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Commit 18f78c1e authored by peastman's avatar peastman
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Integrators control when atom reordering gets done, instead of having it... 

Integrators control when atom reordering gets done, instead of having it happen automatically when forces are evaluated.  This simplifies some code, and also improves unintuitive behavior with CustomIntegrator.
parent 8a8873c6
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Showing with 180 additions and 295 deletions
platforms/cuda/src/CudaContext.cpp
View file @ 18f78c1e
......@@ -67,7 +67,7 @@ bool CudaContext::hasInitializedCuda = false;
CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlockingSync, const string& precision, const string& compiler,
const string& tempDir, CudaPlatform::PlatformData& platformData) : system(system), compiler(compiler),
time(0.0), platformData(platformData), stepCount(0), computeForceCount(0), contextIsValid(false), atomsWereReordered(false), pinnedBuffer(NULL), posq(NULL),
time(0.0), platformData(platformData), stepCount(0), computeForceCount(0), stepsSinceReorder(99999), contextIsValid(false), atomsWereReordered(false), pinnedBuffer(NULL), posq(NULL),
posqCorrection(NULL), velm(NULL), force(NULL), energyBuffer(NULL), integration(NULL), expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
if (!hasInitializedCuda) {
CHECK_RESULT2(cuInit(0), "Error initializing CUDA");
......@@ -282,7 +282,6 @@ void CudaContext::initialize() {
atomIndex[i] = i;
atomIndexDevice->upload(atomIndex);
findMoleculeGroups();
moleculesInvalid = false;
nonbonded->initialize(system);
}
......@@ -821,11 +820,6 @@ void CudaContext::findMoleculeGroups() {
}
void CudaContext::invalidateMolecules() {
moleculesInvalid = true;
}
void CudaContext::validateMolecules() {
moleculesInvalid = false;
if (numAtoms == 0 || nonbonded == NULL || !nonbonded->getUseCutoff())
return;
bool valid = true;
......@@ -925,24 +919,28 @@ void CudaContext::validateMolecules() {
findMoleculeGroups();
for (int i = 0; i < (int) reorderListeners.size(); i++)
reorderListeners[i]->execute();
reorderAtoms();
}
void CudaContext::reorderAtoms(bool enforcePeriodic) {
if (numAtoms == 0 || nonbonded == NULL || !nonbonded->getUseCutoff())
void CudaContext::reorderAtoms() {
atomsWereReordered = false;
if (numAtoms == 0 || nonbonded == NULL || !nonbonded->getUseCutoff() || stepsSinceReorder < 100) {
stepsSinceReorder++;
return;
if (moleculesInvalid)
validateMolecules();
}
atomsWereReordered = true;
stepsSinceReorder = 0;
if (useDoublePrecision)
reorderAtomsImpl<double, double4, double, double4>(enforcePeriodic);
reorderAtomsImpl<double, double4, double, double4>();
else if (useMixedPrecision)
reorderAtomsImpl<float, float4, double, double4>(enforcePeriodic);
reorderAtomsImpl<float, float4, double, double4>();
else
reorderAtomsImpl<float, float4, float, float4>(enforcePeriodic);
reorderAtomsImpl<float, float4, float, float4>();
nonbonded->updateNeighborListSize();
}
template <class Real, class Real4, class Mixed, class Mixed4>
void CudaContext::reorderAtomsImpl(bool enforcePeriodic) {
void CudaContext::reorderAtomsImpl() {
// Find the range of positions and the number of bins along each axis.
Real4 padding = {0, 0, 0, 0};
......@@ -1019,7 +1017,6 @@ void CudaContext::reorderAtomsImpl(bool enforcePeriodic) {
molPos[i].x -= dx;
molPos[i].y -= dy;
molPos[i].z -= dz;
if (enforcePeriodic) {
for (int j = 0; j < (int) atoms.size(); j++) {
int atom = atoms[j]+mol.offsets[i];
Real4 p = oldPosq[atom];
......@@ -1034,7 +1031,6 @@ void CudaContext::reorderAtomsImpl(bool enforcePeriodic) {
}
}
}
}
// Select a bin for each molecule, then sort them by bin.
......
platforms/cuda/src/CudaContext.h
View file @ 18f78c1e
......@@ -298,6 +298,18 @@ public:
void setComputeForceCount(int count) {
computeForceCount = count;
}
/**
* Get the number of time steps since the atoms were reordered.
*/
int getStepsSinceReorder() const {
return stepsSinceReorder;
}
/**
* Set the number of time steps since the atoms were reordered.
*/
void setStepsSinceReorder(int steps) {
stepsSinceReorder = steps;
}
/**
* Get the number of atoms.
*/
......@@ -429,10 +441,8 @@ public:
/**
* Reorder the internal arrays of atoms to try to keep spatially contiguous atoms close
* together in the arrays.
*
* @param enforcePeriodic if true, the atom positions may be altered to enforce periodic boundary conditions
*/
void reorderAtoms(bool enforcePeriodic);
void reorderAtoms();
/**
* Add a listener that should be called whenever atoms get reordered. The CudaContext
* assumes ownership of the object, and deletes it when the context itself is deleted.
......@@ -447,15 +457,9 @@ public:
/**
* Mark that the current molecule definitions (and hence the atom order) may be invalid.
* This should be called whenever force field parameters change. It will cause the definitions
* and order to be revalidated the next to reorderAtoms() is called.
* and order to be revalidated.
*/
void invalidateMolecules();
/**
* Get whether the current molecule definitions are valid.
*/
bool getMoleculesAreInvalid() {
return moleculesInvalid;
}
private:
struct Molecule;
struct MoleculeGroup;
......@@ -472,7 +476,7 @@ private:
* This is the internal implementation of reorderAtoms(), templatized by the numerical precision in use.
