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2c5ae534f2
* First try at using DistViolationContribs only the most basic of testing has been done also add ForceField::distance2 to allow some optimizations * allow testing using old approach * optimization At this point testUFFForceFieldHelpers fails since the check for std::max_element in the e_contribs vector at Embedder.cpp:513 is now doing something totally different (instead of a bunch of small distance violation contribs, we have one big one). We'll need to come up with something for this. With the benchmarking set that I'm using - 500 DG conformers for ~465 COD molecules using 10 threads - this runs in almost 10% less time than master. * backup; builds, tests do not pass * all tests pass except the old failure * more constification * backup/debugging * add fourthdim contribs the same way * tests now pass * deprecations * remove unused vars and code * changes in response to review
100 lines
2.9 KiB
C++
100 lines
2.9 KiB
C++
//
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// Copyright (C) 2024 Greg Landrum 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 "DistViolationContribs.h"
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#include <ForceField/ForceField.h>
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#include <RDGeneral/Invariant.h>
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namespace DistGeom {
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DistViolationContribs::DistViolationContribs(ForceFields::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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auto distance2 = [](const unsigned int idx1, const unsigned int idx2,
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const double *pos, const unsigned int dim) {
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const auto *end1Coords = &(pos[dim * idx1]);
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const auto *end2Coords = &(pos[dim * idx2]);
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double d2 = 0.0;
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for (unsigned int i = 0; i < dim; i++) {
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double d = end1Coords[i] - end2Coords[i];
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d2 += d * d;
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}
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return d2;
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};
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auto distance = [](const unsigned int idx1, const unsigned int idx2,
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const double *pos, const unsigned int dim) {
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return sqrt(distance2(idx1, idx2, pos, dim));
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};
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double DistViolationContribs::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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auto contrib = [&](const auto &c) {
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double d2 = distance2(c.idx1, c.idx2, pos, dp_forceField->dimension());
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double val = 0.0;
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if (d2 > c.ub * c.ub) {
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val = (d2 / (c.ub * c.ub)) - 1.0;
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} else if (d2 < c.lb * c.lb) {
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val = ((2 * c.lb * c.lb) / (c.lb * c.lb + d2)) - 1.0;
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}
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if (val > 0.0) {
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accum += c.weight * val * val;
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}
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};
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for (const auto &c : d_contribs) {
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contrib(c);
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}
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return accum;
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}
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void DistViolationContribs::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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const unsigned int dim = this->dp_forceField->dimension();
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auto contrib = [&](const auto &c) {
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double d = distance(c.idx1, c.idx2, pos, dp_forceField->dimension());
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double preFactor = 0.0;
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if (d > c.ub) {
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double u2 = c.ub * c.ub;
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preFactor = 4. * (((d * d) / u2) - 1.0) * (d / u2);
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} else if (d < c.lb) {
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double d2 = d * d;
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double l2 = c.lb * c.lb;
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double l2d2 = d2 + l2;
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preFactor = 8. * l2 * d * (1. - 2 * l2 / l2d2) / (l2d2 * l2d2);
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} else {
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return;
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}
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for (unsigned int i = 0; i < dim; i++) {
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const auto p1 = dim * c.idx1 + i;
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const auto p2 = dim * c.idx2 + i;
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double dGrad;
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if (d > 0.0) {
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dGrad = c.weight * preFactor * (pos[p1] - pos[p2]) / d;
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} else {
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// FIX: this likely isn't right
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dGrad = c.weight * preFactor * (pos[p1] - pos[p2]);
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}
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grad[p1] += dGrad;
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grad[p2] -= dGrad;
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}
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};
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for (const auto &c : d_contribs) {
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contrib(c);
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}
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}
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} // namespace DistGeom
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