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Commit 94fbbe9c authored by Peter Eastman's avatar Peter Eastman
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Reference implementation of periodic boundary conditions for AMOEBA bonded forces

parent b4dcef47
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Showing with 233 additions and 55 deletions
platforms/reference/include/ReferenceForce.h
View file @ 94fbbe9c
......@@ -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/src/SimTKReference/ReferenceForce.cpp
View file @ 94fbbe9c
......@@ -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;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h
View file @ 94fbbe9c
......@@ -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 @ 94fbbe9c
......@@ -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 @ 94fbbe9c
......@@ -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 @ 94fbbe9c
......@@ -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 @ 94fbbe9c
......@@ -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;
};
/**
......
plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h
View file @ 94fbbe9c
......@@ -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: *
* *
......@@ -119,20 +119,24 @@ 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;
private:
class StretchBendInfo;
std::vector<StretchBendInfo> stretchBends;
bool usePeriodic;
};
/**
......
plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h
View file @ 94fbbe9c
......@@ -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: *
* *
......@@ -137,15 +137,18 @@ public:
* grid[x][y][5] = dEd(xy) value
*/
void setTorsionTorsionGrid(int index, const std::vector<std::vector<std::vector<double> > >& grid);
/**
* 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:
......@@ -153,6 +156,7 @@ private:
class TorsionTorsionGridInfo;
std::vector<TorsionTorsionInfo> torsionTorsions;
std::vector<TorsionTorsionGridInfo> torsionTorsionGrids;
bool usePeriodic;
};
/**
......
plugins/amoeba/openmmapi/src/AmoebaAngleForce.cpp
View file @ 94fbbe9c
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaAngleForce::AmoebaAngleForce() {
AmoebaAngleForce::AmoebaAngleForce() : usePeriodic(false) {
_globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
}
......@@ -102,3 +102,11 @@ ForceImpl* AmoebaAngleForce::createImpl() const {
void AmoebaAngleForce::updateParametersInContext(Context& context) {
dynamic_cast<AmoebaAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void AmoebaAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaAngleForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/openmmapi/src/AmoebaBondForce.cpp
View file @ 94fbbe9c
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaBondForce::AmoebaBondForce() {
AmoebaBondForce::AmoebaBondForce() : usePeriodic(false) {
_globalCubicK = _globalQuarticK = 0.0;
}
......@@ -82,3 +82,11 @@ ForceImpl* AmoebaBondForce::createImpl() const {
void AmoebaBondForce::updateParametersInContext(Context& context) {
dynamic_cast<AmoebaBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void AmoebaBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaBondForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/openmmapi/src/AmoebaInPlaneAngleForce.cpp
View file @ 94fbbe9c
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaInPlaneAngleForce::AmoebaInPlaneAngleForce() {
AmoebaInPlaneAngleForce::AmoebaInPlaneAngleForce() : usePeriodic(false) {
_globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
}
......@@ -104,3 +104,11 @@ ForceImpl* AmoebaInPlaneAngleForce::createImpl() const {
void AmoebaInPlaneAngleForce::updateParametersInContext(Context& context) {
dynamic_cast<AmoebaInPlaneAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void AmoebaInPlaneAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaInPlaneAngleForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/openmmapi/src/AmoebaOutOfPlaneBendForce.cpp
View file @ 94fbbe9c
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaOutOfPlaneBendForce::AmoebaOutOfPlaneBendForce() {
AmoebaOutOfPlaneBendForce::AmoebaOutOfPlaneBendForce() : usePeriodic(false) {
_globalCubicK = -0.1400000E-01;
_globalQuarticK = 0.5600000E-04;
_globalPenticK = -0.7000000E-06;
......@@ -106,3 +106,11 @@ ForceImpl* AmoebaOutOfPlaneBendForce::createImpl() const {
void AmoebaOutOfPlaneBendForce::updateParametersInContext(Context& context) {
dynamic_cast<AmoebaOutOfPlaneBendForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void AmoebaOutOfPlaneBendForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaOutOfPlaneBendForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/openmmapi/src/AmoebaPiTorsionForce.cpp
View file @ 94fbbe9c
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaPiTorsionForce::AmoebaPiTorsionForce() {
AmoebaPiTorsionForce::AmoebaPiTorsionForce() : usePeriodic(false) {
}
int AmoebaPiTorsionForce::addPiTorsion(int particle1, int particle2, int particle3, int particle4, int particle5, int particle6, double k) {
......@@ -71,3 +71,11 @@ ForceImpl* AmoebaPiTorsionForce::createImpl() const {
void AmoebaPiTorsionForce::updateParametersInContext(Context& context) {
dynamic_cast<AmoebaPiTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void AmoebaPiTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaPiTorsionForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/openmmapi/src/AmoebaStretchBendForce.cpp
