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//
// Copyright (C) 2024-2025 Greg Landrum 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 "DistViolationContribs.h"
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
namespace DistGeom {
DistViolationContribs::DistViolationContribs(ForceFields::ForceField *owner) {
PRECONDITION(owner, "bad owner");
dp_forceField = owner;
}
inline double distance2(const unsigned int idx1, const unsigned int idx2,
const double *pos, const unsigned int dim) {
const auto *end1Coords = &(pos[dim * idx1]);
const auto *end2Coords = &(pos[dim * idx2]);
double d2 = 0.0;
for (unsigned int i = 0; i < dim; i++) {
double d = end1Coords[i] - end2Coords[i];
d2 += d * d;
}
return d2;
}
inline double distance(const unsigned int idx1, const unsigned int idx2,
const double *pos, const unsigned int dim) {
return sqrt(distance2(idx1, idx2, pos, dim));
}
double DistViolationContribs::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
double accum = 0.0;
auto contrib = [&](const auto &c) {
double d2 = distance2(c.idx1, c.idx2, pos, dp_forceField->dimension());
double val = 0.0;
if (d2 > c.ub2) {
val = (d2 / (c.ub2)) - 1.0;
} else if (d2 < c.lb2) {
val = ((2 * c.lb2) / (c.lb2 + d2)) - 1.0;
}
if (val > 0.0) {
accum += c.weight * val * val;
}
};
for (const auto &c : d_contribs) {
contrib(c);
}
return accum;
}
void DistViolationContribs::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
const unsigned int dim = this->dp_forceField->dimension();
auto contrib = [&](const auto &c) {
double d2 = distance2(c.idx1, c.idx2, pos, dp_forceField->dimension());
double d;
double preFactor = 0.0;
if (d2 > c.ub2) {
d = sqrt(d2);
preFactor = 4. * (((d * d) / c.ub2) - 1.0) * (d / c.ub2);
} else if (d2 < c.lb2) {
d = sqrt(d2);
double l2d2 = d2 + c.lb2;
preFactor = 8. * c.lb2 * d * (1. - 2 * c.lb2 / l2d2) / (l2d2 * l2d2);
} else {
return;
}
for (unsigned int i = 0; i < dim; i++) {
const auto p1 = dim * c.idx1 + i;
const auto p2 = dim * c.idx2 + i;
double dGrad;
if (d > 0.0) {
dGrad = c.weight * preFactor * (pos[p1] - pos[p2]) / d;
} else {
// FIX: this likely isn't right
dGrad = c.weight * preFactor * (pos[p1] - pos[p2]);
}
grad[p1] += dGrad;
grad[p2] -= dGrad;
}
};
for (const auto &c : d_contribs) {
contrib(c);
}
}
} // namespace DistGeom
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