*/
template <class Real, class Real4, class Mixed, class Mixed4>
void reorderAtomsImpl(bool enforcePeriodic);
void reorderAtomsImpl();
static bool hasInitializedCuda;
const System& system;
double time, computeCapability;
......@@ -481,11 +485,12 @@ private:
int contextIndex;
int stepCount;
int computeForceCount;
int stepsSinceReorder;
int numAtoms;
int paddedNumAtoms;
int numAtomBlocks;
int numThreadBlocks;
bool useBlockingSync, useDoublePrecision, useMixedPrecision, contextIsValid, atomsWereReordered, moleculesInvalid;
bool useBlockingSync, useDoublePrecision, useMixedPrecision, contextIsValid, atomsWereReordered;
std::string compiler, tempDir, gpuArchitecture;
float4 periodicBoxSizeFloat, invPeriodicBoxSizeFloat;
double4 periodicBoxSize, invPeriodicBoxSize;
......
platforms/cuda/src/CudaKernels.cpp
View file @ 18f78c1e
......@@ -86,11 +86,6 @@ void CudaCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool
cu.setAsCurrent();
CudaNonbondedUtilities& nb = cu.getNonbondedUtilities();
bool includeNonbonded = ((groups&(1<<nb.getForceGroup())) != 0);
cu.setAtomsWereReordered(false);
if (nb.getUseCutoff() && includeNonbonded && (cu.getMoleculesAreInvalid() || cu.getComputeForceCount()%100 == 0)) {
cu.reorderAtoms(!cu.getMoleculesAreInvalid());
nb.updateNeighborListSize();
}
cu.setComputeForceCount(cu.getComputeForceCount()+1);
cu.clearAutoclearBuffers();
if (includeNonbonded)
......@@ -220,6 +215,7 @@ void CudaUpdateStateDataKernel::setPositions(ContextImpl& context, const vector<
}
for (int i = 0; i < (int) cu.getPosCellOffsets().size(); i++)
cu.getPosCellOffsets()[i] = make_int4(0, 0, 0, 0);
cu.reorderAtoms();
}
void CudaUpdateStateDataKernel::getVelocities(ContextImpl& context, vector<Vec3>& velocities) {
......@@ -317,8 +313,8 @@ void CudaUpdateStateDataKernel::createCheckpoint(ContextImpl& context, ostream&
stream.write((char*) &time, sizeof(double));
int stepCount = cu.getStepCount();
stream.write((char*) &stepCount, sizeof(int));
int computeForceCount = cu.getComputeForceCount();
stream.write((char*) &computeForceCount, sizeof(int));
int stepsSinceReorder = cu.getStepsSinceReorder();
stream.write((char*) &stepsSinceReorder, sizeof(int));
char* buffer = (char*) cu.getPinnedBuffer();
cu.getPosq().download(buffer);
stream.write(buffer, cu.getPosq().getSize()*cu.getPosq().getElementSize());
......@@ -349,14 +345,14 @@ void CudaUpdateStateDataKernel::loadCheckpoint(ContextImpl& context, istream& st
throw OpenMMException("Checkpoint was created with a different numeric precision");
double time;
stream.read((char*) &time, sizeof(double));
int stepCount, computeForceCount;
int stepCount, stepsSinceReorder;
stream.read((char*) &stepCount, sizeof(int));
stream.read((char*) &computeForceCount, sizeof(int));
stream.read((char*) &stepsSinceReorder, sizeof(int));
vector<CudaContext*>& contexts = cu.getPlatformData().contexts;
for (int i = 0; i < (int) contexts.size(); i++) {
contexts[i]->setTime(time);
contexts[i]->setStepCount(stepCount);
contexts[i]->setComputeForceCount(computeForceCount);
contexts[i]->setStepsSinceReorder(stepsSinceReorder);
}
char* buffer = (char*) cu.getPinnedBuffer();
stream.read(buffer, cu.getPosq().getSize()*cu.getPosq().getElementSize());
......@@ -4134,6 +4130,7 @@ void CudaIntegrateVerletStepKernel::execute(ContextImpl& context, const VerletIn
cu.setTime(cu.getTime()+dt);
cu.setStepCount(cu.getStepCount()+1);
cu.reorderAtoms();
}
double CudaIntegrateVerletStepKernel::computeKineticEnergy(ContextImpl& context, const VerletIntegrator& integrator) {
......@@ -4221,6 +4218,7 @@ void CudaIntegrateLangevinStepKernel::execute(ContextImpl& context, const Langev
cu.setTime(cu.getTime()+stepSize);
cu.setStepCount(cu.getStepCount()+1);
cu.reorderAtoms();
}
double CudaIntegrateLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const LangevinIntegrator& integrator) {
......@@ -4283,6 +4281,7 @@ void CudaIntegrateBrownianStepKernel::execute(ContextImpl& context, const Browni
cu.setTime(cu.getTime()+stepSize);
cu.setStepCount(cu.getStepCount()+1);
cu.reorderAtoms();
}
double CudaIntegrateBrownianStepKernel::computeKineticEnergy(ContextImpl& context, const BrownianIntegrator& integrator) {
......@@ -4363,6 +4362,7 @@ double CudaIntegrateVariableVerletStepKernel::execute(ContextImpl& context, cons
}
cu.setTime(time);
cu.setStepCount(cu.getStepCount()+1);
cu.reorderAtoms();
return dt;
}
......@@ -4457,6 +4457,7 @@ double CudaIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, co
}
cu.setTime(time);
cu.setStepCount(cu.getStepCount()+1);
cu.reorderAtoms();
return dt;
}
......@@ -5129,6 +5130,7 @@ void CudaIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrat
cu.setTime(cu.getTime()+integrator.getStepSize());
cu.setStepCount(cu.getStepCount()+1);
cu.reorderAtoms();
}
double CudaIntegrateCustomStepKernel::computeKineticEnergy(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid) {
......@@ -5359,33 +5361,6 @@ void CudaApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context, d
void CudaApplyMonteCarloBarostatKernel::restoreCoordinates(ContextImpl& context) {
cu.setAsCurrent();
if (cu.getAtomsWereReordered()) {
// The atoms were reordered since we saved the positions, so we need to fix them.
