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Commit 2e9c418a authored by peastman's avatar peastman
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Merge branch 'master' into gayberne

parents 8f532e31 a4d327f5
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Showing with 189 additions and 48 deletions
platforms/cuda/tests/TestCudaFFT3D.cpp
View file @ 2e9c418a
......@@ -56,7 +56,7 @@ void testTransform(bool realToComplex, int xsize, int ysize, int zsize) {
system.addParticle(0.0);
CudaPlatform::PlatformData platformData(NULL, system, "", "true", platform.getPropertyDefaultValue("CudaPrecision"), "false",
platform.getPropertyDefaultValue(CudaPlatform::CudaCompiler()), platform.getPropertyDefaultValue(CudaPlatform::CudaTempDirectory()),
platform.getPropertyDefaultValue(CudaPlatform::CudaHostCompiler()), platform.getPropertyDefaultValue(CudaPlatform::CudaDisablePmeStream()), 1);
platform.getPropertyDefaultValue(CudaPlatform::CudaHostCompiler()), platform.getPropertyDefaultValue(CudaPlatform::CudaDisablePmeStream()), "false", 1);
CudaContext& context = *platformData.contexts[0];
context.initialize();
OpenMM_SFMT::SFMT sfmt;
......
platforms/cuda/tests/TestCudaNonbondedForce.cpp
View file @ 2e9c418a
......@@ -118,9 +118,44 @@ void testReordering() {
}
}
void testDeterministicForces() {
// Check that the CudaDeterministicForces property works correctly.
const int numParticles = 1000;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(2.1, 6, 0), Vec3(-1.5, -0.5, 6));
NonbondedForce *nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::PME);
system.addForce(nonbonded);
vector<Vec3> positions;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
nonbonded->addParticle(i%2 == 0 ? 1 : -1, 1, 0);
positions.push_back(Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5)*6);
}
VerletIntegrator integrator(0.001);
map<string, string> properties;
properties[CudaPlatform::CudaDeterministicForces()] = "true";
Context context(system, integrator, platform, properties);
context.setPositions(positions);
State state1 = context.getState(State::Forces);
State state2 = context.getState(State::Forces);
// All forces should be *exactly* equal.
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL(state1.getForces()[i][0], state2.getForces()[i][0]);
ASSERT_EQUAL(state1.getForces()[i][1], state2.getForces()[i][1]);
ASSERT_EQUAL(state1.getForces()[i][2], state2.getForces()[i][2]);
}
}
void runPlatformTests() {
testParallelComputation(NonbondedForce::NoCutoff);
testParallelComputation(NonbondedForce::Ewald);
testParallelComputation(NonbondedForce::PME);
testReordering();
testDeterministicForces();
}
platforms/cuda/tests/TestCudaRandom.cpp
View file @ 2e9c418a
......@@ -56,7 +56,7 @@ void testGaussian() {
system.addParticle(1.0);
CudaPlatform::PlatformData platformData(NULL, system, "", "true", platform.getPropertyDefaultValue("CudaPrecision"), "false",
platform.getPropertyDefaultValue(CudaPlatform::CudaCompiler()), platform.getPropertyDefaultValue(CudaPlatform::CudaTempDirectory()),
platform.getPropertyDefaultValue(CudaPlatform::CudaHostCompiler()), platform.getPropertyDefaultValue(CudaPlatform::CudaDisablePmeStream()), 1);
platform.getPropertyDefaultValue(CudaPlatform::CudaHostCompiler()), platform.getPropertyDefaultValue(CudaPlatform::CudaDisablePmeStream()), "false", 1);
CudaContext& context = *platformData.contexts[0];
context.initialize();
context.getIntegrationUtilities().initRandomNumberGenerator(0);
......
