Skip to content

GitLab

Commit cc5467e7 authored by Peter Eastman's avatar Peter Eastman
Browse files

Created OpenCL implementations of AndersenThermostat and BrownianIntegrator. Also fixed some bugs.

parent 13d89753
Show whitespace changes
Inline Side-by-side
Showing with 702 additions and 239 deletions
platforms/opencl/src/OpenCLContext.h
View file @ cc5467e7
......@@ -266,7 +266,7 @@ public:
/**
* Get the OpenCLIntegrationUtilities for this context.
*/
OpenCLIntegrationUtilities& getIntegrationUtilties() {
OpenCLIntegrationUtilities& getIntegrationUtilities() {
return *integration;
}
/**
......
platforms/opencl/src/OpenCLIntegrationUtilities.cpp
View file @ cc5467e7
......@@ -68,10 +68,13 @@ struct OpenCLIntegrationUtilities::ShakeCluster {
OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, const System& system) : context(context),
posDelta(NULL), settleAtoms(NULL), settleParams(NULL), shakeAtoms(NULL), shakeParams(NULL),
random(NULL), randomSeed(NULL), randomPos(NULL) {
random(NULL), randomSeed(NULL), randomPos(NULL), stepSize(NULL) {
// Create workspace arrays.
posDelta = new OpenCLArray<mm_float4>(context, context.getPaddedNumAtoms(), "posDelta");
stepSize = new OpenCLArray<mm_float2>(context, 1, "stepSize", true);
stepSize->set(0, (mm_float2) {0.0f, 0.0f});
stepSize->upload();
// Create kernels for enforcing constraints.
......@@ -260,6 +263,8 @@ OpenCLIntegrationUtilities::~OpenCLIntegrationUtilities() {
delete random;
if (randomSeed != NULL)
delete randomSeed;
if (stepSize != NULL)
delete stepSize;
}
void OpenCLIntegrationUtilities::applyConstraints(double tol) {
......
platforms/opencl/src/OpenCLIntegrationUtilities.h
View file @ cc5467e7
......@@ -53,6 +53,12 @@ public:
OpenCLArray<mm_float4>& getRandom() {
return *random;
}
/**
* Get the array which contains the current step size.
*/
OpenCLArray<mm_float2>& getStepSize() {
return *stepSize;
}
/**
* Apply constraints to the atom positions.
*
......@@ -82,6 +88,7 @@ private:
OpenCLArray<mm_float4>* shakeParams;
OpenCLArray<mm_float4>* random;
OpenCLArray<mm_int4>* randomSeed;
OpenCLArray<mm_float2>* stepSize;
int randomPos;
int lastSeed;
struct ShakeCluster;
......
platforms/opencl/src/OpenCLKernelFactory.cpp
View file @ cc5467e7
......@@ -56,14 +56,14 @@ KernelImpl* OpenCLKernelFactory::createKernelImpl(std::string name, const Platfo
return new OpenCLIntegrateVerletStepKernel(name, platform, cl);
if (name == IntegrateLangevinStepKernel::Name())
return new OpenCLIntegrateLangevinStepKernel(name, platform, cl);
// if (name == IntegrateBrownianStepKernel::Name())
// return new OpenCLIntegrateBrownianStepKernel(name, platform, cl);
if (name == IntegrateBrownianStepKernel::Name())
return new OpenCLIntegrateBrownianStepKernel(name, platform, cl);
if (name == IntegrateVariableVerletStepKernel::Name())
return new OpenCLIntegrateVariableVerletStepKernel(name, platform, cl);
if (name == IntegrateVariableLangevinStepKernel::Name())
return new OpenCLIntegrateVariableLangevinStepKernel(name, platform, cl);
// if (name == ApplyAndersenThermostatKernel::Name())
// return new OpenCLApplyAndersenThermostatKernel(name, platform, cl);
if (name == ApplyAndersenThermostatKernel::Name())
return new OpenCLApplyAndersenThermostatKernel(name, platform, cl);
if (name == CalcKineticEnergyKernel::Name())
return new OpenCLCalcKineticEnergyKernel(name, platform, cl);
if (name == RemoveCMMotionKernel::Name())
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ cc5467e7
......@@ -1171,8 +1171,6 @@ double OpenCLCalcGBSAOBCForceKernel::executeEnergy(ContextImpl& context) {
}
OpenCLIntegrateVerletStepKernel::~OpenCLIntegrateVerletStepKernel() {
if (stepSize != NULL)
delete stepSize;
}
void OpenCLIntegrateVerletStepKernel::initialize(const System& system, const VerletIntegrator& integrator) {
......@@ -1180,24 +1178,23 @@ void OpenCLIntegrateVerletStepKernel::initialize(const System& system, const Ver
cl::Program program = cl.createProgram(cl.loadSourceFromFile("verlet.cl"));
kernel1 = cl::Kernel(program, "integrateVerletPart1");
kernel2 = cl::Kernel(program, "integrateVerletPart2");
stepSize = new OpenCLArray<mm_float2>(cl, 1, "stepSize");
prevStepSize = -1.0;
}
void OpenCLIntegrateVerletStepKernel::execute(ContextImpl& context, const VerletIntegrator& integrator) {
OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilties();
OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
int numAtoms = cl.getNumAtoms();
double dt = integrator.getStepSize();
if (!hasInitializedKernels) {
hasInitializedKernels = true;
kernel1.setArg<cl_int>(0, numAtoms);
kernel1.setArg<cl::Buffer>(1, stepSize->getDeviceBuffer());
kernel1.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(4, cl.getForce().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(5, integration.getPosDelta().getDeviceBuffer());
kernel2.setArg<cl_int>(0, numAtoms);
kernel2.setArg<cl::Buffer>(1, stepSize->getDeviceBuffer());
kernel2.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(4, integration.getPosDelta().getDeviceBuffer());
......@@ -1205,7 +1202,7 @@ void OpenCLIntegrateVerletStepKernel::execute(ContextImpl& context, const Verlet
if (dt != prevStepSize) {
vector<mm_float2> stepSizeVec(1);
stepSizeVec[0] = (mm_float2) {dt, dt};
stepSize->upload(stepSizeVec);
cl.getIntegrationUtilities().getStepSize().upload(stepSizeVec);
