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Commit 0843c5f3 authored by Peter Eastman's avatar Peter Eastman
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First stage of a refactoring to clean up the reference platform

parent bacc1eff
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Showing with 159 additions and 198 deletions
platforms/reference/src/ReferenceKernels.cpp
View file @ 0843c5f3
...@@ -90,26 +90,6 @@ static RealOpenMM** allocateRealArray(int length, int width) { ...@@ -90,26 +90,6 @@ static RealOpenMM** allocateRealArray(int length, int width) {
return array; return array;
} }
static int** copyToArray(const vector<vector<int> > vec) {
if (vec.size() == 0)
return new int*[1];
int** array = allocateIntArray(vec.size(), vec[0].size());
for (size_t i = 0; i < vec.size(); ++i)
for (size_t j = 0; j < vec[i].size(); ++j)
array[i][j] = vec[i][j];
return array;
}
static RealOpenMM** copyToArray(const vector<vector<double> > vec) {
if (vec.size() == 0)
return new RealOpenMM*[1];
RealOpenMM** array = allocateRealArray(vec.size(), vec[0].size());
for (size_t i = 0; i < vec.size(); ++i)
for (size_t j = 0; j < vec[i].size(); ++j)
array[i][j] = static_cast<RealOpenMM>(vec[i][j]);
return array;
}
static void disposeIntArray(int** array, int size) { static void disposeIntArray(int** array, int size) {
if (array) { if (array) {
for (int i = 0; i < size; ++i) for (int i = 0; i < size; ++i)
...@@ -126,19 +106,19 @@ static void disposeRealArray(RealOpenMM** array, int size) { ...@@ -126,19 +106,19 @@ static void disposeRealArray(RealOpenMM** array, int size) {
} }
} }
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 RealOpenMM* extractBoxSize(ContextImpl& context) {
...@@ -166,7 +146,7 @@ void ReferenceCalcForcesAndEnergyKernel::initialize(const System& system) { ...@@ -166,7 +146,7 @@ void ReferenceCalcForcesAndEnergyKernel::initialize(const System& system) {
void ReferenceCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy) { void ReferenceCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (includeForces) { if (includeForces) {
int numParticles = context.getSystem().getNumParticles(); int numParticles = context.getSystem().getNumParticles();
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
for (int i = 0; i < numParticles; ++i) { for (int i = 0; i < numParticles; ++i) {
forceData[i][0] = (RealOpenMM) 0.0; forceData[i][0] = (RealOpenMM) 0.0;
forceData[i][1] = (RealOpenMM) 0.0; forceData[i][1] = (RealOpenMM) 0.0;
...@@ -192,7 +172,7 @@ void ReferenceUpdateStateDataKernel::setTime(ContextImpl& context, double time) ...@@ -192,7 +172,7 @@ void ReferenceUpdateStateDataKernel::setTime(ContextImpl& context, double time)
void ReferenceUpdateStateDataKernel::getPositions(ContextImpl& context, std::vector<Vec3>& positions) { void ReferenceUpdateStateDataKernel::getPositions(ContextImpl& context, std::vector<Vec3>& positions) {
int numParticles = context.getSystem().getNumParticles(); int numParticles = context.getSystem().getNumParticles();
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
positions.resize(numParticles); positions.resize(numParticles);
for (int i = 0; i < numParticles; ++i) for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3(posData[i][0], posData[i][1], posData[i][2]); positions[i] = Vec3(posData[i][0], posData[i][1], posData[i][2]);
...@@ -200,7 +180,7 @@ void ReferenceUpdateStateDataKernel::getPositions(ContextImpl& context, std::vec ...@@ -200,7 +180,7 @@ void ReferenceUpdateStateDataKernel::getPositions(ContextImpl& context, std::vec
void ReferenceUpdateStateDataKernel::setPositions(ContextImpl& context, const std::vector<Vec3>& positions) { void ReferenceUpdateStateDataKernel::setPositions(ContextImpl& context, const std::vector<Vec3>& positions) {
int numParticles = context.getSystem().getNumParticles(); int numParticles = context.getSystem().getNumParticles();
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
for (int i = 0; i < numParticles; ++i) { for (int i = 0; i < numParticles; ++i) {
posData[i][0] = (RealOpenMM) positions[i][0]; posData[i][0] = (RealOpenMM) positions[i][0];
posData[i][1] = (RealOpenMM) positions[i][1]; posData[i][1] = (RealOpenMM) positions[i][1];
...@@ -210,7 +190,7 @@ void ReferenceUpdateStateDataKernel::setPositions(ContextImpl& context, const st ...@@ -210,7 +190,7 @@ void ReferenceUpdateStateDataKernel::setPositions(ContextImpl& context, const st
void ReferenceUpdateStateDataKernel::getVelocities(ContextImpl& context, std::vector<Vec3>& velocities) { void ReferenceUpdateStateDataKernel::getVelocities(ContextImpl& context, std::vector<Vec3>& velocities) {
int numParticles = context.getSystem().getNumParticles(); int numParticles = context.getSystem().getNumParticles();
RealOpenMM** velData = extractVelocities(context); vector<RealVec>& velData = extractVelocities(context);
velocities.resize(numParticles); velocities.resize(numParticles);
for (int i = 0; i < numParticles; ++i) for (int i = 0; i < numParticles; ++i)
velocities[i] = Vec3(velData[i][0], velData[i][1], velData[i][2]); velocities[i] = Vec3(velData[i][0], velData[i][1], velData[i][2]);
...@@ -218,7 +198,7 @@ void ReferenceUpdateStateDataKernel::getVelocities(ContextImpl& context, std::ve ...@@ -218,7 +198,7 @@ void ReferenceUpdateStateDataKernel::getVelocities(ContextImpl& context, std::ve
void ReferenceUpdateStateDataKernel::setVelocities(ContextImpl& context, const std::vector<Vec3>& velocities) { void ReferenceUpdateStateDataKernel::setVelocities(ContextImpl& context, const std::vector<Vec3>& velocities) {
int numParticles = context.getSystem().getNumParticles(); int numParticles = context.getSystem().getNumParticles();
RealOpenMM** velData = extractVelocities(context); vector<RealVec>& velData = extractVelocities(context);
for (int i = 0; i < numParticles; ++i) { for (int i = 0; i < numParticles; ++i) {
velData[i][0] = (RealOpenMM) velocities[i][0]; velData[i][0] = (RealOpenMM) velocities[i][0];
velData[i][1] = (RealOpenMM) velocities[i][1]; velData[i][1] = (RealOpenMM) velocities[i][1];
...@@ -228,7 +208,7 @@ void ReferenceUpdateStateDataKernel::setVelocities(ContextImpl& context, const s ...@@ -228,7 +208,7 @@ void ReferenceUpdateStateDataKernel::setVelocities(ContextImpl& context, const s
void ReferenceUpdateStateDataKernel::getForces(ContextImpl& context, std::vector<Vec3>& forces) { void ReferenceUpdateStateDataKernel::getForces(ContextImpl& context, std::vector<Vec3>& forces) {
int numParticles = context.getSystem().getNumParticles(); int numParticles = context.getSystem().getNumParticles();
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
forces.resize(numParticles); forces.resize(numParticles);
for (int i = 0; i < numParticles; ++i) for (int i = 0; i < numParticles; ++i)
forces[i] = Vec3(forceData[i][0], forceData[i][1], forceData[i][2]); forces[i] = Vec3(forceData[i][0], forceData[i][1], forceData[i][2]);
...@@ -250,8 +230,8 @@ void ReferenceUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, ...@@ -250,8 +230,8 @@ void ReferenceUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context,
void ReferenceApplyConstraintsKernel::initialize(const System& system) { void ReferenceApplyConstraintsKernel::initialize(const System& system) {
int numParticles = system.getNumParticles(); int numParticles = system.getNumParticles();
masses = new RealOpenMM[numParticles]; masses.resize(numParticles);
inverseMasses = new RealOpenMM[numParticles]; inverseMasses.resize(numParticles);
for (int i = 0; i < numParticles; ++i) { for (int i = 0; i < numParticles; ++i) {
masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i)); masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
inverseMasses[i] = 1.0/masses[i]; inverseMasses[i] = 1.0/masses[i];