platforms/cuda/tests/TestCudaSort.cpp
View file @ 2e9c418a
......@@ -66,7 +66,7 @@ void verifySorting(vector<float> array) {
system.addParticle(0.0);
CudaPlatform::PlatformData platformData(NULL, system, "", "true", platform.getPropertyDefaultValue("CudaPrecision"), "false",
platform.getPropertyDefaultValue(CudaPlatform::CudaCompiler()), platform.getPropertyDefaultValue(CudaPlatform::CudaTempDirectory()),
platform.getPropertyDefaultValue(CudaPlatform::CudaHostCompiler()), platform.getPropertyDefaultValue(CudaPlatform::CudaDisablePmeStream()), 1);
platform.getPropertyDefaultValue(CudaPlatform::CudaHostCompiler()), platform.getPropertyDefaultValue(CudaPlatform::CudaDisablePmeStream()), "false", 1);
CudaContext& context = *platformData.contexts[0];
context.initialize();
CudaArray data(context, array.size(), 4, "sortData");
......
platforms/opencl/include/OpenCLKernels.h
View file @ 2e9c418a
......@@ -156,7 +156,7 @@ public:
* @param b the vector defining the second edge of the periodic box
* @param c the vector defining the third edge of the periodic box
*/
void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const;
void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c);
/**
* Create a checkpoint recording the current state of the Context.
*
......@@ -698,7 +698,7 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
private:
void initInteractionGroups(const CustomNonbondedForce& force, const std::string& interactionSource);
void initInteractionGroups(const CustomNonbondedForce& force, const std::string& interactionSource, const std::vector<std::string>& tableTypes);
OpenCLContext& cl;
OpenCLParameterSet* params;
OpenCLArray* globals;
......
platforms/opencl/include/OpenCLPlatform.h
View file @ 2e9c418a
......@@ -58,14 +58,14 @@ public:
* This is the name of the parameter for selecting which OpenCL device or devices to use.
*/
static const std::string& OpenCLDeviceIndex() {
static const std::string key = "OpenCLDeviceIndex";
static const std::string key = "DeviceIndex";
return key;
}
/**
* This is the name of the parameter that reports the OpenCL device or devices being used.
*/
static const std::string& OpenCLDeviceName() {
static const std::string key = "OpenCLDeviceName";
static const std::string key = "DeviceName";
return key;
}
/**
......@@ -86,21 +86,21 @@ public:
* This is the name of the parameter for selecting what numerical precision to use.
*/
static const std::string& OpenCLPrecision() {
static const std::string key = "OpenCLPrecision";
static const std::string key = "Precision";
return key;
}
/**
* This is the name of the parameter for selecting whether to use the CPU based PME calculation.
*/
static const std::string& OpenCLUseCpuPme() {
static const std::string key = "OpenCLUseCpuPme";
static const std::string key = "UseCpuPme";
return key;
}
/**
* This is the name of the parameter for selecting whether to disable use of a separate stream for PME.
*/
static const std::string& OpenCLDisablePmeStream() {
static const std::string key = "OpenCLDisablePmeStream";
static const std::string key = "DisablePmeStream";
return key;
}
};
......
platforms/opencl/src/OpenCLContext.cpp
View file @ 2e9c418a
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009-2015 Stanford University and the Authors. *
* Portions copyright (c) 2009-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -84,7 +84,7 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
useMixedPrecision = false;
}
else
throw OpenMMException("Illegal value for OpenCLPrecision: "+precision);
throw OpenMMException("Illegal value for Precision: "+precision);
try {
contextIndex = platformData.contexts.size();
std::vector<cl::Platform> platforms;
......@@ -105,7 +105,7 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
vector<cl::Device> devices;
platforms[j].getDevices(CL_DEVICE_TYPE_ALL, &devices);
if (deviceIndex < -1 || deviceIndex >= (int) devices.size())
throw OpenMMException("Illegal value for OpenCLDeviceIndex: "+intToString(deviceIndex));
throw OpenMMException("Illegal value for DeviceIndex: "+intToString(deviceIndex));
for (int i = 0; i < (int) devices.size(); i++) {
// If they supplied a valid deviceIndex, we only look through that one
......@@ -113,6 +113,11 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
continue;
if (platformVendor == "Apple" && (devices[i].getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU))
continue; // The CPU device on OS X won't work correctly.
if (useMixedPrecision || useDoublePrecision) {
bool supportsDouble = (devices[i].getInfo<CL_DEVICE_EXTENSIONS>().find("cl_khr_fp64") != string::npos);
if (!supportsDouble)
continue; // This device does not support double precision.
