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102 lines
3.1 KiB
C++
102 lines
3.1 KiB
C++
// $Id$
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//
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// Copyright (C) 2004-2008 Greg Landrum and 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 "Nonbonded.h"
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#include "Params.h"
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#include <math.h>
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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 calcNonbondedMinimum(const AtomicParams *at1Params,
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const AtomicParams *at2Params) {
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return sqrt(at1Params->x1 * at2Params->x1);
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}
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double calcNonbondedDepth(const AtomicParams *at1Params,
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const AtomicParams *at2Params) {
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return sqrt(at1Params->D1 * at2Params->D1);
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}
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} // end of namespace utils
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vdWContrib::vdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2,
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const AtomicParams *at1Params,
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const AtomicParams *at2Params, double threshMultiplier) {
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PRECONDITION(owner, "bad owner");
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PRECONDITION(at1Params, "bad params pointer");
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PRECONDITION(at2Params, "bad params pointer");
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URANGE_CHECK(idx1, owner->positions().size() - 1);
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URANGE_CHECK(idx2, owner->positions().size() - 1);
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dp_forceField = owner;
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d_at1Idx = idx1;
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d_at2Idx = idx2;
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// UFF uses the geometric mean of the vdW parameters:
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d_xij = Utils::calcNonbondedMinimum(at1Params, at2Params);
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d_wellDepth = Utils::calcNonbondedDepth(at1Params, at2Params);
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d_thresh = threshMultiplier * d_xij;
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// std::cerr << " non-bonded: " << idx1 << "-" << idx2 << " " << d_xij << " "
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// << d_wellDepth << " " << d_thresh << std::endl;
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}
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double vdWContrib::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 dist = dp_forceField->distance(d_at1Idx, d_at2Idx, pos);
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if (dist > d_thresh || dist <= 0.0) return 0.0;
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double r = d_xij / dist;
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double r6 = int_pow<6>(r);
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double r12 = r6 * r6;
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double res = d_wellDepth * (r12 - 2.0 * r6);
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// if(d_at1Idx==12 && d_at2Idx==21 ) std::cerr << " >: " << d_at1Idx <<
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// "-" << d_at2Idx << " " << r << " = " << res << std::endl;
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return res;
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}
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void vdWContrib::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_at1Idx, d_at2Idx, pos);
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if (dist > d_thresh) return;
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if (dist <= 0) {
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for (int i = 0; i < 3; i++) {
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// move in an arbitrary direction
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double dGrad = 100.0;
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grad[3 * d_at1Idx + i] += dGrad;
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grad[3 * d_at2Idx + i] -= dGrad;
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}
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return;
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}
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double r = d_xij / dist;
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double r7 = int_pow<7>(r);
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double r13 = int_pow<13>(r);
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double preFactor = 12. * d_wellDepth / d_xij * (r7 - r13);
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double *at1Coords = &(pos[3 * d_at1Idx]);
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double *at2Coords = &(pos[3 * d_at2Idx]);
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for (int i = 0; i < 3; i++) {
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double dGrad = preFactor * (at1Coords[i] - at2Coords[i]) / dist;
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grad[3 * d_at1Idx + i] += dGrad;
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grad[3 * d_at2Idx + i] -= dGrad;
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}
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}
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}
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}
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