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Commit a37e41ea authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

Revamp of reference local force classes

parent 3b67aadf
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Showing with 686 additions and 285 deletions
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ a37e41ea
...@@ -97,19 +97,10 @@ void ReferenceCalcAmoebaHarmonicBondForceKernel::initialize(const System& system ...@@ -97,19 +97,10 @@ void ReferenceCalcAmoebaHarmonicBondForceKernel::initialize(const System& system
double ReferenceCalcAmoebaHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcAmoebaHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); RealOpenMM** forceData = extractForces(context);
RealOpenMM energy = 0.0; AmoebaReferenceHarmonicBondForce amoebaReferenceHarmonicBondForce;
for (int ii = 0; ii < numBonds; ii++) { RealOpenMM energy = amoebaReferenceHarmonicBondForce.calculateForceAndEnergy( numBonds, posData, particle1, particle2, length, kQuadratic,
int particle1Index = particle1[ii]; globalHarmonicBondCubic, globalHarmonicBondQuartic,
int particle2Index = particle2[ii]; forceData );
RealOpenMM bondLength = length[ii];
RealOpenMM bondK = kQuadratic[ii];
RealOpenMM* forces[2];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
energy += AmoebaReferenceHarmonicBondForce::calculateForceAndEnergy( posData[particle1Index], posData[particle2Index],
bondLength, bondK, globalHarmonicBondCubic, globalHarmonicBondQuartic,
forces );
}
return static_cast<double>(energy); return static_cast<double>(energy);
} }
...@@ -143,22 +134,9 @@ void ReferenceCalcAmoebaHarmonicAngleForceKernel::initialize(const System& syste ...@@ -143,22 +134,9 @@ void ReferenceCalcAmoebaHarmonicAngleForceKernel::initialize(const System& syste
double ReferenceCalcAmoebaHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcAmoebaHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); RealOpenMM** forceData = extractForces(context);
RealOpenMM energy = 0.0; AmoebaReferenceHarmonicAngleForce amoebaReferenceHarmonicAngleForce;
for (unsigned int ii = 0; ii < numAngles; ii++) { RealOpenMM energy = amoebaReferenceHarmonicAngleForce.calculateForceAndEnergy( numAngles,
int particle1Index = particle1[ii]; posData, particle1, particle2, particle3, angle, kQuadratic, globalHarmonicAngleCubic, globalHarmonicAngleQuartic, globalHarmonicAnglePentic, globalHarmonicAngleSextic, forceData );
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii];
RealOpenMM* forces[3];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
energy += AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy(
posData[particle1Index], posData[particle2Index], posData[particle3Index],
idealAngle, angleK, globalHarmonicAngleCubic, globalHarmonicAngleQuartic,
globalHarmonicAnglePentic, globalHarmonicAngleSextic, forces );
}
return static_cast<double>(energy); return static_cast<double>(energy);
} }
...@@ -190,26 +168,13 @@ void ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::initialize(const System ...@@ -190,26 +168,13 @@ void ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::initialize(const System
} }
double ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); RealOpenMM** forceData = extractForces(context);
RealOpenMM energy = 0.0; AmoebaReferenceHarmonicInPlaneAngleForce amoebaReferenceHarmonicInPlaneAngleForce;
for (unsigned int ii = 0; ii < numAngles; ii++) { RealOpenMM energy = amoebaReferenceHarmonicInPlaneAngleForce.calculateForceAndEnergy( numAngles, posData, particle1, particle2, particle3, particle4,
int particle1Index = particle1[ii]; angle, kQuadratic, globalHarmonicInPlaneAngleCubic, globalHarmonicInPlaneAngleQuartic,
int particle2Index = particle2[ii]; globalHarmonicInPlaneAnglePentic, globalHarmonicInPlaneAngleSextic, forceData );
int particle3Index = particle3[ii];
int particle4Index = particle4[ii];
RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii];
RealOpenMM* forces[4];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
energy += AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy(
posData[particle1Index], posData[particle2Index], posData[particle3Index], posData[particle4Index],
idealAngle, angleK, globalHarmonicInPlaneAngleCubic, globalHarmonicInPlaneAngleQuartic,
globalHarmonicInPlaneAnglePentic, globalHarmonicInPlaneAngleSextic, forces );
}
return static_cast<double>(energy); return static_cast<double>(energy);
} }
...@@ -256,24 +221,9 @@ void ReferenceCalcAmoebaTorsionForceKernel::initialize(const System& system, con ...@@ -256,24 +221,9 @@ void ReferenceCalcAmoebaTorsionForceKernel::initialize(const System& system, con
double ReferenceCalcAmoebaTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcAmoebaTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); RealOpenMM** forceData = extractForces(context);
RealOpenMM energy = 0.0; AmoebaReferenceTorsionForce amoebaReferenceTorsionForce;
for (unsigned int ii = 0; ii < numTorsions; ii++) { RealOpenMM energy = amoebaReferenceTorsionForce.calculateForceAndEnergy( numTorsions, posData, particle1, particle2, particle3, particle4,
torsionParameters1, torsionParameters2, torsionParameters3, forceData );
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
int particle4Index = particle4[ii];
RealOpenMM* forces[4];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
energy += AmoebaReferenceTorsionForce::calculateForceAndEnergy(
posData[particle1Index], posData[particle2Index], posData[particle3Index], posData[particle4Index],
torsionParameters1[ii], torsionParameters2[ii], torsionParameters3[ii], forces );
}
return static_cast<double>(energy); return static_cast<double>(energy);
} }
...@@ -305,28 +255,10 @@ void ReferenceCalcAmoebaPiTorsionForceKernel::initialize(const System& system, c ...@@ -305,28 +255,10 @@ void ReferenceCalcAmoebaPiTorsionForceKernel::initialize(const System& system, c
double ReferenceCalcAmoebaPiTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcAmoebaPiTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); RealOpenMM** forceData = extractForces(context);
RealOpenMM energy = 0.0; AmoebaReferencePiTorsionForce amoebaReferencePiTorsionForce;
for( unsigned int ii = 0; ii < numPiTorsions; ii++ ){ RealOpenMM energy = amoebaReferencePiTorsionForce.calculateForceAndEnergy( numPiTorsions, posData, particle1, particle2,
particle3, particle4, particle5, particle6,
int particle1Index = particle1[ii]; kTorsion, forceData );
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