}
int maxSize = devices[i].getInfo<CL_DEVICE_MAX_WORK_ITEM_SIZES>()[0];
int processingElementsPerComputeUnit = 8;
if (devices[i].getInfo<CL_DEVICE_TYPE>() != CL_DEVICE_TYPE_GPU) {
......
platforms/opencl/src/OpenCLExpressionUtilities.cpp
View file @ 2e9c418a
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009-2015 Stanford University and the Authors. *
* Portions copyright (c) 2009-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -254,7 +254,7 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
for (int k = 3; k >= 0; k--)
for (int m = 0; m < 4; m++) {
int base = 4*m;
string suffix = suffixes[m];
string suffix = suffixes[k];
out << "derivy[" << m << "] = da*derivy[" << m << "] + (3*c[" << (base+3) << "]" << suffix << "*db + 2*c[" << (base+2) << "]" << suffix << ")*db + c[" << (base+1) << "]" << suffix << ";\n";
}
out << nodeNames[j] << " = derivy[0] + dc*(derivy[1] + dc*(derivy[2] + dc*derivy[3]));\n";
......@@ -271,7 +271,7 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
out << nodeNames[j] << " *= " << paramsFloat[11] << ";\n";
}
else
throw OpenMMException("Unsupported derivative order for Continuous2DFunction");
throw OpenMMException("Unsupported derivative order for Continuous3DFunction");
}
out << "}\n";
}
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 2e9c418a
......@@ -369,10 +369,27 @@ void OpenCLUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context, Ve
cl.getPeriodicBoxVectors(a, b, c);
}
void OpenCLUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const {
void OpenCLUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) {
vector<OpenCLContext*>& contexts = cl.getPlatformData().contexts;
// If any particles have been wrapped to the first periodic box, we need to unwrap them
// to avoid changing their positions.
vector<Vec3> positions;
for (int i = 0; i < (int) cl.getPosCellOffsets().size(); i++) {
mm_int4& offset = cl.getPosCellOffsets()[i];
if (offset.x != 0 || offset.y != 0 || offset.z != 0) {
getPositions(context, positions);
break;
}
}
// Update the vectors.
for (int i = 0; i < (int) contexts.size(); i++)
contexts[i]->setPeriodicBoxVectors(a, b, c);
if (positions.size() > 0)
setPositions(context, positions);
}
void OpenCLUpdateStateDataKernel::createCheckpoint(ContextImpl& context, ostream& stream) {
......@@ -527,6 +544,7 @@ void OpenCLCalcHarmonicBondForceKernel::initialize(const System& system, const H
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = OpenCLKernelSources::harmonicBondForce;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float2");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::bondForce, replacements), force.getForceGroup());
......@@ -660,6 +678,7 @@ void OpenCLCalcCustomBondForceKernel::initialize(const System& system, const Cus
vector<pair<string, string> > functionNames;
compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = compute.str();
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::bondForce, replacements), force.getForceGroup());
}
......@@ -756,6 +775,7 @@ void OpenCLCalcHarmonicAngleForceKernel::initialize(const System& system, const
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = OpenCLKernelSources::harmonicAngleForce;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float2");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::angleForce, replacements), force.getForceGroup());
......@@ -890,6 +910,7 @@ void OpenCLCalcCustomAngleForceKernel::initialize(const System& system, const Cu
vector<pair<string, string> > functionNames;
compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = compute.str();
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::angleForce, replacements), force.getForceGroup());
}
......@@ -987,6 +1008,7 @@ void OpenCLCalcPeriodicTorsionForceKernel::initialize(const System& system, cons
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = OpenCLKernelSources::periodicTorsionForce;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float4");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
......@@ -1073,6 +1095,7 @@ void OpenCLCalcRBTorsionForceKernel::initialize(const System& system, const RBTo
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = OpenCLKernelSources::rbTorsionForce;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float8");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
......@@ -1184,6 +1207,7 @@ void OpenCLCalcCMAPTorsionForceKernel::initialize(const System& system, const CM
mapPositions->upload(mapPositionsVec);
torsionMaps->upload(torsionMapsVec);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COEFF"] = cl.getBondedUtilities().addArgument(coefficients->getDeviceBuffer(), "float4");
replacements["MAP_POS"] = cl.getBondedUtilities().addArgument(mapPositions->getDeviceBuffer(), "int2");