prevStepSize = dt;
}
......@@ -1238,8 +1235,11 @@ OpenCLIntegrateLangevinStepKernel::~OpenCLIntegrateLangevinStepKernel() {
void OpenCLIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) {
cl.initialize(system);
cl.getIntegrationUtilties().initRandomNumberGenerator(integrator.getRandomNumberSeed());
cl::Program program = cl.createProgram(cl.loadSourceFromFile("langevin.cl"));
cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
map<string, string> defines;
defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
defines["PADDED_NUM_ATOMS"] = intToString(cl.getPaddedNumAtoms());
cl::Program program = cl.createProgram(cl.loadSourceFromFile("langevin.cl"), defines);
kernel1 = cl::Kernel(program, "integrateLangevinPart1");
kernel2 = cl::Kernel(program, "integrateLangevinPart2");
kernel3 = cl::Kernel(program, "integrateLangevinPart3");
......@@ -1252,32 +1252,28 @@ void OpenCLIntegrateLangevinStepKernel::initialize(const System& system, const L
}
void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const LangevinIntegrator& integrator) {
OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilties();
OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
int numAtoms = cl.getNumAtoms();
if (!hasInitializedKernels) {
hasInitializedKernels = true;
kernel1.setArg<cl_int>(0, numAtoms);
kernel1.setArg<cl::Buffer>(1, cl.getVelm().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(2, cl.getForce().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(3, integration.getPosDelta().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(4, params->getDeviceBuffer());
kernel1.setArg(5, params->getSize()*sizeof(cl_float), NULL);
kernel1.setArg<cl::Buffer>(6, xVector->getDeviceBuffer());
kernel1.setArg<cl::Buffer>(7, vVector->getDeviceBuffer());
kernel1.setArg<cl::Buffer>(8,integration.getRandom().getDeviceBuffer());
kernel2.setArg<cl_int>(0, numAtoms);
kernel2.setArg<cl::Buffer>(1, cl.getVelm().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(3, params->getDeviceBuffer());
kernel2.setArg(4, params->getSize()*sizeof(cl_float), NULL);
kernel2.setArg<cl::Buffer>(5, xVector->getDeviceBuffer());
kernel2.setArg<cl::Buffer>(6, vVector->getDeviceBuffer());
kernel2.setArg<cl::Buffer>(7,integration.getRandom().getDeviceBuffer());
kernel3.setArg<cl_int>(0, numAtoms);
kernel3.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
kernel3.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
}
int numThreads = cl.getNumThreadBlocks()*cl.ThreadBlockSize;
kernel1.setArg<cl::Buffer>(0, cl.getVelm().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(1, cl.getForce().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(3, params->getDeviceBuffer());
kernel1.setArg(4, params->getSize()*sizeof(cl_float), NULL);
kernel1.setArg<cl::Buffer>(5, xVector->getDeviceBuffer());
kernel1.setArg<cl::Buffer>(6, vVector->getDeviceBuffer());
kernel1.setArg<cl::Buffer>(7,integration.getRandom().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(0, cl.getVelm().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(1, integration.getPosDelta().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(2, params->getDeviceBuffer());
kernel2.setArg(3, params->getSize()*sizeof(cl_float), NULL);
kernel2.setArg<cl::Buffer>(4, xVector->getDeviceBuffer());
kernel2.setArg<cl::Buffer>(5, vVector->getDeviceBuffer());
kernel2.setArg<cl::Buffer>(6,integration.getRandom().getDeviceBuffer());
kernel3.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
kernel3.setArg<cl::Buffer>(1, integration.getPosDelta().getDeviceBuffer());
}
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
......@@ -1346,7 +1342,7 @@ void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const Lang
// Call the first integration kernel.
kernel1.setArg<cl_uint>(9, integration.prepareRandomNumbers(2*numThreads));
kernel1.setArg<cl_uint>(8, integration.prepareRandomNumbers(2*cl.getPaddedNumAtoms()));
cl.executeKernel(kernel1, numAtoms);
// Apply constraints.
......@@ -1355,7 +1351,7 @@ void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const Lang
// Call the second integration kernel.
kernel2.setArg<cl_uint>(8, integration.prepareRandomNumbers(2*numThreads));
kernel2.setArg<cl_uint>(7, integration.prepareRandomNumbers(2*cl.getPaddedNumAtoms()));
cl.executeKernel(kernel2, numAtoms);
// Reapply constraints.
......@@ -1371,50 +1367,66 @@ void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const Lang
cl.setTime(cl.getTime()+stepSize);
cl.setStepCount(cl.getStepCount()+1);
}
//
//OpenCLIntegrateBrownianStepKernel::~OpenCLIntegrateBrownianStepKernel() {
//}
//
//void OpenCLIntegrateBrownianStepKernel::initialize(const System& system, const BrownianIntegrator& integrator) {
// initializeIntegration(system, data, integrator);
// _gpuContext* gpu = data.gpu;
// gpu->seed = (unsigned long) integrator.getRandomNumberSeed();
// gpuInitializeRandoms(gpu);
// prevStepSize = -1.0;
//}
//
//void OpenCLIntegrateBrownianStepKernel::execute(ContextImpl& context, const BrownianIntegrator& integrator) {
// _gpuContext* gpu = data.gpu;
// double temperature = integrator.getTemperature();
// double friction = integrator.getFriction();
// double stepSize = integrator.getStepSize();
// if (temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
// // Initialize the GPU parameters.