int particle4Index = particle4[ii];
int particle5Index = particle5[ii];
int particle6Index = particle6[ii];
RealOpenMM* forces[6];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
forces[4] = forceData[particle5Index];
forces[5] = forceData[particle6Index];
energy += AmoebaReferencePiTorsionForce::calculateForceAndEnergy(
posData[particle1Index], posData[particle2Index], posData[particle3Index], posData[particle4Index],
posData[particle5Index], posData[particle6Index], kTorsion[ii], forces );
}
return static_cast<double>(energy); return static_cast<double>(energy);
} }
...@@ -357,23 +289,9 @@ void ReferenceCalcAmoebaStretchBendForceKernel::initialize(const System& system, ...@@ -357,23 +289,9 @@ void ReferenceCalcAmoebaStretchBendForceKernel::initialize(const System& system,
double ReferenceCalcAmoebaStretchBendForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcAmoebaStretchBendForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); RealOpenMM** forceData = extractForces(context);
RealOpenMM energy = 0.0; AmoebaReferenceStretchBendForce amoebaReferenceStretchBendForce;
for( unsigned int ii = 0; ii < numStretchBends; ii++ ){ RealOpenMM energy = amoebaReferenceStretchBendForce.calculateForceAndEnergy( numStretchBends, posData, particle1, particle2, particle3,
lengthABParameters, lengthCBParameters, angleParameters, kParameters, forceData );
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
RealOpenMM* forces[3];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
energy += AmoebaReferenceStretchBendForce::calculateForceAndEnergy(
posData[particle1Index], posData[particle2Index], posData[particle3Index],
lengthABParameters[ii], lengthCBParameters[ii],
angleParameters[ii], kParameters[ii], forces );
}
return static_cast<double>(energy); return static_cast<double>(energy);
} }
...@@ -409,23 +327,14 @@ void ReferenceCalcAmoebaOutOfPlaneBendForceKernel::initialize(const System& syst ...@@ -409,23 +327,14 @@ void ReferenceCalcAmoebaOutOfPlaneBendForceKernel::initialize(const System& syst
double ReferenceCalcAmoebaOutOfPlaneBendForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcAmoebaOutOfPlaneBendForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); RealOpenMM** forceData = extractForces(context);
RealOpenMM energy = 0.0; AmoebaReferenceOutOfPlaneBendForce amoebaReferenceOutOfPlaneBendForce;
for (unsigned int ii = 0; ii < numOutOfPlaneBends; ii++) { RealOpenMM energy = amoebaReferenceOutOfPlaneBendForce.calculateForceAndEnergy( numOutOfPlaneBends, posData,
int particle1Index = particle1[ii]; particle1, particle2, particle3, particle4,
int particle2Index = particle2[ii]; kParameters,
int particle3Index = particle3[ii]; globalOutOfPlaneBendAngleCubic,
int particle4Index = particle4[ii]; globalOutOfPlaneBendAngleQuartic,
RealOpenMM angleK = kParameters[ii]; globalOutOfPlaneBendAnglePentic,
RealOpenMM* forces[4]; globalOutOfPlaneBendAngleSextic, forceData );
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
energy += AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy(
posData[particle1Index], posData[particle2Index], posData[particle3Index], posData[particle4Index],
angleK, globalOutOfPlaneBendAngleCubic, globalOutOfPlaneBendAngleQuartic,
globalOutOfPlaneBendAnglePentic, globalOutOfPlaneBendAngleSextic, forces );
}
return static_cast<double>(energy); return static_cast<double>(energy);
} }
...@@ -482,39 +391,10 @@ double ReferenceCalcAmoebaTorsionTorsionForceKernel::execute(ContextImpl& contex ...@@ -482,39 +391,10 @@ double ReferenceCalcAmoebaTorsionTorsionForceKernel::execute(ContextImpl& contex
RealOpenMM** posData = extractPositions(context); RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); RealOpenMM** forceData = extractForces(context);
RealOpenMM energy = 0.0; AmoebaReferenceTorsionTorsionForce amoebaReferenceTorsionTorsionForce;
RealOpenMM energy = amoebaReferenceTorsionTorsionForce.calculateForceAndEnergy( numTorsionTorsions, posData,
for( unsigned int ii = 0; ii < numTorsionTorsions; ii++ ){ particle1, particle2, particle3, particle4, particle5,
chiralCheckAtom, gridIndices, torsionTorsionGrids, forceData );
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
int particle4Index = particle4[ii];
int particle5Index = particle5[ii];
int chiralCheckAtomIndex = chiralCheckAtom[ii];
int gridIndex = gridIndices[ii];
RealOpenMM* forces[5];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
forces[4] = forceData[particle5Index];
RealOpenMM* chiralCheckAtom;
if( chiralCheckAtomIndex >= 0 ){
chiralCheckAtom = posData[chiralCheckAtomIndex];
} else {
chiralCheckAtom = NULL;
}
energy += AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy(
posData[particle1Index], posData[particle2Index],
posData[particle3Index], posData[particle4Index],
posData[particle5Index], chiralCheckAtom, torsionTorsionGrids[gridIndex],
forces );
}
return static_cast<double>(energy); return static_cast<double>(energy);
} }
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicAngleForce.cpp
View file @ a37e41ea
...@@ -24,7 +24,6 @@ ...@@ -24,7 +24,6 @@
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include "AmoebaReferenceHarmonicAngleForce.h" #include "AmoebaReferenceHarmonicAngleForce.h"
#include <vector>
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -48,7 +47,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::getPrefactorsGivenAngleCosine( Rea ...@@ -48,7 +47,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::getPrefactorsGivenAngleCosine( Rea
RealOpenMM idealAngle, RealOpenMM angleK, RealOpenMM idealAngle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM* dEdR ){ RealOpenMM* dEdR ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -111,12 +110,12 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::getPrefactorsGivenAngleCosine( Rea ...@@ -111,12 +110,12 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::getPrefactorsGivenAngleCosine( Rea
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateAngleIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomC,
RealOpenMM angle, RealOpenMM angleK, RealOpenMM angle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM** forces ){ RealOpenMM** forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -181,3 +180,30 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy( const Rea ...@@ -181,3 +180,30 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy( const Rea
return energy; return energy;
} }
RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy( int numAngles, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<RealOpenMM>& angle,