const vector<int> atomOrder = cu.getAtomIndex();
int numAtoms = cu.getNumAtoms();
if (cu.getUseDoublePrecision()) {
double4* pos = (double4*) cu.getPinnedBuffer();
savedPositions->download(pos);
vector<double4> fixedPos(cu.getPaddedNumAtoms());
for (int i = 0; i < numAtoms; i++)
fixedPos[lastAtomOrder[i]] = pos[i];
for (int i = 0; i < numAtoms; i++)
pos[i] = fixedPos[atomOrder[i]];
cu.getPosq().upload(pos);
}
else {
float4* pos = (float4*) cu.getPinnedBuffer();
savedPositions->download(pos);
vector<float4> fixedPos(cu.getPaddedNumAtoms());
for (int i = 0; i < numAtoms; i++)
fixedPos[lastAtomOrder[i]] = pos[i];
for (int i = 0; i < numAtoms; i++)
pos[i] = fixedPos[atomOrder[i]];
cu.getPosq().upload(pos);
}
}
else {
int bytesToCopy = cu.getPosq().getSize()*(cu.getUseDoublePrecision() ? sizeof(double4) : sizeof(float4));
CUresult result = cuMemcpyDtoD(cu.getPosq().getDevicePointer(), savedPositions->getDevicePointer(), bytesToCopy);
if (result != CUDA_SUCCESS) {
......@@ -5393,7 +5368,6 @@ void CudaApplyMonteCarloBarostatKernel::restoreCoordinates(ContextImpl& context)
m<<"Error restoring positions for MC barostat: "<<cu.getErrorString(result)<<" ("<<result<<")";
throw OpenMMException(m.str());
}
}
}
CudaRemoveCMMotionKernel::~CudaRemoveCMMotionKernel() {
......
platforms/cuda/tests/TestCudaNonbondedForce.cpp
View file @ 18f78c1e
......@@ -739,12 +739,6 @@ void testChangingParameters() {
nonbonded->getParticleParameters(i, charge, sigma, epsilon);
nonbonded->setParticleParameters(i, 1.5*charge, 1.1*sigma, 1.7*epsilon);
}
double total = 0;
for (int i = 0; i < numParticles; i++) {
double charge, sigma, epsilon;
nonbonded->getParticleParameters(i, charge, sigma, epsilon);
total += charge;
}
nonbonded->updateParametersInContext(cuContext);
nonbonded->updateParametersInContext(referenceContext);
cuState = cuContext.getState(State::Forces | State::Energy);
......
platforms/opencl/src/OpenCLContext.cpp
View file @ 18f78c1e
......@@ -66,7 +66,7 @@ static void CL_CALLBACK errorCallback(const char* errinfo, const void* private_i
}
OpenCLContext::OpenCLContext(const System& system, int platformIndex, int deviceIndex, const string& precision, OpenCLPlatform::PlatformData& platformData) :
system(system), time(0.0), platformData(platformData), stepCount(0), computeForceCount(0), atomsWereReordered(false), posq(NULL),
system(system), time(0.0), platformData(platformData), stepCount(0), computeForceCount(0), stepsSinceReorder(99999), atomsWereReordered(false), posq(NULL),
posqCorrection(NULL), velm(NULL), forceBuffers(NULL), longForceBuffer(NULL), energyBuffer(NULL), atomIndexDevice(NULL), integration(NULL),
expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
if (precision == "single") {
......@@ -407,7 +407,6 @@ void OpenCLContext::initialize() {
atomIndex[i] = i;
atomIndexDevice->upload(atomIndex);
findMoleculeGroups();
moleculesInvalid = false;
nonbonded->initialize(system);
}
......@@ -826,11 +825,6 @@ void OpenCLContext::findMoleculeGroups() {
}
void OpenCLContext::invalidateMolecules() {
moleculesInvalid = true;
}
void OpenCLContext::validateMolecules() {
moleculesInvalid = false;
if (numAtoms == 0 || nonbonded == NULL || !nonbonded->getUseCutoff())
return;
bool valid = true;
......@@ -930,24 +924,28 @@ void OpenCLContext::validateMolecules() {
findMoleculeGroups();
for (int i = 0; i < (int) reorderListeners.size(); i++)
reorderListeners[i]->execute();
reorderAtoms();
}
void OpenCLContext::reorderAtoms(bool enforcePeriodic) {
if (numAtoms == 0 || nonbonded == NULL || !nonbonded->getUseCutoff())
void OpenCLContext::reorderAtoms() {
atomsWereReordered = false;
if (numAtoms == 0 || nonbonded == NULL || !nonbonded->getUseCutoff() || stepsSinceReorder < 100) {
stepsSinceReorder++;
return;
if (moleculesInvalid)
validateMolecules();
}
atomsWereReordered = true;
stepsSinceReorder = 0;
if (useDoublePrecision)
reorderAtomsImpl<cl_double, mm_double4, cl_double, mm_double4>(enforcePeriodic);
reorderAtomsImpl<cl_double, mm_double4, cl_double, mm_double4>();
else if (useMixedPrecision)
reorderAtomsImpl<cl_float, mm_float4, cl_double, mm_double4>(enforcePeriodic);
reorderAtomsImpl<cl_float, mm_float4, cl_double, mm_double4>();
else
reorderAtomsImpl<cl_float, mm_float4, cl_float, mm_float4>(enforcePeriodic);
reorderAtomsImpl<cl_float, mm_float4, cl_float, mm_float4>();
nonbonded->updateNeighborListSize();
}
template <class Real, class Real4, class Mixed, class Mixed4>
void OpenCLContext::reorderAtomsImpl(bool enforcePeriodic) {
void OpenCLContext::reorderAtomsImpl() {
// Find the range of positions and the number of bins along each axis.
......@@ -1023,7 +1021,6 @@ void OpenCLContext::reorderAtomsImpl(bool enforcePeriodic) {
molPos[i].x -= dx;
molPos[i].y -= dy;
molPos[i].z -= dz;
if (enforcePeriodic) {
for (int j = 0; j < (int) atoms.size(); j++) {
int atom = atoms[j]+mol.offsets[i];
Real4 p = oldPosq[atom];
......@@ -1038,7 +1035,6 @@ void OpenCLContext::reorderAtomsImpl(bool enforcePeriodic) {
}
}
}
}
// Select a bin for each molecule, then sort them by bin.
