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Commit 908340c1 authored by Peter Eastman's avatar Peter Eastman
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Reference implementation of periodic boundary conditions for bonded forces

parent 4bd2f9d2
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platforms/cpu/include/CpuKernels.h
View file @ 908340c1
......@@ -98,7 +98,7 @@ private:
class CpuCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
public:
CpuCalcHarmonicAngleForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) :
CalcHarmonicAngleForceKernel(name, platform), data(data), angleIndexArray(NULL), angleParamArray(NULL) {
CalcHarmonicAngleForceKernel(name, platform), data(data), angleIndexArray(NULL), angleParamArray(NULL), usePeriodic(false) {
}
~CpuCalcHarmonicAngleForceKernel();
/**
......@@ -130,6 +130,7 @@ private:
int **angleIndexArray;
RealOpenMM **angleParamArray;
CpuBondForce bondForce;
bool usePeriodic;
};
/**
......@@ -138,7 +139,7 @@ private:
class CpuCalcPeriodicTorsionForceKernel : public CalcPeriodicTorsionForceKernel {
public:
CpuCalcPeriodicTorsionForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) :
CalcPeriodicTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL) {
CalcPeriodicTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL), usePeriodic(false) {
}
~CpuCalcPeriodicTorsionForceKernel();
/**
......@@ -170,6 +171,7 @@ private:
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
CpuBondForce bondForce;
bool usePeriodic;
};
/**
......@@ -178,7 +180,7 @@ private:
class CpuCalcRBTorsionForceKernel : public CalcRBTorsionForceKernel {
public:
CpuCalcRBTorsionForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) :
CalcRBTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL) {
CalcRBTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL), usePeriodic(false) {
}
~CpuCalcRBTorsionForceKernel();
/**
......@@ -210,6 +212,7 @@ private:
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
CpuBondForce bondForce;
bool usePeriodic;
};
/**
......
platforms/cpu/src/CpuKernels.cpp
View file @ 908340c1
......@@ -283,6 +283,7 @@ void CpuCalcHarmonicAngleForceKernel::initialize(const System& system, const Har
angleParamArray[i][1] = (RealOpenMM) k;
}
bondForce.initialize(system.getNumParticles(), numAngles, 3, angleIndexArray, data.threads);
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double CpuCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -290,6 +291,8 @@ double CpuCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool inclu
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0;
ReferenceAngleBondIxn angleBond;
if (usePeriodic)
angleBond.setPeriodic(extractBoxVectors(context));
bondForce.calculateForce(posData, angleParamArray, forceData, includeEnergy ? &energy : NULL, angleBond);
return energy;
}
......@@ -343,6 +346,7 @@ void CpuCalcPeriodicTorsionForceKernel::initialize(const System& system, const P
torsionParamArray[i][2] = (RealOpenMM) periodicity;
}
bondForce.initialize(system.getNumParticles(), numTorsions, 4, torsionIndexArray, data.threads);
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double CpuCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -350,6 +354,8 @@ double CpuCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool inc
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0;
ReferenceProperDihedralBond periodicTorsionBond;
if (usePeriodic)
periodicTorsionBond.setPeriodic(extractBoxVectors(context));
bondForce.calculateForce(posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, periodicTorsionBond);
return energy;
}
......@@ -407,6 +413,7 @@ void CpuCalcRBTorsionForceKernel::initialize(const System& system, const RBTorsi
torsionParamArray[i][5] = (RealOpenMM) c5;
}
bondForce.initialize(system.getNumParticles(), numTorsions, 4, torsionIndexArray, data.threads);
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double CpuCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -414,6 +421,8 @@ double CpuCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeFo
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0;
ReferenceRbDihedralBond rbTorsionBond;
if (usePeriodic)
rbTorsionBond.setPeriodic(extractBoxVectors(context));
bondForce.calculateForce(posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, rbTorsionBond);
return energy;
}
......
platforms/reference/include/ReferenceAngleBondIxn.h
View file @ 908340c1
......@@ -33,6 +33,9 @@ class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {
private:
bool usePeriodic;
RealVec boxVectors[3];
public:
/**---------------------------------------------------------------------------------------
......@@ -51,6 +54,16 @@ class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {
~ReferenceAngleBondIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Get dEdR and energy term for angle bond
......
