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Commit 73183c61 authored by ChayaSt's avatar ChayaSt
Browse files

resolved conflict

parents 0e218233 32e08b87
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Showing with 398 additions and 222 deletions
platforms/reference/src/ReferenceKernels.cpp
View file @ 73183c61
......@@ -280,7 +280,7 @@ 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];
......@@ -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/ReferenceTabulatedFunction.cpp
View file @ 73183c61
......@@ -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 @ 73183c61
......@@ -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 @ 73183c61
/* 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 @ 73183c61
/* 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 @ 73183c61
/* 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 @ 73183c61
/* 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 @ 73183c61
/* 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) {
......
platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
View file @ 73183c61
/* 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
......@@ -56,13 +56,11 @@ ReferenceCustomDynamics::ReferenceCustomDynamics(int numberOfAtoms, const Custom
string expression;
integrator.getComputationStep(i, stepType[i], stepVariable[i], expression);
}
kineticEnergyExpression = Lepton::Parser::parse(integrator.getKineticEnergyExpression()).optimize().createProgram();
kineticEnergyExpression = Lepton::Parser::parse(integrator.getKineticEnergyExpression()).optimize().createCompiledExpression();
expressionSet.registerExpression(kineticEnergyExpression);
kineticEnergyNeedsForce = false;
for (int i = 0; i < kineticEnergyExpression.getNumOperations(); i++) {
const Lepton::Operation& op = kineticEnergyExpression.getOperation(i);
if (op.getId() == Lepton::Operation::VARIABLE && op.getName() == "f")
kineticEnergyNeedsForce = true;
}
if (kineticEnergyExpression.getVariables().find("f") != kineticEnergyExpression.getVariables().end())
kineticEnergyNeedsForce = true;
}
/**---------------------------------------------------------------------------------------
......@@ -74,6 +72,75 @@ ReferenceCustomDynamics::ReferenceCustomDynamics(int numberOfAtoms, const Custom
ReferenceCustomDynamics::~ReferenceCustomDynamics() {
}
void ReferenceCustomDynamics::initialize(ContextImpl& context, vector<RealOpenMM>& masses, map<string, RealOpenMM>& globals) {
// Some initialization can't be done in the constructor, since we need a ContextImpl from which to get the list of
// Context parameters. Instead, we do it the first time update() or computeKineticEnergy() is called.
int numSteps = stepType.size();
vector<int> forceGroup;
vector<vector<Lepton::ParsedExpression> > expressions;
CustomIntegratorUtilities::analyzeComputations(context, integrator, expressions, comparisons, blockEnd, invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy, forceGroup);
stepExpressions.resize(expressions.size());
for (int i = 0; i < numSteps; i++) {
stepExpressions[i].resize(expressions[i].size());
for (int j = 0; j < (int) expressions[i].size(); j++) {
stepExpressions[i][j] = expressions[i][j].createCompiledExpression();
expressionSet.registerExpression(stepExpressions[i][j]);
}
if (stepType[i] == CustomIntegrator::WhileBlockStart)
blockEnd[blockEnd[i]] = i; // Record where to branch back to.
}
// Record the variable names and flags for the force and energy in each step.
forceGroupFlags.resize(numSteps, -1);
fIndex = expressionSet.getVariableIndex("f");
energyIndex = expressionSet.getVariableIndex("energy");
forceVariableIndex.resize(numSteps, fIndex);
energyVariableIndex.resize(numSteps, energyIndex);
vector<string> forceGroupName;
vector<string> energyGroupName;
for (int i = 0; i < 32; i++) {
stringstream fname;
fname << "f" << i;
forceGroupName.push_back(fname.str());
stringstream ename;
ename << "energy" << i;
energyGroupName.push_back(ename.str());
}
for (int i = 0; i < numSteps; i++) {
if (needsForces[i] && forceGroup[i] > -1)
forceVariableIndex[i] = expressionSet.getVariableIndex(forceGroupName[forceGroup[i]]);
if (needsEnergy[i] && forceGroup[i] > -1)
energyVariableIndex[i] = expressionSet.getVariableIndex(energyGroupName[forceGroup[i]]);
if (forceGroup[i] > -1)
forceGroupFlags[i] = 1<<forceGroup[i];
}
// Build the list of inverse masses.
int numberOfAtoms = masses.size();
inverseMasses.resize(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; i++) {
if (masses[i] == 0.0)
inverseMasses[i] = 0.0;
else
inverseMasses[i] = 1.0/masses[i];
}
// Record indices of other variables.
