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Commit 669e314e authored by John Chodera (MSKCC)'s avatar John Chodera (MSKCC)
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Merge remote-tracking branch 'upstream/master' into fix-mts

parents 283b1acd 388bf972
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.travis.yml
View file @ 669e314e
......@@ -109,7 +109,7 @@ before_install:
sudo easy_install pytest;
fi
- if [[ "$OPENCL" == "true" ]]; then
wget https://jenkins.choderalab.org/userContent/AMD-APP-SDKInstaller-v3.0.130.135-GA-linux64.tar.bz2;
wget http://s3.amazonaws.com/omnia-ci/AMD-APP-SDKInstaller-v3.0.130.135-GA-linux64.tar.bz2;
tar -xjf AMD-APP-SDK*.tar.bz2;
AMDAPPSDK=${HOME}/AMDAPPSDK;
export OPENCL_VENDOR_PATH=${AMDAPPSDK}/etc/OpenCL/vendors;
......
README.md
View file @ 669e314e
[![Build Status](https://travis-ci.org/pandegroup/openmm.svg?branch=master)](https://travis-ci.org/pandegroup/openmm)
[![Anaconda Cloud Badge](https://anaconda.org/omnia/openmm/badges/downloads.svg)](https://anaconda.org/omnia/openmm)
## OpenMM: A High Performance Molecular Dynamics Library
Introduction
......@@ -10,15 +13,3 @@ Getting Help
------------
Need Help? Check out the [documentation](http://docs.openmm.org/) and [discussion forums](https://simtk.org/forums/viewforum.php?f=161).
[C++ API Reference](http://docs.openmm.org/6.3.0/api-c++/namespaceOpenMM.html)
[Python API Reference](http://docs.openmm.org/6.3.0/api-python/annotated.html)
Badges
------
* Travis CI `linux` and `osx` integration tests:
* GitHub master [![Build Status](https://travis-ci.org/pandegroup/openmm.svg?branch=master)](https://travis-ci.org/pandegroup/openmm)
* `openmm-dev` recipe [![Build Status](https://travis-ci.org/omnia-md/conda-dev-recipes.svg?branch=master)](https://travis-ci.org/omnia-md/conda-dev-recipes)
* Anaconda Cloud `openmm` conda release: [![Binstar `openmm` conda release](https://anaconda.org/omnia/openmm/badges/version.svg)](https://anaconda.org/omnia/openmm)
* Anaconda Cloud `openmm-dev` conda package: [![Binstar `openmm-dev` conda package](https://anaconda.org/omnia/openmm-dev/badges/version.svg)](https://anaconda.org/omnia/openmm-dev)
platforms/cuda/include/CudaNonbondedUtilities.h
View file @ 669e314e
......@@ -78,8 +78,9 @@ public:
* @param exclusionList for each atom, specifies the list of other atoms whose interactions should be excluded
* @param kernel the code to evaluate the interaction
* @param forceGroup the force group in which the interaction should be calculated
* @param supportsPairList specifies whether this interaction can work with a neighbor list that uses a separate pair list
*/
void addInteraction(bool usesCutoff, bool usesPeriodic, bool usesExclusions, double cutoffDistance, const std::vector<std::vector<int> >& exclusionList, const std::string& kernel, int forceGroup);
void addInteraction(bool usesCutoff, bool usesPeriodic, bool usesExclusions, double cutoffDistance, const std::vector<std::vector<int> >& exclusionList, const std::string& kernel, int forceGroup, bool supportsPairList=false);
/**
* Add a per-atom parameter that the default interaction kernel may depend on.
*/
......@@ -189,6 +190,12 @@ public:
CudaArray& getInteractingAtoms() {
return *interactingAtoms;
}
/**
* Get the array containing single pairs in the neighbor list.
*/
CudaArray& getSinglePairs() {
return *singlePairs;
}
/**
* Get the array containing exclusion flags.
*/
......@@ -270,6 +277,8 @@ private:
CudaArray* interactingTiles;
CudaArray* interactingAtoms;
CudaArray* interactionCount;
CudaArray* singlePairs;
CudaArray* singlePairCount;
CudaArray* blockCenter;
CudaArray* blockBoundingBox;
CudaArray* sortedBlocks;
......@@ -288,8 +297,8 @@ private:
std::map<int, double> groupCutoff;
std::map<int, std::string> groupKernelSource;
double lastCutoff;
bool useCutoff, usePeriodic, anyExclusions, usePadding, forceRebuildNeighborList;
int startTileIndex, numTiles, startBlockIndex, numBlocks, maxTiles, maxExclusions, numForceThreadBlocks, forceThreadBlockSize, numAtoms, groupFlags;
bool useCutoff, usePeriodic, anyExclusions, usePadding, forceRebuildNeighborList, canUsePairList;
int startTileIndex, numTiles, startBlockIndex, numBlocks, maxTiles, maxSinglePairs, maxExclusions, numForceThreadBlocks, forceThreadBlockSize, numAtoms, groupFlags;
};
/**
......
platforms/cuda/include/CudaParallelKernels.h
View file @ 669e314e
......@@ -83,7 +83,7 @@ private:
std::vector<Kernel> kernels;
std::vector<long long> completionTimes;
std::vector<double> contextNonbondedFractions;
int* tileCounts;
int2* interactionCounts;
CudaArray* contextForces;
void* pinnedPositionBuffer;
long long* pinnedForceBuffer;
......
platforms/cuda/src/CudaContext.cpp
View file @ 669e314e
......@@ -130,8 +130,10 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
#endif
struct stat info;
isNvccAvailable = (res == 0 && stat(tempDir.c_str(), &info) == 0);
int cudaDriverVersion;
cuDriverGetVersion(&cudaDriverVersion);
static bool hasShownNvccWarning = false;
if (hasCompilerKernel && !isNvccAvailable && !hasShownNvccWarning) {
if (hasCompilerKernel && !isNvccAvailable && !hasShownNvccWarning && cudaDriverVersion < 8000) {
hasShownNvccWarning = true;
printf("Could not find nvcc. Using runtime compiler, which may produce slower performance. ");
#ifdef WIN32
......@@ -208,14 +210,14 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
int major, minor;
CHECK_RESULT(cuDeviceComputeCapability(&major, &minor, device));
int numThreadBlocksPerComputeUnit = (major >= 6 ? 4 : 6);
#if __CUDA_API_VERSION < 7000
if (cudaDriverVersion < 7000) {
// This is a workaround to support GTX 980 with CUDA 6.5. It reports
// its compute capability as 5.2, but the compiler doesn't support
// anything beyond 5.0.
if (major == 5)
minor = 0;
#endif
#if __CUDA_API_VERSION < 8000
}
if (cudaDriverVersion < 8000) {
// This is a workaround to support Pascal with CUDA 7.5. It reports
// its compute capability as 6.x, but the compiler doesn't support
// anything beyond 5.3.