platforms/reference/include/ReferenceCMAPTorsionIxn.h
View file @ 908340c1
......@@ -38,6 +38,8 @@ private:
std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
std::vector<int> torsionMaps;
std::vector<std::vector<int> > torsionIndices;
bool usePeriodic;
RealVec boxVectors[3];
/**---------------------------------------------------------------------------------------
......@@ -65,6 +67,16 @@ public:
const std::vector<int>& torsionMaps,
const std::vector<std::vector<int> >& torsionIndices);
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate torsion interaction
......
platforms/reference/include/ReferenceCustomAngleIxn.h
View file @ 908340c1
/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -39,6 +39,8 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
double* energyTheta;
double* forceTheta;
int numParameters;
bool usePeriodic;
RealVec boxVectors[3];
public:
......@@ -59,6 +61,16 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
~ReferenceCustomAngleIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate Custom Angle Ixn
......
platforms/reference/include/ReferenceCustomBondIxn.h
View file @ 908340c1
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -40,6 +40,8 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
double* energyR;
double* forceR;
int numParameters;
bool usePeriodic;
RealVec boxVectors[3];
public:
......@@ -60,6 +62,16 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
~ReferenceCustomBondIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate Custom Bond Ixn
......
platforms/reference/include/ReferenceCustomCentroidBondIxn.h
View file @ 908340c1
/* Portions copyright (c) 2009-2015 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -50,6 +50,8 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
std::vector<DistanceTermInfo> distanceTerms;
std::vector<AngleTermInfo> angleTerms;
std::vector<DihedralTermInfo> dihedralTerms;
bool usePeriodic;
RealVec boxVectors[3];
/**---------------------------------------------------------------------------------------
......@@ -94,6 +96,16 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
~ReferenceCustomCentroidBondIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Get the list of groups in each bond.
......
platforms/reference/include/ReferenceCustomCompoundBondIxn.h
View file @ 908340c1
/* Portions copyright (c) 2009-2012 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -48,6 +48,8 @@ class ReferenceCustomCompoundBondIxn : public ReferenceBondIxn {
std::vector<DistanceTermInfo> distanceTerms;
std::vector<AngleTermInfo> angleTerms;
std::vector<DihedralTermInfo> dihedralTerms;
bool usePeriodic;
RealVec boxVectors[3];
/**---------------------------------------------------------------------------------------
......@@ -91,6 +93,16 @@ class ReferenceCustomCompoundBondIxn : public ReferenceBondIxn {
~ReferenceCustomCompoundBondIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Get the list atoms in each bond.
......
platforms/reference/include/ReferenceCustomTorsionIxn.h
View file @ 908340c1
/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -39,6 +39,8 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
double* energyTheta;
double* forceTheta;
int numParameters;
bool usePeriodic;
RealVec boxVectors[3];
public:
......@@ -59,6 +61,16 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
~ReferenceCustomTorsionIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate Custom Torsion Ixn
......
platforms/reference/include/ReferenceHarmonicBondIxn.h
View file @ 908340c1
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -32,6 +32,9 @@ namespace OpenMM {
class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
private:
bool usePeriodic;
RealVec boxVectors[3];
public:
......@@ -51,6 +54,16 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
~ReferenceHarmonicBondIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate Harmonic Bond Ixn
......
