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Commit 93900ab2 authored by Peter Eastman's avatar Peter Eastman
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Updated Amoeba plugin based on refactoring of reference platform

parent c27f5d1f
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plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ 93900ab2
...@@ -51,24 +51,24 @@ ...@@ -51,24 +51,24 @@
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
static RealOpenMM** extractPositions(ContextImpl& context) { static vector<RealVec>& extractPositions(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData()); ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return (RealOpenMM**) data->positions; return *((vector<RealVec>*) data->positions);
} }
static RealOpenMM** extractVelocities(ContextImpl& context) { static vector<RealVec>& extractVelocities(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData()); ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return (RealOpenMM**) data->velocities; return *((vector<RealVec>*) data->velocities);
} }
static RealOpenMM** extractForces(ContextImpl& context) { static vector<RealVec>& extractForces(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData()); ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return (RealOpenMM**) data->forces; return *((vector<RealVec>*) data->forces);
} }
static RealOpenMM* extractBoxSize(ContextImpl& context) { static RealVec& extractBoxSize(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData()); ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return (RealOpenMM*) data->periodicBoxSize; return *(RealVec*) data->periodicBoxSize;
} }
// *************************************************************************** // ***************************************************************************
...@@ -99,8 +99,8 @@ void ReferenceCalcAmoebaHarmonicBondForceKernel::initialize(const System& system ...@@ -99,8 +99,8 @@ 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); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceHarmonicBondForce amoebaReferenceHarmonicBondForce; AmoebaReferenceHarmonicBondForce amoebaReferenceHarmonicBondForce;
RealOpenMM energy = amoebaReferenceHarmonicBondForce.calculateForceAndEnergy( numBonds, posData, particle1, particle2, length, kQuadratic, RealOpenMM energy = amoebaReferenceHarmonicBondForce.calculateForceAndEnergy( numBonds, posData, particle1, particle2, length, kQuadratic,
globalHarmonicBondCubic, globalHarmonicBondQuartic, globalHarmonicBondCubic, globalHarmonicBondQuartic,
...@@ -136,8 +136,8 @@ void ReferenceCalcAmoebaUreyBradleyForceKernel::initialize(const System& system, ...@@ -136,8 +136,8 @@ void ReferenceCalcAmoebaUreyBradleyForceKernel::initialize(const System& system,
} }
double ReferenceCalcAmoebaUreyBradleyForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcAmoebaUreyBradleyForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceUreyBradleyForce amoebaReferenceUreyBradleyForce; AmoebaReferenceUreyBradleyForce amoebaReferenceUreyBradleyForce;
RealOpenMM energy = amoebaReferenceUreyBradleyForce.calculateForceAndEnergy( numIxns, posData, particle1, particle2, length, kQuadratic, RealOpenMM energy = amoebaReferenceUreyBradleyForce.calculateForceAndEnergy( numIxns, posData, particle1, particle2, length, kQuadratic,
globalUreyBradleyCubic, globalUreyBradleyQuartic, globalUreyBradleyCubic, globalUreyBradleyQuartic,
...@@ -173,8 +173,8 @@ void ReferenceCalcAmoebaHarmonicAngleForceKernel::initialize(const System& syste ...@@ -173,8 +173,8 @@ 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); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceHarmonicAngleForce amoebaReferenceHarmonicAngleForce; AmoebaReferenceHarmonicAngleForce amoebaReferenceHarmonicAngleForce;
RealOpenMM energy = amoebaReferenceHarmonicAngleForce.calculateForceAndEnergy( numAngles, RealOpenMM energy = amoebaReferenceHarmonicAngleForce.calculateForceAndEnergy( numAngles,
posData, particle1, particle2, particle3, angle, kQuadratic, globalHarmonicAngleCubic, globalHarmonicAngleQuartic, globalHarmonicAnglePentic, globalHarmonicAngleSextic, forceData ); posData, particle1, particle2, particle3, angle, kQuadratic, globalHarmonicAngleCubic, globalHarmonicAngleQuartic, globalHarmonicAnglePentic, globalHarmonicAngleSextic, forceData );
...@@ -210,8 +210,8 @@ void ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::initialize(const System ...@@ -210,8 +210,8 @@ 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); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceHarmonicInPlaneAngleForce amoebaReferenceHarmonicInPlaneAngleForce; AmoebaReferenceHarmonicInPlaneAngleForce amoebaReferenceHarmonicInPlaneAngleForce;
RealOpenMM energy = amoebaReferenceHarmonicInPlaneAngleForce.calculateForceAndEnergy( numAngles, posData, particle1, particle2, particle3, particle4, RealOpenMM energy = amoebaReferenceHarmonicInPlaneAngleForce.calculateForceAndEnergy( numAngles, posData, particle1, particle2, particle3, particle4,
angle, kQuadratic, globalHarmonicInPlaneAngleCubic, globalHarmonicInPlaneAngleQuartic, angle, kQuadratic, globalHarmonicInPlaneAngleCubic, globalHarmonicInPlaneAngleQuartic,
...@@ -260,8 +260,8 @@ void ReferenceCalcAmoebaTorsionForceKernel::initialize(const System& system, con ...@@ -260,8 +260,8 @@ 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); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceTorsionForce amoebaReferenceTorsionForce; AmoebaReferenceTorsionForce amoebaReferenceTorsionForce;
RealOpenMM energy = amoebaReferenceTorsionForce.calculateForceAndEnergy( numTorsions, posData, particle1, particle2, particle3, particle4, RealOpenMM energy = amoebaReferenceTorsionForce.calculateForceAndEnergy( numTorsions, posData, particle1, particle2, particle3, particle4,
torsionParameters1, torsionParameters2, torsionParameters3, forceData ); torsionParameters1, torsionParameters2, torsionParameters3, forceData );
...@@ -294,8 +294,8 @@ void ReferenceCalcAmoebaPiTorsionForceKernel::initialize(const System& system, c ...@@ -294,8 +294,8 @@ 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); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
AmoebaReferencePiTorsionForce amoebaReferencePiTorsionForce; AmoebaReferencePiTorsionForce amoebaReferencePiTorsionForce;
RealOpenMM energy = amoebaReferencePiTorsionForce.calculateForceAndEnergy( numPiTorsions, posData, particle1, particle2, RealOpenMM energy = amoebaReferencePiTorsionForce.calculateForceAndEnergy( numPiTorsions, posData, particle1, particle2,
particle3, particle4, particle5, particle6, particle3, particle4, particle5, particle6,
...@@ -328,8 +328,8 @@ void ReferenceCalcAmoebaStretchBendForceKernel::initialize(const System& system, ...@@ -328,8 +328,8 @@ 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); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceStretchBendForce amoebaReferenceStretchBendForce; AmoebaReferenceStretchBendForce amoebaReferenceStretchBendForce;
RealOpenMM energy = amoebaReferenceStretchBendForce.calculateForceAndEnergy( numStretchBends, posData, particle1, particle2, particle3, RealOpenMM energy = amoebaReferenceStretchBendForce.calculateForceAndEnergy( numStretchBends, posData, particle1, particle2, particle3,
lengthABParameters, lengthCBParameters, angleParameters, kParameters, forceData ); lengthABParameters, lengthCBParameters, angleParameters, kParameters, forceData );