......@@ -223,7 +225,7 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
major = 5;
minor = 3;
}
#endif
}
gpuArchitecture = intToString(major)+intToString(minor);
computeCapability = major+0.1*minor;
......
platforms/cuda/src/CudaKernels.cpp
View file @ 669e314e
......@@ -1920,7 +1920,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
// Add the interaction to the default nonbonded kernel.
string source = cu.replaceStrings(CudaKernelSources::coulombLennardJones, defines);
cu.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, true, force.getCutoffDistance(), exclusionList, source, force.getForceGroup());
cu.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, true, force.getCutoffDistance(), exclusionList, source, force.getForceGroup(), true);
if (hasLJ)
cu.getNonbondedUtilities().addParameter(CudaNonbondedUtilities::ParameterInfo("sigmaEpsilon", "float", 2, sizeof(float2), sigmaEpsilon->getDevicePointer()));
......@@ -2314,7 +2314,7 @@ void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const
if (force.getNumInteractionGroups() > 0)
initInteractionGroups(force, source, tableTypes);
else {
cu.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, true, force.getCutoffDistance(), exclusionList, source, force.getForceGroup());
cu.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, true, force.getCutoffDistance(), exclusionList, source, force.getForceGroup(), true);
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
CudaNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
cu.getNonbondedUtilities().addParameter(CudaNonbondedUtilities::ParameterInfo(prefix+"params"+cu.intToString(i+1), buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
......
platforms/cuda/src/CudaNonbondedUtilities.cpp
View file @ 669e314e
......@@ -64,15 +64,16 @@ private:
CudaNonbondedUtilities::CudaNonbondedUtilities(CudaContext& context) : context(context), useCutoff(false), usePeriodic(false), anyExclusions(false), usePadding(true),
exclusionIndices(NULL), exclusionRowIndices(NULL), exclusionTiles(NULL), exclusions(NULL), interactingTiles(NULL), interactingAtoms(NULL),
interactionCount(NULL), blockCenter(NULL), blockBoundingBox(NULL), sortedBlocks(NULL), sortedBlockCenter(NULL), sortedBlockBoundingBox(NULL),
oldPositions(NULL), rebuildNeighborList(NULL), blockSorter(NULL), pinnedCountBuffer(NULL), forceRebuildNeighborList(true), lastCutoff(0.0), groupFlags(0) {
interactionCount(NULL), singlePairs(NULL), blockCenter(NULL), blockBoundingBox(NULL), sortedBlocks(NULL), sortedBlockCenter(NULL), sortedBlockBoundingBox(NULL),
oldPositions(NULL), rebuildNeighborList(NULL), blockSorter(NULL), pinnedCountBuffer(NULL), forceRebuildNeighborList(true), lastCutoff(0.0), groupFlags(0),
canUsePairList(true) {
// Decide how many thread blocks to use.
string errorMessage = "Error initializing nonbonded utilities";
int multiprocessors;
CHECK_RESULT(cuDeviceGetAttribute(&multiprocessors, CU_DEVICE_ATTRIBUTE_MULTIPROCESSOR_COUNT, context.getDevice()));
CHECK_RESULT(cuEventCreate(&downloadCountEvent, 0));
CHECK_RESULT(cuMemHostAlloc((void**) &pinnedCountBuffer, sizeof(int), CU_MEMHOSTALLOC_PORTABLE));
CHECK_RESULT(cuMemHostAlloc((void**) &pinnedCountBuffer, 2*sizeof(int), CU_MEMHOSTALLOC_PORTABLE));
numForceThreadBlocks = 4*multiprocessors;
forceThreadBlockSize = (context.getComputeCapability() < 2.0 ? 128 : 256);
}
......@@ -92,6 +93,8 @@ CudaNonbondedUtilities::~CudaNonbondedUtilities() {
delete interactingAtoms;
if (interactionCount != NULL)
delete interactionCount;
if (singlePairs != NULL)
delete singlePairs;
if (blockCenter != NULL)
delete blockCenter;
if (blockBoundingBox != NULL)
......@@ -113,7 +116,7 @@ CudaNonbondedUtilities::~CudaNonbondedUtilities() {
cuEventDestroy(downloadCountEvent);
}
void CudaNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic, bool usesExclusions, double cutoffDistance, const vector<vector<int> >& exclusionList, const string& kernel, int forceGroup) {
void CudaNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic, bool usesExclusions, double cutoffDistance, const vector<vector<int> >& exclusionList, const string& kernel, int forceGroup, bool supportsPairList) {
if (groupCutoff.size() > 0) {
if (usesCutoff != useCutoff)
throw OpenMMException("All Forces must agree on whether to use a cutoff");
......@@ -128,6 +131,7 @@ void CudaNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic,
usePeriodic = usesPeriodic;
groupCutoff[forceGroup] = cutoffDistance;
groupFlags |= 1<<forceGroup;
canUsePairList &= supportsPairList;
if (kernel.size() > 0) {
if (groupKernelSource.find(forceGroup) == groupKernelSource.end())
groupKernelSource[forceGroup] = "";
......@@ -279,9 +283,11 @@ void CudaNonbondedUtilities::initialize(const System& system) {
maxTiles = numTiles;
if (maxTiles < 1)
maxTiles = 1;
maxSinglePairs = 5*numAtoms;
interactingTiles = CudaArray::create<int>(context, maxTiles, "interactingTiles");
interactingAtoms = CudaArray::create<int>(context, CudaContext::TileSize*maxTiles, "interactingAtoms");
interactionCount = CudaArray::create<unsigned int>(context, 1, "interactionCount");
