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Commit f5aebbd4 authored by Peter Eastman's avatar Peter Eastman
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Eliminated Stream and related classes, replacing their functionality with UpdateStateDataKernel.

parent 21d67074
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Showing with 176 additions and 115 deletions
platforms/reference/src/ReferenceKernels.cpp
View file @ f5aebbd4
......@@ -30,7 +30,6 @@
* -------------------------------------------------------------------------- */
#include "ReferenceKernels.h"
#include "ReferenceFloatStreamImpl.h"
#include "gbsa/CpuObc.h"
#include "gbsa/CpuGBVI.h"
#include "SimTKReference/ReferenceAndersenThermostat.h"
......@@ -112,6 +111,21 @@ static void disposeRealArray(RealOpenMM** array, int size) {
}
}
static RealOpenMM** extractPositions(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return (RealOpenMM**) data->positions;
}
static RealOpenMM** extractVelocities(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return (RealOpenMM**) data->velocities;
}
static RealOpenMM** extractForces(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return (RealOpenMM**) data->forces;
}
static void findAnglesForCCMA(const System& system, vector<ReferenceCCMAAlgorithm::AngleInfo>& angles) {
for (int i = 0; i < system.getNumForces(); i++) {
const HarmonicAngleForce* force = dynamic_cast<const HarmonicAngleForce*>(&system.getForce(i));
......@@ -130,8 +144,13 @@ void ReferenceCalcForcesAndEnergyKernel::initialize(const System& system) {
}
void ReferenceCalcForcesAndEnergyKernel::beginForceComputation(ContextImpl& context) {
double zero[] = {0.0, 0.0, 0.0};
context.getForces().fillWithValue(zero);
int numParticles = context.getSystem().getNumParticles();
RealOpenMM** forceData = extractForces(context);
for (int i = 0; i < numParticles; ++i) {
forceData[i][0] = (RealOpenMM) 0.0;
forceData[i][1] = (RealOpenMM) 0.0;
forceData[i][2] = (RealOpenMM) 0.0;
}
}
void ReferenceCalcForcesAndEnergyKernel::finishForceComputation(ContextImpl& context) {
......@@ -144,17 +163,61 @@ double ReferenceCalcForcesAndEnergyKernel::finishEnergyComputation(ContextImpl&
return 0.0;
}
void ReferenceUpdateTimeKernel::initialize(const System& system) {
void ReferenceUpdateStateDataKernel::initialize(const System& system) {
}
double ReferenceUpdateTimeKernel::getTime(const ContextImpl& context) const {
double ReferenceUpdateStateDataKernel::getTime(const ContextImpl& context) const {
return data.time;
}
void ReferenceUpdateTimeKernel::setTime(ContextImpl& context, double time) {
void ReferenceUpdateStateDataKernel::setTime(ContextImpl& context, double time) {
data.time = time;
}
void ReferenceUpdateStateDataKernel::getPositions(ContextImpl& context, std::vector<Vec3>& positions) {
int numParticles = context.getSystem().getNumParticles();
RealOpenMM** posData = extractPositions(context);
positions.resize(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3(posData[i][0], posData[i][1], posData[i][2]);
}
void ReferenceUpdateStateDataKernel::setPositions(ContextImpl& context, const std::vector<Vec3>& positions) {
int numParticles = context.getSystem().getNumParticles();
RealOpenMM** posData = extractPositions(context);
for (int i = 0; i < numParticles; ++i) {
posData[i][0] = positions[i][0];
posData[i][1] = positions[i][1];
posData[i][2] = positions[i][2];
}
}
void ReferenceUpdateStateDataKernel::getVelocities(ContextImpl& context, std::vector<Vec3>& velocities) {
int numParticles = context.getSystem().getNumParticles();
RealOpenMM** velData = extractVelocities(context);
velocities.resize(numParticles);
for (int i = 0; i < numParticles; ++i)
velocities[i] = Vec3(velData[i][0], velData[i][1], velData[i][2]);
}
void ReferenceUpdateStateDataKernel::setVelocities(ContextImpl& context, const std::vector<Vec3>& velocities) {
int numParticles = context.getSystem().getNumParticles();
RealOpenMM** velData = extractVelocities(context);
for (int i = 0; i < numParticles; ++i) {
velData[i][0] = velocities[i][0];
velData[i][1] = velocities[i][1];
velData[i][2] = velocities[i][2];
}
}
void ReferenceUpdateStateDataKernel::getForces(ContextImpl& context, std::vector<Vec3>& forces) {
int numParticles = context.getSystem().getNumParticles();
RealOpenMM** forceData = extractForces(context);
forces.resize(numParticles);
for (int i = 0; i < numParticles; ++i)
forces[i] = Vec3(forceData[i][0], forceData[i][1], forceData[i][2]);
}
ReferenceCalcHarmonicBondForceKernel::~ReferenceCalcHarmonicBondForceKernel() {
disposeIntArray(bondIndexArray, numBonds);
disposeRealArray(bondParamArray, numBonds);
......@@ -176,15 +239,15 @@ void ReferenceCalcHarmonicBondForceKernel::initialize(const System& system, cons
}
void ReferenceCalcHarmonicBondForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
