mirror of
https://github.com/openmm/openmm
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157 lines
5.8 KiB
C++
157 lines
5.8 KiB
C++
/* Portions copyright (c) 2006-2009 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 __ReferenceLincsAlgorithm_H__
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#define __ReferenceLincsAlgorithm_H__
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#include "ReferenceConstraintAlgorithm.h"
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#include "SimTKOpenMMRealType.h"
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#include <vector>
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namespace OpenMM {
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class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
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protected:
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int _numTerms;
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int _numberOfConstraints;
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int** _atomIndices;
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double* _distance;
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bool _hasInitialized;
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std::vector<std::vector<int> > _linkedConstraints;
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std::vector<double> _sMatrix;
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std::vector<double> _rhs1;
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std::vector<double> _rhs2;
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std::vector<double> _solution;
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std::vector<std::vector<double> > _couplingMatrix;
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std::vector<OpenMM::Vec3> _constraintDir;
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/**---------------------------------------------------------------------------------------
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Set the number of terms to use in the series expansion
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@param numberOfAtoms number of atoms
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@param inverseMasses 1/mass
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--------------------------------------------------------------------------------------- */
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void initialize(int numberOfAtoms, std::vector<double>& inverseMasses);
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/**---------------------------------------------------------------------------------------
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Solve the matrix equation
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--------------------------------------------------------------------------------------- */
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void solveMatrix();
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/**---------------------------------------------------------------------------------------
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Update the atom position based on the solution to the matrix equation.
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@param numberOfAtoms number of atoms
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@param atomCoordinates atom coordinates
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@param inverseMasses 1/mass
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--------------------------------------------------------------------------------------- */
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void updateAtomPositions(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<double>& inverseMasses);
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public:
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/**---------------------------------------------------------------------------------------
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ReferenceLincsAlgorithm constructor
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@param numberOfConstraints 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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--------------------------------------------------------------------------------------- */
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ReferenceLincsAlgorithm(int numberOfConstraints, int** atomIndices, double* distance);
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/**---------------------------------------------------------------------------------------
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Get number of constraints
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@return number of constraints
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--------------------------------------------------------------------------------------- */
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int getNumberOfConstraints() const;
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/**---------------------------------------------------------------------------------------
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Get the number of terms to use in the series expansion
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@return terms
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--------------------------------------------------------------------------------------- */
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int getNumTerms() const;
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/**---------------------------------------------------------------------------------------
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Set the number of terms to use in the series expansion
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--------------------------------------------------------------------------------------- */
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void setNumTerms(int terms);
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/**---------------------------------------------------------------------------------------
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Apply Lincs algorithm
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@param numberOfAtoms number of atoms
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@param atomCoordinates atom coordinates
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@param atomCoordinatesP atom coordinates prime
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@param inverseMasses 1/mass
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--------------------------------------------------------------------------------------- */
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void apply(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
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std::vector<OpenMM::Vec3>& atomCoordinatesP, std::vector<double>& inverseMasses);
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/**---------------------------------------------------------------------------------------
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Apply constraint algorithm to velocities.
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@param numberOfAtoms number of atoms
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@param atomCoordinates atom coordinates
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@param velocities atom velocities
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@param inverseMasses 1/mass
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--------------------------------------------------------------------------------------- */
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void applyToVelocities(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
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std::vector<OpenMM::Vec3>& velocities, std::vector<double>& inverseMasses);
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};
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} // namespace OpenMM
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#endif // __ReferenceLincsAlgorithm_H__
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