View file @ 94fbbe9c
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaStretchBendForce::AmoebaStretchBendForce() {
AmoebaStretchBendForce::AmoebaStretchBendForce() : usePeriodic(false) {
}
int AmoebaStretchBendForce::addStretchBend(int particle1, int particle2, int particle3,
......@@ -76,3 +76,11 @@ ForceImpl* AmoebaStretchBendForce::createImpl() const {
void AmoebaStretchBendForce::updateParametersInContext(Context& context) {
dynamic_cast<AmoebaStretchBendForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void AmoebaStretchBendForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaStretchBendForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForce.cpp
View file @ 94fbbe9c
......@@ -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: *
* Contributors: *
* *
......@@ -38,7 +38,7 @@
using namespace OpenMM;
using namespace std;
AmoebaTorsionTorsionForce::AmoebaTorsionTorsionForce() {
AmoebaTorsionTorsionForce::AmoebaTorsionTorsionForce() : usePeriodic(false) {
}
int AmoebaTorsionTorsionForce::addTorsionTorsion(int particle1, int particle2, int particle3,
......@@ -183,3 +183,11 @@ AmoebaTorsionTorsionForce::TorsionTorsionGridInfo::TorsionTorsionGridInfo(const
}
}
}
void AmoebaTorsionTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaTorsionTorsionForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ 94fbbe9c
......@@ -104,12 +104,15 @@ void ReferenceCalcAmoebaBondForceKernel::initialize(const System& system, const
}
globalBondCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalBondCubic());
globalBondQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalBondQuartic());
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double ReferenceCalcAmoebaBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceBondForce amoebaReferenceBondForce;
if (usePeriodic)
amoebaReferenceBondForce.setPeriodic(extractBoxVectors(context));
RealOpenMM energy = amoebaReferenceBondForce.calculateForceAndEnergy(numBonds, posData, particle1, particle2, length, kQuadratic,
globalBondCubic, globalBondQuartic,
forceData);
......@@ -160,12 +163,15 @@ void ReferenceCalcAmoebaAngleForceKernel::initialize(const System& system, const
globalAngleQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleQuartic());
globalAnglePentic = static_cast<RealOpenMM>(force.getAmoebaGlobalAnglePentic());
globalAngleSextic = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleSextic());
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double ReferenceCalcAmoebaAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceAngleForce amoebaReferenceAngleForce;
if (usePeriodic)
amoebaReferenceAngleForce.setPeriodic(extractBoxVectors(context));
RealOpenMM energy = amoebaReferenceAngleForce.calculateForceAndEnergy(numAngles,
posData, particle1, particle2, particle3, angle, kQuadratic, globalAngleCubic, globalAngleQuartic, globalAnglePentic, globalAngleSextic, forceData);
return static_cast<double>(energy);
......@@ -213,6 +219,7 @@ void ReferenceCalcAmoebaInPlaneAngleForceKernel::initialize(const System& system
globalInPlaneAngleQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleQuartic());
globalInPlaneAnglePentic = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAnglePentic());
globalInPlaneAngleSextic = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleSextic());
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double ReferenceCalcAmoebaInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -220,6 +227,8 @@ double ReferenceCalcAmoebaInPlaneAngleForceKernel::execute(ContextImpl& context,
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceInPlaneAngleForce amoebaReferenceInPlaneAngleForce;
if (usePeriodic)
amoebaReferenceInPlaneAngleForce.setPeriodic(extractBoxVectors(context));
RealOpenMM energy = amoebaReferenceInPlaneAngleForce.calculateForceAndEnergy(numAngles, posData, particle1, particle2, particle3, particle4,
angle, kQuadratic, globalInPlaneAngleCubic, globalInPlaneAngleQuartic,
globalInPlaneAnglePentic, globalInPlaneAngleSextic, forceData);
......@@ -266,12 +275,15 @@ void ReferenceCalcAmoebaPiTorsionForceKernel::initialize(const System& system, c
particle6.push_back(particle6Index);
kTorsion.push_back(static_cast<RealOpenMM>(kTorsionParameter));
}
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double ReferenceCalcAmoebaPiTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferencePiTorsionForce amoebaReferencePiTorsionForce;
if (usePeriodic)
amoebaReferencePiTorsionForce.setPeriodic(extractBoxVectors(context));
RealOpenMM energy = amoebaReferencePiTorsionForce.calculateForceAndEnergy(numPiTorsions, posData, particle1, particle2,
particle3, particle4, particle5, particle6,
kTorsion, forceData);
......@@ -318,12 +330,15 @@ void ReferenceCalcAmoebaStretchBendForceKernel::initialize(const System& system,
k1Parameters.push_back(static_cast<RealOpenMM>(k1));
k2Parameters.push_back(static_cast<RealOpenMM>(k2));
}
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double ReferenceCalcAmoebaStretchBendForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceStretchBendForce amoebaReferenceStretchBendForce;
if (usePeriodic)
amoebaReferenceStretchBendForce.setPeriodic(extractBoxVectors(context));