//
// double tau = (friction == 0.0 ? 0.0 : 1.0/friction);
// gpuSetBrownianIntegrationParameters(gpu, (float) tau, (float) stepSize, (float) temperature);
// gpuSetConstants(gpu);
// kGenerateRandoms(gpu);
// prevTemp = temperature;
// prevFriction = friction;
// prevStepSize = stepSize;
// }
// kBrownianUpdatePart1(gpu);
// kApplyFirstShake(gpu);
// kApplyFirstSettle(gpu);
// kApplyFirstCCMA(gpu);
// if (data.removeCM)
// if (data.stepCount%data.cmMotionFrequency == 0)
// gpu->bCalculateCM = true;
// kBrownianUpdatePart2(gpu);
// data.time += stepSize;
// data.stepCount++;
//}
//
OpenCLIntegrateBrownianStepKernel::~OpenCLIntegrateBrownianStepKernel() {
}
void OpenCLIntegrateBrownianStepKernel::initialize(const System& system, const BrownianIntegrator& integrator) {
cl.initialize(system);
cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
map<string, string> defines;
defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
cl::Program program = cl.createProgram(cl.loadSourceFromFile("brownian.cl"), defines);
kernel1 = cl::Kernel(program, "integrateBrownianPart1");
kernel2 = cl::Kernel(program, "integrateBrownianPart2");
prevStepSize = -1.0;
}
void OpenCLIntegrateBrownianStepKernel::execute(ContextImpl& context, const BrownianIntegrator& integrator) {
OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
int numAtoms = cl.getNumAtoms();
if (!hasInitializedKernels) {
hasInitializedKernels = true;
kernel1.setArg<cl::Buffer>(2, cl.getForce().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(3, integration.getPosDelta().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(4,integration.getRandom().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(2, cl.getVelm().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(3, integration.getPosDelta().getDeviceBuffer());
}
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
if (temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
double tau = (friction == 0.0 ? 0.0 : 1.0/friction);
kernel1.setArg<cl_float>(0, (cl_float) (tau*stepSize));
kernel1.setArg<cl_float>(1, (cl_float) (sqrt(2.0f*BOLTZ*temperature*stepSize*tau)));
kernel2.setArg<cl_float>(0, (cl_float) (1.0/stepSize));
prevTemp = temperature;
prevFriction = friction;
prevStepSize = stepSize;
}
// Call the first integration kernel.
kernel1.setArg<cl_uint>(5, integration.prepareRandomNumbers(cl.getPaddedNumAtoms()));
cl.executeKernel(kernel1, numAtoms);
// Apply constraints.
integration.applyConstraints(integrator.getConstraintTolerance());
// Call the second integration kernel.
cl.executeKernel(kernel2, numAtoms);
// Update the time and step count.
cl.setTime(cl.getTime()+stepSize);
cl.setStepCount(cl.getStepCount()+1);
}
OpenCLIntegrateVariableVerletStepKernel::~OpenCLIntegrateVariableVerletStepKernel() {
if (stepSize != NULL)
delete stepSize;
}
void OpenCLIntegrateVariableVerletStepKernel::initialize(const System& system, const VariableVerletIntegrator& integrator) {
......@@ -1423,30 +1435,27 @@ void OpenCLIntegrateVariableVerletStepKernel::initialize(const System& system, c
kernel1 = cl::Kernel(program, "integrateVerletPart1");
kernel2 = cl::Kernel(program, "integrateVerletPart2");
selectSizeKernel = cl::Kernel(program, "selectVerletStepSize");
stepSize = new OpenCLArray<mm_float2>(cl, 1, "stepSize", true);
stepSize->set(0, (mm_float2) {0.0f, 0.0f});
stepSize->upload();
blockSize = std::min(std::min(256, system.getNumParticles()), (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
}
void OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilties();
OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
int numAtoms = cl.getNumAtoms();
if (!hasInitializedKernels) {
hasInitializedKernels = true;
kernel1.setArg<cl_int>(0, numAtoms);
kernel1.setArg<cl::Buffer>(1, stepSize->getDeviceBuffer());
kernel1.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(4, cl.getForce().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(5, integration.getPosDelta().getDeviceBuffer());
kernel2.setArg<cl_int>(0, numAtoms);
kernel2.setArg<cl::Buffer>(1, stepSize->getDeviceBuffer());
kernel2.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(4, integration.getPosDelta().getDeviceBuffer());
selectSizeKernel.setArg<cl_int>(0, numAtoms);
selectSizeKernel.setArg<cl::Buffer>(3, stepSize->getDeviceBuffer());
selectSizeKernel.setArg<cl::Buffer>(3, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
selectSizeKernel.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
selectSizeKernel.setArg<cl::Buffer>(5, cl.getForce().getDeviceBuffer());
selectSizeKernel.setArg(6, blockSize*sizeof(cl_float), NULL);
......@@ -1473,8 +1482,8 @@ void OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, cons
// Update the time and step count.