...@@ -366,8 +366,8 @@ void ReferenceCalcAmoebaOutOfPlaneBendForceKernel::initialize(const System& syst ...@@ -366,8 +366,8 @@ 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); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceOutOfPlaneBendForce amoebaReferenceOutOfPlaneBendForce; AmoebaReferenceOutOfPlaneBendForce amoebaReferenceOutOfPlaneBendForce;
RealOpenMM energy = amoebaReferenceOutOfPlaneBendForce.calculateForceAndEnergy( numOutOfPlaneBends, posData, RealOpenMM energy = amoebaReferenceOutOfPlaneBendForce.calculateForceAndEnergy( numOutOfPlaneBends, posData,
particle1, particle2, particle3, particle4, particle1, particle2, particle3, particle4,
...@@ -430,8 +430,8 @@ void ReferenceCalcAmoebaTorsionTorsionForceKernel::initialize(const System& syst ...@@ -430,8 +430,8 @@ void ReferenceCalcAmoebaTorsionTorsionForceKernel::initialize(const System& syst
double ReferenceCalcAmoebaTorsionTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcAmoebaTorsionTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceTorsionTorsionForce amoebaReferenceTorsionTorsionForce; AmoebaReferenceTorsionTorsionForce amoebaReferenceTorsionTorsionForce;
RealOpenMM energy = amoebaReferenceTorsionTorsionForce.calculateForceAndEnergy( numTorsionTorsions, posData, RealOpenMM energy = amoebaReferenceTorsionTorsionForce.calculateForceAndEnergy( numTorsionTorsions, posData,
particle1, particle2, particle3, particle4, particle5, particle1, particle2, particle3, particle4, particle5,
...@@ -524,8 +524,8 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c ...@@ -524,8 +524,8 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
} }
double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceMultipoleForce amoebaReferenceMultipoleForce( AmoebaReferenceMultipoleForce::NoCutoff ); AmoebaReferenceMultipoleForce amoebaReferenceMultipoleForce( AmoebaReferenceMultipoleForce::NoCutoff );
amoebaReferenceMultipoleForce.setMutualInducedDipoleTargetEpsilon( mutualInducedTargetEpsilon ); amoebaReferenceMultipoleForce.setMutualInducedDipoleTargetEpsilon( mutualInducedTargetEpsilon );
...@@ -627,8 +627,8 @@ void ReferenceCalcAmoebaVdwForceKernel::initialize(const System& system, const A ...@@ -627,8 +627,8 @@ void ReferenceCalcAmoebaVdwForceKernel::initialize(const System& system, const A
double ReferenceCalcAmoebaVdwForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcAmoebaVdwForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceVdwForce vdwForce( sigmaCombiningRule, epsilonCombiningRule, AmoebaReferenceVdwForce::NoCutoff ); AmoebaReferenceVdwForce vdwForce( sigmaCombiningRule, epsilonCombiningRule, AmoebaReferenceVdwForce::NoCutoff );
RealOpenMM energy = vdwForce.calculateForceAndEnergy( numParticles, posData, indexIVs, indexClasses, sigmas, epsilons, reductions, allExclusions, forceData); RealOpenMM energy = vdwForce.calculateForceAndEnergy( numParticles, posData, indexIVs, indexClasses, sigmas, epsilons, reductions, allExclusions, forceData);
return static_cast<double>(energy); return static_cast<double>(energy);
...@@ -674,8 +674,8 @@ void ReferenceCalcAmoebaWcaDispersionForceKernel::initialize(const System& syste ...@@ -674,8 +674,8 @@ void ReferenceCalcAmoebaWcaDispersionForceKernel::initialize(const System& syste
} }
double ReferenceCalcAmoebaWcaDispersionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcAmoebaWcaDispersionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceWcaDispersionForce amoebaReferenceWcaDispersionForce( epso, epsh, rmino, rminh, awater, shctd, dispoff, slevy ); AmoebaReferenceWcaDispersionForce amoebaReferenceWcaDispersionForce( epso, epsh, rmino, rminh, awater, shctd, dispoff, slevy );
RealOpenMM energy = amoebaReferenceWcaDispersionForce.calculateForceAndEnergy( numParticles, posData, radii, epsilons, totalMaximumDispersionEnergy, forceData); RealOpenMM energy = amoebaReferenceWcaDispersionForce.calculateForceAndEnergy( numParticles, posData, radii, epsilons, totalMaximumDispersionEnergy, forceData);
return static_cast<double>(energy); return static_cast<double>(energy);
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceForce.cpp
View file @ 93900ab2
...@@ -25,6 +25,8 @@ ...@@ -25,6 +25,8 @@
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include <vector> #include <vector>
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Load delta of two vectors Load delta of two vectors
...@@ -35,7 +37,7 @@ ...@@ -35,7 +37,7 @@
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void AmoebaReferenceForce::loadDeltaR( const RealOpenMM* xVector, const RealOpenMM* yVector, void AmoebaReferenceForce::loadDeltaR( const RealVec& xVector, const RealVec& yVector,
std::vector<RealOpenMM>& deltaR ){ std::vector<RealOpenMM>& deltaR ){
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceForce.h
View file @ 93900ab2
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#ifndef __AmoebaReferenceForce_H__ #ifndef __AmoebaReferenceForce_H__
#define __AmoebaReferenceForce_H__ #define __AmoebaReferenceForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/RealVec.h"
#include "openmm/Vec3.h" #include "openmm/Vec3.h"
#include <vector> #include <vector>
...@@ -62,7 +62,7 @@ public: ...@@ -62,7 +62,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static void loadDeltaR( const RealOpenMM* xVector, const RealOpenMM* yVector, static void loadDeltaR( const OpenMM::RealVec& xVector, const OpenMM::RealVec& yVector,
std::vector<RealOpenMM>& deltaR ); std::vector<RealOpenMM>& deltaR );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicAngleForce.cpp
View file @ 93900ab2
...@@ -25,6 +25,9 @@ ...@@ -25,6 +25,9 @@
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include "AmoebaReferenceHarmonicAngleForce.h" #include "AmoebaReferenceHarmonicAngleForce.h"
using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Get dEdT and energy prefactor given cosine of angle :: the calculation for different Get dEdT and energy prefactor given cosine of angle :: the calculation for different
...@@ -110,12 +113,12 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::getPrefactorsGivenAngleCosine( Rea ...@@ -110,12 +113,12 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::getPrefactorsGivenAngleCosine( Rea
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateAngleIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateAngleIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const RealVec& 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 ) const { RealVec* forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -180,7 +183,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateAngleIxn( const RealOpenM ...@@ -180,7 +183,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateAngleIxn( const RealOpenM
return energy; return energy;
} }
RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy( int numAngles, RealOpenMM** posData, RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy( int numAngles, vector<RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -190,7 +193,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy( int numAn ...@@ -190,7 +193,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy( int numAn
RealOpenMM angleQuartic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM anglePentic,
RealOpenMM angleSextic, RealOpenMM angleSextic,
RealOpenMM** forceData) const { vector<RealVec>& forceData) const {