platforms/reference/include/ReferenceKernels.h
View file @ 908340c1
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -280,6 +280,7 @@ private:
int numBonds;
int **bondIndexArray;
RealOpenMM **bondParamArray;
bool usePeriodic;
};
/**
......@@ -319,6 +320,7 @@ private:
RealOpenMM **bondParamArray;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
bool usePeriodic;
};
/**
......@@ -356,6 +358,7 @@ private:
int numAngles;
int **angleIndexArray;
RealOpenMM **angleParamArray;
bool usePeriodic;
};
/**
......@@ -395,6 +398,7 @@ private:
RealOpenMM **angleParamArray;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
bool usePeriodic;
};
/**
......@@ -432,6 +436,7 @@ private:
int numTorsions;
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
bool usePeriodic;
};
/**
......@@ -469,6 +474,7 @@ private:
int numTorsions;
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
bool usePeriodic;
};
/**
......@@ -505,6 +511,7 @@ private:
std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
std::vector<int> torsionMaps;
std::vector<std::vector<int> > torsionIndices;
bool usePeriodic;
};
/**
......@@ -544,6 +551,7 @@ private:
RealOpenMM **torsionParamArray;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
bool usePeriodic;
};
/**
......@@ -860,6 +868,7 @@ private:
RealOpenMM **bondParamArray;
ReferenceCustomCentroidBondIxn* ixn;
std::vector<std::string> globalParameterNames;
bool usePeriodic;
};
/**
......@@ -898,6 +907,7 @@ private:
RealOpenMM **bondParamArray;
ReferenceCustomCompoundBondIxn* ixn;
std::vector<std::string> globalParameterNames;
bool usePeriodic;
};
/**
......
platforms/reference/include/ReferenceProperDihedralBond.h
View file @ 908340c1
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -33,6 +33,9 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
private:
bool usePeriodic;
RealVec boxVectors[3];
public:
/**---------------------------------------------------------------------------------------
......@@ -51,6 +54,16 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
~ReferenceProperDihedralBond();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate proper dihedral bond ixn
......
platforms/reference/include/ReferenceRbDihedralBond.h
View file @ 908340c1
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -33,6 +33,9 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
private:
bool usePeriodic;
RealVec boxVectors[3];
public:
/**---------------------------------------------------------------------------------------
......@@ -51,6 +54,16 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
~ReferenceRbDihedralBond();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate Ryckaert-Bellemans bond ixn
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 908340c1
......@@ -370,6 +370,7 @@ void ReferenceCalcHarmonicBondForceKernel::initialize(const System& system, cons
bondParamArray[i][0] = (RealOpenMM) length;
bondParamArray[i][1] = (RealOpenMM) k;
}
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double ReferenceCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -378,6 +379,8 @@ double ReferenceCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool
RealOpenMM energy = 0;
ReferenceBondForce refBondForce;
ReferenceHarmonicBondIxn harmonicBond;
if (usePeriodic)
harmonicBond.setPeriodic(extractBoxVectors(context));
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, includeEnergy ? &energy : NULL, harmonicBond);
return energy;
}
......@@ -409,6 +412,7 @@ ReferenceCalcCustomBondForceKernel::~ReferenceCalcCustomBondForceKernel() {
void ReferenceCalcCustomBondForceKernel::initialize(const System& system, const CustomBondForce& force) {
numBonds = force.getNumBonds();
int numParameters = force.getNumPerBondParameters();
usePeriodic = force.usesPeriodicBoundaryConditions();
// Build the arrays.
......@@ -448,8 +452,10 @@ double ReferenceCalcCustomBondForceKernel::execute(ContextImpl& context, bool in
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ReferenceBondForce refBondForce;
ReferenceCustomBondIxn harmonicBond(energyExpression, forceExpression, parameterNames, globalParameters);
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, includeEnergy ? &energy : NULL, harmonicBond);
ReferenceCustomBondIxn bond(energyExpression, forceExpression, parameterNames, globalParameters);
if (usePeriodic)
bond.setPeriodic(extractBoxVectors(context));
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, includeEnergy ? &energy : NULL, bond);
return energy;
}
......@@ -490,6 +496,7 @@ void ReferenceCalcHarmonicAngleForceKernel::initialize(const System& system, con
angleParamArray[i][0] = (RealOpenMM) angle;
angleParamArray[i][1] = (RealOpenMM) k;
}
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double ReferenceCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -498,6 +505,8 @@ double ReferenceCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool
RealOpenMM energy = 0;
ReferenceBondForce refBondForce;
ReferenceAngleBondIxn angleBond;
if (usePeriodic)
angleBond.setPeriodic(extractBoxVectors(context));
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, includeEnergy ? &energy : NULL, angleBond);
return energy;
}
......@@ -527,6 +536,7 @@ ReferenceCalcCustomAngleForceKernel::~ReferenceCalcCustomAngleForceKernel() {
void ReferenceCalcCustomAngleForceKernel::initialize(const System& system, const CustomAngleForce& force) {
numAngles = force.getNumAngles();
int numParameters = force.getNumPerAngleParameters();
usePeriodic = force.usesPeriodicBoundaryConditions();
// Build the arrays.
