mirror of
https://github.com/rdkit/rdkit.git
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a45d4d9857
* add angles and distances * add Inversions * add torsiona angle contribs * use new contribs in test * use new inversion and torsion contribs in dg * use new distance contribs in dg * use new angle constraints in dg * use new constraints in FF tests * update docstrings * remove unused import * include new contribs * cleanup includes * make changes requested by @greglandrum * use std::move instead of release
102 lines
3.7 KiB
C++
102 lines
3.7 KiB
C++
//
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// Copyright (C) 2024 Niels Maeder and other RDKit contributors
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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 "DistanceConstraints.h"
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#include "ForceField.h"
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#include <cmath>
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#include <RDGeneral/Invariant.h>
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namespace ForceFields {
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DistanceConstraintContribs::DistanceConstraintContribs(ForceField *owner) {
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PRECONDITION(owner, "bad owner");
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dp_forceField = owner;
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}
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void DistanceConstraintContribs::addContrib(unsigned int idx1,
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unsigned int idx2, double minLen,
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double maxLen,
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double forceConstant) {
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URANGE_CHECK(idx1, dp_forceField->positions().size());
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URANGE_CHECK(idx2, dp_forceField->positions().size());
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PRECONDITION(maxLen >= minLen, "bad bounds");
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d_contribs.emplace_back(idx1, idx2, minLen, maxLen, forceConstant);
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}
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void DistanceConstraintContribs::addContrib(unsigned int idx1,
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unsigned int idx2, bool relative,
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double minLen, double maxLen,
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double forceConstant) {
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const RDGeom::PointPtrVect &pos = dp_forceField->positions();
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URANGE_CHECK(idx1, pos.size());
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URANGE_CHECK(idx2, pos.size());
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PRECONDITION(maxLen >= minLen, "bad bounds");
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if (relative) {
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const RDGeom::Point3D p1 = *((RDGeom::Point3D *)pos[idx1]);
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const RDGeom::Point3D p2 = *((RDGeom::Point3D *)pos[idx2]);
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const auto distance = (p1 - p2).length();
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minLen = std::max(minLen + distance, 0.0);
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maxLen = std::max(maxLen + distance, 0.0);
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}
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d_contribs.emplace_back(idx1, idx2, minLen, maxLen, forceConstant);
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}
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double DistanceConstraintContribs::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 accum = 0.0;
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for (const auto &contrib : d_contribs) {
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const auto distance2 =
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dp_forceField->distance2(contrib.idx1, contrib.idx2, pos);
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double difference = 0.0;
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if (distance2 < contrib.minLen * contrib.minLen) {
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difference = contrib.minLen - std::sqrt(distance2);
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} else if (distance2 > contrib.maxLen * contrib.maxLen) {
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difference = std::sqrt(distance2) - contrib.maxLen;
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} else {
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continue;
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}
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accum += 0.5 * contrib.forceConstant * difference * difference;
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}
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return accum;
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}
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void DistanceConstraintContribs::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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for (const auto &contrib : d_contribs) {
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double preFactor = 0.0;
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double distance = 0.0;
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const auto distance2 =
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dp_forceField->distance2(contrib.idx1, contrib.idx2, pos);
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if (distance2 < contrib.minLen * contrib.minLen) {
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distance = std::sqrt(distance2);
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preFactor = distance - contrib.minLen;
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} else if (distance2 > contrib.maxLen * contrib.maxLen) {
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distance = std::sqrt(distance2);
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preFactor = distance - contrib.maxLen;
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} else {
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continue;
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}
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preFactor *= contrib.forceConstant;
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preFactor /= std::max(1.0e-8, distance);
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const double *atom1Coords = &(pos[3 * contrib.idx1]);
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const double *atom2Coords = &(pos[3 * contrib.idx2]);
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for (unsigned int i = 0; i < 3; i++) {
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const double dGrad = preFactor * (atom1Coords[i] - atom2Coords[i]);
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grad[3 * contrib.idx1 + i] += dGrad;
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grad[3 * contrib.idx2 + i] -= dGrad;
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}
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}
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}
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} // namespace ForceFields
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