,"no owner");
PRECONDITION(pos,"bad vector");
PRECONDITION(grad,"bad vector");
double dist=this->dp_forceField->distance(this->d_end1Idx,this->d_end2Idx,pos);
double preFactor = this->d_forceConstant*(dist-this->d_restLen);
//std::cout << "\tDist("<<this->d_end1Idx<<","<<this->d_end2Idx<<") " << dist << std::endl;
double *end1Coords = &(pos[3*this->d_end1Idx]);
double *end2Coords = &(pos[3*this->d_end2Idx]);
for(int i=0;i<3;i++){
double dGrad;
if(dist>0.0){
dGrad=preFactor * (end1Coords[i]-end2Coords[i])/dist;
} else {
// move a small amount in an arbitrary direction
dGrad=this->d_forceConstant*.01;
}
grad[3*this->d_end1Idx+i] += dGrad;
grad[3*this->d_end2Idx+i] -= dGrad;
}
}
}
}
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