interactionCount = CudaArray::create<unsigned int>(context, 2, "interactionCount");
singlePairs = CudaArray::create<int2>(context, maxSinglePairs, "singlePairs");
int elementSize = (context.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
blockCenter = new CudaArray(context, numAtomBlocks, 4*elementSize, "blockCenter");
blockBoundingBox = new CudaArray(context, numAtomBlocks, 4*elementSize, "blockBoundingBox");
......@@ -291,7 +297,7 @@ void CudaNonbondedUtilities::initialize(const System& system) {
oldPositions = new CudaArray(context, numAtoms, 4*elementSize, "oldPositions");
rebuildNeighborList = CudaArray::create<int>(context, 1, "rebuildNeighborList");
blockSorter = new CudaSort(context, new BlockSortTrait(context.getUseDoublePrecision()), numAtomBlocks);
vector<unsigned int> count(1, 0);
vector<unsigned int> count(2, 0);
interactionCount->upload(count);
}
......@@ -316,6 +322,8 @@ void CudaNonbondedUtilities::initialize(const System& system) {
forceArgs.push_back(&blockCenter->getDevicePointer());
forceArgs.push_back(&blockBoundingBox->getDevicePointer());
forceArgs.push_back(&interactingAtoms->getDevicePointer());
forceArgs.push_back(&maxSinglePairs);
forceArgs.push_back(&singlePairs->getDevicePointer());
}
for (int i = 0; i < (int) parameters.size(); i++)
forceArgs.push_back(&parameters[i].getMemory());
......@@ -353,8 +361,10 @@ void CudaNonbondedUtilities::initialize(const System& system) {
findInteractingBlocksArgs.push_back(&interactionCount->getDevicePointer());
findInteractingBlocksArgs.push_back(&interactingTiles->getDevicePointer());
findInteractingBlocksArgs.push_back(&interactingAtoms->getDevicePointer());
findInteractingBlocksArgs.push_back(&singlePairs->getDevicePointer());
findInteractingBlocksArgs.push_back(&context.getPosq().getDevicePointer());
findInteractingBlocksArgs.push_back(&maxTiles);
findInteractingBlocksArgs.push_back(&maxSinglePairs);
findInteractingBlocksArgs.push_back(&startBlockIndex);
findInteractingBlocksArgs.push_back(&numBlocks);
findInteractingBlocksArgs.push_back(&sortedBlocks->getDevicePointer());
......@@ -424,12 +434,13 @@ void CudaNonbondedUtilities::computeInteractions(int forceGroups, bool includeFo
bool CudaNonbondedUtilities::updateNeighborListSize() {
if (!useCutoff)
return false;
if (pinnedCountBuffer[0] <= (unsigned int) maxTiles)
if (pinnedCountBuffer[0] <= maxTiles && pinnedCountBuffer[1] <= maxSinglePairs)
return false;
// The most recent timestep had too many interactions to fit in the arrays. Make the arrays bigger to prevent
// this from happening in the future.
if (pinnedCountBuffer[0] > maxTiles) {
maxTiles = (int) (1.2*pinnedCountBuffer[0]);
int totalTiles = context.getNumAtomBlocks()*(context.getNumAtomBlocks()+1)/2;
if (maxTiles > totalTiles)
......@@ -446,6 +457,16 @@ bool CudaNonbondedUtilities::updateNeighborListSize() {
if (forceArgs.size() > 0)
forceArgs[17] = &interactingAtoms->getDevicePointer();
findInteractingBlocksArgs[7] = &interactingAtoms->getDevicePointer();
}
if (pinnedCountBuffer[1] > maxSinglePairs) {
maxSinglePairs = (int) (1.2*pinnedCountBuffer[1]);
delete singlePairs;
singlePairs = NULL; // Avoid an error in the destructor if the following allocation fails
singlePairs = CudaArray::create<int2>(context, maxSinglePairs, "singlePairs");
if (forceArgs.size() > 0)
forceArgs[19] = &singlePairs->getDevicePointer();
findInteractingBlocksArgs[8] = &singlePairs->getDevicePointer();
}
forceRebuildNeighborList = true;
context.setForcesValid(false);
return true;
......@@ -493,6 +514,7 @@ void CudaNonbondedUtilities::createKernelsForGroups(int groups) {
if (usePeriodic)
defines["USE_PERIODIC"] = "1";
defines["MAX_EXCLUSIONS"] = context.intToString(maxExclusions);
defines["MAX_BITS_FOR_PAIRS"] = (canUsePairList ? "2" : "0");
CUmodule interactingBlocksProgram = context.createModule(CudaKernelSources::vectorOps+CudaKernelSources::findInteractingBlocks, defines);
kernels.findBlockBoundsKernel = context.getKernel(interactingBlocksProgram, "findBlockBounds");
kernels.sortBoxDataKernel = context.getKernel(interactingBlocksProgram, "sortBoxData");
......
platforms/cuda/src/CudaParallelKernels.cpp
View file @ 669e314e
......@@ -63,8 +63,8 @@ if (result != CUDA_SUCCESS) { \
class CudaParallelCalcForcesAndEnergyKernel::BeginComputationTask : public CudaContext::WorkTask {
public:
BeginComputationTask(ContextImpl& context, CudaContext& cu, CudaCalcForcesAndEnergyKernel& kernel,
bool includeForce, bool includeEnergy, int groups, void* pinnedMemory, CUevent event, int& numTiles) : context(context), cu(cu), kernel(kernel),
includeForce(includeForce), includeEnergy(includeEnergy), groups(groups), pinnedMemory(pinnedMemory), event(event), numTiles(numTiles) {
bool includeForce, bool includeEnergy, int groups, void* pinnedMemory, CUevent event, int2& interactionCount) : context(context), cu(cu), kernel(kernel),
includeForce(includeForce), includeEnergy(includeEnergy), groups(groups), pinnedMemory(pinnedMemory), event(event), interactionCount(interactionCount) {
}
void execute() {
// Copy coordinates over to this device and execute the kernel.