RealOpenMM energy = 0.0; RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < numAngles; ii++) { for (unsigned int ii = 0; ii < numAngles; ii++) {
int particle1Index = particle1[ii]; int particle1Index = particle1[ii];
...@@ -198,7 +201,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy( int numAn ...@@ -198,7 +201,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy( int numAn
int particle3Index = particle3[ii]; int particle3Index = particle3[ii];
RealOpenMM idealAngle = angle[ii]; RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii]; RealOpenMM angleK = kQuadratic[ii];
RealOpenMM* forces[3]; RealVec forces[3];
forces[0] = forceData[particle1Index]; forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index]; forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index]; forces[2] = forceData[particle3Index];
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicAngleForce.h
View file @ 93900ab2
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#ifndef __AmoebaReferenceHarmonicAngleForce_H__ #ifndef __AmoebaReferenceHarmonicAngleForce_H__
#define __AmoebaReferenceHarmonicAngleForce_H__ #define __AmoebaReferenceHarmonicAngleForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/RealVec.h"
#include <vector> #include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -72,7 +72,7 @@ public: ...@@ -72,7 +72,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numAngles, RealOpenMM** posData, RealOpenMM calculateForceAndEnergy( int numAngles, std::vector<OpenMM::RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -82,7 +82,7 @@ public: ...@@ -82,7 +82,7 @@ public:
RealOpenMM globalHarmonicAngleQuartic, RealOpenMM globalHarmonicAngleQuartic,
RealOpenMM globalHarmonicAnglePentic, RealOpenMM globalHarmonicAnglePentic,
RealOpenMM globalHarmonicAngleSextic, RealOpenMM globalHarmonicAngleSextic,
RealOpenMM** forceData ) const; std::vector<OpenMM::RealVec>& forceData ) const;
private: private:
...@@ -128,12 +128,12 @@ private: ...@@ -128,12 +128,12 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateAngleIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculateAngleIxn( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const OpenMM::RealVec& 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 ) const; OpenMM::RealVec* forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicBondForce.cpp
View file @ 93900ab2
...@@ -25,6 +25,9 @@ ...@@ -25,6 +25,9 @@
#include "AmoebaReferenceHarmonicBondForce.h" #include "AmoebaReferenceHarmonicBondForce.h"
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic bond ixn (force and energy) Calculate Amoeba harmonic bond ixn (force and energy)
...@@ -41,10 +44,10 @@ ...@@ -41,10 +44,10 @@
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicBondForce::calculateBondIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceHarmonicBondForce::calculateBondIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
RealOpenMM bondLength, RealOpenMM bondK, RealOpenMM bondLength, RealOpenMM bondK,
RealOpenMM bondCubic, RealOpenMM bondQuartic, RealOpenMM bondCubic, RealOpenMM bondQuartic,
RealOpenMM** forces ) const { RealVec* forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -85,21 +88,21 @@ RealOpenMM AmoebaReferenceHarmonicBondForce::calculateBondIxn( const RealOpenMM* ...@@ -85,21 +88,21 @@ RealOpenMM AmoebaReferenceHarmonicBondForce::calculateBondIxn( const RealOpenMM*
} }
RealOpenMM AmoebaReferenceHarmonicBondForce::calculateForceAndEnergy( int numBonds, RealOpenMM AmoebaReferenceHarmonicBondForce::calculateForceAndEnergy( int numBonds,
RealOpenMM** particlePositions, vector<RealVec>& particlePositions,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<RealOpenMM>& length, const std::vector<RealOpenMM>& length,
const std::vector<RealOpenMM>& kQuadratic, const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM globalHarmonicBondCubic, RealOpenMM globalHarmonicBondCubic,
RealOpenMM globalHarmonicBondQuartic, RealOpenMM globalHarmonicBondQuartic,
RealOpenMM** forceData ) const { vector<RealVec>& forceData ) const {
RealOpenMM energy = 0.0; RealOpenMM energy = 0.0;
for( int ii = 0; ii < numBonds; ii++ ){ for( int ii = 0; ii < numBonds; ii++ ){
int particle1Index = particle1[ii]; int particle1Index = particle1[ii];
int particle2Index = particle2[ii]; int particle2Index = particle2[ii];
RealOpenMM bondLength = length[ii]; RealOpenMM bondLength = length[ii];
RealOpenMM bondK = kQuadratic[ii]; RealOpenMM bondK = kQuadratic[ii];
RealOpenMM* forces[2]; RealVec forces[2];
forces[0] = forceData[particle1Index]; forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index]; forces[1] = forceData[particle2Index];
energy += calculateBondIxn( particlePositions[particle1Index], particlePositions[particle2Index], energy += calculateBondIxn( particlePositions[particle1Index], particlePositions[particle2Index],
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicBondForce.h
View file @ 93900ab2
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#ifndef __AmoebaReferenceHarmonicBondForce_H__ #ifndef __AmoebaReferenceHarmonicBondForce_H__
#define __AmoebaReferenceHarmonicBondForce_H__ #define __AmoebaReferenceHarmonicBondForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/RealVec.h"
#include <vector> #include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -69,13 +69,13 @@ public: ...@@ -69,13 +69,13 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numBonds, RealOpenMM** posData, RealOpenMM calculateForceAndEnergy( int numBonds, std::vector<OpenMM::RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<RealOpenMM>& bondLength, const std::vector<RealOpenMM>& bondLength,
const std::vector<RealOpenMM>& bondK, const std::vector<RealOpenMM>& bondK,
RealOpenMM bondCubic, RealOpenMM bondQuartic, RealOpenMM bondCubic, RealOpenMM bondQuartic,
RealOpenMM** forceData ) const; std::vector<OpenMM::RealVec>& forceData ) const;
private: private:
...@@ -95,10 +95,10 @@ private: ...@@ -95,10 +95,10 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateBondIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculateBondIxn( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
RealOpenMM bondLength, RealOpenMM bondK, RealOpenMM bondLength, RealOpenMM bondK,
RealOpenMM bondCubic, RealOpenMM bondQuartic, RealOpenMM bondCubic, RealOpenMM bondQuartic,
RealOpenMM** forces ) const; OpenMM::RealVec* forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicInPlaneAngleForce.cpp
View file @ 93900ab2
...@@ -25,6 +25,9 @@ ...@@ -25,6 +25,9 @@
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include "AmoebaReferenceHarmonicInPlaneAngleForce.h" #include "AmoebaReferenceHarmonicInPlaneAngleForce.h"
using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Get dEdT and energy prefactor given cosine of angle :: the calculation for different Get dEdT and energy prefactor given cosine of angle :: the calculation for different
...@@ -111,12 +114,12 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosi ...@@ -111,12 +114,12 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosi
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateAngleIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateAngleIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealVec& positionAtomC, const RealVec& 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 ) const { RealVec* forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -242,7 +245,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateAngleIxn( const Re ...@@ -242,7 +245,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateAngleIxn( const Re