stepSize->download();
double dt = stepSize->get(0).y;
cl.getIntegrationUtilities().getStepSize().download();
double dt = cl.getIntegrationUtilities().getStepSize()[0].y;
double time = cl.getTime()+dt;
if (dt == maxStepSize)
time = maxTime; // Avoid round-off error
......@@ -1489,14 +1498,15 @@ OpenCLIntegrateVariableLangevinStepKernel::~OpenCLIntegrateVariableLangevinStepK
delete xVector;
if (vVector != NULL)
delete vVector;
if (stepSize != NULL)
delete stepSize;
}
void OpenCLIntegrateVariableLangevinStepKernel::initialize(const System& system, const VariableLangevinIntegrator& integrator) {
cl.initialize(system);
cl.getIntegrationUtilties().initRandomNumberGenerator(integrator.getRandomNumberSeed());
cl::Program program = cl.createProgram(cl.loadSourceFromFile("langevin.cl"));
cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
map<string, string> defines;
defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
defines["PADDED_NUM_ATOMS"] = intToString(cl.getPaddedNumAtoms());
cl::Program program = cl.createProgram(cl.loadSourceFromFile("langevin.cl"), defines);
kernel1 = cl::Kernel(program, "integrateLangevinPart1");
kernel2 = cl::Kernel(program, "integrateLangevinPart2");
kernel3 = cl::Kernel(program, "integrateLangevinPart3");
......@@ -1506,61 +1516,53 @@ void OpenCLIntegrateVariableLangevinStepKernel::initialize(const System& system,
vVector = new OpenCLArray<mm_float4>(cl, cl.getPaddedNumAtoms(), "vVector");
vector<mm_float4> initialXVector(xVector->getSize(), (mm_float4) {0.0f, 0.0f, 0.0f, 0.0f});
xVector->upload(initialXVector);
stepSize = new OpenCLArray<mm_float2>(cl, 1, "stepSize", true);
stepSize->set(0, (mm_float2) {0.0f, 0.0f});
stepSize->upload();
blockSize = std::min(256, system.getNumParticles());
blockSize = std::max(blockSize, params->getSize());
blockSize = std::min(blockSize, (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
}
void OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) {
OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilties();
OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
int numAtoms = cl.getNumAtoms();
if (!hasInitializedKernels) {
hasInitializedKernels = true;
kernel1.setArg<cl_int>(0, numAtoms);
kernel1.setArg<cl::Buffer>(1, cl.getVelm().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(2, cl.getForce().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(3, integration.getPosDelta().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(4, params->getDeviceBuffer());
kernel1.setArg(5, params->getSize()*sizeof(cl_float), NULL);
kernel1.setArg<cl::Buffer>(6, xVector->getDeviceBuffer());
kernel1.setArg<cl::Buffer>(7, vVector->getDeviceBuffer());
kernel1.setArg<cl::Buffer>(8,integration.getRandom().getDeviceBuffer());
kernel2.setArg<cl_int>(0, numAtoms);
kernel2.setArg<cl::Buffer>(1, cl.getVelm().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(3, params->getDeviceBuffer());
kernel2.setArg(4, params->getSize()*sizeof(cl_float), NULL);
kernel2.setArg<cl::Buffer>(5, xVector->getDeviceBuffer());
kernel2.setArg<cl::Buffer>(6, vVector->getDeviceBuffer());
kernel2.setArg<cl::Buffer>(7,integration.getRandom().getDeviceBuffer());
kernel3.setArg<cl_int>(0, numAtoms);
kernel3.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
kernel3.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
selectSizeKernel.setArg<cl_int>(0, numAtoms);
selectSizeKernel.setArg<cl::Buffer>(5, stepSize->getDeviceBuffer());
selectSizeKernel.setArg<cl::Buffer>(6, cl.getVelm().getDeviceBuffer());
selectSizeKernel.setArg<cl::Buffer>(7, cl.getForce().getDeviceBuffer());
selectSizeKernel.setArg<cl::Buffer>(8, params->getDeviceBuffer());
selectSizeKernel.setArg(9, params->getSize()*sizeof(cl_float), NULL);
selectSizeKernel.setArg(10, blockSize*sizeof(cl_float), NULL);
kernel1.setArg<cl::Buffer>(0, cl.getVelm().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(1, cl.getForce().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
kernel1.setArg<cl::Buffer>(3, params->getDeviceBuffer());
kernel1.setArg(4, params->getSize()*sizeof(cl_float), NULL);
kernel1.setArg<cl::Buffer>(5, xVector->getDeviceBuffer());
kernel1.setArg<cl::Buffer>(6, vVector->getDeviceBuffer());
kernel1.setArg<cl::Buffer>(7,integration.getRandom().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(0, cl.getVelm().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(1, integration.getPosDelta().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(2, params->getDeviceBuffer());
kernel2.setArg(3, params->getSize()*sizeof(cl_float), NULL);
kernel2.setArg<cl::Buffer>(4, xVector->getDeviceBuffer());
kernel2.setArg<cl::Buffer>(5, vVector->getDeviceBuffer());
kernel2.setArg<cl::Buffer>(6,integration.getRandom().getDeviceBuffer());
kernel3.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
kernel3.setArg<cl::Buffer>(1, integration.getPosDelta().getDeviceBuffer());
selectSizeKernel.setArg<cl::Buffer>(4, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
selectSizeKernel.setArg<cl::Buffer>(5, cl.getVelm().getDeviceBuffer());
selectSizeKernel.setArg<cl::Buffer>(6, cl.getForce().getDeviceBuffer());
selectSizeKernel.setArg<cl::Buffer>(7, params->getDeviceBuffer());
selectSizeKernel.setArg(8, params->getSize()*sizeof(cl_float), NULL);
selectSizeKernel.setArg(9, blockSize*sizeof(cl_float), NULL);
}
// Select the step size to use.
float maxStepSize = (float)(maxTime-cl.getTime());
selectSizeKernel.setArg<cl_float>(1, maxStepSize);
selectSizeKernel.setArg<cl_float>(2, (cl_float) integrator.getErrorTolerance());
selectSizeKernel.setArg<cl_float>(3, (cl_float) (integrator.getFriction() == 0.0 ? 0.0 : 1.0/integrator.getFriction()));
selectSizeKernel.setArg<cl_float>(4, (cl_float) (BOLTZ*integrator.getTemperature()));
selectSizeKernel.setArg<cl_float>(0, maxStepSize);
selectSizeKernel.setArg<cl_float>(1, (cl_float) integrator.getErrorTolerance());
selectSizeKernel.setArg<cl_float>(2, (cl_float) (integrator.getFriction() == 0.0 ? 0.0 : 1.0/integrator.getFriction()));
selectSizeKernel.setArg<cl_float>(3, (cl_float) (BOLTZ*integrator.getTemperature()));
cl.executeKernel(selectSizeKernel, blockSize, blockSize);
// Call the first integration kernel.
int numThreads = cl.getNumThreadBlocks()*cl.ThreadBlockSize;
kernel1.setArg<cl_uint>(9, integration.prepareRandomNumbers(2*numThreads));
kernel1.setArg<cl_uint>(8, integration.prepareRandomNumbers(2*cl.getPaddedNumAtoms()));
cl.executeKernel(kernel1, numAtoms);
// Apply constraints.