xIndex = expressionSet.getVariableIndex("x");
vIndex = expressionSet.getVariableIndex("v");
mIndex = expressionSet.getVariableIndex("m");
gaussianIndex = expressionSet.getVariableIndex("gaussian");
uniformIndex = expressionSet.getVariableIndex("uniform");
for (int i = 0; i < integrator.getNumPerDofVariables(); i++)
perDofVariableIndex.push_back(expressionSet.getVariableIndex(integrator.getPerDofVariableName(i)));
for (int i = 0; i < stepVariable.size(); i++)
stepVariableIndex.push_back(expressionSet.getVariableIndex(stepVariable[i]));
}
/**---------------------------------------------------------------------------------------
Update -- driver routine for performing Custom dynamics update of coordinates
......@@ -93,58 +160,13 @@ ReferenceCustomDynamics::~ReferenceCustomDynamics() {
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses,
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid, RealOpenMM tolerance) {
if (invalidatesForces.size() == 0)
initialize(context, masses, globals);
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, RealOpenMM>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
oldPos = atomCoordinates;
if (invalidatesForces.size() == 0) {
// Some initialization can't be done in the constructor, since we need a ContextImpl from which to get the list of
// Context parameters. Instead, we do it the first time this method is called.
vector<int> forceGroup;
vector<vector<Lepton::ParsedExpression> > expressions;
CustomIntegratorUtilities::analyzeComputations(context, integrator, expressions, comparisons, blockEnd, invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy, forceGroup);
stepExpressions.resize(expressions.size());
for (int i = 0; i < numSteps; i++) {
for (int j = 0; j < (int) expressions[i].size(); j++)
stepExpressions[i].push_back(expressions[i][j].createProgram());
if (stepType[i] == CustomIntegrator::BeginWhileBlock)
blockEnd[blockEnd[i]] = i; // Record where to branch back to.
}
// Record the variable names and flags for the force and energy in each step.
forceGroupFlags.resize(numSteps, -1);
forceName.resize(numSteps, "f");
energyName.resize(numSteps, "energy");
vector<string> forceGroupName;
vector<string> energyGroupName;
for (int i = 0; i < 32; i++) {
stringstream fname;
fname << "f" << i;
forceGroupName.push_back(fname.str());
stringstream ename;
ename << "energy" << i;
energyGroupName.push_back(ename.str());
}
for (int i = 0; i < numSteps; i++) {
if (needsForces[i] && forceGroup[i] > -1)
forceName[i] = forceGroupName[forceGroup[i]];
if (needsEnergy[i] && forceGroup[i] > -1)
energyName[i] = energyGroupName[forceGroup[i]];
if (forceGroup[i] > -1)
forceGroupFlags[i] = 1<<forceGroup[i];
}
// Build the list of inverse masses.
inverseMasses.resize(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; i++) {
if (masses[i] == 0.0)
inverseMasses[i] = 0.0;
else
inverseMasses[i] = 1.0/masses[i];
}
}
// Loop over steps and execute them.
......@@ -160,42 +182,44 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
energy = e;
forcesAreValid = true;
}
globals[energyName[step]] = energy;
expressionSet.setVariable(energyVariableIndex[step], energy);
// Execute the step.
int nextStep = step+1;
switch (stepType[step]) {
case CustomIntegrator::ComputeGlobal: {
map<string, RealOpenMM> variables = globals;
variables["uniform"] = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
variables["gaussian"] = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
globals[stepVariable[step]] = stepExpressions[step][0].evaluate(variables);
expressionSet.setVariable(uniformIndex, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
expressionSet.setVariable(gaussianIndex, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
RealOpenMM result = stepExpressions[step][0].evaluate();
globals[stepVariable[step]] = result;
expressionSet.setVariable(stepVariableIndex[step], result);
break;
}
case CustomIntegrator::ComputePerDof: {
vector<RealVec>* results = NULL;
if (stepVariable[step] == "x")
if (stepVariableIndex[step] == xIndex)
results = &atomCoordinates;
else if (stepVariable[step] == "v")
else if (stepVariableIndex[step] == vIndex)
results = &velocities;
else {
for (int j = 0; j < integrator.getNumPerDofVariables(); j++)
if (stepVariable[step] == integrator.getPerDofVariableName(j))
if (stepVariableIndex[step] == perDofVariableIndex[j])
results = &perDof[j];
}
if (results == NULL)
throw OpenMMException("Illegal per-DOF output variable: "+stepVariable[step]);
computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, globals, perDof, stepExpressions[step][0], forceName[step]);
computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0], forceVariableIndex[step]);
break;
}
case CustomIntegrator::ComputeSum: {
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, globals, perDof, stepExpressions[step][0], forceName[step]);
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0], forceVariableIndex[step]);
RealOpenMM sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
sum += sumBuffer[j][0]+sumBuffer[j][1]+sumBuffer[j][2];
globals[stepVariable[step]] = sum;
expressionSet.setVariable(stepVariableIndex[step], sum);
break;
}
case CustomIntegrator::ConstrainPositions: {
......@@ -211,19 +235,21 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
recordChangedParameters(context, globals);
context.updateContextState();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, RealOpenMM>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
break;
}
case CustomIntegrator::BeginIfBlock: {
if (!evaluateCondition(step, globals))
case CustomIntegrator::IfBlockStart: {
if (!evaluateCondition(step))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::BeginWhileBlock: {
if (!evaluateCondition(step, globals))
case CustomIntegrator::WhileBlockStart: {
if (!evaluateCondition(step))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::EndBlock: {
case CustomIntegrator::BlockEnd: {
if (blockEnd[step] != -1)
nextStep = blockEnd[step]; // Return to the start of a while block.
