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* 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
123 lines
4.5 KiB
C++
123 lines
4.5 KiB
C++
// $Id$
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//
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// Created by Santosh Putta, Nov 2006
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//
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#include "ChiralViolationContrib.h"
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#include "ChiralSet.h"
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#include <ForceField/ForceField.h>
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namespace DistGeom {
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ChiralViolationContrib::ChiralViolationContrib(ForceFields::ForceField *owner,
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const ChiralSet *cset,
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double weight) {
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PRECONDITION(owner, "bad owner");
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PRECONDITION(cset, "bad chiral set")
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URANGE_CHECK(cset->d_idx1, owner->positions().size());
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URANGE_CHECK(cset->d_idx2, owner->positions().size());
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URANGE_CHECK(cset->d_idx3, owner->positions().size());
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URANGE_CHECK(cset->d_idx4, owner->positions().size());
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dp_forceField = owner;
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d_idx1 = cset->d_idx1;
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d_idx2 = cset->d_idx2;
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d_idx3 = cset->d_idx3;
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d_idx4 = cset->d_idx4;
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d_volLower = cset->getLowerVolumeBound();
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d_volUpper = cset->getUpperVolumeBound();
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d_weight = weight;
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}
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double ChiralViolationContrib::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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unsigned int dim = dp_forceField->dimension();
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double vol = calcChiralVolume(d_idx1, d_idx2, d_idx3, d_idx4, pos, dim);
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double res = 0.0;
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if (vol < d_volLower) {
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res = d_weight * (vol - d_volLower) * (vol - d_volLower);
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} else if (vol > d_volUpper) {
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res = d_weight * (vol - d_volUpper) * (vol - d_volUpper);
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}
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// std::cerr<<"Chiral Violation vol: "<<vol<<" E: "<<res<<std::endl;
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return res;
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}
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void ChiralViolationContrib::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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unsigned int dim = dp_forceField->dimension();
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// even if we are minimizing in higher dimension the chiral volume is
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// calculated using only the first 3 dimensions
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RDGeom::Point3D v1(pos[d_idx1 * dim] - pos[d_idx4 * dim],
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pos[d_idx1 * dim + 1] - pos[d_idx4 * dim + 1],
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pos[d_idx1 * dim + 2] - pos[d_idx4 * dim + 2]);
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RDGeom::Point3D v2(pos[d_idx2 * dim] - pos[d_idx4 * dim],
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pos[d_idx2 * dim + 1] - pos[d_idx4 * dim + 1],
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pos[d_idx2 * dim + 2] - pos[d_idx4 * dim + 2]);
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RDGeom::Point3D v3(pos[d_idx3 * dim] - pos[d_idx4 * dim],
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pos[d_idx3 * dim + 1] - pos[d_idx4 * dim + 1],
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pos[d_idx3 * dim + 2] - pos[d_idx4 * dim + 2]);
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RDGeom::Point3D v2xv3 = v2.crossProduct(v3);
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double vol = v1.dotProduct(v2xv3);
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double preFactor;
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// std::cerr << "Chiral Violation grad: " << " " << vol << " "
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// << "idxs: " << d_idx1 << " " << d_idx2 << " " << d_idx3 << " "
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// << d_idx4 << " " << d_volLower << " - " << d_volUpper <<
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// std::endl;
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if (vol < d_volLower) {
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preFactor = d_weight * (vol - d_volLower);
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} else if (vol > d_volUpper) {
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preFactor = d_weight * (vol - d_volUpper);
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} else {
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return;
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}
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// now comes the hard part - there are a total of 12 variables involved
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// 4 x 3 - four points and 3 dimensions
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//
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grad[dim * d_idx1] += preFactor * ((v2.y) * (v3.z) - (v3.y) * (v2.z));
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grad[dim * d_idx1 + 1] += preFactor * ((v3.x) * (v2.z) - (v2.x) * (v3.z));
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grad[dim * d_idx1 + 2] += preFactor * ((v2.x) * (v3.y) - (v3.x) * (v2.y));
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grad[dim * d_idx2] += preFactor * ((v3.y) * (v1.z) - (v3.z) * (v1.y));
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grad[dim * d_idx2 + 1] += preFactor * ((v3.z) * (v1.x) - (v3.x) * (v1.z));
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grad[dim * d_idx2 + 2] += preFactor * ((v3.x) * (v1.y) - (v3.y) * (v1.x));
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grad[dim * d_idx3] += preFactor * ((v2.z) * (v1.y) - (v2.y) * (v1.z));
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grad[dim * d_idx3 + 1] += preFactor * ((v2.x) * (v1.z) - (v2.z) * (v1.x));
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grad[dim * d_idx3 + 2] += preFactor * ((v2.y) * (v1.x) - (v2.x) * (v1.y));
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grad[dim * d_idx4] +=
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preFactor *
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(pos[d_idx1 * dim + 2] * (pos[d_idx2 * dim + 1] - pos[d_idx3 * dim + 1]) +
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pos[d_idx2 * dim + 2] * (pos[d_idx3 * dim + 1] - pos[d_idx1 * dim + 1]) +
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pos[d_idx3 * dim + 2] * (pos[d_idx1 * dim + 1] - pos[d_idx2 * dim + 1]));
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grad[dim * d_idx4 + 1] +=
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preFactor *
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(pos[d_idx1 * dim] * (pos[d_idx2 * dim + 2] - pos[d_idx3 * dim + 2]) +
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pos[d_idx2 * dim] * (pos[d_idx3 * dim + 2] - pos[d_idx1 * dim + 2]) +
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pos[d_idx3 * dim] * (pos[d_idx1 * dim + 2] - pos[d_idx2 * dim + 2]));
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grad[dim * d_idx4 + 2] +=
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preFactor *
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(pos[d_idx1 * dim + 1] * (pos[d_idx2 * dim] - pos[d_idx3 * dim]) +
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pos[d_idx2 * dim + 1] * (pos[d_idx3 * dim] - pos[d_idx1 * dim]) +
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pos[d_idx3 * dim + 1] * (pos[d_idx1 * dim] - pos[d_idx2 * dim]));
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// std::cerr << " " << preFactor << std::endl;
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}
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} // namespace DistGeom
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