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Commit 2e9c418a authored by peastman's avatar peastman
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Merge branch 'master' into gayberne

parents 8f532e31 a4d327f5
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platforms/reference/include/ReferenceCustomAngleIxn.h
View file @ 2e9c418a
/* 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 @ 2e9c418a
/* 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 @ 2e9c418a
/* 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 @ 2e9c418a
/* 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/ReferenceCustomDynamics.h
View file @ 2e9c418a
/* Portions copyright (c) 2011-2015 Stanford University and Simbios.
/* Portions copyright (c) 2011-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -29,7 +29,8 @@
#include "openmm/CustomIntegrator.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/CustomIntegratorUtilities.h"
#include "lepton/ExpressionProgram.h"
#include "openmm/internal/CompiledExpressionSet.h"
#include "lepton/CompiledExpression.h"
#include <map>
#include <string>
......@@ -44,23 +45,27 @@ private:
std::vector<RealOpenMM> inverseMasses;
std::vector<OpenMM::RealVec> sumBuffer, oldPos;
std::vector<OpenMM::CustomIntegrator::ComputationType> stepType;
std::vector<std::string> stepVariable, forceName, energyName;
std::vector<std::vector<Lepton::ExpressionProgram> > stepExpressions;
std::vector<std::string> stepVariable;
std::vector<std::vector<Lepton::CompiledExpression> > stepExpressions;
std::vector<CustomIntegratorUtilities::Comparison> comparisons;
std::vector<bool> invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy;
std::vector<int> forceGroupFlags, blockEnd;
RealOpenMM energy;
Lepton::ExpressionProgram kineticEnergyExpression;
Lepton::CompiledExpression kineticEnergyExpression;
bool kineticEnergyNeedsForce;
CompiledExpressionSet expressionSet;
int xIndex, vIndex, mIndex, fIndex, energyIndex, gaussianIndex, uniformIndex;
std::vector<int> forceVariableIndex, energyVariableIndex, perDofVariableIndex, stepVariableIndex;
void initialize(OpenMM::ContextImpl& context, std::vector<RealOpenMM>& masses, std::map<std::string, RealOpenMM>& globals);
void computePerDof(int numberOfAtoms, std::vector<OpenMM::RealVec>& results, const std::vector<OpenMM::RealVec>& atomCoordinates,
const std::vector<OpenMM::RealVec>& velocities, const std::vector<OpenMM::RealVec>& forces, const std::vector<RealOpenMM>& masses,
const std::map<std::string, RealOpenMM>& globals, const std::vector<std::vector<OpenMM::RealVec> >& perDof,
const Lepton::ExpressionProgram& expression, const std::string& forceName);
const std::vector<std::vector<OpenMM::RealVec> >& perDof, const Lepton::CompiledExpression& expression, int forceIndex);
void recordChangedParameters(OpenMM::ContextImpl& context, std::map<std::string, RealOpenMM>& globals);
bool evaluateCondition(int step, std::map<std::string, RealOpenMM>& globals);
bool evaluateCondition(int step);
public:
......
platforms/reference/include/ReferenceCustomTorsionIxn.h
View file @ 2e9c418a
/* 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/ReferenceForce.h
View file @ 2e9c418a
......@@ -83,6 +83,19 @@ class OPENMM_EXPORT ReferenceForce {
static void getDeltaR(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
RealOpenMM* deltaR);
/**---------------------------------------------------------------------------------------
Get deltaR between atomI and atomJ (static method)
deltaR: j - i
@param atomCoordinatesI atom i coordinates
@param atomCoordinatesI atom j coordinates
@return the displacement
--------------------------------------------------------------------------------------- */
static RealVec getDeltaR(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ);
/**---------------------------------------------------------------------------------------
Get deltaR and distance and distance**2 between atomI and atomJ, assuming periodic
......@@ -113,6 +126,21 @@ class OPENMM_EXPORT ReferenceForce {
static void getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
const OpenMM::RealVec* boxVectors, RealOpenMM* deltaR);
/**---------------------------------------------------------------------------------------
Get deltaR between atomI and atomJ, assuming periodic boundary conditions (static method);
deltaR: j - i
@param atomCoordinatesI atom i coordinates
@param atomCoordinatesI atom j coordinates
@param boxVectors the vectors defining the periodic box
@return the displacement
--------------------------------------------------------------------------------------- */
static RealVec getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
const OpenMM::RealVec* boxVectors);
/**
* Get a pointer to the memory for setting a variable in a CompiledExpression. If the expression
* does not use the specified variable, return NULL.
......
platforms/reference/include/ReferenceHarmonicBondIxn.h
View file @ 2e9c418a
/* 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 @ 2e9c418a
......@@ -173,7 +173,7 @@ public:
* @param b the vector defining the second edge of the periodic box
* @param c the vector defining the third edge of the periodic box
*/
void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const;
void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c);
/**
* Create a checkpoint recording the current state of the Context.