...@@ -272,10 +252,6 @@ void ReferenceApplyConstraintsKernel::initialize(const System& system) { ...@@ -272,10 +252,6 @@ void ReferenceApplyConstraintsKernel::initialize(const System& system) {
ReferenceApplyConstraintsKernel::~ReferenceApplyConstraintsKernel() { ReferenceApplyConstraintsKernel::~ReferenceApplyConstraintsKernel() {
if (constraints) if (constraints)
delete constraints; delete constraints;
if (masses)
delete[] masses;
if (inverseMasses)
delete[] inverseMasses;
if (constraintIndices) if (constraintIndices)
disposeIntArray(constraintIndices, numConstraints); disposeIntArray(constraintIndices, numConstraints);
if (constraintDistances) if (constraintDistances)
...@@ -288,7 +264,7 @@ void ReferenceApplyConstraintsKernel::apply(ContextImpl& context, double tol) { ...@@ -288,7 +264,7 @@ void ReferenceApplyConstraintsKernel::apply(ContextImpl& context, double tol) {
findAnglesForCCMA(context.getSystem(), angles); findAnglesForCCMA(context.getSystem(), angles);
constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, tol); constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, tol);
} }
RealOpenMM** positions = extractPositions(context); vector<RealVec>& positions = extractPositions(context);
constraints->setTolerance(tol); constraints->setTolerance(tol);
constraints->apply(data.numParticles, positions, positions, inverseMasses); constraints->apply(data.numParticles, positions, positions, inverseMasses);
} }
...@@ -314,8 +290,8 @@ void ReferenceCalcHarmonicBondForceKernel::initialize(const System& system, cons ...@@ -314,8 +290,8 @@ void ReferenceCalcHarmonicBondForceKernel::initialize(const System& system, cons
} }
double ReferenceCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcHarmonicBondForceKernel::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);
RealOpenMM energy = 0; RealOpenMM energy = 0;
ReferenceBondForce refBondForce; ReferenceBondForce refBondForce;
ReferenceHarmonicBondIxn harmonicBond; ReferenceHarmonicBondIxn harmonicBond;
...@@ -358,8 +334,8 @@ void ReferenceCalcCustomBondForceKernel::initialize(const System& system, const ...@@ -358,8 +334,8 @@ void ReferenceCalcCustomBondForceKernel::initialize(const System& system, const
} }
double ReferenceCalcCustomBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcCustomBondForceKernel::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);
RealOpenMM energy = 0; RealOpenMM energy = 0;
map<string, double> globalParameters; map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++) for (int i = 0; i < (int) globalParameterNames.size(); i++)
...@@ -392,8 +368,8 @@ void ReferenceCalcHarmonicAngleForceKernel::initialize(const System& system, con ...@@ -392,8 +368,8 @@ void ReferenceCalcHarmonicAngleForceKernel::initialize(const System& system, con
} }
double ReferenceCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcHarmonicAngleForceKernel::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);
RealOpenMM energy = 0; RealOpenMM energy = 0;
ReferenceBondForce refBondForce; ReferenceBondForce refBondForce;
ReferenceAngleBondIxn angleBond; ReferenceAngleBondIxn angleBond;
...@@ -437,8 +413,8 @@ void ReferenceCalcCustomAngleForceKernel::initialize(const System& system, const ...@@ -437,8 +413,8 @@ void ReferenceCalcCustomAngleForceKernel::initialize(const System& system, const
} }
double ReferenceCalcCustomAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcCustomAngleForceKernel::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);
RealOpenMM energy = 0; RealOpenMM energy = 0;
map<string, double> globalParameters; map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++) for (int i = 0; i < (int) globalParameterNames.size(); i++)
...@@ -473,8 +449,8 @@ void ReferenceCalcPeriodicTorsionForceKernel::initialize(const System& system, c ...@@ -473,8 +449,8 @@ void ReferenceCalcPeriodicTorsionForceKernel::initialize(const System& system, c
} }
double ReferenceCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcPeriodicTorsionForceKernel::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);
RealOpenMM energy = 0; RealOpenMM energy = 0;
ReferenceBondForce refBondForce; ReferenceBondForce refBondForce;
ReferenceProperDihedralBond periodicTorsionBond; ReferenceProperDihedralBond periodicTorsionBond;
...@@ -509,8 +485,8 @@ void ReferenceCalcRBTorsionForceKernel::initialize(const System& system, const R ...@@ -509,8 +485,8 @@ void ReferenceCalcRBTorsionForceKernel::initialize(const System& system, const R
} }
double ReferenceCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcRBTorsionForceKernel::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);
RealOpenMM energy = 0; RealOpenMM energy = 0;
ReferenceBondForce refBondForce; ReferenceBondForce refBondForce;
ReferenceRbDihedralBond rbTorsionBond; ReferenceRbDihedralBond rbTorsionBond;
...@@ -545,8 +521,8 @@ void ReferenceCalcCMAPTorsionForceKernel::initialize(const System& system, const ...@@ -545,8 +521,8 @@ void ReferenceCalcCMAPTorsionForceKernel::initialize(const System& system, const
} }
double ReferenceCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcCMAPTorsionForceKernel::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);
RealOpenMM totalEnergy = 0; RealOpenMM totalEnergy = 0;
ReferenceCMAPTorsionIxn torsion(coeff, torsionMaps, torsionIndices); ReferenceCMAPTorsionIxn torsion(coeff, torsionMaps, torsionIndices);
torsion.calculateIxn(posData, forceData, &totalEnergy); torsion.calculateIxn(posData, forceData, &totalEnergy);
...@@ -590,8 +566,8 @@ void ReferenceCalcCustomTorsionForceKernel::initialize(const System& system, con ...@@ -590,8 +566,8 @@ void ReferenceCalcCustomTorsionForceKernel::initialize(const System& system, con
} }
double ReferenceCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcCustomTorsionForceKernel::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);
RealOpenMM energy = 0; RealOpenMM energy = 0;
map<string, double> globalParameters; map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++) for (int i = 0; i < (int) globalParameterNames.size(); i++)
...@@ -684,8 +660,8 @@ void ReferenceCalcNonbondedForceKernel::initialize(const System& system, const N ...@@ -684,8 +660,8 @@ void ReferenceCalcNonbondedForceKernel::initialize(const System& system, const N
} }
double ReferenceCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcNonbondedForceKernel::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);
RealOpenMM energy = 0; RealOpenMM energy = 0;
ReferenceLJCoulombIxn clj; ReferenceLJCoulombIxn clj;
bool periodic = (nonbondedMethod == CutoffPeriodic); bool periodic = (nonbondedMethod == CutoffPeriodic);
...@@ -817,8 +793,8 @@ void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, c ...@@ -817,8 +793,8 @@ void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, c
} }
double ReferenceCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcCustomNonbondedForceKernel::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);
RealOpenMM energy = 0; RealOpenMM energy = 0;
ReferenceCustomNonbondedIxn ixn(energyExpression, forceExpression, parameterNames); ReferenceCustomNonbondedIxn ixn(energyExpression, forceExpression, parameterNames);
bool periodic = (nonbondedMethod == CutoffPeriodic); bool periodic = (nonbondedMethod == CutoffPeriodic);
...@@ -867,8 +843,8 @@ void ReferenceCalcGBSAOBCForceKernel::initialize(const System& system, const GBS ...@@ -867,8 +843,8 @@ void ReferenceCalcGBSAOBCForceKernel::initialize(const System& system, const GBS
} }
double ReferenceCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcGBSAOBCForceKernel::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);
if (isPeriodic) if (isPeriodic)
obc->getObcParameters()->setPeriodic(extractBoxSize(context)); obc->getObcParameters()->setPeriodic(extractBoxSize(context));
obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1); obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
...@@ -908,13 +884,13 @@ void ReferenceCalcGBVIForceKernel::initialize(const System& system, const GBVIFo ...@@ -908,13 +884,13 @@ void ReferenceCalcGBVIForceKernel::initialize(const System& system, const GBVIFo
} }
double ReferenceCalcGBVIForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcGBVIForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealOpenMM* bornRadii = new RealOpenMM[context.getSystem().getNumParticles()]; RealOpenMM* bornRadii = new RealOpenMM[context.getSystem().getNumParticles()];
if (isPeriodic) if (isPeriodic)
gbvi->getGBVIParameters()->setPeriodic(extractBoxSize(context)); gbvi->getGBVIParameters()->setPeriodic(extractBoxSize(context));
gbvi->computeBornRadii(posData, bornRadii, NULL ); gbvi->computeBornRadii(posData, bornRadii, NULL );
if (includeForces) { if (includeForces) {
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
gbvi->computeBornForces(bornRadii, posData, &charges[0], forceData); gbvi->computeBornForces(bornRadii, posData, &charges[0], forceData);
} }
RealOpenMM energy = 0.0; RealOpenMM energy = 0.0;
...@@ -1044,8 +1020,8 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu ...@@ -1044,8 +1020,8 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
} }
double ReferenceCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcCustomGBForceKernel::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);
RealOpenMM energy = 0; RealOpenMM energy = 0;
ReferenceCustomGBIxn ixn(valueExpressions, valueDerivExpressions, valueGradientExpressions, valueNames, valueTypes, energyExpressions, ReferenceCustomGBIxn ixn(valueExpressions, valueDerivExpressions, valueGradientExpressions, valueNames, valueTypes, energyExpressions,
energyDerivExpressions, energyGradientExpressions, energyTypes, particleParameterNames); energyDerivExpressions, energyGradientExpressions, energyTypes, particleParameterNames);
...@@ -1096,8 +1072,8 @@ void ReferenceCalcCustomExternalForceKernel::initialize(const System& system, co ...@@ -1096,8 +1072,8 @@ void ReferenceCalcCustomExternalForceKernel::initialize(const System& system, co
} }
double ReferenceCalcCustomExternalForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcCustomExternalForceKernel::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);
RealOpenMM energy = 0; RealOpenMM energy = 0;
map<string, double> globalParameters; map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++) for (int i = 0; i < (int) globalParameterNames.size(); i++)
...@@ -1206,8 +1182,8 @@ void ReferenceCalcCustomHbondForceKernel::initialize(const System& system, const ...@@ -1206,8 +1182,8 @@ void ReferenceCalcCustomHbondForceKernel::initialize(const System& system, const
} }
double ReferenceCalcCustomHbondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double ReferenceCalcCustomHbondForceKernel::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);
if (isPeriodic) if (isPeriodic)
ixn->setPeriodic(extractBoxSize(context)); ixn->setPeriodic(extractBoxSize(context));
RealOpenMM energy = 0; RealOpenMM energy = 0;
...@@ -1223,8 +1199,6 @@ ReferenceIntegrateVerletStepKernel::~ReferenceIntegrateVerletStepKernel() { ...@@ -1223,8 +1199,6 @@ ReferenceIntegrateVerletStepKernel::~ReferenceIntegrateVerletStepKernel() {
delete dynamics; delete dynamics;
if (constraints) if (constraints)
delete constraints; delete constraints;
if (masses)
delete[] masses;
if (constraintIndices) if (constraintIndices)
disposeIntArray(constraintIndices, numConstraints); disposeIntArray(constraintIndices, numConstraints);
if (constraintDistances) if (constraintDistances)
...@@ -1233,7 +1207,7 @@ ReferenceIntegrateVerletStepKernel::~ReferenceIntegrateVerletStepKernel() { ...@@ -1233,7 +1207,7 @@ ReferenceIntegrateVerletStepKernel::~ReferenceIntegrateVerletStepKernel() {
void ReferenceIntegrateVerletStepKernel::initialize(const System& system, const VerletIntegrator& integrator) { void ReferenceIntegrateVerletStepKernel::initialize(const System& system, const VerletIntegrator& integrator) {
int numParticles = system.getNumParticles(); int numParticles = system.getNumParticles();
masses = new RealOpenMM[numParticles]; masses.resize(numParticles);
for (int i = 0; i < numParticles; ++i) for (int i = 0; i < numParticles; ++i)
masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i)); masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
numConstraints = system.getNumConstraints(); numConstraints = system.getNumConstraints();
...@@ -1251,9 +1225,9 @@ void ReferenceIntegrateVerletStepKernel::initialize(const System& system, const ...@@ -1251,9 +1225,9 @@ void ReferenceIntegrateVerletStepKernel::initialize(const System& system, const
void ReferenceIntegrateVerletStepKernel::execute(ContextImpl& context, const VerletIntegrator& integrator) { void ReferenceIntegrateVerletStepKernel::execute(ContextImpl& context, const VerletIntegrator& integrator) {
double stepSize = integrator.getStepSize(); double stepSize = integrator.getStepSize();
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** velData = extractVelocities(context); vector<RealVec>& velData = extractVelocities(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
if (dynamics == 0 || stepSize != prevStepSize) { if (dynamics == 0 || stepSize != prevStepSize) {
// Recreate the computation objects with the new parameters. // Recreate the computation objects with the new parameters.
...@@ -1278,8 +1252,6 @@ ReferenceIntegrateLangevinStepKernel::~ReferenceIntegrateLangevinStepKernel() { ...@@ -1278,8 +1252,6 @@ ReferenceIntegrateLangevinStepKernel::~ReferenceIntegrateLangevinStepKernel() {
delete dynamics; delete dynamics;
if (constraints) if (constraints)
delete constraints; delete constraints;
if (masses)
delete[] masses;
if (constraintIndices) if (constraintIndices)
disposeIntArray(constraintIndices, numConstraints); disposeIntArray(constraintIndices, numConstraints);
if (constraintDistances) if (constraintDistances)
...@@ -1288,7 +1260,7 @@ ReferenceIntegrateLangevinStepKernel::~ReferenceIntegrateLangevinStepKernel() { ...@@ -1288,7 +1260,7 @@ ReferenceIntegrateLangevinStepKernel::~ReferenceIntegrateLangevinStepKernel() {
void ReferenceIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) { void ReferenceIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) {
int numParticles = system.getNumParticles(); int numParticles = system.getNumParticles();
masses = new RealOpenMM[numParticles]; masses.resize(numParticles);
for (int i = 0; i < numParticles; ++i) for (int i = 0; i < numParticles; ++i)
masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i)); masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
numConstraints = system.getNumConstraints(); numConstraints = system.getNumConstraints();
...@@ -1309,9 +1281,9 @@ void ReferenceIntegrateLangevinStepKernel::execute(ContextImpl& context, const L ...@@ -1309,9 +1281,9 @@ void ReferenceIntegrateLangevinStepKernel::execute(ContextImpl& context, const L
double temperature = integrator.getTemperature(); double temperature = integrator.getTemperature();
double friction = integrator.getFriction(); double friction = integrator.getFriction();
double stepSize = integrator.getStepSize(); double stepSize = integrator.getStepSize();
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** velData = extractVelocities(context); vector<RealVec>& velData = extractVelocities(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) { if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
// Recreate the computation objects with the new parameters. // Recreate the computation objects with the new parameters.