ReferenceBondForce refBondForce;
ReferenceHarmonicBondIxn harmonicBond;
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, 0, 0, 0, harmonicBond);
}
double ReferenceCalcHarmonicBondForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numBonds];
RealOpenMM energy = 0;
......@@ -220,15 +283,15 @@ void ReferenceCalcHarmonicAngleForceKernel::initialize(const System& system, con
}
void ReferenceCalcHarmonicAngleForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
ReferenceBondForce refBondForce;
ReferenceAngleBondIxn angleBond;
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, 0, 0, 0, angleBond);
}
double ReferenceCalcHarmonicAngleForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numAngles];
RealOpenMM energy = 0;
......@@ -266,15 +329,15 @@ void ReferenceCalcPeriodicTorsionForceKernel::initialize(const System& system, c
}
void ReferenceCalcPeriodicTorsionForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
ReferenceBondForce refBondForce;
ReferenceProperDihedralBond periodicTorsionBond;
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, 0, 0, 0, periodicTorsionBond);
}
double ReferenceCalcPeriodicTorsionForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numTorsions];
RealOpenMM energy = 0;
......@@ -315,15 +378,15 @@ void ReferenceCalcRBTorsionForceKernel::initialize(const System& system, const R
}
void ReferenceCalcRBTorsionForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
ReferenceBondForce refBondForce;
ReferenceRbDihedralBond rbTorsionBond;
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, 0, 0, 0, rbTorsionBond);
}
double ReferenceCalcRBTorsionForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numTorsions];
RealOpenMM energy = 0;
......@@ -435,8 +498,8 @@ void ReferenceCalcNonbondedForceKernel::initialize(const System& system, const N
}
void ReferenceCalcNonbondedForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
ReferenceLJCoulombIxn clj;
bool periodic = (nonbondedMethod == CutoffPeriodic);
bool ewald = (nonbondedMethod == Ewald);
......@@ -460,7 +523,7 @@ void ReferenceCalcNonbondedForceKernel::executeForces(ContextImpl& context) {
}
double ReferenceCalcNonbondedForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(numParticles, 3);
RealOpenMM energy = 0;
ReferenceLJCoulombIxn clj;
......@@ -648,8 +711,8 @@ void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, c
}
void ReferenceCalcCustomNonbondedForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
ReferenceCustomNonbondedIxn ixn(energyExpression, forceExpression, parameterNames, combiningRules);
bool periodic = (nonbondedMethod == CutoffPeriodic);
if (nonbondedMethod != NoCutoff) {
......@@ -666,7 +729,7 @@ void ReferenceCalcCustomNonbondedForceKernel::executeForces(ContextImpl& context
}
double ReferenceCalcCustomNonbondedForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(numParticles, 3);
RealOpenMM energy = 0;
ReferenceCustomNonbondedIxn ixn(energyExpression, forceExpression, parameterNames, combiningRules);
......@@ -726,13 +789,13 @@ void ReferenceCalcGBSAOBCForceKernel::initialize(const System& system, const GBS
}
void ReferenceCalcGBSAOBCForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
}
double ReferenceCalcGBSAOBCForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
disposeRealArray(forceData, context.getSystem().getNumParticles());
......@@ -781,8 +844,8 @@ void ReferenceCalcGBVIForceKernel::initialize(const System& system, const GBVIFo
void ReferenceCalcGBVIForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
RealOpenMM* bornRadii = new RealOpenMM[context.getSystem().getNumParticles()];
gbvi->computeBornRadii(posData, bornRadii, NULL );
gbvi->computeBornForces(bornRadii, posData, &charges[0], forceData);
......@@ -790,7 +853,7 @@ void ReferenceCalcGBVIForceKernel::executeForces(ContextImpl& context) {
}
double ReferenceCalcGBVIForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM* bornRadii = new RealOpenMM[context.getSystem().getNumParticles()];
gbvi->computeBornRadii(posData, bornRadii, NULL );
RealOpenMM energy = gbvi->computeBornEnergy(bornRadii ,posData, &charges[0]);
......@@ -831,9 +894,9 @@ void ReferenceIntegrateVerletStepKernel::initialize(const System& system, const
void ReferenceIntegrateVerletStepKernel::execute(ContextImpl& context, const VerletIntegrator& integrator) {
double stepSize = integrator.getStepSize();
RealOpenMM** posData = ((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData();
RealOpenMM** velData = ((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData();
RealOpenMM** forceData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM** velData = extractVelocities(context);
RealOpenMM** forceData = extractForces(context);
if (dynamics == 0 || stepSize != prevStepSize) {
// Recreate the computation objects with the new parameters.