......@@ -77,7 +77,7 @@ public:
}
kernel.beginComputation(context, includeForce, includeEnergy, groups);
if (cu.getNonbondedUtilities().getUsePeriodic())
cu.getNonbondedUtilities().getInteractionCount().download(&numTiles, false);
cu.getNonbondedUtilities().getInteractionCount().download(&interactionCount, false);
}
private:
ContextImpl& context;
......@@ -87,15 +87,15 @@ private:
int groups;
void* pinnedMemory;
CUevent event;
int& numTiles;
int2& interactionCount;
};
class CudaParallelCalcForcesAndEnergyKernel::FinishComputationTask : public CudaContext::WorkTask {
public:
FinishComputationTask(ContextImpl& context, CudaContext& cu, CudaCalcForcesAndEnergyKernel& kernel,
bool includeForce, bool includeEnergy, int groups, double& energy, long long& completionTime, long long* pinnedMemory, CudaArray& contextForces, bool& valid, int& numTiles) :
bool includeForce, bool includeEnergy, int groups, double& energy, long long& completionTime, long long* pinnedMemory, CudaArray& contextForces, bool& valid, int2& interactionCount) :
context(context), cu(cu), kernel(kernel), includeForce(includeForce), includeEnergy(includeEnergy), groups(groups), energy(energy),
completionTime(completionTime), pinnedMemory(pinnedMemory), contextForces(contextForces), valid(valid), numTiles(numTiles) {
completionTime(completionTime), pinnedMemory(pinnedMemory), contextForces(contextForces), valid(valid), interactionCount(interactionCount) {
}
void execute() {
// Execute the kernel, then download forces.
......@@ -120,7 +120,8 @@ public:
cu.getForce().download(&pinnedMemory[(cu.getContextIndex()-1)*numAtoms*3]);
}
}
if (cu.getNonbondedUtilities().getUsePeriodic() && numTiles > cu.getNonbondedUtilities().getInteractingTiles().getSize()) {
if (cu.getNonbondedUtilities().getUsePeriodic() && (interactionCount.x > cu.getNonbondedUtilities().getInteractingTiles().getSize() ||
interactionCount.y > cu.getNonbondedUtilities().getSinglePairs().getSize())) {
valid = false;
cu.getNonbondedUtilities().updateNeighborListSize();
}
......@@ -136,12 +137,12 @@ private:
long long* pinnedMemory;
CudaArray& contextForces;
bool& valid;
int& numTiles;
int2& interactionCount;
};
CudaParallelCalcForcesAndEnergyKernel::CudaParallelCalcForcesAndEnergyKernel(string name, const Platform& platform, CudaPlatform::PlatformData& data) :
CalcForcesAndEnergyKernel(name, platform), data(data), completionTimes(data.contexts.size()), contextNonbondedFractions(data.contexts.size()),
tileCounts(NULL), contextForces(NULL), pinnedPositionBuffer(NULL), pinnedForceBuffer(NULL) {
interactionCounts(NULL), contextForces(NULL), pinnedPositionBuffer(NULL), pinnedForceBuffer(NULL) {
for (int i = 0; i < (int) data.contexts.size(); i++)
kernels.push_back(Kernel(new CudaCalcForcesAndEnergyKernel(name, platform, *data.contexts[i])));
}
......@@ -156,8 +157,8 @@ CudaParallelCalcForcesAndEnergyKernel::~CudaParallelCalcForcesAndEnergyKernel()
cuMemFreeHost(pinnedForceBuffer);
cuEventDestroy(event);
cuStreamDestroy(peerCopyStream);
if (tileCounts != NULL)
cuMemFreeHost(tileCounts);
if (interactionCounts != NULL)
cuMemFreeHost(interactionCounts);
}
void CudaParallelCalcForcesAndEnergyKernel::initialize(const System& system) {
......@@ -172,7 +173,7 @@ void CudaParallelCalcForcesAndEnergyKernel::initialize(const System& system) {
contextNonbondedFractions[i] = 1/(double) numContexts;
CHECK_RESULT(cuEventCreate(&event, 0), "Error creating event");
CHECK_RESULT(cuStreamCreate(&peerCopyStream, CU_STREAM_NON_BLOCKING), "Error creating stream");
CHECK_RESULT(cuMemHostAlloc((void**) &tileCounts, numContexts*sizeof(int), 0), "Error creating tile count buffer");
CHECK_RESULT(cuMemHostAlloc((void**) &interactionCounts, numContexts*sizeof(int2), 0), "Error creating interaction counts buffer");
}
void CudaParallelCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) {
......@@ -202,7 +203,7 @@ void CudaParallelCalcForcesAndEnergyKernel::beginComputation(ContextImpl& contex
data.contextEnergy[i] = 0.0;
CudaContext& cu = *data.contexts[i];
CudaContext::WorkThread& thread = cu.getWorkThread();
thread.addTask(new BeginComputationTask(context, cu, getKernel(i), includeForce, includeEnergy, groups, pinnedPositionBuffer, event, tileCounts[i]));
thread.addTask(new BeginComputationTask(context, cu, getKernel(i), includeForce, includeEnergy, groups, pinnedPositionBuffer, event, interactionCounts[i]));
}
}
......@@ -210,7 +211,7 @@ double CudaParallelCalcForcesAndEnergyKernel::finishComputation(ContextImpl& con
for (int i = 0; i < (int) data.contexts.size(); i++) {
CudaContext& cu = *data.contexts[i];
CudaContext::WorkThread& thread = cu.getWorkThread();
thread.addTask(new FinishComputationTask(context, cu, getKernel(i), includeForce, includeEnergy, groups, data.contextEnergy[i], completionTimes[i], pinnedForceBuffer, *contextForces, valid, tileCounts[i]));
thread.addTask(new FinishComputationTask(context, cu, getKernel(i), includeForce, includeEnergy, groups, data.contextEnergy[i], completionTimes[i], pinnedForceBuffer, *contextForces, valid, interactionCounts[i]));
}
data.syncContexts();
double energy = 0.0;
......
platforms/cuda/src/kernels/findInteractingBlocks.cu
View file @ 669e314e
......@@ -71,9 +71,60 @@ extern "C" __global__ void sortBoxData(const real2* __restrict__ sortedBlock, co
if (rebuild) {
rebuildNeighborList[0] = 1;
interactionCount[0] = 0;
interactionCount[1] = 0;
}
}
__device__ int saveSinglePairs(int x, int* atoms, int* flags, int length, unsigned int maxSinglePairs, unsigned int* singlePairCount, int2* singlePairs, int* sumBuffer, volatile int& pairStartIndex) {
// Record interactions that should be computed as single pairs rather than in blocks.