const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM angleCubic,
RealOpenMM angleQuartic,
RealOpenMM anglePentic,
RealOpenMM angleSextic,
RealOpenMM** forceData) const {
RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < numAngles; ii++) {
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii];
RealOpenMM* forces[3];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
energy += calculateAngleIxn( posData[particle1Index], posData[particle2Index], posData[particle3Index],
idealAngle, angleK, angleCubic, angleQuartic, anglePentic, angleSextic, forces );
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicAngleForce.h
View file @ a37e41ea
...@@ -26,6 +26,7 @@ ...@@ -26,6 +26,7 @@
#define __AmoebaReferenceHarmonicAngleForce_H__ #define __AmoebaReferenceHarmonicAngleForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/SimTKOpenMMRealType.h"
#include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -39,7 +40,7 @@ public: ...@@ -39,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
AmoebaReferenceHarmonicAngleForce( ); AmoebaReferenceHarmonicAngleForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -47,7 +48,43 @@ public: ...@@ -47,7 +48,43 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~AmoebaReferenceHarmonicAngleForce( ); ~AmoebaReferenceHarmonicAngleForce( ){};
/**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixns (force and energy)
@param numBonds number of angles
@param posData particle positions
@param particle1 particle 1 indices
@param particle2 particle 2 indices
@param particle3 particle 3 indices
@param angle ideal angle
@param angleK angle force constant
@param angleCubic cubic force parameter
@param angleQuartic quartic force parameter
@param anglePentic pentic force parameter
@param angleSexic sextic force parameter
@param forces output force vector
@return total energy
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numAngles, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<RealOpenMM>& angle,
const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM globalHarmonicAngleCubic,
RealOpenMM globalHarmonicAngleQuartic,
RealOpenMM globalHarmonicAnglePentic,
RealOpenMM globalHarmonicAngleSextic,
RealOpenMM** forceData ) const;
private:
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -67,10 +104,10 @@ public: ...@@ -67,10 +104,10 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM idealAngle, RealOpenMM angleK, RealOpenMM getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM idealAngle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM* dEdR ); RealOpenMM* dEdR ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -91,12 +128,12 @@ public: ...@@ -91,12 +128,12 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculateAngleIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomC,
RealOpenMM angle, RealOpenMM angleK, RealOpenMM angle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM** forces ); RealOpenMM** forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicBondForce.cpp
View file @ a37e41ea
...@@ -24,7 +24,6 @@ ...@@ -24,7 +24,6 @@
#include "AmoebaReferenceHarmonicBondForce.h" #include "AmoebaReferenceHarmonicBondForce.h"
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include <vector>
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -42,10 +41,10 @@ ...@@ -42,10 +41,10 @@
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicBondForce::calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceHarmonicBondForce::calculateBondIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
RealOpenMM bondLength, RealOpenMM bondK, RealOpenMM bondLength, RealOpenMM bondK,
RealOpenMM bondCubic, RealOpenMM bondQuartic, RealOpenMM bondCubic, RealOpenMM bondQuartic,
RealOpenMM** forces ){ RealOpenMM** forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -85,3 +84,27 @@ RealOpenMM AmoebaReferenceHarmonicBondForce::calculateForceAndEnergy( const Real ...@@ -85,3 +84,27 @@ RealOpenMM AmoebaReferenceHarmonicBondForce::calculateForceAndEnergy( const Real
return energy; return energy;
} }
RealOpenMM AmoebaReferenceHarmonicBondForce::calculateForceAndEnergy( int numBonds,
RealOpenMM** particlePositions,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<RealOpenMM>& length,
const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM globalHarmonicBondCubic,
RealOpenMM globalHarmonicBondQuartic,
RealOpenMM** forceData ) const {
RealOpenMM energy = 0.0;
for( int ii = 0; ii < numBonds; ii++ ){
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
RealOpenMM bondLength = length[ii];
RealOpenMM bondK = kQuadratic[ii];
RealOpenMM* forces[2];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
energy += calculateBondIxn( particlePositions[particle1Index], particlePositions[particle2Index],
bondLength, bondK, globalHarmonicBondCubic, globalHarmonicBondQuartic,
forces );
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicBondForce.h
View file @ a37e41ea
...@@ -26,6 +26,7 @@ ...@@ -26,6 +26,7 @@
#define __AmoebaReferenceHarmonicBondForce_H__ #define __AmoebaReferenceHarmonicBondForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/SimTKOpenMMRealType.h"
#include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -47,12 +48,40 @@ public: ...@@ -47,12 +48,40 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~AmoebaReferenceHarmonicBondForce( ); ~AmoebaReferenceHarmonicBondForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic bond ixn (force and energy) Calculate Amoeba harmonic bond ixns (force and energy)
@param numBonds number of bonds
@param posData particle positions
@param particle1 particle 1 indices
@param particle2 particle 2 indices
@param bondLength bond length
@param bondK bond force
@param bondCubic cubic bond force parameter
@param bondQuartic quartic bond force parameter
@param forces output force vector
@return total energy
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numBonds, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<RealOpenMM>& bondLength,
const std::vector<RealOpenMM>& bondK,
RealOpenMM bondCubic, RealOpenMM bondQuartic,
RealOpenMM** forceData ) const;
private:
/**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic bond ixns (force and energy)
@param positionAtomA Cartesian coordinates of atom A @param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B @param positionAtomB Cartesian coordinates of atom B
...@@ -66,10 +95,10 @@ public: ...@@ -66,10 +95,10 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculateBondIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