RealOpenMM energy = amoebaReferenceStretchBendForce.calculateForceAndEnergy(numStretchBends, posData, particle1, particle2, particle3,
lengthABParameters, lengthCBParameters, angleParameters, k1Parameters,
k2Parameters, forceData);
......@@ -376,13 +391,15 @@ void ReferenceCalcAmoebaOutOfPlaneBendForceKernel::initialize(const System& syst
globalOutOfPlaneBendAngleQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendQuartic());
globalOutOfPlaneBendAnglePentic = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendPentic());
globalOutOfPlaneBendAngleSextic = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendSextic());
usePeriodic = force.usesPeriodicBoundaryConditions();
}
double ReferenceCalcAmoebaOutOfPlaneBendForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceOutOfPlaneBendForce amoebaReferenceOutOfPlaneBendForce;
if (usePeriodic)
amoebaReferenceOutOfPlaneBendForce.setPeriodic(extractBoxVectors(context));
RealOpenMM energy = amoebaReferenceOutOfPlaneBendForce.calculateForceAndEnergy(numOutOfPlaneBends, posData,
particle1, particle2, particle3, particle4,
kParameters,
......@@ -434,6 +451,7 @@ void ReferenceCalcAmoebaTorsionTorsionForceKernel::initialize(const System& syst
chiralCheckAtom.push_back(chiralCheckAtomIndex);
gridIndices.push_back(gridIndex);
}
usePeriodic = force.usesPeriodicBoundaryConditions();
// torsion-torsion grids
......@@ -478,6 +496,8 @@ double ReferenceCalcAmoebaTorsionTorsionForceKernel::execute(ContextImpl& contex
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceTorsionTorsionForce amoebaReferenceTorsionTorsionForce;
if (usePeriodic)
amoebaReferenceTorsionTorsionForce.setPeriodic(extractBoxVectors(context));
RealOpenMM energy = amoebaReferenceTorsionTorsionForce.calculateForceAndEnergy(numTorsionTorsions, posData,
particle1, particle2, particle3, particle4, particle5,
chiralCheckAtom, gridIndices, torsionTorsionGrids, forceData);
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h
View file @ 94fbbe9c
......@@ -77,6 +77,7 @@ private:
RealOpenMM globalBondCubic;
RealOpenMM globalBondQuartic;
const System& system;
bool usePeriodic;
};
/**
......@@ -121,6 +122,7 @@ private:
RealOpenMM globalAnglePentic;
RealOpenMM globalAngleSextic;
const System& system;
bool usePeriodic;
};
/**
......@@ -166,6 +168,7 @@ private:
RealOpenMM globalInPlaneAnglePentic;
RealOpenMM globalInPlaneAngleSextic;
const System& system;
bool usePeriodic;
};
/**
......@@ -208,6 +211,7 @@ private:
std::vector<int> particle6;
std::vector<RealOpenMM> kTorsion;
const System& system;
bool usePeriodic;
};
/**
......@@ -251,6 +255,7 @@ private:
std::vector<RealOpenMM> k1Parameters;
std::vector<RealOpenMM> k2Parameters;
const System& system;
bool usePeriodic;
};
/**
......@@ -295,6 +300,7 @@ private:
RealOpenMM globalOutOfPlaneBendAnglePentic;
RealOpenMM globalOutOfPlaneBendAngleSextic;
const System& system;
bool usePeriodic;
};
/**
......@@ -334,6 +340,7 @@ private:
std::vector< std::vector< std::vector< std::vector<RealOpenMM> > > > torsionTorsionGrids;
const System& system;
bool usePeriodic;
};
/**
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceAngleForce.cpp
View file @ 94fbbe9c
/* 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
......@@ -28,6 +28,13 @@
using std::vector;
using namespace OpenMM;
void AmoebaReferenceAngleForce::setPeriodic(OpenMM::RealVec* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
/**---------------------------------------------------------------------------------------
Get dEdT and energy prefactor given cosine of angle :: the calculation for different
......@@ -132,11 +139,17 @@ RealOpenMM AmoebaReferenceAngleForce::calculateAngleIxn(const RealVec& positionA
// ---------------------------------------------------------------------------------------
std::vector<RealOpenMM> deltaR[2];
AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomB, deltaR[0]);
if (usePeriodic)
AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomA, positionAtomB, deltaR[0], boxVectors);
else
AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomB, deltaR[0]);
RealOpenMM rAB2 = AmoebaReferenceForce::getNormSquared3(deltaR[0]);
RealOpenMM rAB = SQRT(rAB2);
AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomB, deltaR[1]);
if (usePeriodic)
AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomC, positionAtomB, deltaR[1], boxVectors);
else
AmoebaReferenceForce::loadDeltaR(positionAtomC, positionAtomB, deltaR[1]);
RealOpenMM rCB2 = AmoebaReferenceForce::getNormSquared3(deltaR[1]);
RealOpenMM rCB = SQRT(rCB2);
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceAngleForce.h
View file @ 94fbbe9c
/* 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
......@@ -40,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */
AmoebaReferenceAngleForce() {};
AmoebaReferenceAngleForce() : usePeriodic(false) {};
/**---------------------------------------------------------------------------------------
......@@ -50,6 +50,16 @@ public:
~AmoebaReferenceAngleForce() {};
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate Amoeba angle ixns (force and energy)
......@@ -86,6 +96,9 @@ public:
private:
bool usePeriodic;
RealVec boxVectors[3];
/**---------------------------------------------------------------------------------------
Get dEdT and energy prefactor given cosine of angle :: the calculation for different
......
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