......@@ -889,9 +952,9 @@ void ReferenceIntegrateLangevinStepKernel::execute(ContextImpl& context, const L
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
RealOpenMM** posData = ((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData();
RealOpenMM** velData = ((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData();
RealOpenMM** forceData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM** velData = extractVelocities(context);
RealOpenMM** forceData = extractForces(context);
if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
// Recreate the computation objects with the new parameters.
......@@ -954,9 +1017,9 @@ void ReferenceIntegrateBrownianStepKernel::execute(ContextImpl& context, const B
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
RealOpenMM** posData = ((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData();
RealOpenMM** velData = ((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData();
RealOpenMM** forceData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM** velData = extractVelocities(context);
RealOpenMM** forceData = extractForces(context);
if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
// Recreate the computation objects with the new parameters.
......@@ -1018,9 +1081,9 @@ void ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& context,
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double errorTol = integrator.getErrorTolerance();
RealOpenMM** posData = ((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData();
RealOpenMM** velData = ((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData();
RealOpenMM** forceData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM** velData = extractVelocities(context);
RealOpenMM** forceData = extractForces(context);
if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || errorTol != prevErrorTol) {
// Recreate the computation objects with the new parameters.
......@@ -1079,9 +1142,9 @@ void ReferenceIntegrateVariableVerletStepKernel::initialize(const System& system
void ReferenceIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
double errorTol = integrator.getErrorTolerance();
RealOpenMM** posData = ((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData();
RealOpenMM** velData = ((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData();
RealOpenMM** forceData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** posData = extractPositions(context);
RealOpenMM** velData = extractVelocities(context);
RealOpenMM** forceData = extractForces(context);
if (dynamics == 0 || errorTol != prevErrorTol) {
// Recreate the computation objects with the new parameters.
......@@ -1121,9 +1184,9 @@ void ReferenceApplyAndersenThermostatKernel::initialize(const System& system, co
}
void ReferenceApplyAndersenThermostatKernel::execute(ContextImpl& context) {
RealOpenMM** velData = ((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData();
RealOpenMM** velData = extractVelocities(context);
thermostat->applyThermostat(
context.getVelocities().getSize(),
context.getSystem().getNumParticles(),
velData,
masses,
static_cast<RealOpenMM>(context.getParameter(AndersenThermostat::Temperature())),
......@@ -1139,7 +1202,7 @@ void ReferenceCalcKineticEnergyKernel::initialize(const System& system) {
}
double ReferenceCalcKineticEnergyKernel::execute(ContextImpl& context) {
RealOpenMM** velData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** velData = extractVelocities(context);
double energy = 0.0;
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]);
......@@ -1156,7 +1219,7 @@ void ReferenceRemoveCMMotionKernel::initialize(const System& system, const CMMot
void ReferenceRemoveCMMotionKernel::execute(ContextImpl& context) {
if (data.stepCount%frequency != 0)
return;
RealOpenMM** velData = ((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData();
RealOpenMM** velData = extractVelocities(context);
// Calculate the center of mass momentum.
......
platforms/reference/src/ReferenceKernels.h
View file @ f5aebbd4
......@@ -99,11 +99,12 @@ public:
};
/**
* This kernel is invoked to get or set the current time.
* This kernel provides methods for setting and retrieving various state data: time, positions,
* velocities, and forces.
*/
class ReferenceUpdateTimeKernel : public UpdateTimeKernel {
class ReferenceUpdateStateDataKernel : public UpdateStateDataKernel {
public:
ReferenceUpdateTimeKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : UpdateTimeKernel(name, platform), data(data) {
ReferenceUpdateStateDataKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : UpdateStateDataKernel(name, platform), data(data) {
}
/**
* Initialize the kernel.
