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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
164 lines
6.8 KiB
C++
164 lines
6.8 KiB
C++
/* Portions copyright (c) 2006-2023 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 __ReferenceForce_H__
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#define __ReferenceForce_H__
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#include "openmm/Vec3.h"
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#include "lepton/CompiledExpression.h"
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#include "openmm/internal/windowsExport.h"
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namespace OpenMM {
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class OPENMM_EXPORT ReferenceForce {
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private:
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static double periodicDifference(double val1, double val2, double period);
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public:
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/**---------------------------------------------------------------------------------------
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Constructor
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--------------------------------------------------------------------------------------- */
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ReferenceForce();
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/**---------------------------------------------------------------------------------------
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Destructor
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--------------------------------------------------------------------------------------- */
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~ReferenceForce();
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/**---------------------------------------------------------------------------------------
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Static variables
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--------------------------------------------------------------------------------------- */
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static const int XIndex = 0;
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static const int YIndex = 1;
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static const int ZIndex = 2;
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static const int R2Index = 3;
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static const int RIndex = 4;
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static const int LastDeltaRIndex = 5;
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static const int DeltaRMaxIndex = 5;
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/**---------------------------------------------------------------------------------------
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Get deltaR and distance and distance**2 between atomI and atomJ (static method)
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deltaR: j - i
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@param atomCoordinatesI atom i coordinates
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@param atomCoordinatesI atom j coordinates
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@param deltaR deltaX, deltaY, deltaZ, R2, R upon return
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--------------------------------------------------------------------------------------- */
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static void getDeltaR(const OpenMM::Vec3& atomCoordinatesI, const OpenMM::Vec3& atomCoordinatesJ,
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double* deltaR);
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/**---------------------------------------------------------------------------------------
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Get deltaR between atomI and atomJ (static method)
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deltaR: j - i
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@param atomCoordinatesI atom i coordinates
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@param atomCoordinatesI atom j coordinates
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@return the displacement
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--------------------------------------------------------------------------------------- */
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static Vec3 getDeltaR(const OpenMM::Vec3& atomCoordinatesI, const OpenMM::Vec3& atomCoordinatesJ);
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/**---------------------------------------------------------------------------------------
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Get deltaR and distance and distance**2 between atomI and atomJ, assuming periodic
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boundary conditions (static method); deltaR: j - i
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@param atomCoordinatesI atom i coordinates
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@param atomCoordinatesI atom j coordinates
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@param boxSize X, Y, and Z sizes of the periodic box
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@param deltaR deltaX, deltaY, deltaZ, R2, R upon return
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--------------------------------------------------------------------------------------- */
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static void getDeltaRPeriodic(const OpenMM::Vec3& atomCoordinatesI, const OpenMM::Vec3& atomCoordinatesJ,
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const double* boxSize, double* deltaR);
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/**---------------------------------------------------------------------------------------
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Get deltaR and distance and distance**2 between atomI and atomJ, assuming periodic
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boundary conditions (static method); deltaR: j - i
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@param atomCoordinatesI atom i coordinates
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@param atomCoordinatesI atom j coordinates
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@param boxVectors the vectors defining the periodic box
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@param deltaR deltaX, deltaY, deltaZ, R2, R upon return
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--------------------------------------------------------------------------------------- */
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static void getDeltaRPeriodic(const OpenMM::Vec3& atomCoordinatesI, const OpenMM::Vec3& atomCoordinatesJ,
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const OpenMM::Vec3* boxVectors, double* deltaR);
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/**---------------------------------------------------------------------------------------
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Get deltaR between atomI and atomJ, assuming periodic boundary conditions (static method);
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deltaR: j - i
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@param atomCoordinatesI atom i coordinates
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@param atomCoordinatesI atom j coordinates
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@param boxVectors the vectors defining the periodic box
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@return the displacement
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--------------------------------------------------------------------------------------- */
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static Vec3 getDeltaRPeriodic(const OpenMM::Vec3& atomCoordinatesI, const OpenMM::Vec3& atomCoordinatesJ,
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const OpenMM::Vec3* boxVectors);
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/**
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* Invert the periodic box vectors to get the corresponding vectors in reciprocal space.
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*/
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static void invertBoxVectors(const OpenMM::Vec3* boxVectors, OpenMM::Vec3* recipBoxVectors);
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/**
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* Get a pointer to the memory for setting a variable in a CompiledExpression. If the expression
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* does not use the specified variable, return NULL.
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*/
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static double* getVariablePointer(Lepton::CompiledExpression& expression, const std::string& name);
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/**
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* Set the value of a variable in a CompiledExpression, using the pointer that was returned by getVariablePointer().
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*/
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static void setVariable(double* pointer, double value);
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};
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} // namespace OpenMM
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#endif // __ReferenceForce_H__
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