......
platforms/opencl/src/OpenCLContext.h
View file @ 18f78c1e
......@@ -381,6 +381,18 @@ public:
void setComputeForceCount(int count) {
computeForceCount = count;
}
/**
* Get the number of time steps since the atoms were reordered.
*/
int getStepsSinceReorder() const {
return stepsSinceReorder;
}
/**
* Set the number of time steps since the atoms were reordered.
*/
void setStepsSinceReorder(int steps) {
stepsSinceReorder = steps;
}
/**
* Get the number of atoms.
*/
......@@ -529,10 +541,8 @@ public:
/**
* Reorder the internal arrays of atoms to try to keep spatially contiguous atoms close
* together in the arrays.
*
* @param enforcePeriodic if true, the atom positions may be altered to enforce periodic boundary conditions
*/
void reorderAtoms(bool enforcePeriodic);
void reorderAtoms();
/**
* Add a listener that should be called whenever atoms get reordered. The OpenCLContext
* assumes ownership of the object, and deletes it when the context itself is deleted.
......@@ -547,15 +557,9 @@ public:
/**
* Mark that the current molecule definitions (and hence the atom order) may be invalid.
* This should be called whenever force field parameters change. It will cause the definitions
* and order to be revalidated the next to reorderAtoms() is called.
* and order to be revalidated.
*/
void invalidateMolecules();
/**
* Get whether the current molecule definitions are valid.
*/
bool getMoleculesAreInvalid() {
return moleculesInvalid;
}
private:
struct Molecule;
struct MoleculeGroup;
......@@ -572,7 +576,7 @@ private:
* This is the internal implementation of reorderAtoms(), templatized by the numerical precision in use.
*/
template <class Real, class Real4, class Mixed, class Mixed4>
void reorderAtomsImpl(bool enforcePeriodic);
void reorderAtomsImpl();
const System& system;
double time;
OpenCLPlatform::PlatformData& platformData;
......@@ -580,13 +584,14 @@ private:
int contextIndex;
int stepCount;
int computeForceCount;
int stepsSinceReorder;
int numAtoms;
int paddedNumAtoms;
int numAtomBlocks;
int numThreadBlocks;
int numForceBuffers;
int simdWidth;
bool supports64BitGlobalAtomics, supportsDoublePrecision, useDoublePrecision, useMixedPrecision, atomsWereReordered, moleculesInvalid;
bool supports64BitGlobalAtomics, supportsDoublePrecision, useDoublePrecision, useMixedPrecision, atomsWereReordered;
mm_float4 periodicBoxSize, invPeriodicBoxSize;
mm_double4 periodicBoxSizeDouble, invPeriodicBoxSizeDouble;
std::string defaultOptimizationOptions;
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 18f78c1e
......@@ -106,11 +106,6 @@ void OpenCLCalcForcesAndEnergyKernel::initialize(const System& system) {
void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
bool includeNonbonded = ((groups&(1<<nb.getForceGroup())) != 0);
cl.setAtomsWereReordered(false);
if (nb.getUseCutoff() && includeNonbonded && (cl.getMoleculesAreInvalid() || cl.getComputeForceCount()%100 == 0)) {
cl.reorderAtoms(!cl.getMoleculesAreInvalid());
nb.updateNeighborListSize();
}
cl.setComputeForceCount(cl.getComputeForceCount()+1);
cl.clearAutoclearBuffers();
if (includeNonbonded)
......@@ -239,6 +234,7 @@ void OpenCLUpdateStateDataKernel::setPositions(ContextImpl& context, const vecto
}
for (int i = 0; i < (int) cl.getPosCellOffsets().size(); i++)
cl.getPosCellOffsets()[i] = mm_int4(0, 0, 0, 0);
cl.reorderAtoms();
}
void OpenCLUpdateStateDataKernel::getVelocities(ContextImpl& context, vector<Vec3>& velocities) {
......@@ -342,8 +338,8 @@ void OpenCLUpdateStateDataKernel::createCheckpoint(ContextImpl& context, ostream
stream.write((char*) &time, sizeof(double));
int stepCount = cl.getStepCount();
stream.write((char*) &stepCount, sizeof(int));
int computeForceCount = cl.getComputeForceCount();
stream.write((char*) &computeForceCount, sizeof(int));
int stepsSinceReorder = cl.getStepsSinceReorder();
stream.write((char*) &stepsSinceReorder, sizeof(int));
char* buffer = (char*) cl.getPinnedBuffer();
cl.getPosq().download(buffer);
stream.write(buffer, cl.getPosq().getSize()*cl.getPosq().getElementSize());
......@@ -373,14 +369,14 @@ void OpenCLUpdateStateDataKernel::loadCheckpoint(ContextImpl& context, istream&
throw OpenMMException("Checkpoint was created with a different numeric precision");
double time;
stream.read((char*) &time, sizeof(double));
int stepCount, computeForceCount;
int stepCount, stepsSinceReorder;
stream.read((char*) &stepCount, sizeof(int));
stream.read((char*) &computeForceCount, sizeof(int));
stream.read((char*) &stepsSinceReorder, sizeof(int));
vector<OpenCLContext*>& contexts = cl.getPlatformData().contexts;
for (int i = 0; i < (int) contexts.size(); i++) {
contexts[i]->setTime(time);
contexts[i]->setStepCount(stepCount);
contexts[i]->setComputeForceCount(computeForceCount);
contexts[i]->setStepsSinceReorder(stepsSinceReorder);
}
char* buffer = (char*) cl.getPinnedBuffer();
stream.read(buffer, cl.getPosq().getSize()*cl.getPosq().getElementSize());
......@@ -4296,6 +4292,7 @@ void OpenCLIntegrateVerletStepKernel::execute(ContextImpl& context, const Verlet
cl.setTime(cl.getTime()+dt);
cl.setStepCount(cl.getStepCount()+1);
cl.reorderAtoms();
// Reduce UI lag.
