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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 "BondStretch.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 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 /
(restLength * restLength * restLength);
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");
URANGE_CHECK(idx1, owner->positions().size());
URANGE_CHECK(idx2, owner->positions().size());
dp_forceField = owner;
d_end1Idx = idx1;
d_end2Idx = idx2;
d_restLen = Utils::calcBondRestLength(bondOrder, end1Params, end2Params);
d_forceConstant =
Utils::calcBondForceConstant(d_restLen, end1Params, end2Params);
}
double BondStretchContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
double distTerm =
dp_forceField->distance(d_end1Idx, d_end2Idx, pos) - d_restLen;
double res = 0.5 * 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 = dp_forceField->distance(d_end1Idx, d_end2Idx, pos);
double preFactor = d_forceConstant * (dist - d_restLen);
// std::cout << "\tDist("<<d_end1Idx<<","<<d_end2Idx<<") " << dist <<
// std::endl;
double *end1Coords = &(pos[3 * d_end1Idx]);
double *end2Coords = &(pos[3 * 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 = d_forceConstant * .01;
}
grad[3 * d_end1Idx + i] += dGrad;
grad[3 * d_end2Idx + i] -= dGrad;
}
}
}
}
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