...@@ -1343,8 +1315,6 @@ ReferenceIntegrateBrownianStepKernel::~ReferenceIntegrateBrownianStepKernel() { ...@@ -1343,8 +1315,6 @@ ReferenceIntegrateBrownianStepKernel::~ReferenceIntegrateBrownianStepKernel() {
delete dynamics; delete dynamics;
if (constraints) if (constraints)
delete constraints; delete constraints;
if (masses)
delete[] masses;
if (constraintIndices) if (constraintIndices)
disposeIntArray(constraintIndices, numConstraints); disposeIntArray(constraintIndices, numConstraints);
if (constraintDistances) if (constraintDistances)
...@@ -1353,7 +1323,7 @@ ReferenceIntegrateBrownianStepKernel::~ReferenceIntegrateBrownianStepKernel() { ...@@ -1353,7 +1323,7 @@ ReferenceIntegrateBrownianStepKernel::~ReferenceIntegrateBrownianStepKernel() {
void ReferenceIntegrateBrownianStepKernel::initialize(const System& system, const BrownianIntegrator& integrator) { void ReferenceIntegrateBrownianStepKernel::initialize(const System& system, const BrownianIntegrator& integrator) {
int numParticles = system.getNumParticles(); int numParticles = system.getNumParticles();
masses = new RealOpenMM[numParticles]; masses.resize(numParticles);
for (int i = 0; i < numParticles; ++i) for (int i = 0; i < numParticles; ++i)
masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i)); masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
numConstraints = system.getNumConstraints(); numConstraints = system.getNumConstraints();
...@@ -1374,9 +1344,9 @@ void ReferenceIntegrateBrownianStepKernel::execute(ContextImpl& context, const B ...@@ -1374,9 +1344,9 @@ void ReferenceIntegrateBrownianStepKernel::execute(ContextImpl& context, const B
double temperature = integrator.getTemperature(); double temperature = integrator.getTemperature();
double friction = integrator.getFriction(); double friction = integrator.getFriction();
double stepSize = integrator.getStepSize(); double stepSize = integrator.getStepSize();
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** velData = extractVelocities(context); vector<RealVec>& velData = extractVelocities(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) { if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
// Recreate the computation objects with the new parameters. // Recreate the computation objects with the new parameters.
...@@ -1407,8 +1377,6 @@ ReferenceIntegrateVariableLangevinStepKernel::~ReferenceIntegrateVariableLangevi ...@@ -1407,8 +1377,6 @@ ReferenceIntegrateVariableLangevinStepKernel::~ReferenceIntegrateVariableLangevi
delete dynamics; delete dynamics;
if (constraints) if (constraints)
delete constraints; delete constraints;
if (masses)
delete[] masses;
if (constraintIndices) if (constraintIndices)
disposeIntArray(constraintIndices, numConstraints); disposeIntArray(constraintIndices, numConstraints);
if (constraintDistances) if (constraintDistances)
...@@ -1417,7 +1385,7 @@ ReferenceIntegrateVariableLangevinStepKernel::~ReferenceIntegrateVariableLangevi ...@@ -1417,7 +1385,7 @@ ReferenceIntegrateVariableLangevinStepKernel::~ReferenceIntegrateVariableLangevi
void ReferenceIntegrateVariableLangevinStepKernel::initialize(const System& system, const VariableLangevinIntegrator& integrator) { void ReferenceIntegrateVariableLangevinStepKernel::initialize(const System& system, const VariableLangevinIntegrator& integrator) {
int numParticles = system.getNumParticles(); int numParticles = system.getNumParticles();
masses = new RealOpenMM[numParticles]; masses.resize(numParticles);
for (int i = 0; i < numParticles; ++i) for (int i = 0; i < numParticles; ++i)
masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i)); masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
numConstraints = system.getNumConstraints(); numConstraints = system.getNumConstraints();
...@@ -1438,9 +1406,9 @@ void ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, ...@@ -1438,9 +1406,9 @@ void ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& context,
double temperature = integrator.getTemperature(); double temperature = integrator.getTemperature();
double friction = integrator.getFriction(); double friction = integrator.getFriction();
double errorTol = integrator.getErrorTolerance(); double errorTol = integrator.getErrorTolerance();
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** velData = extractVelocities(context); vector<RealVec>& velData = extractVelocities(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || errorTol != prevErrorTol) { if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || errorTol != prevErrorTol) {
// Recreate the computation objects with the new parameters. // Recreate the computation objects with the new parameters.
...@@ -1471,8 +1439,6 @@ ReferenceIntegrateVariableVerletStepKernel::~ReferenceIntegrateVariableVerletSte ...@@ -1471,8 +1439,6 @@ ReferenceIntegrateVariableVerletStepKernel::~ReferenceIntegrateVariableVerletSte
delete dynamics; delete dynamics;
if (constraints) if (constraints)
delete constraints; delete constraints;
if (masses)
delete[] masses;
if (constraintIndices) if (constraintIndices)
disposeIntArray(constraintIndices, numConstraints); disposeIntArray(constraintIndices, numConstraints);
if (constraintDistances) if (constraintDistances)
...@@ -1481,7 +1447,7 @@ ReferenceIntegrateVariableVerletStepKernel::~ReferenceIntegrateVariableVerletSte ...@@ -1481,7 +1447,7 @@ ReferenceIntegrateVariableVerletStepKernel::~ReferenceIntegrateVariableVerletSte
void ReferenceIntegrateVariableVerletStepKernel::initialize(const System& system, const VariableVerletIntegrator& integrator) { void ReferenceIntegrateVariableVerletStepKernel::initialize(const System& system, const VariableVerletIntegrator& integrator) {
int numParticles = system.getNumParticles(); int numParticles = system.getNumParticles();
masses = new RealOpenMM[numParticles]; masses.resize(numParticles);
for (int i = 0; i < numParticles; ++i) for (int i = 0; i < numParticles; ++i)
masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i)); masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
numConstraints = system.getNumConstraints(); numConstraints = system.getNumConstraints();
...@@ -1499,9 +1465,9 @@ void ReferenceIntegrateVariableVerletStepKernel::initialize(const System& system ...@@ -1499,9 +1465,9 @@ void ReferenceIntegrateVariableVerletStepKernel::initialize(const System& system
void ReferenceIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) { void ReferenceIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
double errorTol = integrator.getErrorTolerance(); double errorTol = integrator.getErrorTolerance();
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealOpenMM** velData = extractVelocities(context); vector<RealVec>& velData = extractVelocities(context);
RealOpenMM** forceData = extractForces(context); vector<RealVec>& forceData = extractForces(context);
if (dynamics == 0 || errorTol != prevErrorTol) { if (dynamics == 0 || errorTol != prevErrorTol) {
// Recreate the computation objects with the new parameters. // Recreate the computation objects with the new parameters.