*
......@@ -281,6 +281,7 @@ private:
int numBonds;
int **bondIndexArray;
RealOpenMM **bondParamArray;
bool usePeriodic;
};
/**
......@@ -320,6 +321,7 @@ private:
RealOpenMM **bondParamArray;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
bool usePeriodic;
};
/**
......@@ -357,6 +359,7 @@ private:
int numAngles;
int **angleIndexArray;
RealOpenMM **angleParamArray;
bool usePeriodic;
};
/**
......@@ -396,6 +399,7 @@ private:
RealOpenMM **angleParamArray;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
bool usePeriodic;
};
/**
......@@ -433,6 +437,7 @@ private:
int numTorsions;
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
bool usePeriodic;
};
/**
......@@ -470,6 +475,7 @@ private:
int numTorsions;
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
bool usePeriodic;
};
/**
......@@ -506,6 +512,7 @@ private:
std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
std::vector<int> torsionMaps;
std::vector<std::vector<int> > torsionIndices;
bool usePeriodic;
};
/**
......@@ -545,6 +552,7 @@ private:
RealOpenMM **torsionParamArray;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
bool usePeriodic;
};
/**
......@@ -861,6 +869,7 @@ private:
RealOpenMM **bondParamArray;
ReferenceCustomCentroidBondIxn* ixn;
std::vector<std::string> globalParameterNames;
bool usePeriodic;
};
/**
......@@ -899,6 +908,7 @@ private:
RealOpenMM **bondParamArray;
ReferenceCustomCompoundBondIxn* ixn;
std::vector<std::string> globalParameterNames;
bool usePeriodic;
};
/**
......
platforms/reference/include/ReferenceProperDihedralBond.h
View file @ 2e9c418a
/* 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 @ 2e9c418a
/* 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/include/ReferenceTabulatedFunction.h
View file @ 2e9c418a
......@@ -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) 2014 Stanford University and the Authors. *
* Portions copyright (c) 2014-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -55,6 +55,7 @@ public:
double evaluateDerivative(const double* arguments, const int* derivOrder) const;
CustomFunction* clone() const;
private:
ReferenceContinuous1DFunction(const ReferenceContinuous1DFunction& other);
const Continuous1DFunction& function;
double min, max;
std::vector<double> x, values, derivs;
......@@ -71,6 +72,7 @@ public:
double evaluateDerivative(const double* arguments, const int* derivOrder) const;
CustomFunction* clone() const;
private:
ReferenceContinuous2DFunction(const ReferenceContinuous2DFunction& other);
const Continuous2DFunction& function;
int xsize, ysize;
double xmin, xmax, ymin, ymax;
......@@ -89,6 +91,7 @@ public:
double evaluateDerivative(const double* arguments, const int* derivOrder) const;
CustomFunction* clone() const;
private:
ReferenceContinuous3DFunction(const ReferenceContinuous3DFunction& other);
const Continuous3DFunction& function;
int xsize, ysize, zsize;
double xmin, xmax, ymin, ymax, zmin, zmax;
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 2e9c418a
......@@ -281,7 +281,7 @@ void ReferenceUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context,
c = vectors[2];
}
void ReferenceUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const {
void ReferenceUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) {
RealVec& box = extractBoxSize(context);
box[0] = (RealOpenMM) a[0];
box[1] = (RealOpenMM) b[1];
......@@ -371,6 +371,7 @@ 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) {
......@@ -379,6 +380,8 @@ 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;
}
......@@ -410,6 +413,7 @@ ReferenceCalcCustomBondForceKernel::~ReferenceCalcCustomBondForceKernel() {
void ReferenceCalcCustomBondForceKernel::initialize(const System& system, const CustomBondForce& force) {
numBonds = force.getNumBonds();
int numParameters = force.getNumPerBondParameters();
usePeriodic = force.usesPeriodicBoundaryConditions();
// Build the arrays.
......@@ -449,8 +453,10 @@ 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;
}
......@@ -491,6 +497,7 @@ 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) {
......@@ -499,6 +506,8 @@ 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;
}
......@@ -528,6 +537,7 @@ ReferenceCalcCustomAngleForceKernel::~ReferenceCalcCustomAngleForceKernel() {
void ReferenceCalcCustomAngleForceKernel::initialize(const System& system, const CustomAngleForce& force) {
numAngles = force.getNumAngles();
int numParameters = force.getNumPerAngleParameters();
usePeriodic = force.usesPeriodicBoundaryConditions();
// Build the arrays.