......@@ -1569,7 +1571,7 @@ void OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, co
// Call the second integration kernel.
kernel2.setArg<cl_uint>(8, integration.prepareRandomNumbers(2*numThreads));
kernel2.setArg<cl_uint>(7, integration.prepareRandomNumbers(2*cl.getPaddedNumAtoms()));
cl.executeKernel(kernel2, numAtoms);
// Reapply constraints.
......@@ -1582,8 +1584,8 @@ void OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, co
// Update the time and step count.
stepSize->download();
double dt = stepSize->get(0).y;
cl.getIntegrationUtilities().getStepSize().download();
double dt = cl.getIntegrationUtilities().getStepSize()[0].y;
double time = cl.getTime()+dt;
if (dt == maxStepSize)
time = maxTime; // Avoid round-off error
......@@ -1591,34 +1593,32 @@ void OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, co
cl.setStepCount(cl.getStepCount()+1);
}
//OpenCLApplyAndersenThermostatKernel::~OpenCLApplyAndersenThermostatKernel() {
//}
//
//void OpenCLApplyAndersenThermostatKernel::initialize(const System& system, const AndersenThermostat& thermostat) {
// _gpuContext* gpu = data.gpu;
// gpu->seed = (unsigned long) thermostat.getRandomNumberSeed();
// gpuInitializeRandoms(gpu);
// prevStepSize = -1.0;
//}
//
//void OpenCLApplyAndersenThermostatKernel::execute(ContextImpl& context) {
// _gpuContext* gpu = data.gpu;
// double temperature = context.getParameter(AndersenThermostat::Temperature());
// double frequency = context.getParameter(AndersenThermostat::CollisionFrequency());
// double stepSize = context.getIntegrator().getStepSize();
// if (temperature != prevTemp || frequency != prevFrequency || stepSize != prevStepSize) {
// // Initialize the GPU parameters.
//
// gpuSetAndersenThermostatParameters(gpu, (float) temperature, frequency);
// gpuSetConstants(gpu);
// kGenerateRandoms(gpu);
// prevTemp = temperature;
// prevFrequency = frequency;
// prevStepSize = stepSize;
// }
// kCalculateAndersenThermostat(gpu);
//}
//
OpenCLApplyAndersenThermostatKernel::~OpenCLApplyAndersenThermostatKernel() {
}
void OpenCLApplyAndersenThermostatKernel::initialize(const System& system, const AndersenThermostat& thermostat) {
randomSeed = thermostat.getRandomNumberSeed();
map<string, string> defines;
defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
defines["PADDED_NUM_ATOMS"] = intToString(cl.getPaddedNumAtoms());
cl::Program program = cl.createProgram(cl.loadSourceFromFile("andersenThermostat.cl"), defines);
kernel = cl::Kernel(program, "applyAndersenThermostat");
}
void OpenCLApplyAndersenThermostatKernel::execute(ContextImpl& context) {
if (!hasInitializedKernels) {
hasInitializedKernels = true;
cl.getIntegrationUtilities().initRandomNumberGenerator(randomSeed);
kernel.setArg<cl::Buffer>(2, cl.getVelm().getDeviceBuffer());
kernel.setArg<cl::Buffer>(3, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
kernel.setArg<cl::Buffer>(4, cl.getIntegrationUtilities().getRandom().getDeviceBuffer());
}
kernel.setArg<cl_float>(0, (cl_float) context.getParameter(AndersenThermostat::CollisionFrequency()));
kernel.setArg<cl_float>(1, (cl_float) (BOLTZ*context.getParameter(AndersenThermostat::Temperature())));
kernel.setArg<cl_uint>(5, cl.getIntegrationUtilities().prepareRandomNumbers(cl.getPaddedNumAtoms()));
cl.executeKernel(kernel, cl.getNumAtoms());
}
void OpenCLCalcKineticEnergyKernel::initialize(const System& system) {
int numParticles = system.getNumParticles();
masses.resize(numParticles);
......
platforms/opencl/src/OpenCLKernels.h
View file @ cc5467e7
......@@ -436,7 +436,7 @@ private:
class OpenCLIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
public:
OpenCLIntegrateVerletStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateVerletStepKernel(name, platform), cl(cl),
hasInitializedKernels(false), stepSize(NULL) {
hasInitializedKernels(false) {
}
~OpenCLIntegrateVerletStepKernel();
/**
......@@ -457,7 +457,6 @@ private:
OpenCLContext& cl;
double prevStepSize;
bool hasInitializedKernels;
OpenCLArray<mm_float2>* stepSize;
cl::Kernel kernel1, kernel2;
};
......@@ -494,32 +493,34 @@ private:
cl::Kernel kernel1, kernel2, kernel3;
};
///**
// * This kernel is invoked by BrownianIntegrator to take one time step.
// */
//class OpenCLIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
//public:
// OpenCLIntegrateBrownianStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateBrownianStepKernel(name, platform), cl(cl) {
// }
// ~OpenCLIntegrateBrownianStepKernel();
// /**
// * Initialize the kernel.
// *
// * @param system the System this kernel will be applied to
// * @param integrator the BrownianIntegrator this kernel will be used for
// */
// void initialize(const System& system, const BrownianIntegrator& integrator);
// /**
// * Execute the kernel.
// *
// * @param context the context in which to execute this kernel
// * @param integrator the BrownianIntegrator this kernel is being used for
// */
// void execute(ContextImpl& context, const BrownianIntegrator& integrator);
//private:
// OpenCLContext& cl;
// double prevTemp, prevFriction, prevStepSize;
//};
/**
* This kernel is invoked by BrownianIntegrator to take one time step.