......@@ -4395,6 +4392,7 @@ void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const Lang
cl.setTime(cl.getTime()+stepSize);
cl.setStepCount(cl.getStepCount()+1);
cl.reorderAtoms();
// Reduce UI lag.
......@@ -4473,6 +4471,7 @@ void OpenCLIntegrateBrownianStepKernel::execute(ContextImpl& context, const Brow
cl.setTime(cl.getTime()+stepSize);
cl.setStepCount(cl.getStepCount()+1);
cl.reorderAtoms();
// Reduce UI lag.
......@@ -4578,6 +4577,7 @@ double OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, co
}
cl.setTime(time);
cl.setStepCount(cl.getStepCount()+1);
cl.reorderAtoms();
return dt;
}
......@@ -4691,6 +4691,7 @@ double OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context,
}
cl.setTime(time);
cl.setStepCount(cl.getStepCount()+1);
cl.reorderAtoms();
return dt;
}
......@@ -5354,6 +5355,7 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
cl.setTime(cl.getTime()+integrator.getStepSize());
cl.setStepCount(cl.getStepCount()+1);
cl.reorderAtoms();
// Reduce UI lag.
......@@ -5580,33 +5582,6 @@ void OpenCLApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context,
}
void OpenCLApplyMonteCarloBarostatKernel::restoreCoordinates(ContextImpl& context) {
if (cl.getAtomsWereReordered()) {
// The atoms were reordered since we saved the positions, so we need to fix them.
const vector<int> atomOrder = cl.getAtomIndex();
int numAtoms = cl.getNumAtoms();
if (cl.getUseDoublePrecision()) {
mm_double4* pos = (mm_double4*) cl.getPinnedBuffer();
savedPositions->download(pos);
vector<mm_double4> fixedPos(cl.getPaddedNumAtoms());
for (int i = 0; i < numAtoms; i++)
fixedPos[lastAtomOrder[i]] = pos[i];
for (int i = 0; i < numAtoms; i++)
pos[i] = fixedPos[atomOrder[i]];
cl.getPosq().upload(pos);
}
else {
mm_float4* pos = (mm_float4*) cl.getPinnedBuffer();
savedPositions->download(pos);
vector<mm_float4> fixedPos(cl.getPaddedNumAtoms());
for (int i = 0; i < numAtoms; i++)
fixedPos[lastAtomOrder[i]] = pos[i];
for (int i = 0; i < numAtoms; i++)
pos[i] = fixedPos[atomOrder[i]];
cl.getPosq().upload(pos);
}
}
else
cl.getQueue().enqueueCopyBuffer(savedPositions->getDeviceBuffer(), cl.getPosq().getDeviceBuffer(), 0, 0, cl.getPosq().getSize()*sizeof(mm_float4));
}
......
platforms/opencl/tests/TestOpenCLNonbondedForce.cpp
View file @ 18f78c1e
......@@ -742,12 +742,6 @@ void testChangingParameters() {
nonbonded->getParticleParameters(i, charge, sigma, epsilon);
nonbonded->setParticleParameters(i, 1.5*charge, 1.1*sigma, 1.7*epsilon);
}
double total = 0;
for (int i = 0; i < numParticles; i++) {
double charge, sigma, epsilon;
nonbonded->getParticleParameters(i, charge, sigma, epsilon);
total += charge;
}
nonbonded->updateParametersInContext(clContext);
nonbonded->updateParametersInContext(referenceContext);
clState = clContext.getState(State::Forces | State::Energy);
......
plugins/drude/platforms/cuda/src/CudaDrudeKernels.cpp
View file @ 18f78c1e
......@@ -358,33 +358,13 @@ void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const D
cu.setTime(cu.getTime()+stepSize);
cu.setStepCount(cu.getStepCount()+1);
cu.reorderAtoms();
}
double CudaIntegrateDrudeLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
return cu.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}
class CudaIntegrateDrudeSCFStepKernel::ReorderListener : public CudaContext::ReorderListener {
public:
ReorderListener(CudaContext& cu, const vector<int>& drudeParticles, vector<int>& reorderedDrudeParticles) :
cu(cu), drudeParticles(drudeParticles), reorderedDrudeParticles(reorderedDrudeParticles) {
}
void execute() {
const vector<int>& order = cu.getAtomIndex();
int numParticles = order.size();
vector<int> inverseOrder(numParticles);
for (int i = 0; i < numParticles; i++)
inverseOrder[order[i]] = i;
int numDrudeParticles = drudeParticles.size();
for (int i = 0; i < numDrudeParticles; i++)
reorderedDrudeParticles[i] = inverseOrder[drudeParticles[i]];
}
private:
CudaContext& cu;
const vector<int>& drudeParticles;
vector<int>& reorderedDrudeParticles;
};
CudaIntegrateDrudeSCFStepKernel::~CudaIntegrateDrudeSCFStepKernel() {
if (minimizerPos != NULL)
lbfgs_free(minimizerPos);
......@@ -401,9 +381,7 @@ void CudaIntegrateDrudeSCFStepKernel::initialize(const System& system, const Dru
double charge, polarizability, aniso12, aniso34;
force.getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
drudeParticles.push_back(p);
reorderedDrudeParticles.push_back(p);
}
cu.addReorderListener(new ReorderListener(cu, drudeParticles, reorderedDrudeParticles));
// Initialize the energy minimizer.