......@@ -568,6 +578,8 @@ double ReferenceCalcCustomAngleForceKernel::execute(ContextImpl& context, bool i
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ReferenceBondForce refBondForce;
ReferenceCustomAngleIxn customAngle(energyExpression, forceExpression, parameterNames, globalParameters);
if (usePeriodic)
customAngle.setPeriodic(extractBoxVectors(context));
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, includeEnergy ? &energy : NULL, customAngle);
return energy;
}
......@@ -611,6 +623,7 @@ void ReferenceCalcPeriodicTorsionForceKernel::initialize(const System& system, c
torsionParamArray[i][1] = (RealOpenMM) phase;
torsionParamArray[i][2] = (RealOpenMM) periodicity;
}
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double ReferenceCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -619,6 +632,8 @@ double ReferenceCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bo
RealOpenMM energy = 0;
ReferenceBondForce refBondForce;
ReferenceProperDihedralBond periodicTorsionBond;
if (usePeriodic)
periodicTorsionBond.setPeriodic(extractBoxVectors(context));
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, periodicTorsionBond);
return energy;
}
......@@ -665,6 +680,7 @@ void ReferenceCalcRBTorsionForceKernel::initialize(const System& system, const R
torsionParamArray[i][4] = (RealOpenMM) c4;
torsionParamArray[i][5] = (RealOpenMM) c5;
}
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double ReferenceCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -673,6 +689,8 @@ double ReferenceCalcRBTorsionForceKernel::execute(ContextImpl& context, bool inc
RealOpenMM energy = 0;
ReferenceBondForce refBondForce;
ReferenceRbDihedralBond rbTorsionBond;
if (usePeriodic)
rbTorsionBond.setPeriodic(extractBoxVectors(context));
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, rbTorsionBond);
return energy;
}
......@@ -722,6 +740,7 @@ void ReferenceCalcCMAPTorsionForceKernel::initialize(const System& system, const
force.getTorsionParameters(i, torsionMaps[i], torsionIndices[i][0], torsionIndices[i][1], torsionIndices[i][2],
torsionIndices[i][3], torsionIndices[i][4], torsionIndices[i][5], torsionIndices[i][6], torsionIndices[i][7]);
}
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double ReferenceCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -729,6 +748,8 @@ double ReferenceCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool i
vector<RealVec>& forceData = extractForces(context);
RealOpenMM totalEnergy = 0;
ReferenceCMAPTorsionIxn torsion(coeff, torsionMaps, torsionIndices);
if (usePeriodic)
torsion.setPeriodic(extractBoxVectors(context));
torsion.calculateIxn(posData, forceData, &totalEnergy);
return totalEnergy;
}
......@@ -775,6 +796,7 @@ ReferenceCalcCustomTorsionForceKernel::~ReferenceCalcCustomTorsionForceKernel()
void ReferenceCalcCustomTorsionForceKernel::initialize(const System& system, const CustomTorsionForce& force) {
numTorsions = force.getNumTorsions();
int numParameters = force.getNumPerTorsionParameters();
usePeriodic = force.usesPeriodicBoundaryConditions();
// Build the arrays.
......@@ -817,6 +839,8 @@ double ReferenceCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ReferenceBondForce refBondForce;
ReferenceCustomTorsionIxn customTorsion(energyExpression, forceExpression, parameterNames, globalParameters);
if (usePeriodic)
customTorsion.setPeriodic(extractBoxVectors(context));
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, customTorsion);
return energy;
}
......@@ -1644,6 +1668,7 @@ ReferenceCalcCustomCentroidBondForceKernel::~ReferenceCalcCustomCentroidBondForc
}
void ReferenceCalcCustomCentroidBondForceKernel::initialize(const System& system, const CustomCentroidBondForce& force) {
usePeriodic = force.usesPeriodicBoundaryConditions();
// Build the arrays.
