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* DistViolationContribs optimization. * Update preFactor calculation to avoid numerical instability: use square of distance instead of squared distance directly, to prevent accumulated errors leading to CI test failures on Mac when d2 > c.ub2. * Optimize distance calculations by moving sqrt under condition branches to avoid unnecessary computations when squared distance bounds are not met.
64 lines
2.1 KiB
C++
64 lines
2.1 KiB
C++
//
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// Copyright (C) 2024-2025 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 <RDGeneral/export.h>
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#ifndef RD_DISTVIOLATIONCONTRIBS_H
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#define RD_DISTVIOLATIONCONTRIBS_H
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#include <vector>
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#include <ForceField/Contrib.h>
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namespace DistGeom {
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struct DistViolationContribsParams {
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unsigned int idx1{0}; //!< index of end1 in the ForceField's positions
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unsigned int idx2{0}; //!< index of end2 in the ForceField's positions
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double ub{1000.0}; //!< upper bound on the distance
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double lb{0.0}; //!< lower bound on the distance
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double ub2{1000000.0}; //!< squared upper bound on the distance
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double lb2{0.0}; //!< squared lower bound on the distance
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double weight{1.0}; //!< used to adjust relative contribution weights
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DistViolationContribsParams(unsigned int i1, unsigned int i2, double u,
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double l, double w = 1.0)
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: idx1(i1), idx2(i2), ub(u), lb(l), ub2(u * u), lb2(l * l), weight(w) {};
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};
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//! A term to capture all violations of the upper and lower bounds by
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//! distance between two points
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class RDKIT_DISTGEOMETRY_EXPORT DistViolationContribs
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: public ForceFields::ForceFieldContrib {
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public:
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DistViolationContribs() = default;
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//! Constructor
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/*!
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\param owner pointer to the owning ForceField
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*/
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DistViolationContribs(ForceFields::ForceField *owner);
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double getEnergy(double *pos) const override;
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void getGrad(double *pos, double *grad) const override;
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DistViolationContribs *copy() const override {
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return new DistViolationContribs(*this);
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}
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void addContrib(unsigned int idx1, unsigned int idx2, double ub, double lb,
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double weight = 1.0) {
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d_contribs.emplace_back(idx1, idx2, ub, lb, weight);
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}
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bool empty() const { return d_contribs.empty(); }
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unsigned int size() const { return d_contribs.size(); }
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private:
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std::vector<DistViolationContribsParams> d_contribs;
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};
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} // namespace DistGeom
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#endif
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