...@@ -1527,13 +1493,11 @@ void ReferenceIntegrateVariableVerletStepKernel::execute(ContextImpl& context, c ...@@ -1527,13 +1493,11 @@ void ReferenceIntegrateVariableVerletStepKernel::execute(ContextImpl& context, c
ReferenceApplyAndersenThermostatKernel::~ReferenceApplyAndersenThermostatKernel() { ReferenceApplyAndersenThermostatKernel::~ReferenceApplyAndersenThermostatKernel() {
if (thermostat) if (thermostat)
delete thermostat; delete thermostat;
if (masses)
delete[] masses;
} }
void ReferenceApplyAndersenThermostatKernel::initialize(const System& system, const AndersenThermostat& thermostat) { void ReferenceApplyAndersenThermostatKernel::initialize(const System& system, const AndersenThermostat& thermostat) {
int numParticles = system.getNumParticles(); int numParticles = system.getNumParticles();
masses = new RealOpenMM[numParticles]; masses.resize(numParticles);
for (int i = 0; i < numParticles; ++i) for (int i = 0; i < numParticles; ++i)
masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i)); masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
this->thermostat = new ReferenceAndersenThermostat(); this->thermostat = new ReferenceAndersenThermostat();
...@@ -1542,7 +1506,7 @@ void ReferenceApplyAndersenThermostatKernel::initialize(const System& system, co ...@@ -1542,7 +1506,7 @@ void ReferenceApplyAndersenThermostatKernel::initialize(const System& system, co
} }
void ReferenceApplyAndersenThermostatKernel::execute(ContextImpl& context) { void ReferenceApplyAndersenThermostatKernel::execute(ContextImpl& context) {
RealOpenMM** velData = extractVelocities(context); vector<RealVec>& velData = extractVelocities(context);
thermostat->applyThermostat(particleGroups, velData, masses, thermostat->applyThermostat(particleGroups, velData, masses,
static_cast<RealOpenMM>(context.getParameter(AndersenThermostat::Temperature())), static_cast<RealOpenMM>(context.getParameter(AndersenThermostat::Temperature())),
static_cast<RealOpenMM>(context.getParameter(AndersenThermostat::CollisionFrequency())), static_cast<RealOpenMM>(context.getParameter(AndersenThermostat::CollisionFrequency())),
...@@ -1560,13 +1524,13 @@ void ReferenceApplyMonteCarloBarostatKernel::initialize(const System& system, co ...@@ -1560,13 +1524,13 @@ void ReferenceApplyMonteCarloBarostatKernel::initialize(const System& system, co
void ReferenceApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context, double scale) { void ReferenceApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context, double scale) {
if (barostat == NULL) if (barostat == NULL)
barostat = new ReferenceMonteCarloBarostat(context.getSystem().getNumParticles(), context.getMolecules()); barostat = new ReferenceMonteCarloBarostat(context.getSystem().getNumParticles(), context.getMolecules());
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
RealOpenMM* boxSize = extractBoxSize(context); RealOpenMM* boxSize = extractBoxSize(context);
barostat->applyBarostat(posData, boxSize, scale); barostat->applyBarostat(posData, boxSize, scale);
} }
void ReferenceApplyMonteCarloBarostatKernel::restoreCoordinates(ContextImpl& context) { void ReferenceApplyMonteCarloBarostatKernel::restoreCoordinates(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
barostat->restorePositions(posData); barostat->restorePositions(posData);
} }
...@@ -1578,7 +1542,7 @@ void ReferenceCalcKineticEnergyKernel::initialize(const System& system) { ...@@ -1578,7 +1542,7 @@ void ReferenceCalcKineticEnergyKernel::initialize(const System& system) {
} }
double ReferenceCalcKineticEnergyKernel::execute(ContextImpl& context) { double ReferenceCalcKineticEnergyKernel::execute(ContextImpl& context) {
RealOpenMM** velData = extractVelocities(context); vector<RealVec>& velData = extractVelocities(context);
double energy = 0.0; double energy = 0.0;
for (size_t i = 0; i < masses.size(); ++i) for (size_t i = 0; i < masses.size(); ++i)
energy += masses[i]*(velData[i][0]*velData[i][0]+velData[i][1]*velData[i][1]+velData[i][2]*velData[i][2]); energy += masses[i]*(velData[i][0]*velData[i][0]+velData[i][1]*velData[i][1]+velData[i][2]*velData[i][2]);
...@@ -1595,7 +1559,7 @@ void ReferenceRemoveCMMotionKernel::initialize(const System& system, const CMMot ...@@ -1595,7 +1559,7 @@ void ReferenceRemoveCMMotionKernel::initialize(const System& system, const CMMot
void ReferenceRemoveCMMotionKernel::execute(ContextImpl& context) { void ReferenceRemoveCMMotionKernel::execute(ContextImpl& context) {
if (data.stepCount%frequency != 0) if (data.stepCount%frequency != 0)
return; return;
RealOpenMM** velData = extractVelocities(context); vector<RealVec>& velData = extractVelocities(context);
// Calculate the center of mass momentum. // Calculate the center of mass momentum.
......
platforms/reference/src/ReferenceKernels.h
View file @ 0843c5f3
...@@ -172,7 +172,7 @@ private: ...@@ -172,7 +172,7 @@ private:
class ReferenceApplyConstraintsKernel : public ApplyConstraintsKernel { class ReferenceApplyConstraintsKernel : public ApplyConstraintsKernel {
public: public:
ReferenceApplyConstraintsKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : ReferenceApplyConstraintsKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) :
ApplyConstraintsKernel(name, platform), data(data), constraints(0), masses(0), inverseMasses(0), constraintDistances(0), constraintIndices(0) { ApplyConstraintsKernel(name, platform), data(data), constraints(0), constraintDistances(0), constraintIndices(0) {
} }
~ReferenceApplyConstraintsKernel(); ~ReferenceApplyConstraintsKernel();
/** /**
...@@ -191,8 +191,8 @@ public: ...@@ -191,8 +191,8 @@ public:
private: private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceConstraintAlgorithm* constraints; ReferenceConstraintAlgorithm* constraints;
RealOpenMM* masses; std::vector<RealOpenMM> masses;
RealOpenMM* inverseMasses; std::vector<RealOpenMM> inverseMasses;
RealOpenMM* constraintDistances; RealOpenMM* constraintDistances;
int** constraintIndices; int** constraintIndices;
int numConstraints; int numConstraints;
...@@ -691,7 +691,7 @@ private: ...@@ -691,7 +691,7 @@ private:
class ReferenceIntegrateVerletStepKernel : public IntegrateVerletStepKernel { class ReferenceIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
public: public:
ReferenceIntegrateVerletStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVerletStepKernel(name, platform), ReferenceIntegrateVerletStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVerletStepKernel(name, platform),
data(data), dynamics(0), constraints(0), masses(0), constraintDistances(0), constraintIndices(0) { data(data), dynamics(0), constraints(0), constraintDistances(0), constraintIndices(0) {
} }
~ReferenceIntegrateVerletStepKernel(); ~ReferenceIntegrateVerletStepKernel();
/** /**
...@@ -712,7 +712,7 @@ private: ...@@ -712,7 +712,7 @@ private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceVerletDynamics* dynamics; ReferenceVerletDynamics* dynamics;
ReferenceConstraintAlgorithm* constraints; ReferenceConstraintAlgorithm* constraints;
RealOpenMM* masses; std::vector<RealOpenMM> masses;
RealOpenMM* constraintDistances; RealOpenMM* constraintDistances;
int** constraintIndices; int** constraintIndices;
int numConstraints; int numConstraints;
...@@ -725,7 +725,7 @@ private: ...@@ -725,7 +725,7 @@ private:
class ReferenceIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel { class ReferenceIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
public: public:
ReferenceIntegrateLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateLangevinStepKernel(name, platform), ReferenceIntegrateLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateLangevinStepKernel(name, platform),
data(data), dynamics(0), constraints(0), masses(0), constraintDistances(0), constraintIndices(0) { data(data), dynamics(0), constraints(0), constraintDistances(0), constraintIndices(0) {
} }
~ReferenceIntegrateLangevinStepKernel(); ~ReferenceIntegrateLangevinStepKernel();
/** /**
...@@ -746,7 +746,7 @@ private: ...@@ -746,7 +746,7 @@ private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceStochasticDynamics* dynamics; ReferenceStochasticDynamics* dynamics;
ReferenceConstraintAlgorithm* constraints; ReferenceConstraintAlgorithm* constraints;