} }
RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( int numAngles, RealOpenMM** posData, RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( int numAngles, vector<RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -253,7 +256,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( in ...@@ -253,7 +256,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( in
RealOpenMM angleQuartic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM anglePentic,
RealOpenMM angleSextic, RealOpenMM angleSextic,
RealOpenMM** forceData) const { vector<RealVec>& forceData) const {
RealOpenMM energy = 0.0; RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < numAngles; ii++) { for (unsigned int ii = 0; ii < numAngles; ii++) {
int particle1Index = particle1[ii]; int particle1Index = particle1[ii];
...@@ -262,7 +265,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( in ...@@ -262,7 +265,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( in
int particle4Index = particle4[ii]; int particle4Index = particle4[ii];
RealOpenMM idealAngle = angle[ii]; RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii]; RealOpenMM angleK = kQuadratic[ii];
RealOpenMM* forces[4]; RealVec forces[4];
forces[0] = forceData[particle1Index]; forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index]; forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index]; forces[2] = forceData[particle3Index];
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicInPlaneAngleForce.h
View file @ 93900ab2
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#ifndef __AmoebaReferenceHarmonicInPlaneAngleForce_H__ #ifndef __AmoebaReferenceHarmonicInPlaneAngleForce_H__
#define __AmoebaReferenceHarmonicInPlaneAngleForce_H__ #define __AmoebaReferenceHarmonicInPlaneAngleForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/RealVec.h"
#include <vector> #include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -73,7 +73,7 @@ public: ...@@ -73,7 +73,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numAngles, RealOpenMM** posData, RealOpenMM calculateForceAndEnergy( int numAngles, std::vector<OpenMM::RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -84,7 +84,7 @@ public: ...@@ -84,7 +84,7 @@ public:
RealOpenMM globalHarmonicAngleQuartic, RealOpenMM globalHarmonicAngleQuartic,
RealOpenMM globalHarmonicAnglePentic, RealOpenMM globalHarmonicAnglePentic,
RealOpenMM globalHarmonicAngleSextic, RealOpenMM globalHarmonicAngleSextic,
RealOpenMM** forceData ) const; std::vector<OpenMM::RealVec>& forceData ) const;
private: private:
...@@ -131,12 +131,12 @@ private: ...@@ -131,12 +131,12 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateAngleIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculateAngleIxn( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const OpenMM::RealVec& positionAtomC, const OpenMM::RealVec& 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 ) const; OpenMM::RealVec* forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ 93900ab2
...@@ -27,6 +27,9 @@ ...@@ -27,6 +27,9 @@
#include <sstream> #include <sstream>
#include <algorithm> #include <algorithm>
using std::vector;
using OpenMM::RealVec;
#define AMOEBA_DEBUG #define AMOEBA_DEBUG
AmoebaReferenceMultipoleForce::AmoebaReferenceMultipoleForce( ) : _nonbondedMethod(NoCutoff) { AmoebaReferenceMultipoleForce::AmoebaReferenceMultipoleForce( ) : _nonbondedMethod(NoCutoff) {
...@@ -134,7 +137,7 @@ void AmoebaReferenceMultipoleForce::setMutualInducedDipoleTargetEpsilon( RealOpe ...@@ -134,7 +137,7 @@ void AmoebaReferenceMultipoleForce::setMutualInducedDipoleTargetEpsilon( RealOpe
_mutualInducedDipoleTargetEpsilon = mutualInducedDipoleTargetEpsilon; _mutualInducedDipoleTargetEpsilon = mutualInducedDipoleTargetEpsilon;
} }
void AmoebaReferenceMultipoleForce::getDelta( unsigned int particleI, unsigned int particleJ, RealOpenMM** particlePositions, void AmoebaReferenceMultipoleForce::getDelta( unsigned int particleI, unsigned int particleJ, vector<RealVec>& particlePositions,
RealOpenMM* delta ) const { RealOpenMM* delta ) const {
delta[0] = particlePositions[particleJ][0] - particlePositions[particleI][0]; delta[0] = particlePositions[particleJ][0] - particlePositions[particleI][0];
...@@ -332,7 +335,7 @@ void AmoebaReferenceMultipoleForce::getScaleFactors( unsigned int particleI, uns ...@@ -332,7 +335,7 @@ void AmoebaReferenceMultipoleForce::getScaleFactors( unsigned int particleI, uns
scaleFactors[U_SCALE] = getScaleFactor( particleI, particleJ, U_SCALE ); scaleFactors[U_SCALE] = getScaleFactor( particleI, particleJ, U_SCALE );
} }
void AmoebaReferenceMultipoleForce::loadParticleData( RealOpenMM** particlePositions, void AmoebaReferenceMultipoleForce::loadParticleData( vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges, const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles, const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles, const std::vector<RealOpenMM>& quadrupoles,
...@@ -1023,7 +1026,7 @@ fprintf( stderr, "MIb %3u eps=%15.7e %15.7e %15.7e\n", iteration, epsilonDirect, ...@@ -1023,7 +1026,7 @@ fprintf( stderr, "MIb %3u eps=%15.7e %15.7e %15.7e\n", iteration, epsilonDirect,
RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostaticPairIxn( const MultipoleParticleData& particleI, RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostaticPairIxn( const MultipoleParticleData& particleI,
const MultipoleParticleData& particleK, const MultipoleParticleData& particleK,
RealOpenMM* scalingFactors, RealOpenMM** forces, RealOpenMM* scalingFactors, vector<RealVec>& forces,
std::vector<Vec3>& torque ) const { std::vector<Vec3>& torque ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -1545,7 +1548,7 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForce( const MultipoleParticleDat ...@@ -1545,7 +1548,7 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForce( const MultipoleParticleDat
const MultipoleParticleData& particleU, const MultipoleParticleData& particleU,
const MultipoleParticleData& particleV, const MultipoleParticleData& particleV,
MultipoleParticleData* particleW, MultipoleParticleData* particleW,
int axisType, const Vec3& torque, RealOpenMM** forces ) const { int axisType, const Vec3& torque, vector<RealVec>& forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -1782,7 +1785,7 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForce( const MultipoleParticleDat ...@@ -1782,7 +1785,7 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForce( const MultipoleParticleDat
void AmoebaReferenceMultipoleForce::mapTorqueToForceOld( const MultipoleParticleData& particleI, void AmoebaReferenceMultipoleForce::mapTorqueToForceOld( const MultipoleParticleData& particleI,
const MultipoleParticleData& particleU, const MultipoleParticleData& particleU,
const MultipoleParticleData& particleV, const MultipoleParticleData& particleV,
int axisType, const Vec3& torque, RealOpenMM** forces ) const { int axisType, const Vec3& torque, vector<RealVec>& forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -1877,7 +1880,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::v ...@@ -1877,7 +1880,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::v
const std::vector<int>& multipoleAtomZs, const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs, const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs, const std::vector<int>& multipoleAtomYs,