......@@ -1697,6 +1722,8 @@ double ReferenceCalcCustomCentroidBondForceKernel::execute(ContextImpl& context,
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
if (usePeriodic)
ixn->setPeriodic(extractBoxVectors(context));
ixn->calculatePairIxn(posData, bondParamArray, globalParameters, forceData, includeEnergy ? &energy : NULL);
return energy;
}
......@@ -1728,6 +1755,7 @@ ReferenceCalcCustomCompoundBondForceKernel::~ReferenceCalcCustomCompoundBondForc
}
void ReferenceCalcCustomCompoundBondForceKernel::initialize(const System& system, const CustomCompoundBondForce& force) {
usePeriodic = force.usesPeriodicBoundaryConditions();
// Build the arrays.
......@@ -1774,6 +1802,8 @@ double ReferenceCalcCustomCompoundBondForceKernel::execute(ContextImpl& context,
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
if (usePeriodic)
ixn->setPeriodic(extractBoxVectors(context));
ixn->calculatePairIxn(posData, bondParamArray, globalParameters, forceData, includeEnergy ? &energy : NULL);
return energy;
}
......
platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.cpp
View file @ 908340c1
......@@ -38,7 +38,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceAngleBondIxn::ReferenceAngleBondIxn() {
ReferenceAngleBondIxn::ReferenceAngleBondIxn() : usePeriodic(false) {
// ---------------------------------------------------------------------------------------
......@@ -64,6 +64,13 @@ ReferenceAngleBondIxn::~ReferenceAngleBondIxn() {
}
void ReferenceAngleBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
/**---------------------------------------------------------------------------------------
Get dEdR and energy term for angle bond
......@@ -145,8 +152,14 @@ void ReferenceAngleBondIxn::calculateBondIxn(int* atomIndices,
int atomAIndex = atomIndices[0];
int atomBIndex = atomIndices[1];
int atomCIndex = atomIndices[2];
ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1]);
if (usePeriodic) {
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], boxVectors, deltaR[0]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], boxVectors, deltaR[1]);
}
else {
ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1]);
}
RealOpenMM pVector[threeI];
SimTKOpenMMUtilities::crossProductVector3(deltaR[0], deltaR[1], pVector);
......
platforms/reference/src/SimTKReference/ReferenceCMAPTorsionIxn.cpp
View file @ 908340c1
/* Portions copyright (c) 2010 Stanford University and Simbios.
/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -36,7 +36,14 @@ using namespace OpenMM;
ReferenceCMAPTorsionIxn::ReferenceCMAPTorsionIxn(const vector<vector<vector<RealOpenMM> > >& coeff,
const vector<int>& torsionMaps, const vector<vector<int> >& torsionIndices) :
coeff(coeff), torsionMaps(torsionMaps), torsionIndices(torsionIndices) {
coeff(coeff), torsionMaps(torsionMaps), torsionIndices(torsionIndices), usePeriodic(false) {
}
void ReferenceCMAPTorsionIxn::setPeriodic(OpenMM::RealVec* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
/**---------------------------------------------------------------------------------------
......@@ -83,13 +90,23 @@ void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, vector<RealVec>& atomCo
// Compute deltas between the various atoms involved.
