mirror of
https://github.com/openmm/openmm
synced 2026-06-03 06:39:48 +09:00
bb3073d4f3
* Reference implementation of SymmetrySite * Common implementation of SymmetrySite * Removed duplicated code * Serialization for SymmetrySite * Fixed compilation error building C wrapper * Added SymmetrySite to user guide * Bug fix * Added P21 test case
139 lines
5.5 KiB
C++
139 lines
5.5 KiB
C++
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/* Portions copyright (c) 2006-2024 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 __ReferenceVariableStochasticDynamics_H__
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#define __ReferenceVariableStochasticDynamics_H__
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#include "ReferenceDynamics.h"
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namespace OpenMM {
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class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
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private:
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std::vector<OpenMM::Vec3> xPrime, oldx;
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std::vector<double> inverseMasses;
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double friction, _accuracy;
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public:
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/**---------------------------------------------------------------------------------------
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Constructor
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@param numberOfAtoms number of atoms
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@param friction friction coefficient
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@param temperature temperature
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@param accuracy required accuracy
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--------------------------------------------------------------------------------------- */
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ReferenceVariableStochasticDynamics(int numberOfAtoms, double friction, double temperature, double accuracy);
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/**---------------------------------------------------------------------------------------
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Destructor
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--------------------------------------------------------------------------------------- */
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~ReferenceVariableStochasticDynamics();
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/**---------------------------------------------------------------------------------------
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Get friction coefficient
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--------------------------------------------------------------------------------------- */
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double getFriction() const;
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/**---------------------------------------------------------------------------------------
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Get the required accuracy
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@return accuracy
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--------------------------------------------------------------------------------------- */
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double getAccuracy() const;
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/**---------------------------------------------------------------------------------------
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Set the required accuracy
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--------------------------------------------------------------------------------------- */
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void setAccuracy(double accuracy);
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/**---------------------------------------------------------------------------------------
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Update
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@param system the System to be integrated
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@param atomCoordinates atom coordinates
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@param velocities velocities
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@param forces forces
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@param masses atom masses
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@param maxStepSize maximum time step
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@param tolerance the constraint tolerance
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@param boxVectors the current periodic box vectors
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--------------------------------------------------------------------------------------- */
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void update(const OpenMM::System& system, std::vector<OpenMM::Vec3>& atomCoordinates,
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std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, double maxStepSize, double tolerance, const Vec3* boxVectors);
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/**---------------------------------------------------------------------------------------
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@param numberOfAtoms number of atoms
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@param velocities velocities
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@param forces forces
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@param inverseMasses inverse atom masses
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@param maxStepSize maximum time step
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--------------------------------------------------------------------------------------- */
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void updatePart1(int numberOfAtoms, std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses, double maxStepSize);
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/**---------------------------------------------------------------------------------------
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Second update
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@param numberOfAtoms number of atoms
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@param atomCoordinates atom coordinates
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@param velocities velocities
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@param inverseMasses inverse atom masses
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@param xPrime xPrime
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--------------------------------------------------------------------------------------- */
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void updatePart2(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
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std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
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};
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} // namespace OpenMM
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#endif // __ReferenceVariableStochasticDynamics_H__
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