RealOpenMM** forces ) const { vector<RealVec>& forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -1982,7 +1985,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::v ...@@ -1982,7 +1985,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::v
} }
RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsigned int numParticles, RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsigned int numParticles,
RealOpenMM** particlePositions, vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges, const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles, const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles, const std::vector<RealOpenMM>& quadrupoles,
...@@ -1993,7 +1996,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsig ...@@ -1993,7 +1996,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsig
const std::vector<int>& multipoleAtomZs, const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs, const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs, const std::vector<int>& multipoleAtomYs,
RealOpenMM** forces ){ vector<RealVec>& forces ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -2091,7 +2094,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsig ...@@ -2091,7 +2094,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsig
} }
RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy( int numParticles, RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy( int numParticles,
RealOpenMM** particlePositions, vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges, const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles, const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles, const std::vector<RealOpenMM>& quadrupoles,
...@@ -2103,7 +2106,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy( int numPartic ...@@ -2103,7 +2106,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy( int numPartic
const std::vector<int>& multipoleAtomXs, const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs, const std::vector<int>& multipoleAtomYs,
const std::vector< std::vector< std::vector<int> > >& multipoleParticleCovalentInfo, const std::vector< std::vector< std::vector<int> > >& multipoleParticleCovalentInfo,
RealOpenMM** forces ){ vector<RealVec>& forces ){
setupScaleMaps( multipoleParticleCovalentInfo ); setupScaleMaps( multipoleParticleCovalentInfo );
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 93900ab2
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#ifndef __AmoebaReferenceMultipoleForce_H__ #ifndef __AmoebaReferenceMultipoleForce_H__
#define __AmoebaReferenceMultipoleForce_H__ #define __AmoebaReferenceMultipoleForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/RealVec.h"
#include "openmm/Vec3.h" #include "openmm/Vec3.h"
#include "AmoebaMultipoleForce.h" #include "AmoebaMultipoleForce.h"
#include <string> #include <string>
...@@ -203,7 +203,7 @@ public: ...@@ -203,7 +203,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numParticles, RealOpenMM** particlePositions, RealOpenMM calculateForceAndEnergy( int numParticles, std::vector<OpenMM::RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges, const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles, const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles, const std::vector<RealOpenMM>& quadrupoles,
...@@ -215,7 +215,7 @@ public: ...@@ -215,7 +215,7 @@ public:
const std::vector<int>& multipoleAtomXs, const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs, const std::vector<int>& multipoleAtomYs,
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo, const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
RealOpenMM** forces ); std::vector<OpenMM::RealVec>& forces );
...@@ -270,7 +270,7 @@ private: ...@@ -270,7 +270,7 @@ private:
void initialize( void ); void initialize( void );
void loadParticleData( RealOpenMM** particlePositions, void loadParticleData( std::vector<OpenMM::RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges, const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles, const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles, const std::vector<RealOpenMM>& quadrupoles,
...@@ -319,7 +319,7 @@ private: ...@@ -319,7 +319,7 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void getDelta( unsigned int particleI, unsigned int particleJ, RealOpenMM** particlePositions, RealOpenMM* delta ) const; void getDelta( unsigned int particleI, unsigned int particleJ, std::vector<OpenMM::RealVec>& particlePositions, RealOpenMM* delta ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -464,7 +464,7 @@ private: ...@@ -464,7 +464,7 @@ private:
RealOpenMM calculateNoCutoffElectrostaticPairIxn( const MultipoleParticleData& particleI, RealOpenMM calculateNoCutoffElectrostaticPairIxn( const MultipoleParticleData& particleI,
const MultipoleParticleData& particleK, const MultipoleParticleData& particleK,
RealOpenMM* scalingFactors, RealOpenMM** forces, std::vector<Vec3>& torque ) const; RealOpenMM* scalingFactors, std::vector<OpenMM::RealVec>& forces, std::vector<Vec3>& torque ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -483,19 +483,19 @@ private: ...@@ -483,19 +483,19 @@ private:
const MultipoleParticleData& particleU, const MultipoleParticleData& particleU,
const MultipoleParticleData& particleV, const MultipoleParticleData& particleV,
MultipoleParticleData* particleW, MultipoleParticleData* particleW,
int axisType, const Vec3& torque, RealOpenMM** forces ) const; int axisType, const Vec3& torque, std::vector<OpenMM::RealVec>& forces ) const;
void mapTorqueToForceOld( const MultipoleParticleData& particleI, void mapTorqueToForceOld( const MultipoleParticleData& particleI,
const MultipoleParticleData& particleU, const MultipoleParticleData& particleU,
const MultipoleParticleData& particleV, const MultipoleParticleData& particleV,
int axisType, const Vec3& torque, RealOpenMM** forces ) const; int axisType, const Vec3& torque, std::vector<OpenMM::RealVec>& forces ) const;
RealOpenMM calculateNoCutoffElectrostatic( std::vector<MultipoleParticleData>& particleData, RealOpenMM calculateNoCutoffElectrostatic( std::vector<MultipoleParticleData>& particleData,
const std::vector<int>& axisTypes, const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomZs, const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs, const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs, const std::vector<int>& multipoleAtomYs,
RealOpenMM** forces ) const; std::vector<OpenMM::RealVec>& forces ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -515,7 +515,7 @@ private: ...@@ -515,7 +515,7 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateNoCutoffForceAndEnergy( unsigned int numParticles, RealOpenMM** particlePositions, RealOpenMM calculateNoCutoffForceAndEnergy( unsigned int numParticles, std::vector<OpenMM::RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges, const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles, const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles, const std::vector<RealOpenMM>& quadrupoles,
...@@ -526,7 +526,7 @@ private: ...@@ -526,7 +526,7 @@ private:
const std::vector<int>& multipoleAtomZs, const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs, const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs, const std::vector<int>& multipoleAtomYs,
RealOpenMM** forces ); std::vector<OpenMM::RealVec>& forces );
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceOutOfPlaneBendForce.cpp
