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//
// Copyright (C) 2013-2024 Paolo Tosco 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 "ForceField.h"
#include "DistanceConstraint.h"
#include <RDGeneral/Invariant.h>
#include <cmath>
namespace ForceFields {
DistanceConstraintContrib::DistanceConstraintContrib(
ForceField *owner, unsigned int idx1, unsigned int idx2, double minLen,
double maxLen, double forceConst) {
PRECONDITION(owner, "bad owner");
URANGE_CHECK(idx1, owner->positions().size());
URANGE_CHECK(idx2, owner->positions().size());
PRECONDITION(maxLen >= minLen, "bad bounds");
dp_forceField = owner;
d_end1Idx = idx1;
d_end2Idx = idx2;
d_minLen = minLen;
d_maxLen = maxLen;
d_forceConstant = forceConst;
}
DistanceConstraintContrib::DistanceConstraintContrib(
ForceField *owner, unsigned int idx1, unsigned int idx2, bool relative,
double minLen, double maxLen, double forceConst) {
PRECONDITION(owner, "bad owner");
const RDGeom::PointPtrVect &pos = owner->positions();
URANGE_CHECK(idx1, pos.size());
URANGE_CHECK(idx2, pos.size());
PRECONDITION(maxLen >= minLen, "bad bounds");
if (relative) {
RDGeom::Point3D &p1 = *((RDGeom::Point3D *)pos[idx1]);
RDGeom::Point3D &p2 = *((RDGeom::Point3D *)pos[idx2]);
const auto dist = (p1 - p2).length();
minLen = std::max(dist + minLen, 0.0);
maxLen = std::max(dist + maxLen, 0.0);
}
d_minLen = minLen;
d_maxLen = maxLen;
dp_forceField = owner;
d_end1Idx = idx1;
d_end2Idx = idx2;
d_forceConstant = forceConst;
}
double DistanceConstraintContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
double dist = dp_forceField->distance(d_end1Idx, d_end2Idx, pos);
double distTerm = 0.0;
if (dist < d_minLen) {
distTerm = d_minLen - dist;
} else if (dist > d_maxLen) {
distTerm = dist - d_maxLen;
}
double res = 0.5 * d_forceConstant * distTerm * distTerm;
return res;
}
void DistanceConstraintContrib::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 = 0.0;
if (dist < d_minLen) {
preFactor = dist - d_minLen;
} else if (dist > d_maxLen) {
preFactor = dist - d_maxLen;
} else {
return;
}
preFactor *= d_forceConstant;
double *end1Coords = &(pos[3 * d_end1Idx]);
double *end2Coords = &(pos[3 * d_end2Idx]);
for (unsigned int i = 0; i < 3; ++i) {
double dGrad =
preFactor * (end1Coords[i] - end2Coords[i]) / std::max(dist, 1.0e-8);
grad[3 * d_end1Idx + i] += dGrad;
grad[3 * d_end2Idx + i] -= dGrad;
}
}
} // namespace ForceFields
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