const int indexInWarp = threadIdx.x%32;
int sum = 0;
for (int i = indexInWarp; i < length; i += 32) {
int count = __popc(flags[i]);
sum += (count <= MAX_BITS_FOR_PAIRS ? count : 0);
}
sumBuffer[indexInWarp] = sum;
for (int step = 1; step < 32; step *= 2) {
int add = (indexInWarp >= step ? sumBuffer[indexInWarp-step] : 0);
sumBuffer[indexInWarp] += add;
}
int pairsToStore = sumBuffer[31];
if (indexInWarp == 0)
pairStartIndex = atomicAdd(singlePairCount, pairsToStore);
int pairIndex = pairStartIndex + (indexInWarp > 0 ? sumBuffer[indexInWarp-1] : 0);
for (int i = indexInWarp; i < length; i += 32) {
int count = __popc(flags[i]);
if (count <= MAX_BITS_FOR_PAIRS && pairIndex+count < maxSinglePairs) {
int f = flags[i];
while (f != 0) {
singlePairs[pairIndex] = make_int2(atoms[i], x*TILE_SIZE+__ffs(f)-1);
f &= f-1;
pairIndex++;
}
}
}
// Compact the remaining interactions.
const int warpMask = (1<<indexInWarp)-1;
int numCompacted = 0;
for (int start = 0; start < length; start += 32) {
int i = start+indexInWarp;
int atom = atoms[i];
int flag = flags[i];
bool include = (i < length && __popc(flags[i]) > MAX_BITS_FOR_PAIRS);
int includeFlags = __ballot(include);
if (include) {
int index = numCompacted+__popc(includeFlags&warpMask);
atoms[index] = atom;
flags[index] = flag;
}
numCompacted += __popc(includeFlags);
}
return numCompacted;
}
/**
* Compare the bounding boxes for each pair of atom blocks (comprised of 32 atoms each), forming a tile. If the two
* atom blocks are sufficiently far apart, mark them as non-interacting. There are two stages in the algorithm.
......@@ -124,8 +175,9 @@ extern "C" __global__ void sortBoxData(const real2* __restrict__ sortedBlock, co
*
*/
extern "C" __global__ void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
unsigned int* __restrict__ interactionCount, int* __restrict__ interactingTiles, unsigned int* __restrict__ interactingAtoms, const real4* __restrict__ posq,
unsigned int maxTiles, unsigned int startBlockIndex, unsigned int numBlocks, real2* __restrict__ sortedBlocks, const real4* __restrict__ sortedBlockCenter,
unsigned int* __restrict__ interactionCount, int* __restrict__ interactingTiles, unsigned int* __restrict__ interactingAtoms,
int2* __restrict__ singlePairs, const real4* __restrict__ posq, unsigned int maxTiles, unsigned int maxSinglePairs,
unsigned int startBlockIndex, unsigned int numBlocks, real2* __restrict__ sortedBlocks, const real4* __restrict__ sortedBlockCenter,
const real4* __restrict__ sortedBlockBoundingBox, const unsigned int* __restrict__ exclusionIndices, const unsigned int* __restrict__ exclusionRowIndices,
real4* __restrict__ oldPositions, const int* __restrict__ rebuildNeighborList) {
......@@ -138,12 +190,17 @@ extern "C" __global__ void findBlocksWithInteractions(real4 periodicBoxSize, rea
const int warpIndex = (blockIdx.x*blockDim.x+threadIdx.x)/32;
const int warpMask = (1<<indexInWarp)-1;
__shared__ int workgroupBuffer[BUFFER_SIZE*(GROUP_SIZE/32)];
__shared__ int workgroupFlagsBuffer[BUFFER_SIZE*(GROUP_SIZE/32)];
__shared__ int warpExclusions[MAX_EXCLUSIONS*(GROUP_SIZE/32)];
__shared__ real3 posBuffer[GROUP_SIZE];
__shared__ volatile int workgroupTileIndex[GROUP_SIZE/32];
__shared__ int sumBuffer[GROUP_SIZE];
__shared__ int worksgroupPairStartIndex[GROUP_SIZE/32];
int* buffer = workgroupBuffer+BUFFER_SIZE*(warpStart/32);
int* flagsBuffer = workgroupFlagsBuffer+BUFFER_SIZE*(warpStart/32);
int* exclusionsForX = warpExclusions+MAX_EXCLUSIONS*(warpStart/32);
volatile int& tileStartIndex = workgroupTileIndex[warpStart/32];
volatile int& pairStartIndex = worksgroupPairStartIndex[warpStart/32];
// Loop over blocks.
......@@ -227,7 +284,7 @@ extern "C" __global__ void findBlocksWithInteractions(real4 periodicBoxSize, rea
APPLY_PERIODIC_TO_DELTA(atomDelta)
#endif
int atomFlags = ballot(atomDelta.x*atomDelta.x+atomDelta.y*atomDelta.y+atomDelta.z*atomDelta.z < (PADDED_CUTOFF+blockCenterY.w)*(PADDED_CUTOFF+blockCenterY.w));
bool interacts = false;
int interacts = 0;
if (atom2 < NUM_ATOMS && atomFlags != 0) {
int first = __ffs(atomFlags)-1;
int last = 32-__clz(atomFlags);
......@@ -236,14 +293,14 @@ extern "C" __global__ void findBlocksWithInteractions(real4 periodicBoxSize, rea
for (int j = first; j < last; j++) {
real3 delta = pos2-posBuffer[warpStart+j];
APPLY_PERIODIC_TO_DELTA(delta)
interacts |= (delta.x*delta.x+delta.y*delta.y+delta.z*delta.z < PADDED_CUTOFF_SQUARED);
interacts |= (delta.x*delta.x+delta.y*delta.y+delta.z*delta.z < PADDED_CUTOFF_SQUARED ? 1<<j : 0);
}
}
else {
#endif
for (int j = first; j < last; j++) {
real3 delta = pos2-posBuffer[warpStart+j];
interacts |= (delta.x*delta.x+delta.y*delta.y+delta.z*delta.z < PADDED_CUTOFF_SQUARED);
interacts |= (delta.x*delta.x+delta.y*delta.y+delta.z*delta.z < PADDED_CUTOFF_SQUARED ? 1<<j : 0);
}
#ifdef USE_PERIODIC
}
......@@ -253,15 +310,22 @@ extern "C" __global__ void findBlocksWithInteractions(real4 periodicBoxSize, rea
// Add any interacting atoms to the buffer.
int includeAtomFlags = __ballot(interacts);
if (interacts)
buffer[neighborsInBuffer+__popc(includeAtomFlags&warpMask)] = atom2;
if (interacts) {
int index = neighborsInBuffer+__popc(includeAtomFlags&warpMask);
buffer[index] = atom2;
flagsBuffer[index] = interacts;
}
neighborsInBuffer += __popc(includeAtomFlags);
if (neighborsInBuffer > BUFFER_SIZE-TILE_SIZE) {
// Store the new tiles to memory.
