/* Portions copyright (c) 2009-2018 Stanford University and Simbios. * Contributors: Peter Eastman * * Permission is hereby granted, free of charge, to any person obtaining * a copy of this software and associated documentation files (the * "Software"), to deal in the Software without restriction, including * without limitation the rights to use, copy, modify, merge, publish, * distribute, sublicense, and/or sell copies of the Software, and to * permit persons to whom the Software is furnished to do so, subject * to the following conditions: * * The above copyright notice and this permission notice shall be included * in all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef __ReferenceCustomGBIxn_H__ #define __ReferenceCustomGBIxn_H__ #include "ReferenceNeighborList.h" #include "openmm/internal/CompiledExpressionSet.h" #include "openmm/CustomGBForce.h" #include #include #include namespace OpenMM { class ReferenceCustomGBIxn { private: bool cutoff; bool periodic; const OpenMM::NeighborList* neighborList; OpenMM::Vec3 periodicBoxVectors[3]; double cutoffDistance; CompiledExpressionSet expressionSet; std::vector valueExpressions; std::vector > valueDerivExpressions; std::vector > valueGradientExpressions; std::vector > valueParamDerivExpressions; std::vector valueTypes; std::vector energyExpressions; std::vector > energyDerivExpressions; std::vector > energyGradientExpressions; std::vector > energyParamDerivExpressions; std::vector energyTypes; std::vector paramIndex; std::vector valueIndex; std::vector particleParamIndex; std::vector particleValueIndex; int rIndex, xIndex, yIndex, zIndex; std::vector > values, dEdV; std::vector > > dValuedParam; /**--------------------------------------------------------------------------------------- Calculate a computed value of type SingleParticle @param index the index of the value to compute @param numAtoms number of atoms @param atomCoordinates atom coordinates @param atomParameters atomParameters[atomIndex][paramterIndex] --------------------------------------------------------------------------------------- */ void calculateSingleParticleValue(int index, int numAtoms, std::vector& atomCoordinates, std::vector >& atomParameters); /**--------------------------------------------------------------------------------------- Calculate a computed value that is based on particle pairs @param index the index of the value to compute @param numAtoms number of atoms @param atomCoordinates atom coordinates @param atomParameters atomParameters[atomIndex][paramterIndex] @param exclusions exclusions[i] is the set of excluded indices for atom i @param useExclusions specifies whether to use exclusions --------------------------------------------------------------------------------------- */ void calculateParticlePairValue(int index, int numAtoms, std::vector& atomCoordinates, std::vector >& atomParameters, const std::vector >& exclusions, bool useExclusions); /**--------------------------------------------------------------------------------------- Evaluate a single atom pair as part of calculating a computed value @param index the index of the value to compute @param atom1 the index of the first atom in the pair @param atom2 the index of the second atom in the pair @param atomCoordinates atom coordinates @param atomParameters atomParameters[atomIndex][paramterIndex] --------------------------------------------------------------------------------------- */ void calculateOnePairValue(int index, int atom1, int atom2, std::vector& atomCoordinates, std::vector >& atomParameters); /**--------------------------------------------------------------------------------------- Calculate an energy term of type SingleParticle @param index the index of the value to compute @param numAtoms number of atoms @param atomCoordinates atom coordinates @param atomParameters atomParameters[atomIndex][paramterIndex] @param forces forces on atoms are added to this @param totalEnergy the energy contribution is added to this --------------------------------------------------------------------------------------- */ void calculateSingleParticleEnergyTerm(int index, int numAtoms, std::vector& atomCoordinates, std::vector >& atomParameters, std::vector& forces, double* totalEnergy, double* energyParamDerivs); /**--------------------------------------------------------------------------------------- Calculate an energy term that is based on particle pairs @param index the index of the term to compute @param numAtoms number of atoms @param atomCoordinates atom coordinates @param atomParameters atomParameters[atomIndex][paramterIndex] @param exclusions exclusions[i] is the set of excluded indices for atom i @param useExclusions specifies whether to use exclusions @param forces forces on atoms are added to this @param totalEnergy the energy contribution is added to this --------------------------------------------------------------------------------------- */ void calculateParticlePairEnergyTerm(int index, int numAtoms, std::vector& atomCoordinates, std::vector >& atomParameters, const std::vector >& exclusions, bool useExclusions, std::vector& forces, double* totalEnergy, double* energyParamDerivs); /**--------------------------------------------------------------------------------------- Evaluate a single atom pair as part of calculating an energy term @param index the index of the term to compute @param atom1 the index of the first atom in the pair @param atom2 the index of the second atom in the pair @param atomCoordinates atom coordinates @param atomParameters atomParameters[atomIndex][paramterIndex] @param forces forces on atoms are added to this @param totalEnergy the energy contribution is added to this --------------------------------------------------------------------------------------- */ void calculateOnePairEnergyTerm(int index, int atom1, int atom2, std::vector& atomCoordinates, std::vector >& atomParameters, std::vector& forces, double* totalEnergy, double* energyParamDerivs); /**--------------------------------------------------------------------------------------- Apply the chain rule to compute forces on atoms @param numAtoms number of atoms @param atomCoordinates atom coordinates @param atomParameters atomParameters[atomIndex][paramterIndex] @param exclusions exclusions[i] is the set of excluded indices for atom i @param forces forces on atoms are added to this --------------------------------------------------------------------------------------- */ void calculateChainRuleForces(int numAtoms, std::vector& atomCoordinates, std::vector >& atomParameters, const std::vector >& exclusions, std::vector& forces, double* energyParamDerivs); /**--------------------------------------------------------------------------------------- Evaluate a single atom pair as part of applying the chain rule @param atom1 the index of the first atom in the pair @param atom2 the index of the second atom in the pair @param atomCoordinates atom coordinates @param atomParameters atomParameters[atomIndex][paramterIndex] @param forces forces on atoms are added to this @param isExcluded specifies whether this is an excluded pair --------------------------------------------------------------------------------------- */ void calculateOnePairChainRule(int atom1, int atom2, std::vector& atomCoordinates, std::vector >& atomParameters, std::vector& forces, bool isExcluded); public: /**--------------------------------------------------------------------------------------- Constructor --------------------------------------------------------------------------------------- */ ReferenceCustomGBIxn(const std::vector& valueExpressions, const std::vector > valueDerivExpressions, const std::vector > valueGradientExpressions, const std::vector > valueParamDerivExpressions, const std::vector& valueNames, const std::vector& valueTypes, const std::vector& energyExpressions, const std::vector > energyDerivExpressions, const std::vector > energyGradientExpressions, const std::vector > energyParamDerivExpressions, const std::vector& energyTypes, const std::vector& parameterNames); /**--------------------------------------------------------------------------------------- Destructor --------------------------------------------------------------------------------------- */ ~ReferenceCustomGBIxn(); /**--------------------------------------------------------------------------------------- Set the force to use a cutoff. @param distance the cutoff distance @param neighbors the neighbor list to use --------------------------------------------------------------------------------------- */ void setUseCutoff(double distance, const OpenMM::NeighborList& neighbors); /**--------------------------------------------------------------------------------------- Set the force to use periodic boundary conditions. This requires that a cutoff has already been set, and the smallest side of the periodic box is at least twice the cutoff distance. @param vectors the vectors defining the periodic box --------------------------------------------------------------------------------------- */ void setPeriodic(OpenMM::Vec3* vectors); /**--------------------------------------------------------------------------------------- Calculate custom GB ixn @param numberOfAtoms number of atoms @param atomCoordinates atom coordinates @param atomParameters atomParameters[atomIndex][paramterIndex] @param exclusions exclusions[i] is the set of excluded indices for atom i @param globalParameters the values of global parameters @param forces force array (forces added) @param totalEnergy total energy --------------------------------------------------------------------------------------- */ void calculateIxn(int numberOfAtoms, std::vector& atomCoordinates, std::vector >& atomParameters, const std::vector >& exclusions, std::map& globalParameters, std::vector& forces, double* totalEnergy, double* energyParamDerivs); // --------------------------------------------------------------------------------------- }; } // namespace OpenMM #endif // __ReferenceCustomGBIxn_H__