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// $Id$
//
// 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>
#include <RDGeneral/utils.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");
URANGE_CHECK(idx1, owner->positions().size());
URANGE_CHECK(idx2, owner->positions().size());
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
// UFF uses the geometric mean of the vdW parameters:
d_xij = Utils::calcNonbondedMinimum(at1Params, at2Params);
d_wellDepth = Utils::calcNonbondedDepth(at1Params, at2Params);
d_thresh = threshMultiplier * d_xij;
// std::cerr << " non-bonded: " << idx1 << "-" << idx2 << " " << d_xij << " "
// << d_wellDepth << " " << d_thresh << std::endl;
}
double vdWContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
double dist = dp_forceField->distance(d_at1Idx, d_at2Idx, pos);
if (dist > d_thresh || dist <= 0.0) return 0.0;
double r = d_xij / dist;
double r6 = int_pow<6>(r);
double r12 = r6 * r6;
double res = 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 = dp_forceField->distance(d_at1Idx, d_at2Idx, pos);
if (dist > d_thresh) return;
if (dist <= 0) {
for (int i = 0; i < 3; i++) {
// move in an arbitrary direction
double dGrad = 100.0;
grad[3 * d_at1Idx + i] += dGrad;
grad[3 * d_at2Idx + i] -= dGrad;
}
return;
}
double r = d_xij / dist;
double r7 = int_pow<7>(r);
double r13 = int_pow<13>(r);
double preFactor = 12. * d_wellDepth / d_xij * (r7 - r13);
double *at1Coords = &(pos[3 * d_at1Idx]);
double *at2Coords = &(pos[3 * d_at2Idx]);
for (int i = 0; i < 3; i++) {
double dGrad = preFactor * (at1Coords[i] - at2Coords[i]) / dist;
grad[3 * d_at1Idx + i] += dGrad;
grad[3 * d_at2Idx + i] -= dGrad;
}
}
}
}
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