RealOpenMM bondLength, RealOpenMM bondK, RealOpenMM bondLength, RealOpenMM bondK,
RealOpenMM bondCubic, RealOpenMM bondQuartic, RealOpenMM bondCubic, RealOpenMM bondQuartic,
RealOpenMM** forces ); RealOpenMM** forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicInPlaneAngleForce.cpp
View file @ a37e41ea
...@@ -24,7 +24,6 @@ ...@@ -24,7 +24,6 @@
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include "AmoebaReferenceHarmonicInPlaneAngleForce.h" #include "AmoebaReferenceHarmonicInPlaneAngleForce.h"
#include <vector>
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -48,7 +47,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosi ...@@ -48,7 +47,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosi
RealOpenMM idealAngle, RealOpenMM angleK, RealOpenMM idealAngle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM* dEdR ){ RealOpenMM* dEdR ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -112,12 +111,12 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosi ...@@ -112,12 +111,12 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosi
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateAngleIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD,
RealOpenMM angle, RealOpenMM angleK, RealOpenMM angle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM** forces ){ RealOpenMM** forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -242,3 +241,35 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( co ...@@ -242,3 +241,35 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( co
return energy; return energy;
} }
RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( int numAngles, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<int>& particle4,
const std::vector<RealOpenMM>& angle,
const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM angleCubic,
RealOpenMM angleQuartic,
RealOpenMM anglePentic,
RealOpenMM angleSextic,
RealOpenMM** forceData) const {
RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < numAngles; ii++) {
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
int particle4Index = particle4[ii];
RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii];
RealOpenMM* forces[4];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
energy += calculateAngleIxn( posData[particle1Index], posData[particle2Index], posData[particle3Index], posData[particle4Index],
idealAngle, angleK, angleCubic, angleQuartic, anglePentic, angleSextic, forces );
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicInPlaneAngleForce.h
View file @ a37e41ea
...@@ -26,6 +26,7 @@ ...@@ -26,6 +26,7 @@
#define __AmoebaReferenceHarmonicInPlaneAngleForce_H__ #define __AmoebaReferenceHarmonicInPlaneAngleForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/SimTKOpenMMRealType.h"
#include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -39,7 +40,7 @@ public: ...@@ -39,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
AmoebaReferenceHarmonicInPlaneAngleForce( ); AmoebaReferenceHarmonicInPlaneAngleForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -47,7 +48,45 @@ public: ...@@ -47,7 +48,45 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~AmoebaReferenceHarmonicInPlaneAngleForce( ); ~AmoebaReferenceHarmonicInPlaneAngleForce( ){};
/**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic in-plane angle ixns (force and energy)
@param numBonds number of angles
@param posData particle positions
@param particle1 particle 1 indices
@param particle2 particle 2 indices
@param particle3 particle 3 indices
@param particle4 particle 4 indices
@param angle ideal angle
@param angleK angle force constant
@param angleCubic cubic force parameter
@param angleQuartic quartic force parameter
@param anglePentic pentic force parameter
@param angleSexic sextic force parameter
@param forces output force vector
@return total energy
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numAngles, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<int>& particle4,
const std::vector<RealOpenMM>& angle,
const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM globalHarmonicAngleCubic,
RealOpenMM globalHarmonicAngleQuartic,
RealOpenMM globalHarmonicAnglePentic,
RealOpenMM globalHarmonicAngleSextic,
RealOpenMM** forceData ) const;
private:
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -67,10 +106,10 @@ public: ...@@ -67,10 +106,10 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM idealAngle, RealOpenMM angleK, RealOpenMM getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM idealAngle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM* dEdR ); RealOpenMM* dEdR ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -92,12 +131,12 @@ public: ...@@ -92,12 +131,12 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculateAngleIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD,
RealOpenMM angle, RealOpenMM angleK, RealOpenMM angle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM** forces ); RealOpenMM** forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceOutOfPlaneBendForce.cpp
View file @ a37e41ea
...@@ -24,11 +24,10 @@ ...@@ -24,11 +24,10 @@
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include "AmoebaReferenceOutOfPlaneBendForce.h" #include "AmoebaReferenceOutOfPlaneBendForce.h"
#include <vector>
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixn (force and energy) Calculate Amoeba Out-Of-Plane-Bend ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A @param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B @param positionAtomB Cartesian coordinates of atom B
...@@ -46,12 +45,12 @@ ...@@ -46,12 +45,12 @@
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateOutOfPlaneBendIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD,
RealOpenMM angleK, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM** forces ){ RealOpenMM** forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -193,3 +192,33 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy( const Re ...@@ -193,3 +192,33 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy( const Re
return energy; return energy;
} }
RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy( int numOutOfPlaneBends, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<int>& particle4,
const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM angleCubic,
RealOpenMM angleQuartic,
RealOpenMM anglePentic,
RealOpenMM angleSextic,
RealOpenMM** forceData) const {
RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < numOutOfPlaneBends; ii++) {
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
int particle4Index = particle4[ii];
RealOpenMM kAngle = kQuadratic[ii];
RealOpenMM* forces[4];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
energy += calculateOutOfPlaneBendIxn( posData[particle1Index], posData[particle2Index], posData[particle3Index], posData[particle4Index],
kAngle, angleCubic, angleQuartic, anglePentic, angleSextic, forces );
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceOutOfPlaneBendForce.h
View file @ a37e41ea
...@@ -26,6 +26,7 @@ ...@@ -26,6 +26,7 @@
#define __AmoebaReferenceOutOfPlaneBendForce_H__ #define __AmoebaReferenceOutOfPlaneBendForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/SimTKOpenMMRealType.h"
#include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -39,7 +40,7 @@ public: ...@@ -39,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
AmoebaReferenceOutOfPlaneBendForce( ); AmoebaReferenceOutOfPlaneBendForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -47,11 +48,47 @@ public: ...@@ -47,11 +48,47 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~AmoebaReferenceOutOfPlaneBendForce( ); ~AmoebaReferenceOutOfPlaneBendForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixn (force and energy) Calculate Amoeba out-of-plane-bend angle (force and energy)
@param numOutOfPlaneBends number of angles
@param posData particle positions
@param particle1 particle 1 indices
@param particle2 particle 2 indices
@param particle3 particle 3 indices
@param particle4 particle 4 indices
@param kAngle angle force constant
@param angleCubic cubic force parameter
@param angleQuartic quartic force parameter
@param anglePentic pentic force parameter
@param angleSexic sextic force parameter
@param forces output force vector
@return total energy
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numOutOfPlaneBends, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<int>& particle4,
const std::vector<RealOpenMM>& kAngle,
RealOpenMM angleCubic,
RealOpenMM angleQuartic,
RealOpenMM anglePentic,
RealOpenMM angleSextic,
RealOpenMM** forceData) const;
private:
/**---------------------------------------------------------------------------------------
Calculate Amoeba Out-Of-Plane-Bend ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A @param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B @param positionAtomB Cartesian coordinates of atom B
...@@ -68,12 +105,12 @@ public: ...@@ -68,12 +105,12 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculateOutOfPlaneBendIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD,
RealOpenMM angleK, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM** forces ); RealOpenMM** forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferencePiTorsionForce.cpp
View file @ a37e41ea
...@@ -43,10 +43,10 @@ ...@@ -43,10 +43,10 @@
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferencePiTorsionForce::calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferencePiTorsionForce::calculatePiTorsionIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD,
const RealOpenMM* positionAtomE, const RealOpenMM* positionAtomF, const RealOpenMM* positionAtomE, const RealOpenMM* positionAtomF,
RealOpenMM piTorsionK, RealOpenMM** forces ){ RealOpenMM piTorsionK, RealOpenMM** forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -182,3 +182,37 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculateForceAndEnergy( const RealOpe ...@@ -182,3 +182,37 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculateForceAndEnergy( const RealOpe
return piTorsionK*phi2; return piTorsionK*phi2;
} }
RealOpenMM AmoebaReferencePiTorsionForce::calculateForceAndEnergy( int numPiTorsions, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<int>& particle4,
const std::vector<int>& particle5,
const std::vector<int>& particle6,
const std::vector<RealOpenMM>& kTorsion,
RealOpenMM** forceData ) const {
RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < numPiTorsions; ii++) {
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
int particle4Index = particle4[ii];
int particle5Index = particle5[ii];
int particle6Index = particle6[ii];
RealOpenMM* forces[6];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
forces[4] = forceData[particle5Index];
forces[5] = forceData[particle6Index];
energy += calculatePiTorsionIxn( posData[particle1Index], posData[particle2Index],
posData[particle3Index], posData[particle4Index],
posData[particle5Index], posData[particle6Index],
kTorsion[ii], forces );
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferencePiTorsionForce.h
View file @ a37e41ea
...@@ -26,6 +26,7 @@ ...@@ -26,6 +26,7 @@
#define __AmoebaReferencePiTorsionForce_H__ #define __AmoebaReferencePiTorsionForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/SimTKOpenMMRealType.h"
#include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -39,7 +40,7 @@ public: ...@@ -39,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
AmoebaReferencePiTorsionForce( ); AmoebaReferencePiTorsionForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -47,11 +48,46 @@ public: ...@@ -47,11 +48,46 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~AmoebaReferencePiTorsionForce( ); ~AmoebaReferencePiTorsionForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixn (force and energy) Calculate Amoeba torsion ixns (force and energy)
@param numTorsions number of torsions
@param posData particle positions
@param particle1 particle 1 indices
@param particle2 particle 2 indices
@param particle3 particle 3 indices
@param particle4 particle 4 indices
@param particle5 particle 5 indices
@param particle6 particle 6 indices
@param torsionParameters1 first index torsion parameters (amplitude, phase, fold)
@param torsionParameters2 second index torsion parameters (amplitude, phase, fold)
@param torsionParameters3 third index torsion parameters (amplitude, phase, fold)
@param forces output force vector
@return total energy
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numPiTorsions, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<int>& particle4,
const std::vector<int>& particle5,
const std::vector<int>& particle6,
const std::vector<RealOpenMM>& kTorsion,
RealOpenMM** forceData ) const;
private:
/**---------------------------------------------------------------------------------------
Calculate Amoeba pi-torsion ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A @param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B @param positionAtomB Cartesian coordinates of atom B