break;
......@@ -240,36 +266,33 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
void ReferenceCustomDynamics::computePerDof(int numberOfAtoms, vector<RealVec>& results, const vector<RealVec>& atomCoordinates,
const vector<RealVec>& velocities, const vector<RealVec>& forces, const vector<RealOpenMM>& masses,
const map<string, RealOpenMM>& globals, const vector<vector<RealVec> >& perDof,
const Lepton::ExpressionProgram& expression, const std::string& forceName) {
const vector<vector<RealVec> >& perDof, const Lepton::CompiledExpression& expression, int forceIndex) {
// Loop over all degrees of freedom.
map<string, RealOpenMM> variables = globals;
for (int i = 0; i < numberOfAtoms; i++) {
if (masses[i] != 0.0) {
variables["m"] = masses[i];
expressionSet.setVariable(mIndex, masses[i]);
for (int j = 0; j < 3; j++) {
// Compute the expression.
variables["x"] = atomCoordinates[i][j];
variables["v"] = velocities[i][j];
variables[forceName] = forces[i][j];
variables["uniform"] = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
variables["gaussian"] = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
expressionSet.setVariable(xIndex, atomCoordinates[i][j]);
expressionSet.setVariable(vIndex, velocities[i][j]);
expressionSet.setVariable(forceIndex, forces[i][j]);
expressionSet.setVariable(uniformIndex, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
expressionSet.setVariable(gaussianIndex, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
for (int k = 0; k < (int) perDof.size(); k++)
variables[integrator.getPerDofVariableName(k)] = perDof[k][i][j];
results[i][j] = expression.evaluate(variables);
expressionSet.setVariable(perDofVariableIndex[k], perDof[k][i][j]);
results[i][j] = expression.evaluate();
}
}
}
}
bool ReferenceCustomDynamics::evaluateCondition(int step, map<string, RealOpenMM>& globals) {
map<string, RealOpenMM> variables = globals;
variables["uniform"] = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
variables["gaussian"] = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
double lhs = stepExpressions[step][0].evaluate(variables);
double rhs = stepExpressions[step][1].evaluate(variables);
bool ReferenceCustomDynamics::evaluateCondition(int step) {
expressionSet.setVariable(uniformIndex, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
expressionSet.setVariable(gaussianIndex, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
double lhs = stepExpressions[step][0].evaluate();
double rhs = stepExpressions[step][1].evaluate();
switch (comparisons[step]) {
case CustomIntegratorUtilities::EQUAL:
return (lhs == rhs);
......@@ -318,12 +341,16 @@ void ReferenceCustomDynamics::recordChangedParameters(OpenMM::ContextImpl& conte
double ReferenceCustomDynamics::computeKineticEnergy(OpenMM::ContextImpl& context, int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses,
std::map<std::string, RealOpenMM>& globals, std::vector<std::vector<OpenMM::RealVec> >& perDof, bool& forcesAreValid) {
if (invalidatesForces.size() == 0)
initialize(context, masses, globals);
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, RealOpenMM>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
if (kineticEnergyNeedsForce) {
energy = context.calcForcesAndEnergy(true, true, -1);
forcesAreValid = true;
}
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, globals, perDof, kineticEnergyExpression, "f");
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, kineticEnergyExpression, fIndex);
RealOpenMM sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
......
platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp
View file @ 73183c61
/* 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 OpenMM;
ReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn(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 @@ ReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn(const Lepton::CompiledExpre
--------------------------------------------------------------------------------------- */
ReferenceCustomTorsionIxn::~ReferenceCustomTorsionIxn() {
}
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomTorsionIxn::~ReferenceCustomTorsionIxn";
// ---------------------------------------------------------------------------------------
void ReferenceCustomTorsionIxn::setPeriodic(OpenMM::RealVec* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
/**---------------------------------------------------------------------------------------
......@@ -107,9 +107,16 @@ void ReferenceCustomTorsionIxn::calculateBondIxn(int* atomIndices,
int atomBIndex = atomIndices[1];
int atomCIndex = atomIndices[2];
int atomDIndex = atomIndices[3];
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1]);
ReferenceForce::getDeltaR(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2]);
if (usePeriodic) {
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], boxVectors, deltaR[0]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], boxVectors, deltaR[1]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], boxVectors, deltaR[2]);
}
else {
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1]);
ReferenceForce::getDeltaR(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2]);
}
// Visual Studio complains if crossProduct declared as 'crossProduct[2][3]'
......
platforms/reference/src/SimTKReference/ReferenceForce.cpp
View file @ 73183c61
......@@ -73,6 +73,10 @@ void ReferenceForce::getDeltaR(const RealVec& atomCoordinatesI, const RealVec& a
deltaR[RIndex] = (RealOpenMM) SQRT(deltaR[R2Index]);
}
RealVec ReferenceForce::getDeltaR(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ) {
return atomCoordinatesJ-atomCoordinatesI;
}
void ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
const RealOpenMM* boxSize, RealOpenMM* deltaR) {
deltaR[XIndex] = periodicDifference(atomCoordinatesJ[0], atomCoordinatesI[0], boxSize[0]);
......@@ -96,6 +100,15 @@ void ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const Re
deltaR[RIndex] = SQRT(deltaR[R2Index]);
}
RealVec ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
const RealVec* boxVectors) {
RealVec diff = atomCoordinatesJ-atomCoordinatesI;
diff -= boxVectors[2]*floor(diff[2]/boxVectors[2][2]+0.5);
diff -= boxVectors[1]*floor(diff[1]/boxVectors[1][1]+0.5);
diff -= boxVectors[0]*floor(diff[0]/boxVectors[0][0]+0.5);
return diff;
}
double* ReferenceForce::getVariablePointer(Lepton::CompiledExpression& expression, const std::string& name) {
if (expression.getVariables().find(name) == expression.getVariables().end())
return NULL;
......
platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.cpp
View file @ 73183c61
/* 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
......@@ -38,14 +38,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn";
// ---------------------------------------------------------------------------------------
ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn() : usePeriodic(false) {
}
/**---------------------------------------------------------------------------------------
......@@ -55,13 +48,13 @@ ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn() {
--------------------------------------------------------------------------------------- */
ReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn() {
}
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn";
// ---------------------------------------------------------------------------------------
void ReferenceHarmonicBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
/**---------------------------------------------------------------------------------------
......@@ -99,7 +92,10 @@ void ReferenceHarmonicBondIxn::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);
// deltaIdeal = r - r_0
......
platforms/reference/src/SimTKReference/ReferenceProperDihedralBond.cpp
View file @ 73183c61
/* 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
......@@ -38,14 +38,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceProperDihedralBond::ReferenceProperDihedralBond() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceProperDihedralBond::ReferenceProperDihedralBond";
// ---------------------------------------------------------------------------------------
ReferenceProperDihedralBond::ReferenceProperDihedralBond() : usePeriodic(false) {
}
/**---------------------------------------------------------------------------------------
......@@ -55,13 +48,13 @@ ReferenceProperDihedralBond::ReferenceProperDihedralBond() {
--------------------------------------------------------------------------------------- */
ReferenceProperDihedralBond::~ReferenceProperDihedralBond() {
}
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceProperDihedralBond::~ReferenceProperDihedralBond";
// ---------------------------------------------------------------------------------------
void ReferenceProperDihedralBond::setPeriodic(OpenMM::RealVec* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
/**---------------------------------------------------------------------------------------
......@@ -110,9 +103,16 @@ void ReferenceProperDihedralBond::calculateBondIxn(int* atomIndices,
int atomBIndex = atomIndices[1];
int atomCIndex = atomIndices[2];
int atomDIndex = atomIndices[3];
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1]);
ReferenceForce::getDeltaR(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2]);
if (usePeriodic) {
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], boxVectors, deltaR[0]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], boxVectors, deltaR[1]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], boxVectors, deltaR[2]);
}
else {
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1]);
ReferenceForce::getDeltaR(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2]);
}
RealOpenMM dotDihedral;
RealOpenMM signOfAngle;
......