*/
class OpenCLIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
public:
OpenCLIntegrateBrownianStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateBrownianStepKernel(name, platform), cl(cl) {
}
~OpenCLIntegrateBrownianStepKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param integrator the BrownianIntegrator this kernel will be used for
*/
void initialize(const System& system, const BrownianIntegrator& integrator);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the BrownianIntegrator this kernel is being used for
*/
void execute(ContextImpl& context, const BrownianIntegrator& integrator);
private:
OpenCLContext& cl;
double prevTemp, prevFriction, prevStepSize;
bool hasInitializedKernels;
cl::Kernel kernel1, kernel2;
};
/**
* This kernel is invoked by VariableVerletIntegrator to take one time step.
......@@ -527,7 +528,7 @@ private:
class OpenCLIntegrateVariableVerletStepKernel : public IntegrateVariableVerletStepKernel {
public:
OpenCLIntegrateVariableVerletStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateVariableVerletStepKernel(name, platform), cl(cl),
hasInitializedKernels(false), stepSize(NULL) {
hasInitializedKernels(false) {
}
~OpenCLIntegrateVariableVerletStepKernel();
/**
......@@ -549,7 +550,6 @@ private:
OpenCLContext& cl;
bool hasInitializedKernels;
int blockSize;
OpenCLArray<mm_float2>* stepSize;
cl::Kernel kernel1, kernel2, selectSizeKernel;
};
......@@ -559,7 +559,7 @@ private:
class OpenCLIntegrateVariableLangevinStepKernel : public IntegrateVariableLangevinStepKernel {
public:
OpenCLIntegrateVariableLangevinStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateVariableLangevinStepKernel(name, platform), cl(cl),
hasInitializedKernels(false), stepSize(NULL) {
hasInitializedKernels(false) {
}
~OpenCLIntegrateVariableLangevinStepKernel();
/**
......@@ -584,36 +584,39 @@ private:
OpenCLArray<cl_float>* params;
OpenCLArray<mm_float4>* xVector;
OpenCLArray<mm_float4>* vVector;
OpenCLArray<mm_float2>* stepSize;
cl::Kernel kernel1, kernel2, kernel3, selectSizeKernel;
double prevTemp, prevFriction, prevErrorTol;
};
//
///**
// * This kernel is invoked by AndersenThermostat at the start of each time step to adjust the particle velocities.
// */
//class OpenCLApplyAndersenThermostatKernel : public ApplyAndersenThermostatKernel {
//public:
// OpenCLApplyAndersenThermostatKernel(std::string name, const Platform& platform, OpenCLContext& cl) : ApplyAndersenThermostatKernel(name, platform), cl(cl) {
// }
// ~OpenCLApplyAndersenThermostatKernel();
// /**
// * Initialize the kernel.
// *
// * @param system the System this kernel will be applied to
// * @param thermostat the AndersenThermostat this kernel will be used for
// */
// void initialize(const System& system, const AndersenThermostat& thermostat);
// /**
// * Execute the kernel.
// *
// * @param context the context in which to execute this kernel
// */
// void execute(ContextImpl& context);
//private:
// OpenCLContext& cl;
// double prevTemp, prevFrequency, prevStepSize;
//};
/**
* This kernel is invoked by AndersenThermostat at the start of each time step to adjust the particle velocities.
*/
class OpenCLApplyAndersenThermostatKernel : public ApplyAndersenThermostatKernel {
public:
OpenCLApplyAndersenThermostatKernel(std::string name, const Platform& platform, OpenCLContext& cl) : ApplyAndersenThermostatKernel(name, platform), cl(cl),
hasInitializedKernels(false) {
}
~OpenCLApplyAndersenThermostatKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param thermostat the AndersenThermostat this kernel will be used for
*/
void initialize(const System& system, const AndersenThermostat& thermostat);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
*/
void execute(ContextImpl& context);
private:
OpenCLContext& cl;
bool hasInitializedKernels;
int randomSeed;
cl::Kernel kernel;
double prevTemp, prevFriction, prevStepSize;
};
/**
* This kernel is invoked to calculate the kinetic energy of the system.
......
platforms/opencl/src/OpenCLPlatform.cpp
View file @ cc5467e7
......@@ -56,10 +56,10 @@ OpenCLPlatform::OpenCLPlatform() {
registerKernelFactory(CalcGBSAOBCForceKernel::Name(), factory);
registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
// registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableLangevinStepKernel::Name(), factory);
// registerKernelFactory(ApplyAndersenThermostatKernel::Name(), factory);
registerKernelFactory(ApplyAndersenThermostatKernel::Name(), factory);
registerKernelFactory(CalcKineticEnergyKernel::Name(), factory);
registerKernelFactory(RemoveCMMotionKernel::Name(), factory);
platformProperties.push_back(OpenCLDeviceIndex());
......
platforms/opencl/src/kernels/andersenThermostat.cl 0 → 100644
View file @ cc5467e7
/**
* Apply the Andersen thermostat to adjust particle velocities.
*/
__kernel void applyAndersenThermostat(float collisionFrequency, float kT, __global float4* velm, __global float2* stepSize, __global float4* random, unsigned int randomIndex) {
randomIndex += get_global_id(0);
float collisionProbability = 1.0f-exp(-collisionFrequency*stepSize[0].y);
for (int index = get_global_id(0); index < NUM_ATOMS; index += get_global_size(0)) {
float4 velocity = velm[index];
float4 rand = random[randomIndex];
float scale = (rand.w < collisionProbability ? 0.0 : 1.0);
float add = (1.0-scale)*sqrt(kT*velocity.w);
velocity.xyz = scale*velocity.xyz + add*rand.xyz;
velm[index] = velocity;
randomIndex += get_global_size(0);
}
}
platforms/opencl/src/kernels/brownian.cl 0 → 100644
View file @ cc5467e7
/**
* Perform the first step of Brownian integration.
*/
__kernel void integrateBrownianPart1(float tauDeltaT, float noiseAmplitude, __global float4* force,
__global float4* posDelta, __global float4* random, unsigned int randomIndex) {
randomIndex += get_global_id(0);
for (int index = get_global_id(0); index < NUM_ATOMS; index += get_global_size(0)) {
posDelta[index] = (float4) (tauDeltaT*force[index].xyz + noiseAmplitude*random[randomIndex].xyz, 0.0f);
randomIndex += get_global_size(0);
}
}
/**
* Perform the second step of Brownian integration.