replacements["MAPS"] = cl.getBondedUtilities().addArgument(torsionMaps->getDeviceBuffer(), "int");
......@@ -1338,6 +1362,7 @@ void OpenCLCalcCustomTorsionForceKernel::initialize(const System& system, const
vector<pair<string, string> > functionNames;
compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = compute.str();
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
}
......@@ -1502,9 +1527,9 @@ public:
events[0] = event;
event = cl::Event();
cl.getQueue().enqueueWaitForEvents(events);
if (includeEnergy)
cl.executeKernel(addEnergyKernel, pmeEnergyBuffer.getSize());
}
if (includeEnergy)
cl.executeKernel(addEnergyKernel, pmeEnergyBuffer.getSize());
return 0.0;
}
private:
......@@ -2222,6 +2247,7 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
map<string, Lepton::CustomFunction*> functions;
vector<pair<string, string> > functionDefinitions;
vector<const TabulatedFunction*> functionList;
vector<string> tableTypes;
for (int i = 0; i < force.getNumFunctions(); i++) {
functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i);
......@@ -2233,6 +2259,10 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(arrayName, "float", width, width*sizeof(float), tabulatedFunctions[tabulatedFunctions.size()-1]->getDeviceBuffer()));
if (width == 1)
tableTypes.push_back("float");
else
tableTypes.push_back("float"+cl.intToString(width));
}
// Record information for the expressions.
......@@ -2285,7 +2315,7 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
}
string source = cl.replaceStrings(OpenCLKernelSources::customNonbonded, replacements);
if (force.getNumInteractionGroups() > 0)
initInteractionGroups(force, source);
initInteractionGroups(force, source, tableTypes);
else {
cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, true, force.getCutoffDistance(), exclusionList, source, force.getForceGroup());
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
......@@ -2311,7 +2341,7 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
}
}
void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbondedForce& force, const string& interactionSource) {
void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbondedForce& force, const string& interactionSource, const vector<string>& tableTypes) {
// Process groups to form tiles.
vector<vector<int> > atomLists;
......@@ -2502,6 +2532,8 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
stringstream args;
for (int i = 0; i < (int) buffers.size(); i++)
args<<", __global const "<<buffers[i].getType()<<"* restrict global_params"<<(i+1);
for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
args << ", __global const " << tableTypes[i]<< "* restrict table" << i;
if (globals != NULL)
args<<", __global const float* restrict globals";
replacements["PARAMETER_ARGUMENTS"] = args.str();
......@@ -2591,6 +2623,8 @@ double OpenCLCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool
index += 5;
for (int i = 0; i < (int) params->getBuffers().size(); i++)
interactionGroupKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
interactionGroupKernel.setArg<cl::Memory>(index++, tabulatedFunctions[i]->getDeviceBuffer());
if (globals != NULL)
interactionGroupKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
}
......@@ -4712,7 +4746,7 @@ void OpenCLCalcCustomCentroidBondForceKernel::initialize(const System& system, c
const vector<int>& groups = iter->second;
string deltaName = atomNames[groups[0]]+atomNames[groups[1]];
if (computedDeltas.count(deltaName) == 0) {
compute<<"real4 delta"<<deltaName<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<");\n";
compute<<"real4 delta"<<deltaName<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName);
}
compute<<"real r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
......@@ -4726,11 +4760,11 @@ void OpenCLCalcCustomCentroidBondForceKernel::initialize(const System& system, c
string deltaName2 = atomNames[groups[1]]+atomNames[groups[2]];
string angleName = "angle_"+atomNames[groups[0]]+atomNames[groups[1]]+atomNames[groups[2]];
if (computedDeltas.count(deltaName1) == 0) {
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[0]]<<");\n";
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[0]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName1);
}
if (computedDeltas.count(deltaName2) == 0) {
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[2]]<<");\n";
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[2]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName2);
}
compute<<"real "<<angleName<<" = computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
......@@ -4747,15 +4781,15 @@ void OpenCLCalcCustomCentroidBondForceKernel::initialize(const System& system, c
string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