platforms/reference/src/SimTKReference/ReferenceRbDihedralBond.cpp
View file @ 73183c61
/* 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
......@@ -38,14 +38,7 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceRbDihedralBond::ReferenceRbDihedralBond() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceRbDihedralBond::ReferenceRbDihedralBond";
// ---------------------------------------------------------------------------------------
ReferenceRbDihedralBond::ReferenceRbDihedralBond() : usePeriodic(false) {
}
/**---------------------------------------------------------------------------------------
......@@ -55,13 +48,13 @@ ReferenceRbDihedralBond::ReferenceRbDihedralBond() {
--------------------------------------------------------------------------------------- */
ReferenceRbDihedralBond::~ReferenceRbDihedralBond() {
}
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceRbDihedralBond::~ReferenceRbDihedralBond";
// ---------------------------------------------------------------------------------------
void ReferenceRbDihedralBond::setPeriodic(OpenMM::RealVec* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
/**---------------------------------------------------------------------------------------
......@@ -112,9 +105,16 @@ void ReferenceRbDihedralBond::calculateBondIxn(int* atomIndices,
int atomBIndex = atomIndices[1];
int atomCIndex = atomIndices[2];
int atomDIndex = atomIndices[3];
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1]);
ReferenceForce::getDeltaR(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2]);
if (usePeriodic) {
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], boxVectors, deltaR[0]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], boxVectors, deltaR[1]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], boxVectors, deltaR[2]);
}
else {
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1]);
ReferenceForce::getDeltaR(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2]);
}
RealOpenMM cosPhi;
RealOpenMM signOfAngle;
......
platforms/reference/tests/TestReferenceMonteCarloMembraneBarostat.cpp
View file @ 73183c61
......@@ -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) 2008-2014 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -82,7 +82,7 @@ void testIdealGas(MonteCarloMembraneBarostat::XYMode xymode, MonteCarloMembraneB
// Test it for three different temperatures.
for (int i = 0; i < 3; i++) {
barostat->setTemperature(temp[i]);
barostat->setDefaultTemperature(temp[i]);
LangevinIntegrator integrator(temp[i], 0.1, 0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
......
plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h
View file @ 73183c61
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -166,21 +166,25 @@ public:
* in an angle cannot be changed, nor can new angles be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if nonbondedMethod uses PBC and false otherwise
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
double _globalCubicK, _globalQuarticK, _globalPenticK, _globalSexticK;
private:
class AngleInfo;
std::vector<AngleInfo> angles;
bool usePeriodic;
};
/**
......
plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h
View file @ 73183c61
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -138,21 +138,25 @@ public:
* in a bond cannot be changed, nor can new bonds be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if nonbondedMethod uses PBC and false otherwise
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
double _globalQuarticK, _globalCubicK;
ForceImpl* createImpl() const;
private:
class BondInfo;
std::vector<BondInfo> bonds;
bool usePeriodic;
};
/**
......
plugins/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.h
View file @ 73183c61
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -171,21 +171,25 @@ public:
* in an angle cannot be changed, nor can new angles be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if nonbondedMethod uses PBC and false otherwise
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
double _globalCubicK, _globalQuarticK, _globalPenticK, _globalSexticK;
private:
class AngleInfo;
std::vector<AngleInfo> angles;
bool usePeriodic;
};
/**
......
plugins/amoeba/openmmapi/include/openmm/AmoebaOutOfPlaneBendForce.h
View file @ 73183c61
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -163,21 +163,25 @@ public:
* in a term cannot be changed, nor can new terms be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if nonbondedMethod uses PBC and false otherwise
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
double _globalCubicK, _globalQuarticK, _globalPenticK, _globalSexticK;
private:
class OutOfPlaneBendInfo;
std::vector<OutOfPlaneBendInfo> outOfPlaneBends;
bool usePeriodic;
};
/**
......
plugins/amoeba/openmmapi/include/openmm/AmoebaPiTorsionForce.h
View file @ 73183c61
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -113,20 +113,24 @@ public:
* in a torsion cannot be changed, nor can new torsions be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if nonbondedMethod uses PBC and false otherwise
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
class PiTorsionInfo;
std::vector<PiTorsionInfo> piTorsions;
bool usePeriodic;
};
/**
......
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