......@@ -469,6 +447,7 @@ void CudaIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const DrudeS
cu.setTime(cu.getTime()+dt);
cu.setStepCount(cu.getStepCount()+1);
cu.reorderAtoms();
}
double CudaIntegrateDrudeSCFStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeSCFIntegrator& integrator) {
......@@ -478,39 +457,36 @@ double CudaIntegrateDrudeSCFStepKernel::computeKineticEnergy(ContextImpl& contex
struct MinimizerData {
ContextImpl& context;
CudaContext& cu;
vector<int>& reorderedDrudeParticles;
MinimizerData(ContextImpl& context, CudaContext& cu, vector<int>& reorderedDrudeParticles) : context(context), cu(cu), reorderedDrudeParticles(reorderedDrudeParticles) {}
vector<int>& drudeParticles;
MinimizerData(ContextImpl& context, CudaContext& cu, vector<int>& drudeParticles) : context(context), cu(cu), drudeParticles(drudeParticles) {}
};
static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsfloatval_t *g, const int n, const lbfgsfloatval_t step) {
MinimizerData* data = reinterpret_cast<MinimizerData*>(instance);
ContextImpl& context = data->context;
CudaContext& cu = data->cu;
vector<int>& reorderedDrudeParticles = data->reorderedDrudeParticles;
int numDrudeParticles = reorderedDrudeParticles.size();
vector<int>& drudeParticles = data->drudeParticles;
int numDrudeParticles = drudeParticles.size();
// Set the particle positions.
cu.getPosq().download(cu.getPinnedBuffer());
double4 periodicBoxSize = cu.getPeriodicBoxSize();
if (cu.getUseDoublePrecision()) {
double4* posq = (double4*) cu.getPinnedBuffer();
for (int i = 0; i < numDrudeParticles; ++i) {
double4& p = posq[reorderedDrudeParticles[i]];
int4 offset = cu.getPosCellOffsets()[reorderedDrudeParticles[i]];
p.x = x[3*i]+offset.x*periodicBoxSize.x;
p.y = x[3*i+1]+offset.y*periodicBoxSize.y;
p.z = x[3*i+2]+offset.z*periodicBoxSize.z;
double4& p = posq[drudeParticles[i]];
p.x = x[3*i];
p.y = x[3*i+1];
p.z = x[3*i+2];
}
}
else {
float4* posq = (float4*) cu.getPinnedBuffer();
for (int i = 0; i < numDrudeParticles; ++i) {
float4& p = posq[reorderedDrudeParticles[i]];
int4 offset = cu.getPosCellOffsets()[reorderedDrudeParticles[i]];
p.x = x[3*i]+offset.x*periodicBoxSize.x;
p.y = x[3*i+1]+offset.y*periodicBoxSize.y;
p.z = x[3*i+2]+offset.z*periodicBoxSize.z;
float4& p = posq[drudeParticles[i]];
p.x = x[3*i];
p.y = x[3*i+1];
p.z = x[3*i+2];
}
}
cu.getPosq().upload(cu.getPinnedBuffer());
......@@ -523,7 +499,7 @@ static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsf
double forceScale = -1.0/0x100000000;
int paddedNumAtoms = cu.getPaddedNumAtoms();
for (int i = 0; i < numDrudeParticles; ++i) {
int index = reorderedDrudeParticles[i];
int index = drudeParticles[i];
g[3*i] = forceScale*force[index];
g[3*i+1] = forceScale*force[index+paddedNumAtoms];
g[3*i+2] = forceScale*force[index+paddedNumAtoms*2];
......@@ -534,27 +510,24 @@ static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsf
void CudaIntegrateDrudeSCFStepKernel::minimize(ContextImpl& context, double tolerance) {
// Record the initial positions.
int numDrudeParticles = reorderedDrudeParticles.size();
int numDrudeParticles = drudeParticles.size();
cu.getPosq().download(cu.getPinnedBuffer());
double4 periodicBoxSize = cu.getPeriodicBoxSize();
if (cu.getUseDoublePrecision()) {
double4* posq = (double4*) cu.getPinnedBuffer();
for (int i = 0; i < numDrudeParticles; ++i) {
double4 p = posq[reorderedDrudeParticles[i]];
int4 offset = cu.getPosCellOffsets()[reorderedDrudeParticles[i]];
minimizerPos[3*i] = p.x-offset.x*periodicBoxSize.x;
minimizerPos[3*i+1] = p.y-offset.y*periodicBoxSize.y;
minimizerPos[3*i+2] = p.z-offset.z*periodicBoxSize.z;
double4 p = posq[drudeParticles[i]];
minimizerPos[3*i] = p.x;
minimizerPos[3*i+1] = p.y;
minimizerPos[3*i+2] = p.z;
}
}
else {
float4* posq = (float4*) cu.getPinnedBuffer();
for (int i = 0; i < numDrudeParticles; ++i) {
float4 p = posq[reorderedDrudeParticles[i]];
int4 offset = cu.getPosCellOffsets()[reorderedDrudeParticles[i]];
minimizerPos[3*i] = p.x-offset.x*periodicBoxSize.x;
minimizerPos[3*i+1] = p.y-offset.y*periodicBoxSize.y;
minimizerPos[3*i+2] = p.z-offset.z*periodicBoxSize.z;
float4 p = posq[drudeParticles[i]];
minimizerPos[3*i] = p.x;
minimizerPos[3*i+1] = p.y;
minimizerPos[3*i+2] = p.z;
}
minimizerParams.xtol = 1e-7;
}
......@@ -571,6 +544,6 @@ void CudaIntegrateDrudeSCFStepKernel::minimize(ContextImpl& context, double tole
// Perform the minimization.
lbfgsfloatval_t fx;
MinimizerData data(context, cu, reorderedDrudeParticles);
MinimizerData data(context, cu, drudeParticles);
lbfgs(numDrudeParticles*3, minimizerPos, &fx, evaluate, NULL, &data, &minimizerParams);
}
\ No newline at end of file
plugins/drude/platforms/cuda/src/CudaDrudeKernels.h
View file @ 18f78c1e
......@@ -148,12 +148,10 @@ public:
*/
double computeKineticEnergy(ContextImpl& context, const DrudeSCFIntegrator& integrator);
private:
class ReorderListener;
void minimize(ContextImpl& context, double tolerance);
CudaContext& cu;
double prevStepSize;
std::vector<int> drudeParticles;
std::vector<int> reorderedDrudeParticles;
lbfgsfloatval_t *minimizerPos;
lbfgs_parameter_t minimizerParams;
CUfunction kernel1, kernel2;
......