RealOpenMM deltaA[3][ReferenceForce::LastDeltaRIndex];
ReferenceForce::getDeltaR(atomCoordinates[a2], atomCoordinates[a1], deltaA[0]);
ReferenceForce::getDeltaR(atomCoordinates[a2], atomCoordinates[a3], deltaA[1]);
ReferenceForce::getDeltaR(atomCoordinates[a4], atomCoordinates[a3], deltaA[2]);
RealOpenMM deltaB[3][ReferenceForce::LastDeltaRIndex];
ReferenceForce::getDeltaR(atomCoordinates[b2], atomCoordinates[b1], deltaB[0]);
ReferenceForce::getDeltaR(atomCoordinates[b2], atomCoordinates[b3], deltaB[1]);
ReferenceForce::getDeltaR(atomCoordinates[b4], atomCoordinates[b3], deltaB[2]);
if (usePeriodic) {
ReferenceForce::getDeltaRPeriodic(atomCoordinates[a2], atomCoordinates[a1], boxVectors, deltaA[0]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[a2], atomCoordinates[a3], boxVectors, deltaA[1]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[a4], atomCoordinates[a3], boxVectors, deltaA[2]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[b2], atomCoordinates[b1], boxVectors, deltaB[0]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[b2], atomCoordinates[b3], boxVectors, deltaB[1]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[b4], atomCoordinates[b3], boxVectors, deltaB[2]);
}
else {
ReferenceForce::getDeltaR(atomCoordinates[a2], atomCoordinates[a1], deltaA[0]);
ReferenceForce::getDeltaR(atomCoordinates[a2], atomCoordinates[a3], deltaA[1]);
ReferenceForce::getDeltaR(atomCoordinates[a4], atomCoordinates[a3], deltaA[2]);
ReferenceForce::getDeltaR(atomCoordinates[b2], atomCoordinates[b1], deltaB[0]);
ReferenceForce::getDeltaR(atomCoordinates[b2], atomCoordinates[b3], deltaB[1]);
ReferenceForce::getDeltaR(atomCoordinates[b4], atomCoordinates[b3], deltaB[2]);
}
// Visual Studio complains if crossProduct declared as 'crossProduct[2][3]'
......
platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp
View file @ 908340c1
/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -39,7 +39,7 @@ using namespace std;
ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::CompiledExpression& energyExpression,
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
energyExpression(energyExpression), forceExpression(forceExpression) {
energyExpression(energyExpression), forceExpression(forceExpression), usePeriodic(false) {
energyTheta = ReferenceForce::getVariablePointer(this->energyExpression, "theta");
forceTheta = ReferenceForce::getVariablePointer(this->forceExpression, "theta");
......@@ -61,13 +61,13 @@ ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::CompiledExpressio
--------------------------------------------------------------------------------------- */
ReferenceCustomAngleIxn::~ReferenceCustomAngleIxn() {
}
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomAngleIxn::~ReferenceCustomAngleIxn";
// ---------------------------------------------------------------------------------------
void ReferenceCustomAngleIxn::setPeriodic(OpenMM::RealVec* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
/**---------------------------------------------------------------------------------------
......@@ -106,8 +106,14 @@ void ReferenceCustomAngleIxn::calculateBondIxn(int* atomIndices,
int atomAIndex = atomIndices[0];
int atomBIndex = atomIndices[1];
int atomCIndex = atomIndices[2];
ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1]);
if (usePeriodic) {
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], boxVectors, deltaR[0]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], boxVectors, deltaR[1]);
}
else {
ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1]);
}
RealOpenMM pVector[3];
SimTKOpenMMUtilities::crossProductVector3(deltaR[0], deltaR[1], pVector);
RealOpenMM rp = SQRT(DOT3(pVector, pVector));
......
platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp
View file @ 908340c1
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -40,7 +40,7 @@ using namespace OpenMM;
ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::CompiledExpression& energyExpression,
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
energyExpression(energyExpression), forceExpression(forceExpression) {
energyExpression(energyExpression), forceExpression(forceExpression), usePeriodic(false) {
energyR = ReferenceForce::getVariablePointer(this->energyExpression, "r");
forceR = ReferenceForce::getVariablePointer(this->forceExpression, "r");
numParameters = parameterNames.size();
......@@ -61,13 +61,13 @@ ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::CompiledExpression&
--------------------------------------------------------------------------------------- */
ReferenceCustomBondIxn::~ReferenceCustomBondIxn() {
}
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomBondIxn::~ReferenceCustomBondIxn";
// ---------------------------------------------------------------------------------------
void ReferenceCustomBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
/**---------------------------------------------------------------------------------------
......@@ -108,7 +108,10 @@ void ReferenceCustomBondIxn::calculateBondIxn(int* atomIndices,
int atomAIndex = atomIndices[0];
int atomBIndex = atomIndices[1];
ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR);
if (usePeriodic)
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], boxVectors, deltaR);
else
ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR);
ReferenceForce::setVariable(energyR, deltaR[ReferenceForce::RIndex]);
ReferenceForce::setVariable(forceR, deltaR[ReferenceForce::RIndex]);
......