string dihedralName = "dihedral_"+atomNames[groups[0]]+atomNames[groups[1]]+atomNames[groups[2]]+atomNames[groups[3]];
if (computedDeltas.count(deltaName1) == 0) {
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<");\n";
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName1);
}
if (computedDeltas.count(deltaName2) == 0) {
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[1]]<<");\n";
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName2);
}
if (computedDeltas.count(deltaName3) == 0) {
compute<<"real4 delta"<<deltaName3<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[3]]<<");\n";
compute<<"real4 delta"<<deltaName3<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[3]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName3);
}
compute<<"real4 "<<crossName1<<" = computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
......@@ -4876,6 +4910,7 @@ void OpenCLCalcCustomCentroidBondForceKernel::initialize(const System& system, c
index++; // Energy buffer hasn't been created yet
groupForcesKernel.setArg<cl::Buffer>(index++, centerPositions->getDeviceBuffer());
groupForcesKernel.setArg<cl::Buffer>(index++, bondGroups->getDeviceBuffer());
index += 5; // Periodic box information
for (int i = 0; i < tabulatedFunctions.size(); i++)
groupForcesKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
if (globals != NULL)
......@@ -4906,6 +4941,7 @@ double OpenCLCalcCustomCentroidBondForceKernel::execute(ContextImpl& context, bo
}
cl.executeKernel(computeCentersKernel, OpenCLContext::TileSize*numGroups);
groupForcesKernel.setArg<cl::Buffer>(1, cl.getEnergyBuffer().getDeviceBuffer());
setPeriodicBoxArgs(cl, groupForcesKernel, 4);
cl.executeKernel(groupForcesKernel, numBonds);
applyForcesKernel.setArg<cl::Buffer>(4, cl.getLongForceBuffer().getDeviceBuffer());
cl.executeKernel(applyForcesKernel, OpenCLContext::TileSize*numGroups);
......@@ -5061,7 +5097,7 @@ void OpenCLCalcCustomCompoundBondForceKernel::initialize(const System& system, c
const vector<int>& atoms = iter->second;
string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
if (computedDeltas.count(deltaName) == 0) {
compute<<"real4 delta"<<deltaName<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<");\n";
compute<<"real4 delta"<<deltaName<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName);
}
compute<<"real r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
......@@ -5075,11 +5111,11 @@ void OpenCLCalcCustomCompoundBondForceKernel::initialize(const System& system, c
string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
string angleName = "angle_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]];
if (computedDeltas.count(deltaName1) == 0) {
compute<<"real4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[0]]<<");\n";
compute<<"real4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[0]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName1);
}
if (computedDeltas.count(deltaName2) == 0) {
compute<<"real4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[2]]<<");\n";
compute<<"real4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[2]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName2);
}
compute<<"real "<<angleName<<" = ccb_computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
......@@ -5096,15 +5132,15 @@ void OpenCLCalcCustomCompoundBondForceKernel::initialize(const System& system, c
string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
string dihedralName = "dihedral_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]]+atomNames[atoms[3]];
if (computedDeltas.count(deltaName1) == 0) {
compute<<"real4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<");\n";
compute<<"real4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName1);
}
if (computedDeltas.count(deltaName2) == 0) {
compute<<"real4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[1]]<<");\n";
compute<<"real4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName2);
}
if (computedDeltas.count(deltaName3) == 0) {
compute<<"real4 delta"<<deltaName3<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[3]]<<");\n";
compute<<"real4 delta"<<deltaName3<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[3]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName3);
}
compute<<"real4 "<<crossName1<<" = ccb_computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
......@@ -6513,9 +6549,9 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
for (int step = 0; step < numSteps; step++) {
string expr;
integrator.getComputationStep(step, stepType[step], variable[step], expr);
if (stepType[step] == CustomIntegrator::BeginWhileBlock)
if (stepType[step] == CustomIntegrator::WhileBlockStart)
blockEnd[blockEnd[step]] = step; // Record where to branch back to.
