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https://github.com/openmm/openmm
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05472c9a81
* Replace SimTK-containing file headers * Update file headers for new Tinker reader files added
93 lines
4.5 KiB
C++
93 lines
4.5 KiB
C++
#ifndef OPENMM_REFERENCESETTLEALGORITHM_H_
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#define OPENMM_REFERENCESETTLEALGORITHM_H_
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/* -------------------------------------------------------------------------- *
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* OpenMM *
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* -------------------------------------------------------------------------- *
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* This is part of the OpenMM molecular simulation toolkit. *
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* See https://openmm.org/development. *
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* *
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* Portions copyright (c) 2013 Stanford University and the Authors. *
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* Authors: Peter Eastman *
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* Contributors: *
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* *
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* Permission is hereby granted, free of charge, to any person obtaining a *
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* copy of this software and associated documentation files (the "Software"), *
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* to deal in the Software without restriction, including without limitation *
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* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
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* and/or sell copies of the Software, and to permit persons to whom the *
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* Software is furnished to do so, subject to the following conditions: *
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* *
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* The above copyright notice and this permission notice shall be included in *
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* 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 OR *
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
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* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
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* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
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* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
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* USE OR OTHER DEALINGS IN THE SOFTWARE. *
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* -------------------------------------------------------------------------- */
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#include "ReferenceConstraintAlgorithm.h"
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#include <vector>
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namespace OpenMM {
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/**
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* This implements the SETTLE algorithm for constraining water molecules.
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*/
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class OPENMM_EXPORT ReferenceSETTLEAlgorithm : public ReferenceConstraintAlgorithm {
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public:
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ReferenceSETTLEAlgorithm(const std::vector<int>& atom1, const std::vector<int>& atom2, const std::vector<int>& atom3,
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const std::vector<double>& distance1, const std::vector<double>& distance2, std::vector<double>& masses);
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/**
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* Get the number of clusters.
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*/
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int getNumClusters() const;
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/**
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* Get the parameters describing one cluster.
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*
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* @param index the index of the cluster to get
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* @param atom1 the index of the first atom in the cluster
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* @param atom2 the index of the second atom in the cluster
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* @param atom3 the index of the third atom in the cluster
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* @param distance1 the distance between atoms 1 and 2
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* @param distance2 the distance between atoms 2 and 3
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*/
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void getClusterParameters(int index, int& atom1, int& atom2, int& atom3, double& distance1, double& distance2) const;
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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, 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 velocities 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, std::vector<OpenMM::Vec3>& velocities, std::vector<double>& inverseMasses, double tolerance);
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private:
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std::vector<int> atom1;
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std::vector<int> atom2;
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std::vector<int> atom3;
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std::vector<double> distance1;
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std::vector<double> distance2;
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std::vector<double> masses;
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};
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} // namespace OpenMM
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#endif /*OPENMM_REFERENCESETTLEALGORITHM_H_*/
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