...@@ -66,10 +102,10 @@ public: ...@@ -66,10 +102,10 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculatePiTorsionIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD,
const RealOpenMM* positionAtomE, const RealOpenMM* positionAtomF, const RealOpenMM* positionAtomE, const RealOpenMM* positionAtomF,
RealOpenMM kTorsion, RealOpenMM** forces ); RealOpenMM kTorsion, RealOpenMM** forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceStretchBendForce.cpp
View file @ a37e41ea
...@@ -28,7 +28,7 @@ ...@@ -28,7 +28,7 @@
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixn (force and energy) Calculate Amoeba stretch bend angle ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A @param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B @param positionAtomB Cartesian coordinates of atom B
...@@ -46,11 +46,11 @@ ...@@ -46,11 +46,11 @@
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceStretchBendForce::calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceStretchBendForce::calculateStretchBendIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomC,
RealOpenMM lengthAB, RealOpenMM lengthCB, RealOpenMM lengthAB, RealOpenMM lengthCB,
RealOpenMM idealAngle, RealOpenMM kParameter, RealOpenMM idealAngle, RealOpenMM kParameter,
RealOpenMM** forces ){ RealOpenMM** forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -141,6 +141,34 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateForceAndEnergy( const RealO ...@@ -141,6 +141,34 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateForceAndEnergy( const RealO
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// return energy
return (kParameter*dt*dr); return (kParameter*dt*dr);
} }
RealOpenMM AmoebaReferenceStretchBendForce::calculateForceAndEnergy( int numStretchBends, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<RealOpenMM>& lengthABParameters,
const std::vector<RealOpenMM>& lengthCBParameters,
const std::vector<RealOpenMM>& angle,
const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM** forceData) const {
RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < numStretchBends; ii++) {
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
RealOpenMM abLength = lengthABParameters[ii];
RealOpenMM cbLength = lengthCBParameters[ii];
RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii];
RealOpenMM* forces[3];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
energy += calculateStretchBendIxn( posData[particle1Index], posData[particle2Index], posData[particle3Index],
abLength, cbLength, idealAngle, angleK, forces );
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceStretchBendForce.h
View file @ a37e41ea
...@@ -26,6 +26,7 @@ ...@@ -26,6 +26,7 @@
#define __AmoebaReferenceStretchBendForce_H__ #define __AmoebaReferenceStretchBendForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/SimTKOpenMMRealType.h"
#include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -39,7 +40,7 @@ public: ...@@ -39,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
AmoebaReferenceStretchBendForce( ); AmoebaReferenceStretchBendForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -47,11 +48,44 @@ public: ...@@ -47,11 +48,44 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~AmoebaReferenceStretchBendForce( ); ~AmoebaReferenceStretchBendForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixn (force and energy) Calculate Amoeba stretch bend ixns (force and energy)
@param numBonds number of angles
@param posData particle positions
@param particle1 particle 1 indices
@param particle2 particle 2 indices
@param particle3 particle 3 indices
@param lengthABParameters ideal AB bond length
@param lengthCBParameters ideal CB bond length
@param angle ideal angle
@param kQuadratic force constant
@param forces output force vector
@return total energy
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numAngles, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<RealOpenMM>& lengthABParameters,
const std::vector<RealOpenMM>& lengthCBParameters,
const std::vector<RealOpenMM>& angle,
const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM** forceData ) const;
private:
/**---------------------------------------------------------------------------------------
Calculate Amoeba stretch bend angle ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A @param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B @param positionAtomB Cartesian coordinates of atom B
...@@ -65,11 +99,12 @@ public: ...@@ -65,11 +99,12 @@ public:
@return energy @return energy
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
RealOpenMM calculateStretchBendIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomC,
RealOpenMM lengthAB, RealOpenMM lengthCB, RealOpenMM lengthAB, RealOpenMM lengthCB,
RealOpenMM idealAngle, RealOpenMM kParameter, RealOpenMM idealAngle, RealOpenMM kParameter,
RealOpenMM** forces ); RealOpenMM** forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionForce.cpp
View file @ a37e41ea
/* Portions copyright (c) 2006 Stanford University and Simbios. /* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
...@@ -24,7 +23,6 @@ ...@@ -24,7 +23,6 @@
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include "AmoebaReferenceTorsionForce.h" #include "AmoebaReferenceTorsionForce.h"
#include <vector>
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -43,12 +41,12 @@ ...@@ -43,12 +41,12 @@
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceTorsionForce::calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceTorsionForce::calculateTorsionIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD,
const std::vector<RealOpenMM>& torsionParameters1, const std::vector<RealOpenMM>& torsionParameters1,
const std::vector<RealOpenMM>& torsionParameters2, const std::vector<RealOpenMM>& torsionParameters2,
const std::vector<RealOpenMM>& torsionParameters3, const std::vector<RealOpenMM>& torsionParameters3,
RealOpenMM** forces ){ RealOpenMM** forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -210,3 +208,31 @@ RealOpenMM AmoebaReferenceTorsionForce::calculateForceAndEnergy( const RealOpenM ...@@ -210,3 +208,31 @@ RealOpenMM AmoebaReferenceTorsionForce::calculateForceAndEnergy( const RealOpenM
return energy; return energy;
} }
RealOpenMM AmoebaReferenceTorsionForce::calculateForceAndEnergy( int numTorsions, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<int>& particle4,
const std::vector< std::vector<RealOpenMM> >& torsionParameters1,