if (stepType[step] == CustomIntegrator::ComputeGlobal || stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock)
if (stepType[step] == CustomIntegrator::ComputeGlobal || stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart)
for (int i = 0; i < (int) expression[step].size(); i++)
globalExpressions[step].push_back(expression[step][i].createCompiledExpression());
}
......@@ -6961,15 +6997,15 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
else if (stepType[step] == CustomIntegrator::ConstrainVelocities) {
cl.getIntegrationUtilities().applyVelocityConstraints(integrator.getConstraintTolerance());
}
else if (stepType[step] == CustomIntegrator::BeginIfBlock) {
else if (stepType[step] == CustomIntegrator::IfBlockStart) {
if (!evaluateCondition(step))
nextStep = blockEnd[step]+1;
}
else if (stepType[step] == CustomIntegrator::BeginWhileBlock) {
else if (stepType[step] == CustomIntegrator::WhileBlockStart) {
if (!evaluateCondition(step))
nextStep = blockEnd[step]+1;
}
else if (stepType[step] == CustomIntegrator::EndBlock) {
else if (stepType[step] == CustomIntegrator::BlockEnd) {
if (blockEnd[step] != -1)
nextStep = blockEnd[step]; // Return to the start of a while block.
}
......@@ -7053,6 +7089,7 @@ void OpenCLIntegrateCustomStepKernel::recordGlobalValue(double value, GlobalTarg
case DT:
if (value != globalValuesDouble[dtVariableIndex])
deviceGlobalsAreCurrent = false;
expressionSet.setVariable(dtVariableIndex, value);
globalValuesDouble[dtVariableIndex] = value;
cl.getIntegrationUtilities().setNextStepSize(value);
break;
......
platforms/opencl/src/OpenCLPlatform.cpp
View file @ 2e9c418a
......@@ -56,6 +56,11 @@ extern "C" OPENMM_EXPORT_OPENCL void registerPlatforms() {
#endif
OpenCLPlatform::OpenCLPlatform() {
deprecatedPropertyReplacements["OpenCLDeviceIndex"] = OpenCLDeviceIndex();
deprecatedPropertyReplacements["OpenCLDeviceName"] = OpenCLDeviceName();
deprecatedPropertyReplacements["OpenCLPrecision"] = OpenCLPrecision();
deprecatedPropertyReplacements["OpenCLUseCpuPme"] = OpenCLUseCpuPme();
deprecatedPropertyReplacements["OpenCLDisablePmeStream"] = OpenCLDisablePmeStream();
OpenCLKernelFactory* factory = new OpenCLKernelFactory();
registerKernelFactory(CalcForcesAndEnergyKernel::Name(), factory);
registerKernelFactory(UpdateStateDataKernel::Name(), factory);
......@@ -139,7 +144,10 @@ bool OpenCLPlatform::isPlatformSupported() {
const string& OpenCLPlatform::getPropertyValue(const Context& context, const string& property) const {
const ContextImpl& impl = getContextImpl(context);
const PlatformData* data = reinterpret_cast<const PlatformData*>(impl.getPlatformData());
map<string, string>::const_iterator value = data->propertyValues.find(property);
string propertyName = property;
if (deprecatedPropertyReplacements.find(property) != deprecatedPropertyReplacements.end())
propertyName = deprecatedPropertyReplacements.find(property)->second;
map<string, string>::const_iterator value = data->propertyValues.find(propertyName);
if (value != data->propertyValues.end())
return value->second;
return Platform::getPropertyValue(context, property);
......
platforms/opencl/src/kernels/angleForce.cl
View file @ 2e9c418a
real4 v0 = pos2-pos1;
real4 v1 = pos2-pos3;
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(v0)
APPLY_PERIODIC_TO_DELTA(v1)
#endif
real4 cp = cross(v0, v1);
real rp = cp.x*cp.x + cp.y*cp.y + cp.z*cp.z;
rp = max(SQRT(rp), (real) 1.0e-06f);
......