View file @ 93900ab2
...@@ -25,6 +25,9 @@ ...@@ -25,6 +25,9 @@
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include "AmoebaReferenceOutOfPlaneBendForce.h" #include "AmoebaReferenceOutOfPlaneBendForce.h"
using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba Out-Of-Plane-Bend ixn (force and energy) Calculate Amoeba Out-Of-Plane-Bend ixn (force and energy)
...@@ -45,12 +48,12 @@ ...@@ -45,12 +48,12 @@
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateOutOfPlaneBendIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateOutOfPlaneBendIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealVec& positionAtomC, const RealVec& positionAtomD,
RealOpenMM angleK, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM** forces ) const { RealVec* forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -193,7 +196,7 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateOutOfPlaneBendIxn( const ...@@ -193,7 +196,7 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateOutOfPlaneBendIxn( const
return energy; return energy;
} }
RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy( int numOutOfPlaneBends, RealOpenMM** posData, RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy( int numOutOfPlaneBends, vector<RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -203,7 +206,7 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy( int numO ...@@ -203,7 +206,7 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy( int numO
RealOpenMM angleQuartic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM anglePentic,
RealOpenMM angleSextic, RealOpenMM angleSextic,
RealOpenMM** forceData) const { vector<RealVec>& forceData) const {
RealOpenMM energy = 0.0; RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < static_cast<unsigned int>(numOutOfPlaneBends); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(numOutOfPlaneBends); ii++) {
int particle1Index = particle1[ii]; int particle1Index = particle1[ii];
...@@ -211,7 +214,7 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy( int numO ...@@ -211,7 +214,7 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy( int numO
int particle3Index = particle3[ii]; int particle3Index = particle3[ii];
int particle4Index = particle4[ii]; int particle4Index = particle4[ii];
RealOpenMM kAngle = kQuadratic[ii]; RealOpenMM kAngle = kQuadratic[ii];
RealOpenMM* forces[4]; RealVec forces[4];
forces[0] = forceData[particle1Index]; forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index]; forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index]; forces[2] = forceData[particle3Index];
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceOutOfPlaneBendForce.h
View file @ 93900ab2
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#ifndef __AmoebaReferenceOutOfPlaneBendForce_H__ #ifndef __AmoebaReferenceOutOfPlaneBendForce_H__
#define __AmoebaReferenceOutOfPlaneBendForce_H__ #define __AmoebaReferenceOutOfPlaneBendForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/RealVec.h"
#include <vector> #include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -72,7 +72,7 @@ public: ...@@ -72,7 +72,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numOutOfPlaneBends, RealOpenMM** posData, RealOpenMM calculateForceAndEnergy( int numOutOfPlaneBends, std::vector<OpenMM::RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -82,7 +82,7 @@ public: ...@@ -82,7 +82,7 @@ public:
RealOpenMM angleQuartic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM anglePentic,
RealOpenMM angleSextic, RealOpenMM angleSextic,
RealOpenMM** forceData) const; std::vector<OpenMM::RealVec>& forceData) const;
private: private:
...@@ -105,12 +105,12 @@ private: ...@@ -105,12 +105,12 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateOutOfPlaneBendIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculateOutOfPlaneBendIxn( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const OpenMM::RealVec& positionAtomC, const OpenMM::RealVec& positionAtomD,
RealOpenMM angleK, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM** forces ) const; OpenMM::RealVec* forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferencePiTorsionForce.cpp
View file @ 93900ab2
...@@ -26,6 +26,9 @@ ...@@ -26,6 +26,9 @@
#include "AmoebaReferencePiTorsionForce.h" #include "AmoebaReferencePiTorsionForce.h"
#include <vector> #include <vector>
using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba pi-torsion ixn (force and energy) Calculate Amoeba pi-torsion ixn (force and energy)
...@@ -43,10 +46,10 @@ ...@@ -43,10 +46,10 @@
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferencePiTorsionForce::calculatePiTorsionIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferencePiTorsionForce::calculatePiTorsionIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealVec& positionAtomC, const RealVec& positionAtomD,
const RealOpenMM* positionAtomE, const RealOpenMM* positionAtomF, const RealVec& positionAtomE, const RealVec& positionAtomF,
RealOpenMM piTorsionK, RealOpenMM** forces ) const { RealOpenMM piTorsionK, RealVec* forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -183,7 +186,7 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculatePiTorsionIxn( const RealOpenM ...@@ -183,7 +186,7 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculatePiTorsionIxn( const RealOpenM
} }
RealOpenMM AmoebaReferencePiTorsionForce::calculateForceAndEnergy( int numPiTorsions, RealOpenMM** posData, RealOpenMM AmoebaReferencePiTorsionForce::calculateForceAndEnergy( int numPiTorsions, vector<RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -191,7 +194,7 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculateForceAndEnergy( int numPiTors ...@@ -191,7 +194,7 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculateForceAndEnergy( int numPiTors
const std::vector<int>& particle5, const std::vector<int>& particle5,
const std::vector<int>& particle6, const std::vector<int>& particle6,
const std::vector<RealOpenMM>& kTorsion, const std::vector<RealOpenMM>& kTorsion,
RealOpenMM** forceData ) const { vector<RealVec>& forceData ) const {
RealOpenMM energy = 0.0; RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < static_cast<unsigned int>(numPiTorsions); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(numPiTorsions); ii++) {
...@@ -202,7 +205,7 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculateForceAndEnergy( int numPiTors ...@@ -202,7 +205,7 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculateForceAndEnergy( int numPiTors
int particle5Index = particle5[ii]; int particle5Index = particle5[ii];
int particle6Index = particle6[ii]; int particle6Index = particle6[ii];
RealOpenMM* forces[6]; RealVec forces[6];
forces[0] = forceData[particle1Index]; forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index]; forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index]; forces[2] = forceData[particle3Index];
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferencePiTorsionForce.h
View file @ 93900ab2
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#ifndef __AmoebaReferencePiTorsionForce_H__ #ifndef __AmoebaReferencePiTorsionForce_H__
#define __AmoebaReferencePiTorsionForce_H__ #define __AmoebaReferencePiTorsionForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/RealVec.h"
