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