platforms/opencl/src/kernels/bondForce.cl
View file @ 2e9c418a
real4 delta = pos2-pos1;
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r = SQRT(delta.x*delta.x + delta.y*delta.y + delta.z*delta.z);
COMPUTE_FORCE
dEdR = (r > 0.0f) ? (dEdR / r) : 0.0f;
......
platforms/opencl/src/kernels/cmapTorsionForce.cl
View file @ 2e9c418a
......@@ -5,6 +5,11 @@ const real PI = 3.14159265358979323846f;
real4 v0a = (real4) (pos1.xyz-pos2.xyz, 0.0f);
real4 v1a = (real4) (pos3.xyz-pos2.xyz, 0.0f);
real4 v2a = (real4) (pos3.xyz-pos4.xyz, 0.0f);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(v0a)
APPLY_PERIODIC_TO_DELTA(v1a)
APPLY_PERIODIC_TO_DELTA(v2a)
#endif
real4 cp0a = cross(v0a, v1a);
real4 cp1a = cross(v1a, v2a);
real cosangle = dot(normalize(cp0a), normalize(cp1a));
......@@ -28,6 +33,11 @@ angleA = fmod(angleA+2.0f*PI, 2.0f*PI);
real4 v0b = (real4) (pos5.xyz-pos6.xyz, 0.0f);
real4 v1b = (real4) (pos7.xyz-pos6.xyz, 0.0f);
real4 v2b = (real4) (pos7.xyz-pos8.xyz, 0.0f);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(v0b)
APPLY_PERIODIC_TO_DELTA(v1b)
APPLY_PERIODIC_TO_DELTA(v2b)
#endif
real4 cp0b = cross(v0b, v1b);
real4 cp1b = cross(v1b, v2b);
cosangle = dot(normalize(cp0b), normalize(cp1b));
......
platforms/opencl/src/kernels/customCentroidBond.cl
View file @ 2e9c418a
......@@ -70,8 +70,11 @@ __kernel void computeGroupCenters(__global const real4* restrict posq, __global
/**
* Compute the difference between two vectors, setting the fourth component to the squared magnitude.
*/
real4 delta(real4 vec1, real4 vec2) {
real4 delta(real4 vec1, real4 vec2, bool periodic, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ) {
real4 result = (real4) (vec1.x-vec2.x, vec1.y-vec2.y, vec1.z-vec2.z, 0);
if (periodic)
APPLY_PERIODIC_TO_DELTA(result);
result.w = result.x*result.x + result.y*result.y + result.z*result.z;
return result;
}
......@@ -110,7 +113,7 @@ real4 computeCross(real4 vec1, real4 vec2) {
* Compute the forces on groups based on the bonds.
*/
__kernel void computeGroupForces(__global long* restrict groupForce, __global mixed* restrict energyBuffer, __global const real4* restrict centerPositions,
__global const int* restrict bondGroups
__global const int* restrict bondGroups, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ
EXTRA_ARGS) {
mixed energy = 0;
for (int index = get_global_id(0); index < NUM_BONDS; index += get_global_size(0)) {
......
platforms/opencl/src/kernels/customCompoundBond.cl
View file @ 2e9c418a
/**
* Compute the difference between two vectors, setting the fourth component to the squared magnitude.
*/
real4 ccb_delta(real4 vec1, real4 vec2) {
real4 ccb_delta(real4 vec1, real4 vec2, bool periodic, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ) {
real4 result = (real4) (vec1.x-vec2.x, vec1.y-vec2.y, vec1.z-vec2.z, 0);
if (periodic)
APPLY_PERIODIC_TO_DELTA(result);
result.w = result.x*result.x + result.y*result.y + result.z*result.z;
return result;
}
......
platforms/opencl/src/kernels/customManyParticle.cl
View file @ 2e9c418a
......@@ -55,7 +55,7 @@ inline real4 computeCross(real4 vec1, real4 vec2) {
/**
* Determine whether a particular interaction is in the list of exclusions.