platforms/reference/src/SimTKReference/ReferenceCustomCentroidBondIxn.cpp
View file @ 908340c1
/* Portions copyright (c) 2009-2015 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -41,7 +41,7 @@ ReferenceCustomCentroidBondIxn::ReferenceCustomCentroidBondIxn(int numGroupsPerB
const vector<vector<double> >& normalizedWeights, const vector<vector<int> >& bondGroups,
const Lepton::ParsedExpression& energyExpression, const vector<string>& bondParameterNames,
const map<string, vector<int> >& distances, const map<string, vector<int> >& angles, const map<string, vector<int> >& dihedrals) :
groupAtoms(groupAtoms), normalizedWeights(normalizedWeights), bondGroups(bondGroups), energyExpression(energyExpression.createProgram()), bondParamNames(bondParameterNames) {
groupAtoms(groupAtoms), normalizedWeights(normalizedWeights), bondGroups(bondGroups), energyExpression(energyExpression.createProgram()), bondParamNames(bondParameterNames), usePeriodic(false) {
for (int i = 0; i < numGroupsPerBond; i++) {
stringstream xname, yname, zname;
xname << 'x' << (i+1);
......@@ -62,6 +62,13 @@ ReferenceCustomCentroidBondIxn::ReferenceCustomCentroidBondIxn(int numGroupsPerB
ReferenceCustomCentroidBondIxn::~ReferenceCustomCentroidBondIxn() {
}
void ReferenceCustomCentroidBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
void ReferenceCustomCentroidBondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates, RealOpenMM** bondParameters,
const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
......@@ -215,7 +222,10 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>&
}
void ReferenceCustomCentroidBondIxn::computeDelta(int group1, int group2, RealOpenMM* delta, vector<RealVec>& groupCenters) const {
ReferenceForce::getDeltaR(groupCenters[group1], groupCenters[group2], delta);
if (usePeriodic)
ReferenceForce::getDeltaRPeriodic(groupCenters[group1], groupCenters[group2], boxVectors, delta);
else
ReferenceForce::getDeltaR(groupCenters[group1], groupCenters[group2], delta);
}
RealOpenMM ReferenceCustomCentroidBondIxn::computeAngle(RealOpenMM* vec1, RealOpenMM* vec2) {
......
platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.cpp
View file @ 908340c1
/* Portions copyright (c) 2009-2015 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -46,7 +46,7 @@ using namespace OpenMM;
ReferenceCustomCompoundBondIxn::ReferenceCustomCompoundBondIxn(int numParticlesPerBond, const vector<vector<int> >& bondAtoms,
const Lepton::ParsedExpression& energyExpression, const vector<string>& bondParameterNames,
const map<string, vector<int> >& distances, const map<string, vector<int> >& angles, const map<string, vector<int> >& dihedrals) :
bondAtoms(bondAtoms), energyExpression(energyExpression.createProgram()), bondParamNames(bondParameterNames) {
bondAtoms(bondAtoms), energyExpression(energyExpression.createProgram()), bondParamNames(bondParameterNames), usePeriodic(false) {
for (int i = 0; i < numParticlesPerBond; i++) {
stringstream xname, yname, zname;
xname << 'x' << (i+1);
......@@ -73,6 +73,13 @@ ReferenceCustomCompoundBondIxn::ReferenceCustomCompoundBondIxn(int numParticlesP
ReferenceCustomCompoundBondIxn::~ReferenceCustomCompoundBondIxn() {
}
void ReferenceCustomCompoundBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
/**---------------------------------------------------------------------------------------
Calculate custom hbond interaction
......@@ -232,7 +239,10 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
}
void ReferenceCustomCompoundBondIxn::computeDelta(int atom1, int atom2, RealOpenMM* delta, vector<RealVec>& atomCoordinates) const {
ReferenceForce::getDeltaR(atomCoordinates[atom1], atomCoordinates[atom2], delta);
if (usePeriodic)
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atom1], atomCoordinates[atom2], boxVectors, delta);
else
ReferenceForce::getDeltaR(atomCoordinates[atom1], atomCoordinates[atom2], delta);
}
RealOpenMM ReferenceCustomCompoundBondIxn::computeAngle(RealOpenMM* vec1, RealOpenMM* vec2) {
......
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