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.cpp
View file @ 18f78c1e
......@@ -364,33 +364,13 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
cl.setTime(cl.getTime()+stepSize);
cl.setStepCount(cl.getStepCount()+1);
cl.reorderAtoms();
}
double OpenCLIntegrateDrudeLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
return cl.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}
class OpenCLIntegrateDrudeSCFStepKernel::ReorderListener : public OpenCLContext::ReorderListener {
public:
ReorderListener(OpenCLContext& cl, const vector<int>& drudeParticles, vector<int>& reorderedDrudeParticles) :
cl(cl), drudeParticles(drudeParticles), reorderedDrudeParticles(reorderedDrudeParticles) {
}
void execute() {
const vector<int>& order = cl.getAtomIndex();
int numParticles = order.size();
vector<int> inverseOrder(numParticles);
for (int i = 0; i < numParticles; i++)
inverseOrder[order[i]] = i;
int numDrudeParticles = drudeParticles.size();
for (int i = 0; i < numDrudeParticles; i++)
reorderedDrudeParticles[i] = inverseOrder[drudeParticles[i]];
}
private:
OpenCLContext& cl;
const vector<int>& drudeParticles;
vector<int>& reorderedDrudeParticles;
};
OpenCLIntegrateDrudeSCFStepKernel::~OpenCLIntegrateDrudeSCFStepKernel() {
if (minimizerPos != NULL)
lbfgs_free(minimizerPos);
......@@ -406,9 +386,7 @@ void OpenCLIntegrateDrudeSCFStepKernel::initialize(const System& system, const D
double charge, polarizability, aniso12, aniso34;
force.getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
drudeParticles.push_back(p);
reorderedDrudeParticles.push_back(p);
}
cl.addReorderListener(new ReorderListener(cl, drudeParticles, reorderedDrudeParticles));
// Initialize the energy minimizer.
......@@ -481,6 +459,7 @@ void OpenCLIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const Drud
cl.setTime(cl.getTime()+dt);
cl.setStepCount(cl.getStepCount()+1);
cl.reorderAtoms();
// Reduce UI lag.
......@@ -496,39 +475,36 @@ double OpenCLIntegrateDrudeSCFStepKernel::computeKineticEnergy(ContextImpl& cont
struct MinimizerData {
ContextImpl& context;
OpenCLContext& cl;
vector<int>& reorderedDrudeParticles;
MinimizerData(ContextImpl& context, OpenCLContext& cl, vector<int>& reorderedDrudeParticles) : context(context), cl(cl), reorderedDrudeParticles(reorderedDrudeParticles) {}
vector<int>& drudeParticles;
MinimizerData(ContextImpl& context, OpenCLContext& cl, vector<int>& drudeParticles) : context(context), cl(cl), drudeParticles(drudeParticles) {}
};
static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsfloatval_t *g, const int n, const lbfgsfloatval_t step) {
MinimizerData* data = reinterpret_cast<MinimizerData*>(instance);
ContextImpl& context = data->context;
OpenCLContext& cl = data->cl;
vector<int>& reorderedDrudeParticles = data->reorderedDrudeParticles;
int numDrudeParticles = reorderedDrudeParticles.size();
vector<int>& drudeParticles = data->drudeParticles;
int numDrudeParticles = drudeParticles.size();
// Set the particle positions.
cl.getPosq().download(cl.getPinnedBuffer());
mm_double4 periodicBoxSize = cl.getPeriodicBoxSizeDouble();
if (cl.getUseDoublePrecision()) {
mm_double4* posq = (mm_double4*) cl.getPinnedBuffer();
for (int i = 0; i < numDrudeParticles; ++i) {
mm_double4& p = posq[reorderedDrudeParticles[i]];
mm_int4 offset = cl.getPosCellOffsets()[reorderedDrudeParticles[i]];
p.x = x[3*i]+offset.x*periodicBoxSize.x;
p.y = x[3*i+1]+offset.y*periodicBoxSize.y;
p.z = x[3*i+2]+offset.z*periodicBoxSize.z;
mm_double4& p = posq[drudeParticles[i]];
p.x = x[3*i];
p.y = x[3*i+1];
p.z = x[3*i+2];
}
}
else {
mm_float4* posq = (mm_float4*) cl.getPinnedBuffer();
for (int i = 0; i < numDrudeParticles; ++i) {
mm_float4& p = posq[reorderedDrudeParticles[i]];
mm_int4 offset = cl.getPosCellOffsets()[reorderedDrudeParticles[i]];
p.x = x[3*i]+offset.x*periodicBoxSize.x;
p.y = x[3*i+1]+offset.y*periodicBoxSize.y;
p.z = x[3*i+2]+offset.z*periodicBoxSize.z;
mm_float4& p = posq[drudeParticles[i]];
p.x = x[3*i];
p.y = x[3*i+1];
p.z = x[3*i+2];
}
}
cl.getPosq().upload(cl.getPinnedBuffer());
......@@ -540,7 +516,7 @@ static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsf
if (cl.getUseDoublePrecision()) {
mm_double4* force = (mm_double4*) cl.getPinnedBuffer();
for (int i = 0; i < numDrudeParticles; ++i) {
int index = reorderedDrudeParticles[i];
int index = drudeParticles[i];
g[3*i] = -force[index].x;
g[3*i+1] = -force[index].y;
g[3*i+2] = -force[index].z;
......@@ -549,7 +525,7 @@ static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsf
else {
mm_float4* force = (mm_float4*) cl.getPinnedBuffer();
for (int i = 0; i < numDrudeParticles; ++i) {
int index = reorderedDrudeParticles[i];
int index = drudeParticles[i];
g[3*i] = -force[index].x;
g[3*i+1] = -force[index].y;
g[3*i+2] = -force[index].z;
......@@ -561,27 +537,24 @@ static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsf
void OpenCLIntegrateDrudeSCFStepKernel::minimize(ContextImpl& context, double tolerance) {
// Record the initial positions.