*/
inline bool isInteractionExcluded(int atom1, int atom2, __global int* restrict exclusions, __global int* restrict exclusionStartIndex) {
inline bool isInteractionExcluded(int atom1, int atom2, __global const int* restrict exclusions, __global const int* restrict exclusionStartIndex) {
int first = exclusionStartIndex[atom1];
int last = exclusionStartIndex[atom1+1];
for (int i = last-1; i >= first; i--) {
......@@ -174,7 +174,7 @@ __kernel void findNeighbors(real4 periodicBoxSize, real4 invPeriodicBoxSize, rea
__global const real4* restrict posq, __global const real4* restrict blockCenter, __global const real4* restrict blockBoundingBox, __global int2* restrict neighborPairs,
__global int* restrict numNeighborPairs, __global int* restrict numNeighborsForAtom, int maxNeighborPairs
#ifdef USE_EXCLUSIONS
, __global int* restrict exclusions, __global int* restrict exclusionStartIndex
, __global const int* restrict exclusions, __global const int* restrict exclusionStartIndex
#endif
) {
__local real4 positionCache[FIND_NEIGHBORS_WORKGROUP_SIZE];
......@@ -264,7 +264,9 @@ __kernel void findNeighbors(real4 periodicBoxSize, real4 invPeriodicBoxSize, rea
}
}
}
numNeighborsForAtom[atom1] = totalNeighborsForAtom1;
if (atom1 < NUM_ATOMS)
numNeighborsForAtom[atom1] = totalNeighborsForAtom1;
SYNC_WARPS;
}
}
......@@ -307,6 +309,7 @@ __kernel void computeNeighborStartIndices(__global int* restrict numNeighborsFor
numNeighborsForAtom[globalIndex] = 0; // Clear this so the next kernel can use it as a counter
}
globalOffset += posBuffer[get_local_size(0)-1];
barrier(CLK_LOCAL_MEM_FENCE);
}
if (get_local_id(0) == 0)
neighborStartIndex[0] = 0;
......
platforms/opencl/src/kernels/torsionForce.cl
View file @ 2e9c418a
......@@ -2,6 +2,11 @@ const real PI = 3.14159265358979323846f;
real4 v0 = (real4) (pos1.xyz-pos2.xyz, 0.0f);
real4 v1 = (real4) (pos3.xyz-pos2.xyz, 0.0f);
real4 v2 = (real4) (pos3.xyz-pos4.xyz, 0.0f);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(v0)
APPLY_PERIODIC_TO_DELTA(v1)
APPLY_PERIODIC_TO_DELTA(v2)
#endif
real4 cp0 = cross(v0, v1);
real4 cp1 = cross(v1, v2);
real cosangle = dot(normalize(cp0), normalize(cp1));
......
platforms/opencl/tests/OpenCLTests.h
View file @ 2e9c418a
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Portions copyright (c) 2015-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -39,9 +39,9 @@ OpenMM::OpenCLPlatform platform;
void initializeTests(int argc, char* argv[]) {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", std::string(argv[1]));
platform.setPropertyDefaultValue("Precision", std::string(argv[1]));
if (argc > 2)
platform.setPropertyDefaultValue("OpenCLPlatformIndex", std::string(argv[2]));
if (argc > 3)
platform.setPropertyDefaultValue("OpenCLDeviceIndex", std::string(argv[3]));
platform.setPropertyDefaultValue("DeviceIndex", std::string(argv[3]));
}
platforms/reference/include/ReferenceAngleBondIxn.h
View file @ 2e9c418a
......@@ -33,6 +33,9 @@ class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {
private:
bool usePeriodic;
RealVec boxVectors[3];
public:
/**---------------------------------------------------------------------------------------
......@@ -51,6 +54,16 @@ class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {
~ReferenceAngleBondIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Get dEdR and energy term for angle bond
......
platforms/reference/include/ReferenceCMAPTorsionIxn.h
View file @ 2e9c418a
......@@ -38,6 +38,8 @@ private:
std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
std::vector<int> torsionMaps;
std::vector<std::vector<int> > torsionIndices;
bool usePeriodic;
RealVec boxVectors[3];
/**---------------------------------------------------------------------------------------
......@@ -65,6 +67,16 @@ public:
const std::vector<int>& torsionMaps,
const std::vector<std::vector<int> >& torsionIndices);
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate torsion interaction
......
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