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
149 lines
7.2 KiB
C++
149 lines
7.2 KiB
C++
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/* Portions copyright (c) 2011-2023 Stanford University and Simbios.
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* Contributors: Peter Eastman
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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 __ReferenceCustomDynamics_H__
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#define __ReferenceCustomDynamics_H__
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#include "ReferenceDynamics.h"
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#include "openmm/CustomIntegrator.h"
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#include "openmm/internal/ContextImpl.h"
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#include "openmm/internal/CustomIntegratorUtilities.h"
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#include "openmm/internal/CompiledExpressionSet.h"
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#include "openmm/internal/VectorExpression.h"
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#include "lepton/CompiledExpression.h"
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#include <map>
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#include <string>
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#include <vector>
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namespace OpenMM {
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class ReferenceCustomDynamics : public ReferenceDynamics {
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private:
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class DerivFunction;
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bool initialized;
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const OpenMM::CustomIntegrator& integrator;
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std::vector<double> inverseMasses;
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std::vector<OpenMM::Vec3> sumBuffer, oldPos;
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std::vector<OpenMM::CustomIntegrator::ComputationType> stepType;
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std::vector<std::string> stepVariable;
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std::vector<std::vector<Lepton::CompiledExpression> > stepExpressions;
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std::vector<std::vector<VectorExpression> > stepVectorExpressions;
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std::vector<CustomIntegratorUtilities::Comparison> comparisons;
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std::vector<bool> invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy;
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std::vector<int> forceGroupFlags, blockEnd;
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std::map<std::string, double> energyParamDerivs;
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Lepton::CompiledExpression kineticEnergyExpression;
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bool kineticEnergyNeedsForce;
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CompiledExpressionSet expressionSet;
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double x, v, m, f, energy, gaussian, uniform;
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int xIndex, vIndex;
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std::vector<int> perDofVariableIndex, stepVariableIndex;
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std::vector<double> perDofVariable;
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void initialize(OpenMM::ContextImpl& context, std::vector<double>& masses, std::map<std::string, double>& globals);
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Lepton::ExpressionTreeNode replaceDerivFunctions(const Lepton::ExpressionTreeNode& node, OpenMM::ContextImpl& context);
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void computePerDof(int numberOfAtoms, std::vector<OpenMM::Vec3>& results, const std::vector<OpenMM::Vec3>& atomCoordinates,
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const std::vector<OpenMM::Vec3>& velocities, const std::vector<OpenMM::Vec3>& forces, const std::vector<double>& masses,
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const std::vector<std::vector<OpenMM::Vec3> >& perDof, const Lepton::CompiledExpression& expression);
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void computePerParticle(int numberOfAtoms, std::vector<OpenMM::Vec3>& results, const std::vector<OpenMM::Vec3>& atomCoordinates,
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const std::vector<OpenMM::Vec3>& velocities, const std::vector<OpenMM::Vec3>& forces, const std::vector<double>& masses,
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const std::vector<std::vector<OpenMM::Vec3> >& perDof, const std::map<std::string, double>& globals, const VectorExpression& expression);
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void recordChangedParameters(OpenMM::ContextImpl& context, std::map<std::string, double>& globals);
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bool evaluateCondition(int step);
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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 integrator the integrator definition to use
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--------------------------------------------------------------------------------------- */
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ReferenceCustomDynamics(int numberOfAtoms, const OpenMM::CustomIntegrator& integrator);
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/**---------------------------------------------------------------------------------------
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Destructor
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--------------------------------------------------------------------------------------- */
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~ReferenceCustomDynamics();
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/**---------------------------------------------------------------------------------------
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Update
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@param context the context this integrator is updating
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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 forces forces
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@param masses atom masses
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@param globals a map containing values of global variables
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@param perDof the values of per-DOF variables
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@param forcesAreValid whether the current forces are valid or need to be recomputed
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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, int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
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std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses,
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std::map<std::string, double>& globals, std::vector<std::vector<OpenMM::Vec3> >& perDof, bool& forcesAreValid, double tolerance, const Vec3* boxVectors);
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/**---------------------------------------------------------------------------------------
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Compute the kinetic energy of the system.
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@param context the context this integrator is updating
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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 forces forces
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@param masses atom masses
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@param globals a map containing values of global variables
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@param perDof the values of per-DOF variables
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@param forcesAreValid whether the current forces are valid or need to be recomputed
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--------------------------------------------------------------------------------------- */
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double computeKineticEnergy(OpenMM::ContextImpl& context, int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
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std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses,
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std::map<std::string, double>& globals, std::vector<std::vector<OpenMM::Vec3> >& perDof, bool& forcesAreValid);
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};
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} // namespace OpenMM
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#endif // __ReferenceCustomDynamics_H__
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