int numDrudeParticles = reorderedDrudeParticles.size();
int numDrudeParticles = drudeParticles.size();
cl.getPosq().download(cl.getPinnedBuffer());
mm_double4 periodicBoxSize = cl.getPeriodicBoxSizeDouble();
if (cl.getUseDoublePrecision()) {
mm_double4* posq = (mm_double4*) cl.getPinnedBuffer();
for (int i = 0; i < numDrudeParticles; ++i) {
mm_double4 p = posq[reorderedDrudeParticles[i]];
mm_int4 offset = cl.getPosCellOffsets()[reorderedDrudeParticles[i]];
minimizerPos[3*i] = p.x-offset.x*periodicBoxSize.x;
minimizerPos[3*i+1] = p.y-offset.y*periodicBoxSize.y;
minimizerPos[3*i+2] = p.z-offset.z*periodicBoxSize.z;
mm_double4 p = posq[drudeParticles[i]];
minimizerPos[3*i] = p.x;
minimizerPos[3*i+1] = p.y;
minimizerPos[3*i+2] = p.z;
}
}
else {
mm_float4* posq = (mm_float4*) cl.getPinnedBuffer();
for (int i = 0; i < numDrudeParticles; ++i) {
mm_float4 p = posq[reorderedDrudeParticles[i]];
mm_int4 offset = cl.getPosCellOffsets()[reorderedDrudeParticles[i]];
minimizerPos[3*i] = p.x-offset.x*periodicBoxSize.x;
minimizerPos[3*i+1] = p.y-offset.y*periodicBoxSize.y;
minimizerPos[3*i+2] = p.z-offset.z*periodicBoxSize.z;
mm_float4 p = posq[drudeParticles[i]];
minimizerPos[3*i] = p.x;
minimizerPos[3*i+1] = p.y;
minimizerPos[3*i+2] = p.z;
}
minimizerParams.xtol = 1e-7;
}
......@@ -598,6 +571,6 @@ void OpenCLIntegrateDrudeSCFStepKernel::minimize(ContextImpl& context, double to
// Perform the minimization.
lbfgsfloatval_t fx;
MinimizerData data(context, cl, reorderedDrudeParticles);
MinimizerData data(context, cl, drudeParticles);
lbfgs(numDrudeParticles*3, minimizerPos, &fx, evaluate, NULL, &data, &minimizerParams);
}
\ No newline at end of file
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.h
View file @ 18f78c1e
......@@ -149,13 +149,11 @@ public:
*/
double computeKineticEnergy(ContextImpl& context, const DrudeSCFIntegrator& integrator);
private:
class ReorderListener;
void minimize(ContextImpl& context, double tolerance);
OpenCLContext& cl;
bool hasInitializedKernels;
double prevStepSize;
std::vector<int> drudeParticles;
std::vector<int> reorderedDrudeParticles;
lbfgsfloatval_t *minimizerPos;
lbfgs_parameter_t minimizerParams;
cl::Kernel kernel1, kernel2;
......
plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.cpp
View file @ 18f78c1e
......@@ -132,6 +132,7 @@ void CudaIntegrateRPMDStepKernel::initialize(const System& system, const RPMDInt
}
void CudaIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDIntegrator& integrator, bool forcesAreValid) {
cu.setAsCurrent();
CudaIntegrationUtilities& integration = cu.getIntegrationUtilities();
// Loop over copies and compute the force on each one.
......@@ -178,6 +179,15 @@ void CudaIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDIntegr
cu.setTime(cu.getTime()+dt);
cu.setStepCount(cu.getStepCount()+1);
cu.reorderAtoms();
if (cu.getAtomsWereReordered() && cu.getNonbondedUtilities().getUsePeriodic()) {
// Atoms may have been translated into a different periodic box, so apply
// the same translation to all the beads.
int i = numCopies-1;
void* args[] = {&positions->getDevicePointer(), &cu.getPosq().getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};
cu.executeKernel(translateKernel, args, cu.getNumAtoms());
}
}
void CudaIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
......@@ -188,13 +198,6 @@ void CudaIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
context.computeVirtualSites();
context.updateContextState();
context.calcForcesAndEnergy(true, false);
if (cu.getAtomsWereReordered() && cu.getNonbondedUtilities().getUsePeriodic()) {
// Atoms may have been translated into a different periodic box, so apply
// the same translation to all the beads.
void* args[] = {&positions->getDevicePointer(), &cu.getPosq().getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};
cu.executeKernel(translateKernel, args, cu.getNumAtoms());
}
void* copyFromContextArgs[] = {&cu.getForce().getDevicePointer(), &forces->getDevicePointer(), &cu.getVelm().getDevicePointer(),
&velocities->getDevicePointer(), &cu.getPosq().getDevicePointer(), &positions->getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};
cu.executeKernel(copyFromContextKernel, copyFromContextArgs, cu.getNumAtoms());
......
plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernels.cpp
View file @ 18f78c1e
......@@ -190,6 +190,14 @@ void OpenCLIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDInte
cl.setTime(cl.getTime()+dt);
cl.setStepCount(cl.getStepCount()+1);
cl.reorderAtoms();
if (cl.getAtomsWereReordered() && cl.getNonbondedUtilities().getUsePeriodic()) {
// Atoms may have been translated into a different periodic box, so apply
// the same translation to all the beads.
translateKernel.setArg<cl_int>(3, numCopies-1);
cl.executeKernel(translateKernel, cl.getNumAtoms());
}
}
void OpenCLIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
......@@ -199,13 +207,6 @@ void OpenCLIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
context.computeVirtualSites();
context.updateContextState();
context.calcForcesAndEnergy(true, false);
if (cl.getAtomsWereReordered() && cl.getNonbondedUtilities().getUsePeriodic()) {
// Atoms may have been translated into a different periodic box, so apply
// the same translation to all the beads.
translateKernel.setArg<cl_int>(3, i);
cl.executeKernel(translateKernel, cl.getNumAtoms());
}
copyFromContextKernel.setArg<cl_int>(7, i);
cl.executeKernel(copyFromContextKernel, cl.getNumAtoms());
}
......
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