mirror of
https://github.com/openmm/openmm
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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
105 lines
3.8 KiB
C++
105 lines
3.8 KiB
C++
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/* Portions copyright (c) 2006-2025 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 __ReferenceDPDDynamics_H__
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#define __ReferenceDPDDynamics_H__
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#include "ReferenceDynamics.h"
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#include "ReferenceNeighborList.h"
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#include "openmm/DPDIntegrator.h"
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#include "openmm/Vec3.h"
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#include "openmm/internal/ContextImpl.h"
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#include "openmm/internal/windowsExport.h"
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#include <vector>
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namespace OpenMM {
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class OPENMM_EXPORT ReferenceDPDDynamics : public ReferenceDynamics {
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protected:
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std::vector<Vec3> xPrime, oldx;
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std::vector<double> masses, inverseMasses;
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bool periodic;
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Vec3 periodicBoxVectors[3];
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NeighborList neighborList;
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std::vector<int> particleType;
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std::vector<std::vector<double> > frictionTable, cutoffTable;
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double maxCutoff;
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public:
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/**
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* Constructor
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*
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* @param system the system to simulate
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* @param integrator the integrator being used
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*/
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ReferenceDPDDynamics(const System& system, const DPDIntegrator& integrator);
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/**
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* Destructor
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*/
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~ReferenceDPDDynamics();
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/**
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* Set the periodic box vectors.
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*/
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void setPeriodicBoxVectors(OpenMM::Vec3* vectors);
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/**
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* Get the maximum cutoff distance for any pair of types.
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*/
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double getMaxCutoff() const;
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/**
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* Perform a time step, updating the positions and velocities.
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*
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* @param context the context this integrator is updating
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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 masses atom masses
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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(OpenMM::ContextImpl& context, std::vector<OpenMM::Vec3>& atomCoordinates,
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std::vector<OpenMM::Vec3>& velocities, std::vector<double>& masses, double tolerance, const Vec3* boxVectors);
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/**
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* The first stage of the update algorithm.
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*/
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virtual void updatePart1(int numParticles, std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces);
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/**
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* The second stage of the update algorithm.
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*/
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virtual void updatePart2(int numParticles, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
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std::vector<OpenMM::Vec3>& xPrime);
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/**
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* The third stage of the update algorithm.
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*/
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virtual void updatePart3(OpenMM::ContextImpl& context, int numParticles, std::vector<OpenMM::Vec3>& atomCoordinates,
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std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& xPrime);
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};
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} // namespace OpenMM
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#endif // __ReferenceDPDDynamics_H__
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