mirror of
https://github.com/openmm/openmm
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131 lines
4.7 KiB
C++
131 lines
4.7 KiB
C++
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/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
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* Contributors: Pande Group
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*
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* Permission is hereby granted, free of charge, to any person obtaining
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* a copy of this software and associated documentation files (the
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* "Software"), to deal in the Software without restriction, including
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* without limitation the rights to use, copy, modify, merge, publish,
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* distribute, sublicense, and/or sell copies of the Software, and to
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* permit persons to whom the Software is furnished to do so, subject
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* to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included
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* in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
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* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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#ifndef __ReferenceCCMAAlgorithm_H__
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#define __ReferenceCCMAAlgorithm_H__
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#include "ReferenceConstraintAlgorithm.h"
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#include <utility>
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#include <vector>
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#include <set>
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namespace OpenMM {
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class OPENMM_EXPORT ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm {
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protected:
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int _maximumNumberOfIterations;
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double _elementCutoff;
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int _numberOfConstraints;
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std::vector<std::pair<int, int> > _atomIndices;
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std::vector<double> _distance;
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std::vector<OpenMM::Vec3> r_ij;
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std::vector<double> d_ij2, _distanceTolerance, reducedMasses;
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bool _hasInitializedMasses;
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std::vector<std::vector<std::pair<int, double> > > _matrix;
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private:
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void applyConstraints(std::vector<OpenMM::Vec3>& atomCoordinates,
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std::vector<OpenMM::Vec3>& atomCoordinatesP, std::vector<double>& inverseMasses, bool constrainingVelocities, double tolerance);
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public:
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class AngleInfo;
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/**
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* Create a ReferenceCCMAAlgorithm object.
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*
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* @param numberOfAtoms the number of atoms in the system
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* @param numberOfConstraints the number of constraints
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* @param atomIndices atom indices for contraints
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* @param distance distances for constraints
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* @param masses atom masses
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* @param angles angle force field terms
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* @param elementCutoff the cutoff for which elements of the inverse matrix to keep
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*/
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ReferenceCCMAAlgorithm(int numberOfAtoms, int numberOfConstraints, const std::vector<std::pair<int, int> >& atomIndices, const std::vector<double>& distance, std::vector<double>& masses, std::vector<AngleInfo>& angles, double elementCutoff);
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/**
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* Get the number of constraints.
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*/
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int getNumberOfConstraints() const;
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/**
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* Get the maximum number of iterations to perform.
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*/
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int getMaximumNumberOfIterations() const;
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/**
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* Set the maximum number of iterations to perform.
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*/
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void setMaximumNumberOfIterations(int maximumNumberOfIterations);
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/**
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* Apply the constraint algorithm.
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*
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* @param atomCoordinates the original atom coordinates
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* @param atomCoordinatesP the new atom coordinates
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* @param inverseMasses 1/mass
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* @param tolerance the constraint tolerance
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*/
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void apply(std::vector<OpenMM::Vec3>& atomCoordinates,
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std::vector<OpenMM::Vec3>& atomCoordinatesP, std::vector<double>& inverseMasses, double tolerance);
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/**
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* Apply the constraint algorithm to velocities.
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*
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* @param atomCoordinates the atom coordinates
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* @param atomCoordinatesP the velocities to modify
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* @param inverseMasses 1/mass
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* @param tolerance the constraint tolerance
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*/
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void applyToVelocities(std::vector<OpenMM::Vec3>& atomCoordinates,
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std::vector<OpenMM::Vec3>& velocities, std::vector<double>& inverseMasses, double tolerance);
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/**
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* Get the inverse constraint matrix. Each element represents one column, and contains a list
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* of all non-zero elements in the form (index, value).
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*/
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const std::vector<std::vector<std::pair<int, double> > >& getMatrix() const;
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};
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class ReferenceCCMAAlgorithm::AngleInfo
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{
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public:
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int atom1, atom2, atom3;
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double angle;
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AngleInfo(int atom1, int atom2, int atom3, double angle) :
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atom1(atom1), atom2(atom2), atom3(atom3), angle(angle)
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{
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}
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};
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} // namespace OpenMM
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#endif // __ReferenceCCMAAlgorithm_H__
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