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// $Id: Nonbonded.cpp 1528 2010-09-26 17:04:37Z glandrum $
//
// Copyright (C) 2004-2008 Greg Landrum and 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 "Nonbonded.h"
#include "Params.h"
#include <math.h>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
namespace ForceFields {
namespace UFF {
namespace Utils {
double calcNonbondedMinimum(const AtomicParams *at1Params,
const AtomicParams *at2Params){
return sqrt(at1Params->x1*at2Params->x1);
}
double calcNonbondedDepth(const AtomicParams *at1Params,
const AtomicParams *at2Params){
return sqrt(at1Params->D1*at2Params->D1);
}
} // end of namespace utils
vdWContrib::vdWContrib(ForceField *owner,
unsigned int idx1,unsigned int idx2,
const AtomicParams *at1Params,
const AtomicParams *at2Params,
double threshMultiplier){
PRECONDITION(owner,"bad owner");
PRECONDITION(at1Params,"bad params pointer");
PRECONDITION(at2Params,"bad params pointer");
RANGE_CHECK(0,idx1,owner->positions().size()-1);
RANGE_CHECK(0,idx2,owner->positions().size()-1);
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
// UFF uses the geometric mean of the vdW parameters:
this->d_xij = Utils::calcNonbondedMinimum(at1Params,at2Params);
this->d_wellDepth = Utils::calcNonbondedDepth(at1Params,at2Params);
this->d_thresh = threshMultiplier*this->d_xij;
//std::cerr << " non-bonded: " << idx1 << "-" << idx2 << " " << this->d_xij << " " << this->d_wellDepth << " " << this->d_thresh << std::endl;
}
double vdWContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField,"no owner");
PRECONDITION(pos,"bad vector");
double dist=this->dp_forceField->distance(this->d_at1Idx,this->d_at2Idx,pos);
if(dist>this->d_thresh || dist<=0.0) return 0.0;
double r=this->d_xij/dist;
double r6=pow(r,6);
double r12=r6*r6;
double res = this->d_wellDepth*(r12 - 2.0*r6);
//if(d_at1Idx==12 && d_at2Idx==21 ) std::cerr << " >: " << d_at1Idx << "-" << d_at2Idx << " " << r << " = " << res << std::endl;
return res;
}
void vdWContrib::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_at1Idx,this->d_at2Idx,pos);
if(dist>this->d_thresh) return;
if(dist<=0){
for(int i=0;i<3;i++){
// move in an arbitrary direction
double dGrad=100.0;
grad[3*this->d_at1Idx+i] += dGrad;
grad[3*this->d_at2Idx+i] -= dGrad;
}
return;
}
double r = this->d_xij/dist;
double r7 = pow(r,7);
double r13= pow(r,13);
double preFactor = 12.*this->d_wellDepth/this->d_xij * (r7-r13);
double *at1Coords = &(pos[3*this->d_at1Idx]);
double *at2Coords = &(pos[3*this->d_at2Idx]);
for(int i=0;i<3;i++){
double dGrad=preFactor * (at1Coords[i]-at2Coords[i])/dist;
grad[3*this->d_at1Idx+i] += dGrad;
grad[3*this->d_at2Idx+i] -= dGrad;
}
}
}
}
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