#include <vector> #include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -72,7 +72,7 @@ public: ...@@ -72,7 +72,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numPiTorsions, RealOpenMM** posData, RealOpenMM calculateForceAndEnergy( int numPiTorsions, std::vector<OpenMM::RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -80,7 +80,7 @@ public: ...@@ -80,7 +80,7 @@ public:
const std::vector<int>& particle5, const std::vector<int>& particle5,
const std::vector<int>& particle6, const std::vector<int>& particle6,
const std::vector<RealOpenMM>& kTorsion, const std::vector<RealOpenMM>& kTorsion,
RealOpenMM** forceData ) const; std::vector<OpenMM::RealVec>& forceData ) const;
private: private:
...@@ -102,10 +102,10 @@ private: ...@@ -102,10 +102,10 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculatePiTorsionIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculatePiTorsionIxn( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const OpenMM::RealVec& positionAtomC, const OpenMM::RealVec& positionAtomD,
const RealOpenMM* positionAtomE, const RealOpenMM* positionAtomF, const OpenMM::RealVec& positionAtomE, const OpenMM::RealVec& positionAtomF,
RealOpenMM kTorsion, RealOpenMM** forces ) const; RealOpenMM kTorsion, OpenMM::RealVec* forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceStretchBendForce.cpp
View file @ 93900ab2
...@@ -26,6 +26,9 @@ ...@@ -26,6 +26,9 @@
#include "AmoebaReferenceStretchBendForce.h" #include "AmoebaReferenceStretchBendForce.h"
#include <vector> #include <vector>
using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba stretch bend angle ixn (force and energy) Calculate Amoeba stretch bend angle ixn (force and energy)
...@@ -46,11 +49,11 @@ ...@@ -46,11 +49,11 @@
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceStretchBendForce::calculateStretchBendIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceStretchBendForce::calculateStretchBendIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const RealVec& positionAtomC,
RealOpenMM lengthAB, RealOpenMM lengthCB, RealOpenMM lengthAB, RealOpenMM lengthCB,
RealOpenMM idealAngle, RealOpenMM kParameter, RealOpenMM idealAngle, RealOpenMM kParameter,
RealOpenMM** forces ) const { RealVec* forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -144,7 +147,7 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateStretchBendIxn( const RealO ...@@ -144,7 +147,7 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateStretchBendIxn( const RealO
return (kParameter*dt*dr); return (kParameter*dt*dr);
} }
RealOpenMM AmoebaReferenceStretchBendForce::calculateForceAndEnergy( int numStretchBends, RealOpenMM** posData, RealOpenMM AmoebaReferenceStretchBendForce::calculateForceAndEnergy( int numStretchBends, vector<RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -152,7 +155,7 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateForceAndEnergy( int numStre ...@@ -152,7 +155,7 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateForceAndEnergy( int numStre
const std::vector<RealOpenMM>& lengthCBParameters, const std::vector<RealOpenMM>& lengthCBParameters,
const std::vector<RealOpenMM>& angle, const std::vector<RealOpenMM>& angle,
const std::vector<RealOpenMM>& kQuadratic, const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM** forceData) const { vector<RealVec>& forceData) const {
RealOpenMM energy = 0.0; RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < static_cast<unsigned int>(numStretchBends); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(numStretchBends); ii++) {
int particle1Index = particle1[ii]; int particle1Index = particle1[ii];
...@@ -162,7 +165,7 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateForceAndEnergy( int numStre ...@@ -162,7 +165,7 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateForceAndEnergy( int numStre
RealOpenMM cbLength = lengthCBParameters[ii]; RealOpenMM cbLength = lengthCBParameters[ii];
RealOpenMM idealAngle = angle[ii]; RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii]; RealOpenMM angleK = kQuadratic[ii];
RealOpenMM* forces[3]; RealVec forces[3];
forces[0] = forceData[particle1Index]; forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index]; forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index]; forces[2] = forceData[particle3Index];
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceStretchBendForce.h
View file @ 93900ab2
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#ifndef __AmoebaReferenceStretchBendForce_H__ #ifndef __AmoebaReferenceStretchBendForce_H__
#define __AmoebaReferenceStretchBendForce_H__ #define __AmoebaReferenceStretchBendForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/RealVec.h"
#include <vector> #include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -70,7 +70,7 @@ public: ...@@ -70,7 +70,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numAngles, RealOpenMM** posData, RealOpenMM calculateForceAndEnergy( int numAngles, std::vector<OpenMM::RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -78,7 +78,7 @@ public: ...@@ -78,7 +78,7 @@ public:
const std::vector<RealOpenMM>& lengthCBParameters, const std::vector<RealOpenMM>& lengthCBParameters,
const std::vector<RealOpenMM>& angle, const std::vector<RealOpenMM>& angle,
const std::vector<RealOpenMM>& kQuadratic, const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM** forceData ) const; std::vector<OpenMM::RealVec>& forceData ) const;
private: private:
...@@ -100,11 +100,11 @@ private: ...@@ -100,11 +100,11 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateStretchBendIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculateStretchBendIxn( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const OpenMM::RealVec& positionAtomC,
RealOpenMM lengthAB, RealOpenMM lengthCB, RealOpenMM lengthAB, RealOpenMM lengthCB,
RealOpenMM idealAngle, RealOpenMM kParameter, RealOpenMM idealAngle, RealOpenMM kParameter,
RealOpenMM** forces ) const; OpenMM::RealVec* forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionForce.cpp
View file @ 93900ab2
...@@ -24,6 +24,9 @@ ...@@ -24,6 +24,9 @@
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include "AmoebaReferenceTorsionForce.h" #include "AmoebaReferenceTorsionForce.h"
using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba torsion ixn (force and energy) Calculate Amoeba torsion ixn (force and energy)
...@@ -41,12 +44,12 @@ ...@@ -41,12 +44,12 @@
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceTorsionForce::calculateTorsionIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceTorsionForce::calculateTorsionIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealVec& positionAtomC, const RealVec& 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 ) const { RealVec* forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -209,7 +212,7 @@ RealOpenMM AmoebaReferenceTorsionForce::calculateTorsionIxn( const RealOpenMM* p ...@@ -209,7 +212,7 @@ RealOpenMM AmoebaReferenceTorsionForce::calculateTorsionIxn( const RealOpenMM* p
return energy; return energy;
} }
RealOpenMM AmoebaReferenceTorsionForce::calculateForceAndEnergy( int numTorsions, RealOpenMM** posData, RealOpenMM AmoebaReferenceTorsionForce::calculateForceAndEnergy( int numTorsions, vector<RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -217,14 +220,14 @@ RealOpenMM AmoebaReferenceTorsionForce::calculateForceAndEnergy( int numTorsions ...@@ -217,14 +220,14 @@ RealOpenMM AmoebaReferenceTorsionForce::calculateForceAndEnergy( int numTorsions
const std::vector< std::vector<RealOpenMM> >& torsionParameters1, const std::vector< std::vector<RealOpenMM> >& torsionParameters1,