*/
__kernel void integrateBrownianPart2(float oneOverDeltaT, __global float4* posq, __global float4* velm, __global float4* posDelta) {
for (int index = get_global_id(0); index < NUM_ATOMS; index += get_global_size(0)) {
float4 delta = posDelta[index];
velm[index].xyz = oneOverDeltaT*delta.xyz;
posq[index].xyz = posq[index].xyz + delta.xyz;
}
}
platforms/opencl/src/kernels/langevin.cl
View file @ cc5467e7
......@@ -4,7 +4,7 @@ enum {EM, EM_V, DOverTauC, TauOneMinusEM_V, TauDOverEMMinusOne, V, X, Yv, Yx, Fi
* Perform the first step of Langevin integration.
*/
__kernel void integrateLangevinPart1(int numAtoms, __global float4* velm, __global float4* force, __global float4* posDelta,
__kernel void integrateLangevinPart1(__global float4* velm, __global float4* force, __global float4* posDelta,
__global float* paramBuffer, __local float* params, __global float4* xVector, __global float4* vVector,
__global float4* random, unsigned int randomIndex) {
......@@ -15,12 +15,11 @@ __kernel void integrateLangevinPart1(int numAtoms, __global float4* velm, __glob
params[index] = paramBuffer[index];
barrier(CLK_LOCAL_MEM_FENCE);
randomIndex += index;
while (index < numAtoms) {
while (index < NUM_ATOMS) {
float4 velocity = velm[index];
float sqrtInvMass = sqrt(velocity.w);
float4 vmh = (float4) (xVector[index].xyz*params[DOverTauC] + sqrtInvMass*params[Yv]*random[randomIndex].xyz, 0.0f);
randomIndex += get_global_size(0);
float4 vVec = (float4) (sqrtInvMass*params[V]*random[randomIndex].xyz, 0.0f);
float4 vVec = (float4) (sqrtInvMass*params[V]*random[randomIndex+PADDED_NUM_ATOMS].xyz, 0.0f);
randomIndex += get_global_size(0);
vVector[index] = vVec;
velocity.xyz = velocity.xyz*params[EM_V] + velocity.w*force[index].xyz*params[TauOneMinusEM_V] + vVec.xyz - params[EM]*vmh.xyz;
......@@ -34,7 +33,7 @@ __kernel void integrateLangevinPart1(int numAtoms, __global float4* velm, __glob
* Perform the second step of Langevin integration.
*/
__kernel void integrateLangevinPart2(int numAtoms, __global float4* velm, __global float4* posDelta, __global float* paramBuffer,
__kernel void integrateLangevinPart2(__global float4* velm, __global float4* posDelta, __global float* paramBuffer,
__local float* params, __global float4* xVector, __global float4* vVector, __global float4* random, unsigned int randomIndex) {
// Load the parameters into local memory for faster access.
......@@ -44,14 +43,13 @@ __kernel void integrateLangevinPart2(int numAtoms, __global float4* velm, __glob
params[index] = paramBuffer[index];
barrier(CLK_LOCAL_MEM_FENCE);
randomIndex += index;
while (index < numAtoms) {
while (index < NUM_ATOMS) {
float4 delta = posDelta[index];
float4 velocity = velm[index];
float sqrtInvMass = sqrt(velocity.w);
velocity.xyz = delta.xyz*params[OneOverFix1];
float4 xmh = (float4) (vVector[index].xyz*params[TauDOverEMMinusOne] + sqrtInvMass*params[Yx]*random[randomIndex].xyz, 0.0f);
randomIndex += get_global_size(0);
float4 xVec = (float4) (sqrtInvMass*params[X]*random[randomIndex].xyz, 0.0f);
float4 xVec = (float4) (sqrtInvMass*params[X]*random[randomIndex+PADDED_NUM_ATOMS].xyz, 0.0f);
randomIndex += get_global_size(0);
delta.xyz += xVec.xyz - xmh.xyz;
posDelta[index] = delta;
......@@ -65,9 +63,9 @@ __kernel void integrateLangevinPart2(int numAtoms, __global float4* velm, __glob
* Perform the third step of Langevin integration.
*/
__kernel void integrateLangevinPart3(int numAtoms, __global float4* posq, __global float4* posDelta) {
__kernel void integrateLangevinPart3(__global float4* posq, __global float4* posDelta) {
int index = get_global_id(0);
while (index < numAtoms) {
while (index < NUM_ATOMS) {
float4 pos = posq[index];
float4 delta = posDelta[index];
pos.xyz += delta.xyz;
......@@ -80,13 +78,13 @@ __kernel void integrateLangevinPart3(int numAtoms, __global float4* posq, __glob
* Select the step size to use for the next step.
*/
__kernel void selectLangevinStepSize(int numAtoms, float maxStepSize, float errorTol, float tau, float kT, __global float2* dt,
__kernel void selectLangevinStepSize(float maxStepSize, float errorTol, float tau, float kT, __global float2* dt,
__global float4* velm, __global float4* force, __global float* paramBuffer, __local float* params, __local float* error) {
// Calculate the error.
float err = 0.0f;
unsigned int index = get_local_id(0);
while (index < numAtoms) {
while (index < NUM_ATOMS) {
float4 f = force[index];
float invMass = velm[index].w;
err += (f.x*f.x + f.y*f.y + f.z*f.z)*invMass;
......@@ -105,7 +103,7 @@ __kernel void selectLangevinStepSize(int numAtoms, float maxStepSize, float erro
if (get_global_id(0) == 0) {
// Select the new step size.
float totalError = sqrt(error[0]/(numAtoms*3));
float totalError = sqrt(error[0]/(NUM_ATOMS*3));
float newStepSize = sqrt(errorTol/totalError);
float oldStepSize = dt[0].y;
if (oldStepSize > 0.0f)
......
platforms/opencl/tests/TestOpenCLAndersenThermostat.cpp 0 → 100644
View file @ cc5467e7
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of AndersenThermostat.
