mirror of
https://github.com/openmm/openmm
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de180e4e94
* Created DPDIntegrator class * Reference implementation of DPDIntegrator * Build neighbor list for DPDIntegrator * Minor fixes * Documentation for DPDIntegrator * Python API for DPDIntegrator * Preliminary OpenCL implementation of DPDIntegrator * Enable USE_PERIODIC * Use updated positions in DPD thermostat * Working on neighbor list for OpenCL DPDIntegrator * ReorderListener for particle types * Serialization for DPDIntegrator * CUDA implementation of DPDIntegrator * HIP implementation of DPDIntegrator * Fixed compile error in Python wrapper * Fixed compile error in wrappers * Fixed uninitialized memory in reference neighbor list * Added DPDIntegrator to C++ API docs * Fixed incorrect launch size * Fixed nan in DPD random number generator * Minor optimizations * Improved load balancing * Fixed an indexing error * Neighbor list uses the maximum cutoff of any force * Fixed HIP compilation error * Fixed access to invalid memory * Added test case for diffusion coefficient * Try to debug segfaults on CI * Debugging * Debugging * Debugging * Debugging * Debugging * Debugging * Possible fix * Debugging * Debugging * Debugging * Use correct block size on CPU OpenCL * Workaround for bug in Intel's OpenCL for CPUs * Removed an unnecessary define * Removed debugging code * Include Dart * More Intel workarounds * Workaround for error in NVIDIA OpenCL
198 lines
6.7 KiB
C++
198 lines
6.7 KiB
C++
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/* Portions copyright (c) 2006-2012 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 __ReferenceDynamics_H__
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#define __ReferenceDynamics_H__
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#include "ReferenceConstraintAlgorithm.h"
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#include "ReferenceVirtualSites.h"
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#include "openmm/System.h"
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#include <cstddef>
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#include <vector>
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namespace OpenMM {
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/**---------------------------------------------------------------------------------------
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Abstract class for dynamics
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Main method (virtual) is update()
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'Random' numbers are currently fixed to allow testing
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--------------------------------------------------------------------------------------- */
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class OPENMM_EXPORT ReferenceDynamics {
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private:
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int _numberOfAtoms;
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int _timeStep;
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double _deltaT;
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double _temperature;
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ReferenceConstraintAlgorithm* _referenceConstraint;
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const ReferenceVirtualSites* virtualSites;
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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 deltaT delta t for dynamics
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@param temperature temperature
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--------------------------------------------------------------------------------------- */
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ReferenceDynamics(int numberOfAtoms, double _deltaT, double temperature);
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/**---------------------------------------------------------------------------------------
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Destructor
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--------------------------------------------------------------------------------------- */
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virtual ~ReferenceDynamics();
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/**---------------------------------------------------------------------------------------
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Get number of atoms
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@return number of atoms
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--------------------------------------------------------------------------------------- */
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int getNumberOfAtoms() const;
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/**---------------------------------------------------------------------------------------
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Get time step
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@return time step
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--------------------------------------------------------------------------------------- */
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int getTimeStep() const;
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/**---------------------------------------------------------------------------------------
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Increment time step
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@return incremented time step
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--------------------------------------------------------------------------------------- */
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int incrementTimeStep();
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/**---------------------------------------------------------------------------------------
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Get delta t
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@return deltaT
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--------------------------------------------------------------------------------------- */
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double getDeltaT() const;
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/**---------------------------------------------------------------------------------------
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Set delta t
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--------------------------------------------------------------------------------------- */
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void setDeltaT(double deltaT);
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/**---------------------------------------------------------------------------------------
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Get temperature
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@return temperature
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--------------------------------------------------------------------------------------- */
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double getTemperature() const;
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/**---------------------------------------------------------------------------------------
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Set the temperature
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--------------------------------------------------------------------------------------- */
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void setTemperature(double temperature);
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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 tolerance the constraint tolerance
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--------------------------------------------------------------------------------------- */
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virtual 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 tolerance);
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/**---------------------------------------------------------------------------------------
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Get ReferenceConstraint
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@return referenceConstraint object
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--------------------------------------------------------------------------------------- */
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ReferenceConstraintAlgorithm* getReferenceConstraintAlgorithm() const;
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/**---------------------------------------------------------------------------------------
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Set ReferenceConstraint
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@param referenceConstraint referenceConstraint object
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--------------------------------------------------------------------------------------- */
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void setReferenceConstraintAlgorithm(ReferenceConstraintAlgorithm* referenceConstraint);
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/**
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* Get the object used to compute virtual sites.
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*/
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const ReferenceVirtualSites& getVirtualSites() const;
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/**
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* Set the object used to compute virtual sites.
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*/
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void setVirtualSites(const ReferenceVirtualSites& sites);
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};
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} // namespace OpenMM
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#endif // __ReferenceDynamics_H__
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