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//
// Copyright (C) 2024 Niels Maeder and other RDKit contributors
//
// @@ 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 "DistanceConstraints.h"
#include "ForceField.h"
#include <cmath>
#include <RDGeneral/Invariant.h>
namespace ForceFields {
DistanceConstraintContribs::DistanceConstraintContribs(ForceField *owner) {
PRECONDITION(owner, "bad owner");
dp_forceField = owner;
}
void DistanceConstraintContribs::addContrib(unsigned int idx1,
unsigned int idx2, double minLen,
double maxLen,
double forceConstant) {
URANGE_CHECK(idx1, dp_forceField->positions().size());
URANGE_CHECK(idx2, dp_forceField->positions().size());
PRECONDITION(maxLen >= minLen, "bad bounds");
d_contribs.emplace_back(idx1, idx2, minLen, maxLen, forceConstant);
}
void DistanceConstraintContribs::addContrib(unsigned int idx1,
unsigned int idx2, bool relative,
double minLen, double maxLen,
double forceConstant) {
const RDGeom::PointPtrVect &pos = dp_forceField->positions();
URANGE_CHECK(idx1, pos.size());
URANGE_CHECK(idx2, pos.size());
PRECONDITION(maxLen >= minLen, "bad bounds");
if (relative) {
const RDGeom::Point3D p1 = *((RDGeom::Point3D *)pos[idx1]);
const RDGeom::Point3D p2 = *((RDGeom::Point3D *)pos[idx2]);
const auto distance = (p1 - p2).length();
minLen = std::max(minLen + distance, 0.0);
maxLen = std::max(maxLen + distance, 0.0);
}
d_contribs.emplace_back(idx1, idx2, minLen, maxLen, forceConstant);
}
double DistanceConstraintContribs::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
double accum = 0.0;
for (const auto &contrib : d_contribs) {
const auto distance2 =
dp_forceField->distance2(contrib.idx1, contrib.idx2, pos);
double difference = 0.0;
if (distance2 < contrib.minLen * contrib.minLen) {
difference = contrib.minLen - std::sqrt(distance2);
} else if (distance2 > contrib.maxLen * contrib.maxLen) {
difference = std::sqrt(distance2) - contrib.maxLen;
} else {
continue;
}
accum += 0.5 * contrib.forceConstant * difference * difference;
}
return accum;
}
void DistanceConstraintContribs::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
for (const auto &contrib : d_contribs) {
double preFactor = 0.0;
double distance = 0.0;
const auto distance2 =
dp_forceField->distance2(contrib.idx1, contrib.idx2, pos);
if (distance2 < contrib.minLen * contrib.minLen) {
distance = std::sqrt(distance2);
preFactor = distance - contrib.minLen;
} else if (distance2 > contrib.maxLen * contrib.maxLen) {
distance = std::sqrt(distance2);
preFactor = distance - contrib.maxLen;
} else {
continue;
}
preFactor *= contrib.forceConstant;
preFactor /= std::max(1.0e-8, distance);
const double *atom1Coords = &(pos[3 * contrib.idx1]);
const double *atom2Coords = &(pos[3 * contrib.idx2]);
for (unsigned int i = 0; i < 3; i++) {
const double dGrad = preFactor * (atom1Coords[i] - atom2Coords[i]);
grad[3 * contrib.idx1 + i] += dGrad;
grad[3 * contrib.idx2 + i] -= dGrad;
}
}
}
} // namespace ForceFields
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