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// $Id$
//
// 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 "DistViolationContrib.h"
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
namespace DistGeom {
DistViolationContrib::DistViolationContrib(ForceFields::ForceField *owner,unsigned int idx1,
unsigned int idx2,
double ub, double lb, double weight) {
PRECONDITION(owner,"bad owner");
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;
d_ub = ub;
d_lb = lb;
d_weight = weight;
}
double DistViolationContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField,"no owner");
PRECONDITION(pos,"bad vector");
double d = this->dp_forceField->distance(this->d_end1Idx,this->d_end2Idx,pos);
double val=0.0;
if (d > d_ub) {
val = ((d*d)/(d_ub*d_ub)) - 1.0;
} else if (d < d_lb) {
val = ((2*d_lb*d_lb)/(d_lb*d_lb + d*d)) - 1.0;
}
double res;
if(val>0.0){
res=d_weight*val*val;
}else{
res=0;
}
return res;
}
void DistViolationContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField,"no owner");
PRECONDITION(pos,"bad vector");
PRECONDITION(grad,"bad vector");
unsigned int dim=this->dp_forceField->dimension();
double d = this->dp_forceField->distance(this->d_end1Idx,this->d_end2Idx,pos);
double preFactor = 0.0;
if (d > d_ub) {
double u2 = d_ub*d_ub;
preFactor = 4.*(((d*d)/u2) - 1.0)*(d/u2);
} else if (d < d_lb) {
double d2 = d*d;
double l2 = d_lb*d_lb;
double l2d2 = d2+l2;
preFactor = 8.*l2*d * (1.-2*l2/l2d2) / (l2d2*l2d2);
//preFactor = -8.*((l2-d2)/pow(l2+d2,3))*d*l2;
} else {
return;
}
double *end1Coords = &(pos[dim*this->d_end1Idx]);
double *end2Coords = &(pos[dim*this->d_end2Idx]);
for(unsigned int i=0;i<dim;i++){
double dGrad;
if(d>0.0){
dGrad= d_weight*preFactor * (end1Coords[i]-end2Coords[i])/d;
} else {
// FIX: this likely isn't right
dGrad= d_weight*preFactor * (end1Coords[i]-end2Coords[i]);
}
grad[dim*this->d_end1Idx+i] += dGrad;
grad[dim*this->d_end2Idx+i] -= dGrad;
}
}
}
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