......@@ -569,6 +579,8 @@ 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;
}
......@@ -612,6 +624,7 @@ 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) {
......@@ -620,6 +633,8 @@ 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;
}
......@@ -666,6 +681,7 @@ 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) {
......@@ -674,6 +690,8 @@ 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;
}
......@@ -723,6 +741,7 @@ 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) {
......@@ -730,6 +749,8 @@ 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;
}
......@@ -776,6 +797,7 @@ ReferenceCalcCustomTorsionForceKernel::~ReferenceCalcCustomTorsionForceKernel()
void ReferenceCalcCustomTorsionForceKernel::initialize(const System& system, const CustomTorsionForce& force) {
numTorsions = force.getNumTorsions();
int numParameters = force.getNumPerTorsionParameters();
usePeriodic = force.usesPeriodicBoundaryConditions();
// Build the arrays.
......@@ -818,6 +840,8 @@ 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;
}
......@@ -1645,6 +1669,7 @@ ReferenceCalcCustomCentroidBondForceKernel::~ReferenceCalcCustomCentroidBondForc
}
void ReferenceCalcCustomCentroidBondForceKernel::initialize(const System& system, const CustomCentroidBondForce& force) {
usePeriodic = force.usesPeriodicBoundaryConditions();
// Build the arrays.
......@@ -1698,6 +1723,8 @@ 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;
}
......@@ -1729,6 +1756,7 @@ ReferenceCalcCustomCompoundBondForceKernel::~ReferenceCalcCustomCompoundBondForc
}
void ReferenceCalcCustomCompoundBondForceKernel::initialize(const System& system, const CustomCompoundBondForce& force) {
usePeriodic = force.usesPeriodicBoundaryConditions();
// Build the arrays.
......@@ -1775,6 +1803,8 @@ 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/ReferenceTabulatedFunction.cpp
View file @ 2e9c418a
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2014 Stanford University and the Authors. *
* Portions copyright (c) 2014-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -80,6 +80,13 @@ ReferenceContinuous1DFunction::ReferenceContinuous1DFunction(const Continuous1DF
SplineFitter::createNaturalSpline(x, values, derivs);
}
ReferenceContinuous1DFunction::ReferenceContinuous1DFunction(const ReferenceContinuous1DFunction& other) : function(other.function) {
function.getFunctionParameters(values, min, max);
x = other.x;
values = other.values;
derivs = other.derivs;
}
int ReferenceContinuous1DFunction::getNumArguments() const {
return 1;
}
......@@ -99,7 +106,7 @@ double ReferenceContinuous1DFunction::evaluateDerivative(const double* arguments
}
CustomFunction* ReferenceContinuous1DFunction::clone() const {
return new ReferenceContinuous1DFunction(function);
return new ReferenceContinuous1DFunction(*this);
}
ReferenceContinuous2DFunction::ReferenceContinuous2DFunction(const Continuous2DFunction& function) : function(function) {
......@@ -113,6 +120,14 @@ ReferenceContinuous2DFunction::ReferenceContinuous2DFunction(const Continuous2DF
SplineFitter::create2DNaturalSpline(x, y, values, c);
}
ReferenceContinuous2DFunction::ReferenceContinuous2DFunction(const ReferenceContinuous2DFunction& other) : function(other.function) {
function.getFunctionParameters(xsize, ysize, values, xmin, xmax, ymin, ymax);
x = other.x;
y = other.y;
values = other.values;
c = other.c;
}
int ReferenceContinuous2DFunction::getNumArguments() const {
return 2;
}
......@@ -144,7 +159,7 @@ double ReferenceContinuous2DFunction::evaluateDerivative(const double* arguments
}
CustomFunction* ReferenceContinuous2DFunction::clone() const {
return new ReferenceContinuous2DFunction(function);
return new ReferenceContinuous2DFunction(*this);
}
ReferenceContinuous3DFunction::ReferenceContinuous3DFunction(const Continuous3DFunction& function) : function(function) {
......@@ -161,6 +176,15 @@ ReferenceContinuous3DFunction::ReferenceContinuous3DFunction(const Continuous3DF
SplineFitter::create3DNaturalSpline(x, y, z, values, c);
}
ReferenceContinuous3DFunction::ReferenceContinuous3DFunction(const ReferenceContinuous3DFunction& other) : function(other.function) {
function.getFunctionParameters(xsize, ysize, zsize, values, xmin, xmax, ymin, ymax, zmin, zmax);
x = other.x;
y = other.y;
z = other.z;
values = other.values;
c = other.c;
}
int ReferenceContinuous3DFunction::getNumArguments() const {
return 3;
}
......@@ -200,7 +224,7 @@ double ReferenceContinuous3DFunction::evaluateDerivative(const double* arguments
}
CustomFunction* ReferenceContinuous3DFunction::clone() const {
return new ReferenceContinuous3DFunction(function);
return new ReferenceContinuous3DFunction(*this);
}
ReferenceDiscrete1DFunction::ReferenceDiscrete1DFunction(const Discrete1DFunction& function) : function(function) {
......
platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.cpp
View file @ 2e9c418a
......@@ -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 @ 2e9c418a
/* 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 @ 2e9c418a
/* 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 @ 2e9c418a
/* 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 @ 2e9c418a
/* 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 @ 2e9c418a
/* 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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