const std::vector< std::vector<RealOpenMM> >& torsionParameters2,
const std::vector< std::vector<RealOpenMM> >& torsionParameters3,
RealOpenMM** forceData ) const {
RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < numTorsions; ii++) {
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
int particle4Index = particle4[ii];
RealOpenMM* forces[4];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
energy += calculateTorsionIxn( posData[particle1Index], posData[particle2Index], posData[particle3Index], posData[particle4Index],
torsionParameters1[ii], torsionParameters2[ii], torsionParameters3[ii], forces );
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionForce.h
View file @ a37e41ea
...@@ -26,6 +26,7 @@ ...@@ -26,6 +26,7 @@
#define __AmoebaReferenceTorsionForce_H__ #define __AmoebaReferenceTorsionForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/SimTKOpenMMRealType.h"
#include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -39,7 +40,7 @@ public: ...@@ -39,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
AmoebaReferenceTorsionForce( ); AmoebaReferenceTorsionForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -47,7 +48,39 @@ public: ...@@ -47,7 +48,39 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~AmoebaReferenceTorsionForce( ); ~AmoebaReferenceTorsionForce( ){};
/**---------------------------------------------------------------------------------------
Calculate Amoeba torsion ixns (force and energy)
@param numTorsions number of torsions
@param posData particle positions
@param particle1 particle 1 indices
@param particle2 particle 2 indices
@param particle3 particle 3 indices
@param particle4 particle 4 indices
@param torsionParameters1 first index torsion parameters (amplitude, phase, fold)
@param torsionParameters2 second index torsion parameters (amplitude, phase, fold)
@param torsionParameters3 third index torsion parameters (amplitude, phase, fold)
@param forces output force vector
@return total energy
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numTorsions, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<int>& particle4,
const std::vector< std::vector<RealOpenMM> >& torsionParameters1,
const std::vector< std::vector<RealOpenMM> >& torsionParameters2,
const std::vector< std::vector<RealOpenMM> >& torsionParameters3,
RealOpenMM** forceData ) const;
private:
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -66,15 +99,16 @@ public: ...@@ -66,15 +99,16 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculateTorsionIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD,
const std::vector<RealOpenMM>& torsionParameters1, const std::vector<RealOpenMM>& torsionParameters1,
const std::vector<RealOpenMM>& torsionParameters2, const std::vector<RealOpenMM>& torsionParameters2,
const std::vector<RealOpenMM>& torsionParameters3, const std::vector<RealOpenMM>& torsionParameters3,
RealOpenMM** forces ); RealOpenMM** forces ) const;
}; };
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
#endif // _AmoebaReferenceTorsionForce___ #endif // _AmoebaReferenceTorsionForce___
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.cpp
View file @ a37e41ea
...@@ -24,11 +24,10 @@ ...@@ -24,11 +24,10 @@
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include "AmoebaReferenceTorsionTorsionForce.h" #include "AmoebaReferenceTorsionTorsionForce.h"
#include <vector>
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Load grid values from rectangle enclosing angles Load grid values from rectenclosing angles
@param grid grid values [ angle1, angle2, f, df1, df2, df12 ] @param grid grid values [ angle1, angle2, f, df1, df2, df12 ]
@param angle1 angle in first dimension @param angle1 angle in first dimension
...@@ -50,7 +49,7 @@ ...@@ -50,7 +49,7 @@
void AmoebaReferenceTorsionTorsionForce::loadGridValuesFromEnclosingRectangle( void AmoebaReferenceTorsionTorsionForce::loadGridValuesFromEnclosingRectangle(
const std::vector< std::vector< std::vector<RealOpenMM> > >& grid, const std::vector< std::vector< std::vector<RealOpenMM> > >& grid,
RealOpenMM angle1, RealOpenMM angle2, RealOpenMM corners[2][2], RealOpenMM angle1, RealOpenMM angle2, RealOpenMM corners[2][2],
RealOpenMM* fValues, RealOpenMM* fValues1, RealOpenMM* fValues2, RealOpenMM* fValues12 ){ RealOpenMM* fValues, RealOpenMM* fValues1, RealOpenMM* fValues2, RealOpenMM* fValues12 ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -119,7 +118,7 @@ void AmoebaReferenceTorsionTorsionForce::loadGridValuesFromEnclosingRectangle( ...@@ -119,7 +118,7 @@ void AmoebaReferenceTorsionTorsionForce::loadGridValuesFromEnclosingRectangle(
void AmoebaReferenceTorsionTorsionForce::getBicubicCoefficientMatrix( const RealOpenMM* y, void AmoebaReferenceTorsionTorsionForce::getBicubicCoefficientMatrix( const RealOpenMM* y,
const RealOpenMM* y1, const RealOpenMM* y2, const RealOpenMM* y12, const RealOpenMM d1, const RealOpenMM d2, const RealOpenMM* y1, const RealOpenMM* y2, const RealOpenMM* y12, const RealOpenMM d1, const RealOpenMM d2,
RealOpenMM c[4][4] ){ RealOpenMM c[4][4] ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -221,7 +220,7 @@ void AmoebaReferenceTorsionTorsionForce::getBicubicValues( ...@@ -221,7 +220,7 @@ void AmoebaReferenceTorsionTorsionForce::getBicubicValues(
const RealOpenMM x1Lower, const RealOpenMM x1Upper, const RealOpenMM x1Lower, const RealOpenMM x1Upper,
const RealOpenMM x2Lower, const RealOpenMM x2Upper, const RealOpenMM x2Lower, const RealOpenMM x2Upper,
const RealOpenMM gridValue1, const RealOpenMM gridValue2, const RealOpenMM gridValue1, const RealOpenMM gridValue2,
RealOpenMM* functionValue, RealOpenMM* functionValue1, RealOpenMM* functionValue2 ){ RealOpenMM* functionValue, RealOpenMM* functionValue1, RealOpenMM* functionValue2 ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -275,7 +274,7 @@ void AmoebaReferenceTorsionTorsionForce::getBicubicValues( ...@@ -275,7 +274,7 @@ void AmoebaReferenceTorsionTorsionForce::getBicubicValues(
int AmoebaReferenceTorsionTorsionForce::checkTorsionSign( int AmoebaReferenceTorsionTorsionForce::checkTorsionSign(
const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD ){ const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -324,11 +323,11 @@ int AmoebaReferenceTorsionTorsionForce::checkTorsionSign( ...@@ -324,11 +323,11 @@ int AmoebaReferenceTorsionTorsionForce::checkTorsionSign(
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD,
const RealOpenMM* positionAtomE, const RealOpenMM* positionChiralCheckAtom, const RealOpenMM* positionAtomE, const RealOpenMM* positionChiralCheckAtom,