const std::vector< std::vector<RealOpenMM> >& torsionParameters2, const std::vector< std::vector<RealOpenMM> >& torsionParameters2,
const std::vector< std::vector<RealOpenMM> >& torsionParameters3, const std::vector< std::vector<RealOpenMM> >& torsionParameters3,
RealOpenMM** forceData ) const { vector<RealVec>& forceData ) const {
RealOpenMM energy = 0.0; RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < static_cast<unsigned int>(numTorsions); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(numTorsions); ii++) {
int particle1Index = particle1[ii]; int particle1Index = particle1[ii];
int particle2Index = particle2[ii]; int particle2Index = particle2[ii];
int particle3Index = particle3[ii]; int particle3Index = particle3[ii];
int particle4Index = particle4[ii]; int particle4Index = particle4[ii];
RealOpenMM* forces[4]; RealVec forces[4];
forces[0] = forceData[particle1Index]; forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index]; forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index]; forces[2] = forceData[particle3Index];
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionForce.h
View file @ 93900ab2
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#ifndef __AmoebaReferenceTorsionForce_H__ #ifndef __AmoebaReferenceTorsionForce_H__
#define __AmoebaReferenceTorsionForce_H__ #define __AmoebaReferenceTorsionForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/RealVec.h"
#include <vector> #include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -70,7 +70,7 @@ public: ...@@ -70,7 +70,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numTorsions, RealOpenMM** posData, RealOpenMM calculateForceAndEnergy( int numTorsions, std::vector<OpenMM::RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -78,7 +78,7 @@ public: ...@@ -78,7 +78,7 @@ public:
const std::vector< std::vector<RealOpenMM> >& torsionParameters1, const std::vector< std::vector<RealOpenMM> >& torsionParameters1,
const std::vector< std::vector<RealOpenMM> >& torsionParameters2, const std::vector< std::vector<RealOpenMM> >& torsionParameters2,
const std::vector< std::vector<RealOpenMM> >& torsionParameters3, const std::vector< std::vector<RealOpenMM> >& torsionParameters3,
RealOpenMM** forceData ) const; std::vector<OpenMM::RealVec>& forceData ) const;
private: private:
...@@ -99,12 +99,12 @@ private: ...@@ -99,12 +99,12 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM calculateTorsionIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM calculateTorsionIxn( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const OpenMM::RealVec& positionAtomC, const OpenMM::RealVec& 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 ) const; OpenMM::RealVec* forces ) const;
}; };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.cpp
View file @ 93900ab2
...@@ -25,6 +25,9 @@ ...@@ -25,6 +25,9 @@
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include "AmoebaReferenceTorsionTorsionForce.h" #include "AmoebaReferenceTorsionTorsionForce.h"
using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Load grid values from rectenclosing angles Load grid values from rectenclosing angles
...@@ -273,8 +276,8 @@ void AmoebaReferenceTorsionTorsionForce::getBicubicValues( ...@@ -273,8 +276,8 @@ void AmoebaReferenceTorsionTorsionForce::getBicubicValues(
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int AmoebaReferenceTorsionTorsionForce::checkTorsionSign( int AmoebaReferenceTorsionTorsionForce::checkTorsionSign(
const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, const RealVec& positionAtomA, const RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD ) const { const RealVec& positionAtomC, const RealVec& positionAtomD ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -323,11 +326,11 @@ int AmoebaReferenceTorsionTorsionForce::checkTorsionSign( ...@@ -323,11 +326,11 @@ int AmoebaReferenceTorsionTorsionForce::checkTorsionSign(
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn( const RealOpenMM* positionAtomA, const RealOpenMM* positionAtomB, RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
const RealOpenMM* positionAtomC, const RealOpenMM* positionAtomD, const RealVec& positionAtomC, const RealVec& positionAtomD,
const RealOpenMM* positionAtomE, const RealOpenMM* positionChiralCheckAtom, const RealVec& positionAtomE, const RealVec* positionChiralCheckAtom,
const std::vector< std::vector< std::vector<RealOpenMM> > >& grid, const std::vector< std::vector< std::vector<RealOpenMM> > >& grid,
RealOpenMM** forces ) const { RealVec* forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -421,7 +424,7 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn( const ...@@ -421,7 +424,7 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn( const
// is 'negative' // is 'negative'
if( positionChiralCheckAtom ){ if( positionChiralCheckAtom ){
sign = checkTorsionSign( positionChiralCheckAtom, positionAtomB, positionAtomC, positionAtomD ); sign = checkTorsionSign( *positionChiralCheckAtom, positionAtomB, positionAtomC, positionAtomD );
if( sign < zero ){ if( sign < zero ){
angle1 = -angle1; angle1 = -angle1;
angle2 = -angle2; angle2 = -angle2;
...@@ -549,7 +552,7 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn( const ...@@ -549,7 +552,7 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn( const
return gridEnergy; return gridEnergy;
} }
RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( int numTorsionTorsions, RealOpenMM** posData, RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( int numTorsionTorsions, vector<RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
...@@ -558,7 +561,7 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( int numT ...@@ -558,7 +561,7 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( int numT
const std::vector<int>& chiralCheckAtom, const std::vector<int>& chiralCheckAtom,
const std::vector<int>& gridIndices, const std::vector<int>& gridIndices,
const std::vector< std::vector< std::vector< std::vector<RealOpenMM> > > >& torsionTorsionGrids, const std::vector< std::vector< std::vector< std::vector<RealOpenMM> > > >& torsionTorsionGrids,
RealOpenMM** forceData ) const { vector<RealVec>& forceData ) const {
RealOpenMM energy = 0.0; RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < static_cast<unsigned int>(numTorsionTorsions); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(numTorsionTorsions); ii++) {
...@@ -572,16 +575,16 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( int numT ...@@ -572,16 +575,16 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( int numT
int gridIndex = gridIndices[ii]; int gridIndex = gridIndices[ii];
RealOpenMM* forces[5]; RealVec forces[5];
forces[0] = forceData[particle1Index]; forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index]; forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index]; forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index]; forces[3] = forceData[particle4Index];
forces[4] = forceData[particle5Index]; forces[4] = forceData[particle5Index];
RealOpenMM* chiralCheckAtom; RealVec* chiralCheckAtom;
if( chiralCheckAtomIndex >= 0 ){ if( chiralCheckAtomIndex >= 0 ){
chiralCheckAtom = posData[chiralCheckAtomIndex]; chiralCheckAtom = &posData[chiralCheckAtomIndex];
} else { } else {
chiralCheckAtom = NULL; chiralCheckAtom = NULL;
} }
......
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