#if MAX_BITS_FOR_PAIRS > 0
neighborsInBuffer = saveSinglePairs(x, buffer, flagsBuffer, neighborsInBuffer, maxSinglePairs, &interactionCount[1], singlePairs, sumBuffer+warpStart, pairStartIndex);
#endif
int tilesToStore = neighborsInBuffer/TILE_SIZE;
if (tilesToStore > 0) {
if (indexInWarp == 0)
tileStartIndex = atomicAdd(interactionCount, tilesToStore);
tileStartIndex = atomicAdd(&interactionCount[0], tilesToStore);
int newTileStartIndex = tileStartIndex;
if (newTileStartIndex+tilesToStore <= maxTiles) {
if (indexInWarp < tilesToStore)
......@@ -274,13 +338,18 @@ extern "C" __global__ void findBlocksWithInteractions(real4 periodicBoxSize, rea
}
}
}
}
// If we have a partially filled buffer, store it to memory.
#if MAX_BITS_FOR_PAIRS > 0
if (neighborsInBuffer > 32)
neighborsInBuffer = saveSinglePairs(x, buffer, flagsBuffer, neighborsInBuffer, maxSinglePairs, &interactionCount[1], singlePairs, sumBuffer+warpStart, pairStartIndex);
#endif
if (neighborsInBuffer > 0) {
int tilesToStore = (neighborsInBuffer+TILE_SIZE-1)/TILE_SIZE;
if (indexInWarp == 0)
tileStartIndex = atomicAdd(interactionCount, tilesToStore);
tileStartIndex = atomicAdd(&interactionCount[0], tilesToStore);
int newTileStartIndex = tileStartIndex;
if (newTileStartIndex+tilesToStore <= maxTiles) {
if (indexInWarp < tilesToStore)
......
platforms/cuda/src/kernels/nonbonded.cu
View file @ 669e314e
......@@ -103,9 +103,10 @@ extern "C" __global__ void computeNonbonded(
unsigned long long* __restrict__ forceBuffers, mixed* __restrict__ energyBuffer, const real4* __restrict__ posq, const tileflags* __restrict__ exclusions,
const ushort2* __restrict__ exclusionTiles, unsigned int startTileIndex, unsigned int numTileIndices
#ifdef USE_CUTOFF
, const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount,real4 periodicBoxSize, real4 invPeriodicBoxSize,
, const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, const real4* __restrict__ blockCenter,
const real4* __restrict__ blockSize, const unsigned int* __restrict__ interactingAtoms
const real4* __restrict__ blockSize, const unsigned int* __restrict__ interactingAtoms, unsigned int maxSinglePairs,
const int2* __restrict__ singlePairs
#endif
PARAMETER_ARGUMENTS) {
const unsigned int totalWarps = (blockDim.x*gridDim.x)/TILE_SIZE;
......@@ -278,10 +279,10 @@ extern "C" __global__ void computeNonbonded(
localData[tbx+tj].fz += dEdR2.z;
#endif
#endif // end USE_SYMMETRIC
#endif
#ifdef ENABLE_SHUFFLE
SHUFFLE_WARP_DATA
#endif
#endif
#ifdef USE_EXCLUSIONS
excl >>= 1;
#endif
......@@ -484,9 +485,9 @@ extern "C" __global__ void computeNonbonded(
localData[tbx+tj].fz += dEdR2.z;
#endif
#endif // end USE_SYMMETRIC
#endif
#ifdef ENABLE_SHUFFLE
SHUFFLE_WARP_DATA
#endif
#endif
tj = (tj + 1) & (TILE_SIZE - 1);
}
......@@ -555,9 +556,9 @@ extern "C" __global__ void computeNonbonded(
localData[tbx+tj].fz += dEdR2.z;
#endif
#endif // end USE_SYMMETRIC
#endif
#ifdef ENABLE_SHUFFLE
SHUFFLE_WARP_DATA
#endif
#endif
tj = (tj + 1) & (TILE_SIZE - 1);
}
......@@ -588,6 +589,59 @@ extern "C" __global__ void computeNonbonded(
}
pos++;
}
// Third loop: single pairs that aren't part of a tile.
#if USE_CUTOFF
const unsigned int numPairs = interactionCount[1];
if (numPairs > maxSinglePairs)
return; // There wasn't enough memory for the neighbor list.
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < numPairs; i += blockDim.x*gridDim.x) {
int2 pair = singlePairs[i];
int atom1 = pair.x;
int atom2 = pair.y;
real4 posq1 = posq[atom1];
real4 posq2 = posq[atom2];
LOAD_ATOM1_PARAMETERS
int j = atom2;
atom2 = threadIdx.x;
DECLARE_LOCAL_PARAMETERS
LOAD_LOCAL_PARAMETERS_FROM_GLOBAL
LOAD_ATOM2_PARAMETERS
atom2 = pair.y;
real3 delta = make_real3(posq2.x-posq1.x, posq2.y-posq1.y, posq2.z-posq1.z);
#ifdef USE_PERIODIC
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
real invR = RSQRT(r2);
real r = r2*invR;
#ifdef USE_SYMMETRIC
real dEdR = 0.0f;
#else
real3 dEdR1 = make_real3(0);
real3 dEdR2 = make_real3(0);
#endif
bool hasExclusions = false;
bool isExcluded = false;
real tempEnergy = 0.0f;
const real interactionScale = 1.0f;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
#ifdef USE_SYMMETRIC
real3 dEdR1 = delta*dEdR;
real3 dEdR2 = -dEdR1;
#endif
atomicAdd(&forceBuffers[atom1], static_cast<unsigned long long>((long long) (-dEdR1.x*0x100000000)));
atomicAdd(&forceBuffers[atom1+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (-dEdR1.y*0x100000000)));
atomicAdd(&forceBuffers[atom1+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (-dEdR1.z*0x100000000)));
atomicAdd(&forceBuffers[atom2], static_cast<unsigned long long>((long long) (-dEdR2.x*0x100000000)));
atomicAdd(&forceBuffers[atom2+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (-dEdR2.y*0x100000000)));
atomicAdd(&forceBuffers[atom2+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (-dEdR2.z*0x100000000)));
#endif
}
#endif
#ifdef INCLUDE_ENERGY
energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += energy;
#endif
......
platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.cpp
View file @ 669e314e
......@@ -266,11 +266,11 @@ void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, v
// copy xPrime -> atomCoordinates
RealOpenMM invStepSize = 1.0/getDeltaT();
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] != 0.0) {
atomCoordinates[ii][0] = xPrime[ii][0];
atomCoordinates[ii][1] = xPrime[ii][1];
atomCoordinates[ii][2] = xPrime[ii][2];
velocities[ii] = (xPrime[ii]-atomCoordinates[ii])*invStepSize;
atomCoordinates[ii] = xPrime[ii];
}
}
......
wrappers/python/src/swig_doxygen/swig_lib/python/extend.i
View file @ 669e314e
......@@ -28,6 +28,7 @@
int getForces,
int getEnergy,
int getParameters,
int getParameterDerivatives,
int enforcePeriodic,
bitmask32t groups) {
State state;
......@@ -38,6 +39,7 @@
if (getForces) types |= State::Forces;
if (getEnergy) types |= State::Energy;
if (getParameters) types |= State::Parameters;
if (getParameterDerivatives) types |= State::ParameterDerivatives;
try {
state = self->getState(types, enforcePeriodic, groups);
}
......@@ -53,7 +55,7 @@
%pythoncode %{
def getState(self, getPositions=False, getVelocities=False,
getForces=False, getEnergy=False, getParameters=False,
enforcePeriodicBox=False, groups=-1):
getParameterDerivatives=False, enforcePeriodicBox=False, groups=-1):
"""Get a State object recording the current state information stored in this context.
Parameters
......@@ -66,8 +68,10 @@
whether to store the forces acting on particles in the State
getEnergy : bool=False
whether to store potential and kinetic energy in the State
getParameter : bool=False
getParameters : bool=False
whether to store context parameters in the State
getParameterDerivatives : bool=False
whether to store parameter derivatives in the State
enforcePeriodicBox : bool=False
if false, the position of each particle will be whatever position
is stored in the Context, regardless of periodic boundary conditions.
......@@ -79,9 +83,9 @@
can also be passed as an unsigned integer interpreted as a bitmask,
in which case group i will be included if (groups&(1<<i)) != 0.
"""
getP, getV, getF, getE, getPa, enforcePeriodic = map(bool,
getP, getV, getF, getE, getPa, getPd, enforcePeriodic = map(bool,
(getPositions, getVelocities, getForces, getEnergy, getParameters,
enforcePeriodicBox))
getParameterDerivatives, enforcePeriodicBox))
try:
# is the input integer-like?
......@@ -95,8 +99,8 @@
raise TypeError('%s is neither an int nor set' % groups)
(simTime, periodicBoxVectorsList, energy, coordList, velList,
forceList, paramMap) = \
self._getStateAsLists(getP, getV, getF, getE, getPa, enforcePeriodic, groups_mask)
forceList, paramMap, paramDerivMap) = \
self._getStateAsLists(getP, getV, getF, getE, getPa, getPd, enforcePeriodic, groups_mask)
state = State(simTime=simTime,
energy=energy,
......@@ -104,7 +108,8 @@
velList=velList,
forceList=forceList,
periodicBoxVectorsList=periodicBoxVectorsList,
paramMap=paramMap)
paramMap=paramMap,
paramDerivMap=paramDerivMap)
return state
def setState(self, state):
......@@ -176,6 +181,7 @@ Parameters:
int getForces,
int getEnergy,
int getParameters,
int getParameterDerivatives,
int enforcePeriodic,
int groups) {
State state;
......@@ -186,6 +192,7 @@ Parameters:
if (getForces) types |= State::Forces;
if (getEnergy) types |= State::Energy;
if (getParameters) types |= State::Parameters;
if (getParameterDerivatives) types |= State::ParameterDerivatives;
try {
state = self->getState(copy, types, enforcePeriodic, groups);
}
......@@ -206,6 +213,7 @@ Parameters:
getForces=False,
getEnergy=False,
getParameters=False,
getParameterDerivatives=False,
enforcePeriodicBox=False,
groups=-1):
"""Get a State object recording the current state information about one copy of the system.
......@@ -222,8 +230,10 @@ Parameters:
whether to store the forces acting on particles in the State
getEnergy : bool=False
whether to store potential and kinetic energy in the State
getParameter : bool=False
getParameters : bool=False
whether to store context parameters in the State
getParameterDerivatives : bool=False
whether to store parameter derivatives in the State
enforcePeriodicBox : bool=False
if false, the position of each particle will be whatever position
is stored in the Context, regardless of periodic boundary conditions.
......@@ -235,9 +245,9 @@ Parameters:
can also be passed as an unsigned integer interpreted as a bitmask,
in which case group i will be included if (groups&(1<<i)) != 0.