const std::vector< std::vector< std::vector<RealOpenMM> > >& grid, const std::vector< std::vector< std::vector<RealOpenMM> > >& grid,
RealOpenMM** forces ){ RealOpenMM** forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -549,3 +548,48 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( const Re ...@@ -549,3 +548,48 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( const Re
return gridEnergy; return gridEnergy;
} }
RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( int numTorsionTorsions, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<int>& particle4,
const std::vector<int>& particle5,
const std::vector<int>& chiralCheckAtom,
const std::vector<int>& gridIndices,
const std::vector< std::vector< std::vector< std::vector<RealOpenMM> > > >& torsionTorsionGrids,
RealOpenMM** forceData ) const {
RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < numTorsionTorsions; ii++) {
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
int particle4Index = particle4[ii];
int particle5Index = particle5[ii];
int chiralCheckAtomIndex = chiralCheckAtom[ii];
int gridIndex = gridIndices[ii];
RealOpenMM* forces[5];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
forces[4] = forceData[particle5Index];
RealOpenMM* chiralCheckAtom;
if( chiralCheckAtomIndex >= 0 ){
chiralCheckAtom = posData[chiralCheckAtomIndex];
} else {
chiralCheckAtom = NULL;
}
energy += calculateTorsionTorsionIxn( posData[particle1Index], posData[particle2Index],
posData[particle3Index], posData[particle4Index],
posData[particle5Index], chiralCheckAtom, torsionTorsionGrids[gridIndex],
forces );
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.h
View file @ a37e41ea
...@@ -26,6 +26,7 @@ ...@@ -26,6 +26,7 @@
#define __AmoebaReferenceTorsionTorsionForce_H__ #define __AmoebaReferenceTorsionTorsionForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/SimTKOpenMMRealType.h"
#include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -39,7 +40,7 @@ public: ...@@ -39,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
AmoebaReferenceTorsionTorsionForce( ); AmoebaReferenceTorsionTorsionForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -47,7 +48,41 @@ public: ...@@ -47,7 +48,41 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~AmoebaReferenceTorsionTorsionForce( ); ~AmoebaReferenceTorsionTorsionForce( ){};
/**---------------------------------------------------------------------------------------
Calculate Amoeba torsion-torsion ixns (force and energy)
@param numTorsions number of torsions
@param posData particle positions
@param particle1 particle 1 indices
@param particle2 particle 2 indices
@param particle3 particle 3 indices
@param particle4 particle 4 indices
@param particle5 particle 5 indices
@param chiralCheckAtom chiralCheckAtom (-1 if no chiral check is to be performed)
@param gridIndices grid indices
@param torsionTorsionGrids torsion-torsion grids
@param forces output force vector
@return total energy
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numTorsionTorsions, RealOpenMM** posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<int>& particle4,
const std::vector<int>& particle5,
const std::vector<int>& chiralCheckAtom,
const std::vector<int>& gridIndices,
const std::vector< std::vector< std::vector< std::vector<RealOpenMM> > > >& torsionTorsionGrids,
RealOpenMM** forceData ) const;
private:
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -67,10 +102,10 @@ public: ...@@ -67,10 +102,10 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void loadGridValuesFromEnclosingRectangle( void loadGridValuesFromEnclosingRectangle(
const std::vector< std::vector< std::vector<RealOpenMM> > >& grid, const std::vector< std::vector< std::vector<RealOpenMM> > >& grid,
RealOpenMM angle1, RealOpenMM angle2, RealOpenMM corners[2][2], RealOpenMM angle1, RealOpenMM angle2, RealOpenMM corners[2][2],
RealOpenMM* fValues, RealOpenMM* fValues1, RealOpenMM* fValues2, RealOpenMM* fValues12 ); RealOpenMM* fValues, RealOpenMM* fValues1, RealOpenMM* fValues2, RealOpenMM* fValues12 ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -93,9 +128,8 @@ public: ...@@ -93,9 +128,8 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void getBicubicCoefficientMatrix( const RealOpenMM* y, void getBicubicCoefficientMatrix( const RealOpenMM* y, const RealOpenMM* y1, const RealOpenMM* y2, const RealOpenMM* y12,
const RealOpenMM* y1, const RealOpenMM* y2, const RealOpenMM* y12, const RealOpenMM d1, const RealOpenMM d2, const RealOpenMM d1, const RealOpenMM d2, RealOpenMM c[4][4] ) const;
RealOpenMM c[4][4] );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -130,12 +164,12 @@ public: ...@@ -130,12 +164,12 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void getBicubicValues( void getBicubicValues(
const RealOpenMM* y, const RealOpenMM* y1, const RealOpenMM* y2, const RealOpenMM* y12, const RealOpenMM* y, const RealOpenMM* y1, const RealOpenMM* y2, const RealOpenMM* y12,
const RealOpenMM x1Lower, const RealOpenMM x1Upper, const RealOpenMM x1Lower, const RealOpenMM x1Upper,
const RealOpenMM x2Lower, const RealOpenMM x2Upper, const RealOpenMM x2Lower, const RealOpenMM x2Upper,
const RealOpenMM gridValue1, const RealOpenMM gridValue2, const RealOpenMM gridValue1, const RealOpenMM gridValue2,
RealOpenMM* functionValue, RealOpenMM* functionValue1, RealOpenMM* functionValue2 ); RealOpenMM* functionValue, RealOpenMM* functionValue1, RealOpenMM* functionValue2 ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -151,9 +185,8 @@ public: ...@@ -151,9 +185,8 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static int checkTorsionSign( int checkTorsionSign( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD ) const;
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -173,11 +206,11 @@ public: ...@@ -173,11 +206,11 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static RealOpenMM calculateForceAndEnergy( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculateTorsionTorsionIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD,
const RealOpenMM* positionAtomE, const RealOpenMM* chiralCheckAtom, const RealOpenMM* positionAtomE, const RealOpenMM* chiralCheckAtom,
const std::vector< std::vector< std::vector<RealOpenMM> > >& grid, const std::vector< std::vector< std::vector<RealOpenMM> > >& grid,
RealOpenMM** forces ); RealOpenMM** forces ) const;
}; };
......
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