RealOpenMM* masses; std::vector<RealOpenMM> masses;
RealOpenMM* constraintDistances; RealOpenMM* constraintDistances;
int** constraintIndices; int** constraintIndices;
int numConstraints; int numConstraints;
...@@ -759,7 +759,7 @@ private: ...@@ -759,7 +759,7 @@ private:
class ReferenceIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel { class ReferenceIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
public: public:
ReferenceIntegrateBrownianStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateBrownianStepKernel(name, platform), ReferenceIntegrateBrownianStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateBrownianStepKernel(name, platform),
data(data), dynamics(0), constraints(0), masses(0), constraintDistances(0), constraintIndices(0) { data(data), dynamics(0), constraints(0), constraintDistances(0), constraintIndices(0) {
} }
~ReferenceIntegrateBrownianStepKernel(); ~ReferenceIntegrateBrownianStepKernel();
/** /**
...@@ -780,7 +780,7 @@ private: ...@@ -780,7 +780,7 @@ private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceBrownianDynamics* dynamics; ReferenceBrownianDynamics* dynamics;
ReferenceConstraintAlgorithm* constraints; ReferenceConstraintAlgorithm* constraints;
RealOpenMM* masses; std::vector<RealOpenMM> masses;
RealOpenMM* constraintDistances; RealOpenMM* constraintDistances;
int** constraintIndices; int** constraintIndices;
int numConstraints; int numConstraints;
...@@ -793,7 +793,7 @@ private: ...@@ -793,7 +793,7 @@ private:
class ReferenceIntegrateVariableLangevinStepKernel : public IntegrateVariableLangevinStepKernel { class ReferenceIntegrateVariableLangevinStepKernel : public IntegrateVariableLangevinStepKernel {
public: public:
ReferenceIntegrateVariableLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVariableLangevinStepKernel(name, platform), ReferenceIntegrateVariableLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVariableLangevinStepKernel(name, platform),
data(data), dynamics(0), constraints(0), masses(0), constraintDistances(0), constraintIndices(0) { data(data), dynamics(0), constraints(0), constraintDistances(0), constraintIndices(0) {
} }
~ReferenceIntegrateVariableLangevinStepKernel(); ~ReferenceIntegrateVariableLangevinStepKernel();
/** /**
...@@ -815,7 +815,7 @@ private: ...@@ -815,7 +815,7 @@ private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceVariableStochasticDynamics* dynamics; ReferenceVariableStochasticDynamics* dynamics;
ReferenceConstraintAlgorithm* constraints; ReferenceConstraintAlgorithm* constraints;
RealOpenMM* masses; std::vector<RealOpenMM> masses;
RealOpenMM* constraintDistances; RealOpenMM* constraintDistances;
int** constraintIndices; int** constraintIndices;
int numConstraints; int numConstraints;
...@@ -828,7 +828,7 @@ private: ...@@ -828,7 +828,7 @@ private:
class ReferenceIntegrateVariableVerletStepKernel : public IntegrateVariableVerletStepKernel { class ReferenceIntegrateVariableVerletStepKernel : public IntegrateVariableVerletStepKernel {
public: public:
ReferenceIntegrateVariableVerletStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVariableVerletStepKernel(name, platform), ReferenceIntegrateVariableVerletStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVariableVerletStepKernel(name, platform),
data(data), dynamics(0), constraints(0), masses(0), constraintDistances(0), constraintIndices(0) { data(data), dynamics(0), constraints(0), constraintDistances(0), constraintIndices(0) {
} }
~ReferenceIntegrateVariableVerletStepKernel(); ~ReferenceIntegrateVariableVerletStepKernel();
/** /**
...@@ -850,7 +850,7 @@ private: ...@@ -850,7 +850,7 @@ private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceVariableVerletDynamics* dynamics; ReferenceVariableVerletDynamics* dynamics;
ReferenceConstraintAlgorithm* constraints; ReferenceConstraintAlgorithm* constraints;
RealOpenMM* masses; std::vector<RealOpenMM> masses;
RealOpenMM* constraintDistances; RealOpenMM* constraintDistances;
int** constraintIndices; int** constraintIndices;
int numConstraints; int numConstraints;
...@@ -881,7 +881,7 @@ public: ...@@ -881,7 +881,7 @@ public:
private: private:
ReferenceAndersenThermostat* thermostat; ReferenceAndersenThermostat* thermostat;
std::vector<std::vector<int> > particleGroups; std::vector<std::vector<int> > particleGroups;
RealOpenMM* masses; std::vector<RealOpenMM> masses;
}; };
/** /**
......
platforms/reference/src/ReferencePlatform.cpp
View file @ 0843c5f3
...@@ -34,6 +34,8 @@ ...@@ -34,6 +34,8 @@
#include "ReferenceKernels.h" #include "ReferenceKernels.h"
#include "openmm/internal/ContextImpl.h" #include "openmm/internal/ContextImpl.h"
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKUtilities/SimTKOpenMMRealType.h"
#include "SimTKUtilities/RealVec.h"
#include <vector>
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
...@@ -83,32 +85,16 @@ void ReferencePlatform::contextDestroyed(ContextImpl& context) const { ...@@ -83,32 +85,16 @@ void ReferencePlatform::contextDestroyed(ContextImpl& context) const {
} }
ReferencePlatform::PlatformData::PlatformData(int numParticles) : time(0.0), stepCount(0), numParticles(numParticles) { ReferencePlatform::PlatformData::PlatformData(int numParticles) : time(0.0), stepCount(0), numParticles(numParticles) {
RealOpenMM** positions = new RealOpenMM*[numParticles]; positions = new vector<RealVec>(numParticles);
RealOpenMM** velocities = new RealOpenMM*[numParticles]; velocities = new vector<RealVec>(numParticles);
RealOpenMM** forces = new RealOpenMM*[numParticles]; forces = new vector<RealVec>(numParticles);
for (int i = 0; i < numParticles; ++i) {
positions[i] = new RealOpenMM[3];
velocities[i] = new RealOpenMM[3];
forces[i] = new RealOpenMM[3];
}
this->positions = positions;
this->velocities = velocities;
this->forces = forces;
periodicBoxSize = new RealOpenMM[3]; periodicBoxSize = new RealOpenMM[3];
} }
ReferencePlatform::PlatformData::~PlatformData() { ReferencePlatform::PlatformData::~PlatformData() {
RealOpenMM** positions = (RealOpenMM**) this->positions; delete (vector<RealVec>*) positions;
RealOpenMM** velocities = (RealOpenMM**) this->velocities; delete (vector<RealVec>*) velocities;
RealOpenMM** forces = (RealOpenMM**) this->forces; delete (vector<RealVec>*) forces;
RealOpenMM* periodicBoxSize = (RealOpenMM*) this->periodicBoxSize; RealOpenMM* periodicBoxSize = (RealOpenMM*) this->periodicBoxSize;
for (int i = 0; i < numParticles; ++i) {
delete[] positions[i];
delete[] velocities[i];
delete[] forces[i];
}
delete[] positions;
delete[] velocities;
delete[] forces;
delete[] periodicBoxSize; delete[] periodicBoxSize;
} }
platforms/reference/src/SimTKReference/PME.cpp
View file @ 0843c5f3
...@@ -36,6 +36,8 @@ ...@@ -36,6 +36,8 @@
#include "PME.h" #include "PME.h"
#include "fftpack.h" #include "fftpack.h"
using std::vector;
using OpenMM::RealVec;
typedef int ivec[3]; typedef int ivec[3];
...@@ -193,7 +195,7 @@ pme_calculate_bsplines_moduli(pme_t pme) ...@@ -193,7 +195,7 @@ pme_calculate_bsplines_moduli(pme_t pme)
static void static void
pme_update_grid_index_and_fraction(pme_t pme, pme_update_grid_index_and_fraction(pme_t pme,
RealOpenMM ** atomCoordinates, vector<RealVec>& atomCoordinates,
const RealOpenMM periodicBoxSize[3]) const RealOpenMM periodicBoxSize[3])
{ {
int i; int i;
...@@ -522,7 +524,7 @@ static void ...@@ -522,7 +524,7 @@ static void
pme_grid_interpolate_force(pme_t pme, pme_grid_interpolate_force(pme_t pme,
const RealOpenMM periodicBoxSize[3], const RealOpenMM periodicBoxSize[3],
RealOpenMM ** atomParameters, RealOpenMM ** atomParameters,
RealOpenMM ** forces) vector<RealVec>& forces)
{ {
static const int QIndex = 2; // atom charges are stored in atomParameters[atomID][2] static const int QIndex = 2; // atom charges are stored in atomParameters[atomID][2]
int i; int i;
...@@ -667,8 +669,8 @@ pme_init(pme_t * ppme, ...@@ -667,8 +669,8 @@ pme_init(pme_t * ppme,
int pme_exec(pme_t pme, int pme_exec(pme_t pme,
RealOpenMM ** atomCoordinates, vector<RealVec>& atomCoordinates,
RealOpenMM ** forces, vector<RealVec>& forces,
RealOpenMM ** atomParameters, RealOpenMM ** atomParameters,
const RealOpenMM periodicBoxSize[3], const RealOpenMM periodicBoxSize[3],
RealOpenMM * energy, RealOpenMM * energy,
......
platforms/reference/src/SimTKReference/PME.h
View file @ 0843c5f3
...@@ -30,6 +30,7 @@ ...@@ -30,6 +30,7 @@
*/ */
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "../SimTKUtilities/SimTKOpenMMCommon.h"
#include <vector>
typedef RealOpenMM rvec[3]; typedef RealOpenMM rvec[3];
...@@ -74,8 +75,8 @@ pme_init(pme_t * ppme, ...@@ -74,8 +75,8 @@ pme_init(pme_t * ppme,
*/ */
int int
pme_exec(pme_t pme, pme_exec(pme_t pme,
RealOpenMM ** atomCoordinates, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM ** forces, std::vector<OpenMM::RealVec>& forces,
RealOpenMM ** atomParameters, RealOpenMM ** atomParameters,
const RealOpenMM periodicBoxSize[3], const RealOpenMM periodicBoxSize[3],
RealOpenMM * energy, RealOpenMM * energy,
......
platforms/reference/src/SimTKReference/ReferenceAndersenThermostat.cpp
View file @ 0843c5f3
...@@ -29,6 +29,7 @@ ...@@ -29,6 +29,7 @@
#include "ReferenceAndersenThermostat.h" #include "ReferenceAndersenThermostat.h"
using std::vector; using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -60,7 +61,7 @@ using std::vector; ...@@ -60,7 +61,7 @@ using std::vector;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceAndersenThermostat::applyThermostat( const vector<vector<int> >& atomGroups, RealOpenMM** atomVelocities, RealOpenMM* atomMasses, void ReferenceAndersenThermostat::applyThermostat( const vector<vector<int> >& atomGroups, vector<RealVec>& atomVelocities, vector<RealOpenMM>& atomMasses,
RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize ) const { RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize ) const {
const RealOpenMM collisionProbability = 1.0f - EXP(-collisionFrequency*stepSize); const RealOpenMM collisionProbability = 1.0f - EXP(-collisionFrequency*stepSize);
......
platforms/reference/src/SimTKReference/ReferenceAndersenThermostat.h
View file @ 0843c5f3
...@@ -65,7 +65,7 @@ class ReferenceAndersenThermostat { ...@@ -65,7 +65,7 @@ class ReferenceAndersenThermostat {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void applyThermostat( const std::vector<std::vector<int> >& atomGroups, RealOpenMM** atomVelocities, RealOpenMM* atomMasses, void applyThermostat( const std::vector<std::vector<int> >& atomGroups, std::vector<OpenMM::RealVec>& atomVelocities, std::vector<RealOpenMM>& atomMasses,
RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize ) const; RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize ) const;
}; };
......
platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.cpp
View file @ 0843c5f3
...@@ -31,6 +31,9 @@ ...@@ -31,6 +31,9 @@
#include "ReferenceAngleBondIxn.h" #include "ReferenceAngleBondIxn.h"
#include "ReferenceForce.h" #include "ReferenceForce.h"
using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
ReferenceAngleBondIxn constructor ReferenceAngleBondIxn constructor
...@@ -122,9 +125,9 @@ int ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine( RealOpenMM cosine, Rea ...@@ -122,9 +125,9 @@ int ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine( RealOpenMM cosine, Rea
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices, void ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices,
RealOpenMM** atomCoordinates, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM* parameters,
RealOpenMM** forces, vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const { RealOpenMM* totalEnergy ) const {
// constants -- reduce Visual Studio warnings regarding conversions between float & double // constants -- reduce Visual Studio warnings regarding conversions between float & double
......
platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.h
View file @ 0843c5f3
...@@ -81,8 +81,8 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn { ...@@ -81,8 +81,8 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates, void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces, RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy ) const; RealOpenMM* totalEnergy ) const;
......
platforms/reference/src/SimTKReference/ReferenceBondForce.cpp
View file @ 0843c5f3
...@@ -30,6 +30,9 @@ ...@@ -30,6 +30,9 @@
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "../SimTKUtilities/SimTKOpenMMUtilities.h"
#include "ReferenceBondForce.h" #include "ReferenceBondForce.h"
using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
ReferenceBondForce constructor ReferenceBondForce constructor
...@@ -78,9 +81,9 @@ ReferenceBondForce::~ReferenceBondForce( ){ ...@@ -78,9 +81,9 @@ ReferenceBondForce::~ReferenceBondForce( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceBondForce::calculateForce( int numberOfBonds, int** atomIndices, void ReferenceBondForce::calculateForce( int numberOfBonds, int** atomIndices,
RealOpenMM** atomCoordinates, vector<RealVec>& atomCoordinates,
RealOpenMM** parameters, RealOpenMM** parameters,
RealOpenMM** forces, vector<RealVec>& forces,
RealOpenMM *totalEnergy, RealOpenMM *totalEnergy,
ReferenceBondIxn& referenceBondIxn ){ ReferenceBondIxn& referenceBondIxn ){
......
platforms/reference/src/SimTKReference/ReferenceBondForce.h
View file @ 0843c5f3
...@@ -68,8 +68,8 @@ class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce { ...@@ -68,8 +68,8 @@ class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateForce( int numberOfBonds, int** atomIndices, void calculateForce( int numberOfBonds, int** atomIndices,
RealOpenMM** atomCoordinates, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** parameters, RealOpenMM** forces, RealOpenMM** parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn ); RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn );
}; };
......
platforms/reference/src/SimTKReference/ReferenceBondIxn.cpp
View file @ 0843c5f3
...@@ -31,6 +31,9 @@ ...@@ -31,6 +31,9 @@
#include "ReferenceForce.h" #include "ReferenceForce.h"
#include "ReferenceBondIxn.h" #include "ReferenceBondIxn.h"
using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
ReferenceBondIxn constructor ReferenceBondIxn constructor
...@@ -75,8 +78,8 @@ ReferenceBondIxn::~ReferenceBondIxn( ){ ...@@ -75,8 +78,8 @@ ReferenceBondIxn::~ReferenceBondIxn( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceBondIxn::calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates, void ReferenceBondIxn::calculateBondIxn( int* atomIndices, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces, RealOpenMM* parameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy ) const { RealOpenMM* totalEnergy ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceBondIxn.h
View file @ 0843c5f3
...@@ -63,8 +63,8 @@ class OPENMM_EXPORT ReferenceBondIxn { ...@@ -63,8 +63,8 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
virtual void calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates, virtual void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces, RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy ) const; RealOpenMM* totalEnergy ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp
View file @ 0843c5f3
...@@ -32,6 +32,9 @@ ...@@ -32,6 +32,9 @@
#include <cstdio> #include <cstdio>
using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
ReferenceBrownianDynamics constructor ReferenceBrownianDynamics constructor
...@@ -67,9 +70,8 @@ ReferenceBrownianDynamics::ReferenceBrownianDynamics( int numberOfAtoms, ...@@ -67,9 +70,8 @@ ReferenceBrownianDynamics::ReferenceBrownianDynamics( int numberOfAtoms,
this->friction = one; this->friction = one;
} }
allocate2DArrays( numberOfAtoms, 3, Max2DArrays ); xPrime.resize(numberOfAtoms);
allocate1DArrays( numberOfAtoms, Max1DArrays ); inverseMasses.resize(numberOfAtoms);
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -122,9 +124,9 @@ RealOpenMM ReferenceBrownianDynamics::getFriction( void ) const { ...@@ -122,9 +124,9 @@ RealOpenMM ReferenceBrownianDynamics::getFriction( void ) const {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceBrownianDynamics::update( int numberOfAtoms, RealOpenMM** atomCoordinates, int ReferenceBrownianDynamics::update( int numberOfAtoms, vector<RealVec>& atomCoordinates,
RealOpenMM** velocities, vector<RealVec>& velocities,
RealOpenMM** forces, RealOpenMM* masses ){ vector<RealVec>& forces, vector<RealOpenMM>& masses ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -135,11 +137,6 @@ int ReferenceBrownianDynamics::update( int numberOfAtoms, RealOpenMM** atomCoord ...@@ -135,11 +137,6 @@ int ReferenceBrownianDynamics::update( int numberOfAtoms, RealOpenMM** atomCoord
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// get work arrays
RealOpenMM** xPrime = get2DArrayAtIndex( xPrime2D );
RealOpenMM* inverseMasses = get1DArrayAtIndex( InverseMasses );
// first-time-through initialization // first-time-through initialization
if( getTimeStep() == 0 ){ if( getTimeStep() == 0 ){
......
platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.h
View file @ 0843c5f3
...@@ -33,9 +33,8 @@ class ReferenceBrownianDynamics : public ReferenceDynamics { ...@@ -33,9 +33,8 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
private: private:
enum TwoDArrayIndicies { xPrime2D, Max2DArrays }; std::vector<OpenMM::RealVec> xPrime;
enum OneDArrayIndicies { InverseMasses, Max1DArrays }; std::vector<RealOpenMM> inverseMasses;
RealOpenMM friction; RealOpenMM friction;
public: public:
...@@ -85,8 +84,8 @@ class ReferenceBrownianDynamics : public ReferenceDynamics { ...@@ -85,8 +84,8 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int update( int numberOfAtoms, RealOpenMM** atomCoordinates, int update( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses ); std::vector<OpenMM::RealVec>& velocities, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses );
}; };
......
platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
View file @ 0843c5f3
...@@ -39,6 +39,7 @@ using std::pair; ...@@ -39,6 +39,7 @@ using std::pair;
using std::vector; using std::vector;
using std::set; using std::set;
using OpenMM::Vec3; using OpenMM::Vec3;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -58,7 +59,7 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm( int numberOfAtoms, ...@@ -58,7 +59,7 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm( int numberOfAtoms,
int numberOfConstraints, int numberOfConstraints,
int** atomIndices, int** atomIndices,
RealOpenMM* distance, RealOpenMM* distance,
RealOpenMM* masses, vector<RealOpenMM>& masses,
vector<AngleInfo>& angles, vector<AngleInfo>& angles,
RealOpenMM tolerance){ RealOpenMM tolerance){
...@@ -348,9 +349,9 @@ void ReferenceCCMAAlgorithm::setTolerance( RealOpenMM tolerance ){ ...@@ -348,9 +349,9 @@ void ReferenceCCMAAlgorithm::setTolerance( RealOpenMM tolerance ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceCCMAAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordinates, int ReferenceCCMAAlgorithm::apply( int numberOfAtoms, vector<RealVec>& atomCoordinates,
RealOpenMM** atomCoordinatesP, vector<RealVec>& atomCoordinatesP,
RealOpenMM* inverseMasses ){ vector<RealOpenMM>& inverseMasses ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -479,7 +480,7 @@ int ReferenceCCMAAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordinat ...@@ -479,7 +480,7 @@ int ReferenceCCMAAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordinat
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceCCMAAlgorithm::reportCCMA( int numberOfAtoms, RealOpenMM** atomCoordinates, int ReferenceCCMAAlgorithm::reportCCMA( int numberOfAtoms, vector<RealVec>& atomCoordinates,
std::stringstream& message ){ std::stringstream& message ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.h
View file @ 0843c5f3
...@@ -67,7 +67,7 @@ class OPENMM_EXPORT ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm ...@@ -67,7 +67,7 @@ class OPENMM_EXPORT ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceCCMAAlgorithm( int numberOfAtoms, int numberOfConstraints, int** atomIndices, RealOpenMM* distance, RealOpenMM* masses, std::vector<AngleInfo>& angles, RealOpenMM tolerance ); ReferenceCCMAAlgorithm( int numberOfAtoms, int numberOfConstraints, int** atomIndices, RealOpenMM* distance, std::vector<RealOpenMM>& masses, std::vector<AngleInfo>& angles, RealOpenMM tolerance );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -142,8 +142,8 @@ class OPENMM_EXPORT ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm ...@@ -142,8 +142,8 @@ class OPENMM_EXPORT ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int apply( int numberOfAtoms, RealOpenMM** atomCoordinates, int apply( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomCoordinatesP, RealOpenMM* inverseMasses ); std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -157,7 +157,7 @@ class OPENMM_EXPORT ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm ...@@ -157,7 +157,7 @@ class OPENMM_EXPORT ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int reportCCMA( int numberOfAtoms, RealOpenMM** atomCoordinates, std::stringstream& message ); int reportCCMA( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::stringstream& message );
}; };
class ReferenceCCMAAlgorithm::AngleInfo class ReferenceCCMAAlgorithm::AngleInfo
......
platforms/reference/src/SimTKReference/ReferenceCMAPTorsionIxn.cpp
View file @ 0843c5f3
...@@ -26,6 +26,7 @@ ...@@ -26,6 +26,7 @@
#include "ReferenceForce.h" #include "ReferenceForce.h"
using std::vector; using std::vector;
using OpenMM::RealVec;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -51,7 +52,7 @@ ReferenceCMAPTorsionIxn::ReferenceCMAPTorsionIxn(const vector<vector<vector<Real ...@@ -51,7 +52,7 @@ ReferenceCMAPTorsionIxn::ReferenceCMAPTorsionIxn(const vector<vector<vector<Real
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceCMAPTorsionIxn::calculateIxn(RealOpenMM** atomCoordinates, RealOpenMM** forces, RealOpenMM* totalEnergy) const { void ReferenceCMAPTorsionIxn::calculateIxn(vector<RealVec>& atomCoordinates, vector<RealVec>& forces, RealOpenMM* totalEnergy) const {
for (unsigned int i = 0; i < torsionMaps.size(); i++) for (unsigned int i = 0; i < torsionMaps.size(); i++)
calculateOneIxn(i, atomCoordinates, forces, totalEnergy); calculateOneIxn(i, atomCoordinates, forces, totalEnergy);
} }
...@@ -67,7 +68,7 @@ void ReferenceCMAPTorsionIxn::calculateIxn(RealOpenMM** atomCoordinates, RealOpe ...@@ -67,7 +68,7 @@ void ReferenceCMAPTorsionIxn::calculateIxn(RealOpenMM** atomCoordinates, RealOpe
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, RealOpenMM** atomCoordinates, RealOpenMM** forces, void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, vector<RealVec>& atomCoordinates, vector<RealVec>& forces,
RealOpenMM* totalEnergy) const { RealOpenMM* totalEnergy) const {
int map = torsionMaps[index]; int map = torsionMaps[index];
int a1 = torsionIndices[index][0]; int a1 = torsionIndices[index][0];
...@@ -188,6 +189,6 @@ void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, RealOpenMM** atomCoordi ...@@ -188,6 +189,6 @@ void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, RealOpenMM** atomCoordi
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceCMAPTorsionIxn::calculateBondIxn(int* atomIndices, RealOpenMM** atomCoordinates, void ReferenceCMAPTorsionIxn::calculateBondIxn(int* atomIndices, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces, RealOpenMM* totalEnergy) const { RealOpenMM* parameters, vector<RealVec>& forces, RealOpenMM* totalEnergy) const {
} }
platforms/reference/src/SimTKReference/ReferenceCMAPTorsionIxn.h
View file @ 0843c5f3
...@@ -51,7 +51,7 @@ private: ...@@ -51,7 +51,7 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateOneIxn(int index, RealOpenMM** atomCoordinates, RealOpenMM** forces, void calculateOneIxn(int index, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const; RealOpenMM* totalEnergy) const;
public: public:
...@@ -76,7 +76,7 @@ public: ...@@ -76,7 +76,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateIxn(RealOpenMM** atomCoordinates, RealOpenMM** forces, RealOpenMM* totalEnergy) const; void calculateIxn(std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -84,8 +84,8 @@ public: ...@@ -84,8 +84,8 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateBondIxn(int* atomIndices, RealOpenMM** atomCoordinates, void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces, RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const; RealOpenMM* totalEnergy) const;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceConstraintAlgorithm.h
View file @ 0843c5f3
...@@ -65,8 +65,8 @@ public: ...@@ -65,8 +65,8 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
virtual int apply(int numberOfAtoms, RealOpenMM** atomCoordinates, virtual int apply(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomCoordinatesP, RealOpenMM* inverseMasses) = 0; std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses) = 0;
}; };
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
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