......@@ -123,6 +124,36 @@ public:
* @param context the context in which to execute this kernel
*/
void setTime(ContextImpl& context, double time);
/**
* Get the positions of all particles.
*
* @param positions on exit, this contains the particle positions
*/
void getPositions(ContextImpl& context, std::vector<Vec3>& positions);
/**
* Set the positions of all particles.
*
* @param positions a vector containg the particle positions
*/
void setPositions(ContextImpl& context, const std::vector<Vec3>& positions);
/**
* Get the velocities of all particles.
*
* @param velocities on exit, this contains the particle velocities
*/
void getVelocities(ContextImpl& context, std::vector<Vec3>& velocities);
/**
* Set the velocities of all particles.
*
* @param velocities a vector containg the particle velocities
*/
void setVelocities(ContextImpl& context, const std::vector<Vec3>& velocities);
/**
* Get the current forces on all particles.
*
* @param forces on exit, this contains the forces
*/
void getForces(ContextImpl& context, std::vector<Vec3>& forces);
private:
ReferencePlatform::PlatformData& data;
};
......
platforms/reference/src/ReferencePlatform.cpp
View file @ f5aebbd4
......@@ -40,7 +40,7 @@ using namespace OpenMM;
ReferencePlatform::ReferencePlatform() {
ReferenceKernelFactory* factory = new ReferenceKernelFactory();
registerKernelFactory(CalcForcesAndEnergyKernel::Name(), factory);
registerKernelFactory(UpdateTimeKernel::Name(), factory);
registerKernelFactory(UpdateStateDataKernel::Name(), factory);
registerKernelFactory(CalcHarmonicBondForceKernel::Name(), factory);
registerKernelFactory(CalcHarmonicAngleForceKernel::Name(), factory);
registerKernelFactory(CalcPeriodicTorsionForceKernel::Name(), factory);
......@@ -63,15 +63,39 @@ bool ReferencePlatform::supportsDoublePrecision() const {
return (sizeof(RealOpenMM) >= sizeof(double));
}
const StreamFactory& ReferencePlatform::getDefaultStreamFactory() const {
return defaultStreamFactory;
}
void ReferencePlatform::contextCreated(ContextImpl& context) const {
context.setPlatformData(new PlatformData());
context.setPlatformData(new PlatformData(context.getSystem().getNumParticles()));
}
void ReferencePlatform::contextDestroyed(ContextImpl& context) const {
PlatformData* data = reinterpret_cast<PlatformData*>(context.getPlatformData());
delete data;
}
ReferencePlatform::PlatformData::PlatformData(int numParticles) : time(0.0), stepCount(0), numParticles(numParticles) {
RealOpenMM** positions = new RealOpenMM*[numParticles];
RealOpenMM** velocities = new RealOpenMM*[numParticles];
RealOpenMM** forces = new RealOpenMM*[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;
}
ReferencePlatform::PlatformData::~PlatformData() {
RealOpenMM** positions = (RealOpenMM**) this->positions;
RealOpenMM** velocities = (RealOpenMM**) this->velocities;
RealOpenMM** forces = (RealOpenMM**) this->forces;
for (int i = 0; i < numParticles; ++i) {
delete[] positions[i];
delete[] velocities[i];
delete[] forces[i];
}
delete[] positions;
delete[] velocities;
delete[] forces;
}
platforms/reference/src/ReferenceStreamFactory.cpp deleted 100644 → 0
View file @ 21d67074
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/OpenMMException.h"
#include "ReferenceStreamFactory.h"
#include "ReferenceFloatStreamImpl.h"
#include "ReferenceIntStreamImpl.h"
using namespace OpenMM;
StreamImpl* ReferenceStreamFactory::createStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, ContextImpl& context) const {
switch (type) {
case Stream::Float:
case Stream::Float2:
case Stream::Float3:
case Stream::Float4:
case Stream::Double:
case Stream::Double2:
case Stream::Double3:
case Stream::Double4:
return new ReferenceFloatStreamImpl(name, size, type, platform);
case Stream::Integer:
case Stream::Integer2:
case Stream::Integer3:
case Stream::Integer4:
return new ReferenceIntStreamImpl(name, size, type, platform);
}
throw OpenMMException("Tried to create a Stream with an illegal DataType.");
}
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