"""
getP, getV, getF, getE, getPa, enforcePeriodic = map(bool,
getP, getV, getF, getE, getPa, getPd, enforcePeriodic = map(bool,
(getPositions, getVelocities, getForces, getEnergy, getParameters,
enforcePeriodicBox))
getParameterDerivatives, enforcePeriodicBox))
try:
# is the input integer-like?
......@@ -250,8 +260,8 @@ Parameters:
raise TypeError('%s is neither an int nor set' % groups)
(simTime, periodicBoxVectorsList, energy, coordList, velList,
forceList, paramMap) = \
self._getStateAsLists(copy, getP, getV, getF, getE, getPa, enforcePeriodic, groups_mask)
forceList, paramMap, paramDerivMap) = \
self._getStateAsLists(getP, getV, getF, getE, getPa, getPd, enforcePeriodic, groups_mask)
state = State(simTime=simTime,
energy=energy,
......@@ -259,7 +269,8 @@ Parameters:
velList=velList,
forceList=forceList,
periodicBoxVectorsList=periodicBoxVectorsList,
paramMap=paramMap)
paramMap=paramMap,
paramDerivMap=paramDerivMap)
return state
%}
}
......@@ -361,8 +372,9 @@ Parameters:
double time,
const std::vector<Vec3>& boxVectors,
const std::map<string, double>& params,
const std::map<string, double>& paramDerivs,
int types) {
OpenMM::State myState = _convertListsToState(pos,vel,forces,kineticEnergy,potentialEnergy,time,boxVectors,params,types);
OpenMM::State myState = _convertListsToState(pos,vel,forces,kineticEnergy,potentialEnergy,time,boxVectors,params,paramDerivs,types);
std::stringstream buffer;
OpenMM::XmlSerializer::serialize<OpenMM::State>(&myState, "State", buffer);
return buffer.str();
......@@ -386,6 +398,7 @@ Parameters:
kineticEnergy = 0.0
potentialEnergy = 0.0
params = {}
paramDerivs = {}
types = 0
try:
positions = pythonState.getPositions().value_in_unit(unit.nanometers)
......@@ -413,16 +426,21 @@ Parameters:
types |= 16
except:
pass
try:
params = pythonState.getEnergyParameterDerivatives()
types |= 32
except:
pass
time = pythonState.getTime().value_in_unit(unit.picoseconds)
boxVectors = pythonState.getPeriodicBoxVectors().value_in_unit(unit.nanometers)
string = XmlSerializer._serializeStateAsLists(positions, velocities, forces, kineticEnergy, potentialEnergy, time, boxVectors, params, types)
string = XmlSerializer._serializeStateAsLists(positions, velocities, forces, kineticEnergy, potentialEnergy, time, boxVectors, params, paramDerivs, types)
return string
@staticmethod
def _deserializeState(pythonString):
(simTime, periodicBoxVectorsList, energy, coordList, velList,
forceList, paramMap) = XmlSerializer._deserializeStringIntoLists(pythonString)
forceList, paramMap, paramDerivMap) = XmlSerializer._deserializeStringIntoLists(pythonString)
state = State(simTime=simTime,
energy=energy,
......@@ -430,7 +448,8 @@ Parameters:
velList=velList,
forceList=forceList,
periodicBoxVectorsList=periodicBoxVectorsList,
paramMap=paramMap)
paramMap=paramMap,
paramDerivMap=paramDerivMap)
return state
@staticmethod
......
wrappers/python/src/swig_doxygen/swig_lib/python/header.i
View file @ 669e314e
......@@ -28,6 +28,7 @@ State _convertListsToState( const std::vector<Vec3> &pos,
double time,
const std::vector<Vec3> &boxVectors,
const std::map<std::string, double> &params,
const std::map<std::string, double> &paramDerivs,
int types ) {
State::StateBuilder sb(time);
if(types & State::Positions)
......@@ -40,6 +41,8 @@ State _convertListsToState( const std::vector<Vec3> &pos,
sb.setEnergy(kineticEnergy, potentialEnergy);
if(types & State::Parameters)
sb.setParameters(params);
if(types & State::ParameterDerivatives)
sb.setEnergyParameterDerivatives(paramDerivs);
sb.setPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
return sb.getState();
}
......@@ -53,6 +56,7 @@ PyObject *_convertStateToLists(const State& state) {
PyObject *pForces;
PyObject *pyTuple;
PyObject *pParameters;
PyObject *pParameterDerivs;
simTime=state.getTime();
OpenMM::Vec3 myVecA;
......@@ -112,11 +116,21 @@ PyObject *_convertStateToLists(const State& state) {
pParameters = Py_None;
Py_INCREF(Py_None);
}
try {
pParameterDerivs = PyDict_New();
const std::map<std::string, double>& params = state.getEnergyParameterDerivatives();
for (std::map<std::string, double>::const_iterator iter = params.begin(); iter != params.end(); ++iter)
PyDict_SetItemString(pParameterDerivs, iter->first.c_str(), Py_BuildValue("d", iter->second));
}
catch (std::exception& ex) {
pParameterDerivs = Py_None;
Py_INCREF(Py_None);
}
pyTuple=Py_BuildValue("(d,N,N,N,N,N,N)",
pyTuple=Py_BuildValue("(d,N,N,N,N,N,N,N)",
simTime, pPeriodicBoxVectorsList, pEnergy,
pPositions, pVelocities,
pForces, pParameters);
pForces, pParameters, pParameterDerivs);
return pyTuple;
}
......
wrappers/python/src/swig_doxygen/swig_lib/python/pythoncode.i
View file @ 669e314e
......@@ -63,7 +63,8 @@ class State(_object):
velList=None,
forceList=None,
periodicBoxVectorsList=None,
paramMap=None):
paramMap=None,
paramDerivMap=None):
self._simTime=simTime
self._periodicBoxVectorsList=periodicBoxVectorsList
self._periodicBoxVectorsListNumpy=None
......@@ -80,6 +81,7 @@ class State(_object):
self._forceList=forceList
self._forceListNumpy=None
self._paramMap=paramMap
self._paramDerivMap=paramDerivMap
def __getstate__(self):
serializationString = XmlSerializer.serialize(self)
......@@ -221,6 +223,18 @@ class State(_object):
raise TypeError('Parameters were not requested in getState() call, so are not available.')
return self._paramMap
def getEnergyParameterDerivatives(self):
"""Get a map containing derivatives of the potential energy with respect to context parameters.
In most cases derivatives are only calculated if the corresponding Force objects have been
specifically told to compute them. Otherwise, the values in the map will be zero. Likewise,
if multiple Forces depend on the same parameter but only some have been told to compute
derivatives with respect to it, the returned value will include only the contributions from
the Forces that were told to compute it."""
if self._paramDerivMap is None:
raise TypeError('Parameter derivatives were not requested in getState() call, so are not available.')
return self._paramDerivMap
%}
%pythonappend OpenMM::Context::Context %{
......
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