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/AndersenThermostat.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "../src/sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
void testTemperature() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
OpenCLPlatform platform;
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
AndersenThermostat* thermstat = new AndersenThermostat(temp, collisionFreq);
system.addForce(thermstat);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
context.setPositions(positions);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the temperature is correct.
double ke = 0.0;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Energy);
ke += state.getKineticEnergy();
integrator.step(1);
}
ke /= 1000;
double expected = 0.5*numParticles*3*BOLTZ*temp;
ASSERT_EQUAL_TOL(expected, ke, 3*expected/std::sqrt(1000.0));
}
void testRandomSeed() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
OpenCLPlatform platform;
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
AndersenThermostat* thermostat = new AndersenThermostat(temp, collisionFreq);
system.addForce(thermostat);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
velocities[i] = Vec3(0, 0, 0);
}
// Try twice with the same random seed.
thermostat->setRandomNumberSeed(5);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state1 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state2 = context.getState(State::Positions);
// Try twice with a different random seed.
thermostat->setRandomNumberSeed(10);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state3 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state4 = context.getState(State::Positions);
// Compare the results.
for (int i = 0; i < numParticles; i++) {
for (int j = 0; j < 3; j++) {
ASSERT(state1.getPositions()[i][j] == state2.getPositions()[i][j]);
ASSERT(state3.getPositions()[i][j] == state4.getPositions()[i][j]);
ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
}
}
}
int main() {
try {
testTemperature();
testRandomSeed();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/opencl/tests/TestOpenCLBrownianIntegrator.cpp 0 → 100644
View file @ cc5467e7
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/System.h"
/**
* This tests the OpenCL implementation of BrownianIntegrator.
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/BrownianIntegrator.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "../src/sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
void testSingleBond() {
OpenCLPlatform platform;
System system;
system.addParticle(2.0);
system.addParticle(2.0);
double dt = 0.01;
BrownianIntegrator integrator(0, 0.1, dt);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// This is simply an overdamped harmonic oscillator, so compare it to the analytical solution.
double rate = 2*1.0/0.1;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Velocities);
double time = state.getTime();
double expectedDist = 1.5+0.5*std::exp(-rate*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
if (i > 0) {
double expectedSpeed = -0.5*rate*std::exp(-rate*(time-0.5*dt));
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.11);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.11);
}
integrator.step(1);
}
}
void testTemperature() {
const int numParticles = 8;
const int numBonds = numParticles-1;
const double temp = 10.0;
OpenCLPlatform platform;
System system;
BrownianIntegrator integrator(temp, 2.0, 0.01);
HarmonicBondForce* forceField = new HarmonicBondForce();
for (int i = 0; i < numParticles; ++i)
system.addParticle(2.0);
for (int i = 0; i < numBonds; ++i)
forceField->addBond(i, i+1, 1.0, 5.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3(i, 0, 0);
context.setPositions(positions);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the temperature is correct.
double pe = 0.0;
const int steps = 50000;
for (int i = 0; i < steps; ++i) {
State state = context.getState(State::Energy);
pe += state.getPotentialEnergy();
integrator.step(1);
}
pe /= steps;
double expected = 0.5*numBonds*BOLTZ*temp;
ASSERT_EQUAL_TOL(expected, pe, 0.1*expected);
}
void testConstraints() {
const int numParticles = 8;
const int numConstraints = 5;
const double temp = 20.0;
OpenCLPlatform platform;
System system;
BrownianIntegrator integrator(temp, 2.0, 0.001);
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(10.0);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
system.addConstraint(0, 1, 1.0);
system.addConstraint(1, 2, 1.0);
system.addConstraint(2, 3, 1.0);
system.addConstraint(4, 5, 1.0);
system.addConstraint(6, 7, 1.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i, 0, 0);
velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions);
for (int j = 0; j < numConstraints; ++j) {
int particle1, particle2;
double distance;
system.getConstraintParameters(j, particle1, particle2, distance);
Vec3 p1 = state.getPositions()[particle1];
Vec3 p2 = state.getPositions()[particle2];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 1e-4);
}
integrator.step(1);
}
}
void testRandomSeed() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
OpenCLPlatform platform;
System system;
BrownianIntegrator integrator(temp, 2.0, 0.001);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
velocities[i] = Vec3(0, 0, 0);
}
// Try twice with the same random seed.
integrator.setRandomNumberSeed(5);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state1 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state2 = context.getState(State::Positions);
// Try twice with a different random seed.
integrator.setRandomNumberSeed(10);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state3 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state4 = context.getState(State::Positions);
// Compare the results.
for (int i = 0; i < numParticles; i++) {
for (int j = 0; j < 3; j++) {
ASSERT(state1.getPositions()[i][j] == state2.getPositions()[i][j]);
ASSERT(state3.getPositions()[i][j] == state4.getPositions()[i][j]);
ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
}
}
}
int main() {
try {
testSingleBond();
testTemperature();
// testConstraints();
testRandomSeed();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/opencl/tests/TestOpenCLRandom.cpp
View file @ cc5467e7
......@@ -50,9 +50,9 @@ void testGaussian() {
system.addParticle(1.0);
OpenCLContext context(numAtoms, -1);
context.initialize(system);
context.getIntegrationUtilties().initRandomNumberGenerator(0);
OpenCLArray<mm_float4>& random = context.getIntegrationUtilties().getRandom();
context.getIntegrationUtilties().prepareRandomNumbers(random.getSize());
context.getIntegrationUtilities().initRandomNumberGenerator(0);
OpenCLArray<mm_float4>& random = context.getIntegrationUtilities().getRandom();
context.getIntegrationUtilities().prepareRandomNumbers(random.getSize());
const int numValues = random.getSize()*4;
vector<mm_float4> values(numValues);
random.download(values);
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment