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Commit f51a85b9 authored by Peter Eastman's avatar Peter Eastman
Browse files

Converted more forces to use OpenCLBondedUtilities

parent 42b9d891
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Showing with 225 additions and 557 deletions
platforms/opencl/src/OpenCLKernels.cpp
View file @ f51a85b9
......@@ -290,8 +290,6 @@ private:
OpenCLCalcCustomBondForceKernel::~OpenCLCalcCustomBondForceKernel() {
if (params != NULL)
delete params;
if (indices != NULL)
delete indices;
if (globals != NULL)
delete globals;
}
......@@ -303,31 +301,18 @@ void OpenCLCalcCustomBondForceKernel::initialize(const System& system, const Cus
numBonds = endIndex-startIndex;
if (numBonds == 0)
return;
vector<vector<int> > atoms(numBonds, vector<int>(2));
params = new OpenCLParameterSet(cl, force.getNumPerBondParameters(), numBonds, "customBondParams");
indices = new OpenCLArray<mm_int4>(cl, numBonds, "customBondIndices");
string extraArguments;
if (force.getNumGlobalParameters() > 0) {
globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customBondGlobals", false, CL_MEM_READ_ONLY);
extraArguments += ", __constant float* globals";
}
vector<int> forceBufferCounter(system.getNumParticles(), 0);
vector<vector<cl_float> > paramVector(numBonds);
vector<mm_int4> indicesVector(numBonds);
for (int i = 0; i < numBonds; i++) {
int particle1, particle2;
vector<double> parameters;
force.getBondParameters(startIndex+i, particle1, particle2, parameters);
force.getBondParameters(startIndex+i, atoms[i][0], atoms[i][1], parameters);
paramVector[i].resize(parameters.size());
for (int j = 0; j < (int) parameters.size(); j++)
paramVector[i][j] = (cl_float) parameters[j];
indicesVector[i] = mm_int4(particle1, particle2, forceBufferCounter[particle1]++, forceBufferCounter[particle2]++);
}
params->setParameterValues(paramVector);
indices->upload(indicesVector);
int maxBuffers = 1;
for (int i = 0; i < (int) forceBufferCounter.size(); i++)
maxBuffers = max(maxBuffers, forceBufferCounter[i]);
cl.addForce(new OpenCLCustomBondForceInfo(maxBuffers, force));
cl.addForce(new OpenCLCustomBondForceInfo(0, force));
// Record information for the expressions.
......@@ -337,8 +322,6 @@ void OpenCLCalcCustomBondForceKernel::initialize(const System& system, const Cus
globalParamNames[i] = force.getGlobalParameterName(i);
globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
}
if (globals != NULL)
globals->upload(globalParamValues);
Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
Lepton::ParsedExpression forceExpression = energyExpression.differentiate("r").optimize();
map<string, Lepton::ParsedExpression> expressions;
......@@ -353,29 +336,30 @@ void OpenCLCalcCustomBondForceKernel::initialize(const System& system, const Cus
const string& name = force.getPerBondParameterName(i);
variables[name] = "bondParams"+params->getParameterSuffix(i);
}
if (force.getNumGlobalParameters() > 0) {
globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customBondGlobals", false, CL_MEM_READ_ONLY);
globals->upload(globalParamValues);
string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
const string& name = force.getGlobalParameterName(i);
string value = "globals["+intToString(i)+"]";
string value = argName+"["+intToString(i)+"]";
variables[name] = value;
}
}
stringstream compute;
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
extraArguments += ", __global "+buffer.getType()+"* "+buffer.getName();
compute<<buffer.getType()<<" bondParams"<<(i+1)<<" = "<<buffer.getName()<<"[index];\n";
string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
compute<<buffer.getType()<<" bondParams"<<(i+1)<<" = "<<argName<<"[index];\n";
}
vector<pair<string, string> > functions;
compute << OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "temp", "");
map<string, string> replacements;
replacements["COMPUTE_FORCE"] = compute.str();
replacements["EXTRA_ARGUMENTS"] = extraArguments;
cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customBondForce, replacements));
kernel = cl::Kernel(program, "computeCustomBondForces");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::customBondForce, replacements));
}
double OpenCLCalcCustomBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numBonds == 0)
return 0.0;
if (globals != NULL) {
bool changed = false;
for (int i = 0; i < (int) globalParamNames.size(); i++) {
......@@ -387,23 +371,6 @@ double OpenCLCalcCustomBondForceKernel::execute(ContextImpl& context, bool inclu
if (changed)
globals->upload(globalParamValues);
}
if (!hasInitializedKernel) {
hasInitializedKernel = true;
kernel.setArg<cl_int>(0, cl.getPaddedNumAtoms());
kernel.setArg<cl_int>(1, numBonds);
kernel.setArg<cl::Buffer>(2, cl.getForceBuffers().getDeviceBuffer());
kernel.setArg<cl::Buffer>(3, cl.getEnergyBuffer().getDeviceBuffer());
kernel.setArg<cl::Buffer>(4, cl.getPosq().getDeviceBuffer());
kernel.setArg<cl::Buffer>(5, indices->getDeviceBuffer());
int nextIndex = 6;
if (globals != NULL)
kernel.setArg<cl::Buffer>(nextIndex++, globals->getDeviceBuffer());
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
kernel.setArg<cl::Memory>(nextIndex++, buffer.getMemory());
}
}
cl.executeKernel(kernel, numBonds);
return 0.0;
}
......@@ -499,8 +466,6 @@ private:
OpenCLCalcCustomAngleForceKernel::~OpenCLCalcCustomAngleForceKernel() {
if (params != NULL)
delete params;
if (indices != NULL)
delete indices;
if (globals != NULL)
delete globals;
}
......@@ -512,32 +477,18 @@ void OpenCLCalcCustomAngleForceKernel::initialize(const System& system, const Cu
numAngles = endIndex-startIndex;
if (numAngles == 0)
return;
vector<vector<int> > atoms(numAngles, vector<int>(3));
params = new OpenCLParameterSet(cl, force.getNumPerAngleParameters(), numAngles, "customAngleParams");
indices = new OpenCLArray<mm_int8>(cl, numAngles, "customAngleIndices");
string extraArguments;
if (force.getNumGlobalParameters() > 0) {
globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customAngleGlobals", false, CL_MEM_READ_ONLY);
extraArguments += ", __constant float* globals";
}
vector<int> forceBufferCounter(system.getNumParticles(), 0);
vector<vector<cl_float> > paramVector(numAngles);
vector<mm_int8> indicesVector(numAngles);
for (int i = 0; i < numAngles; i++) {
int particle1, particle2, particle3;
vector<double> parameters;
force.getAngleParameters(startIndex+i, particle1, particle2, particle3, parameters);
force.getAngleParameters(startIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], parameters);
paramVector[i].resize(parameters.size());
for (int j = 0; j < (int) parameters.size(); j++)
paramVector[i][j] = (cl_float) parameters[j];
indicesVector[i] = mm_int8(particle1, particle2, particle3, forceBufferCounter[particle1]++,
forceBufferCounter[particle2]++, forceBufferCounter[particle3]++, 0, 0);
}
params->setParameterValues(paramVector);
indices->upload(indicesVector);
int maxBuffers = 1;
for (int i = 0; i < (int) forceBufferCounter.size(); i++)
maxBuffers = max(maxBuffers, forceBufferCounter[i]);
cl.addForce(new OpenCLCustomAngleForceInfo(maxBuffers, force));
cl.addForce(new OpenCLCustomAngleForceInfo(0, force));
// Record information for the expressions.
......@@ -547,8 +498,6 @@ void OpenCLCalcCustomAngleForceKernel::initialize(const System& system, const Cu
globalParamNames[i] = force.getGlobalParameterName(i);
globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
}
if (globals != NULL)
globals->upload(globalParamValues);
Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
Lepton::ParsedExpression forceExpression = energyExpression.differentiate("theta").optimize();
map<string, Lepton::ParsedExpression> expressions;
......@@ -563,29 +512,30 @@ void OpenCLCalcCustomAngleForceKernel::initialize(const System& system, const Cu
const string& name = force.getPerAngleParameterName(i);
variables[name] = "angleParams"+params->getParameterSuffix(i);
}
if (force.getNumGlobalParameters() > 0) {
globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customAngleGlobals", false, CL_MEM_READ_ONLY);
globals->upload(globalParamValues);
string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
const string& name = force.getGlobalParameterName(i);
string value = "globals["+intToString(i)+"]";
string value = argName+"["+intToString(i)+"]";
variables[name] = value;
}
}
stringstream compute;
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
extraArguments += ", __global "+buffer.getType()+"* "+buffer.getName();
compute<<buffer.getType()<<" angleParams"<<(i+1)<<" = "<<buffer.getName()<<"[index];\n";
string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
compute<<buffer.getType()<<" angleParams"<<(i+1)<<" = "<<argName<<"[index];\n";
}
vector<pair<string, string> > functions;
compute << OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "temp", "");
map<string, string> replacements;
replacements["COMPUTE_FORCE"] = compute.str();
replacements["EXTRA_ARGUMENTS"] = extraArguments;
cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customAngleForce, replacements));
kernel = cl::Kernel(program, "computeCustomAngleForces");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::customAngleForce, replacements));
}
double OpenCLCalcCustomAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numAngles == 0)
return 0.0;
if (globals != NULL) {
bool changed = false;
for (int i = 0; i < (int) globalParamNames.size(); i++) {
......@@ -597,23 +547,6 @@ double OpenCLCalcCustomAngleForceKernel::execute(ContextImpl& context, bool incl
if (changed)
globals->upload(globalParamValues);
}
if (!hasInitializedKernel) {
hasInitializedKernel = true;
kernel.setArg<cl_int>(0, cl.getPaddedNumAtoms());
kernel.setArg<cl_int>(1, numAngles);
kernel.setArg<cl::Buffer>(2, cl.getForceBuffers().getDeviceBuffer());
kernel.setArg<cl::Buffer>(3, cl.getEnergyBuffer().getDeviceBuffer());
kernel.setArg<cl::Buffer>(4, cl.getPosq().getDeviceBuffer());
kernel.setArg<cl::Buffer>(5, indices->getDeviceBuffer());
int nextIndex = 6;
if (globals != NULL)
kernel.setArg<cl::Buffer>(nextIndex++, globals->getDeviceBuffer());
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
kernel.setArg<cl::Memory>(nextIndex++, buffer.getMemory());
}
}
cl.executeKernel(kernel, numAngles);
return 0.0;
}
......@@ -775,8 +708,6 @@ OpenCLCalcCMAPTorsionForceKernel::~OpenCLCalcCMAPTorsionForceKernel() {
delete mapPositions;
if (torsionMaps != NULL)
delete torsionMaps;
if (torsionIndices != NULL)
delete torsionIndices;
}
void OpenCLCalcCMAPTorsionForceKernel::initialize(const System& system, const CMAPTorsionForce& force) {
......@@ -805,53 +736,25 @@ void OpenCLCalcCMAPTorsionForceKernel::initialize(const System& system, const CM
coeffVec.push_back(mm_float4((float) c[j][12], (float) c[j][13], (float) c[j][14], (float) c[j][15]));
}
}
vector<int> forceBufferCounter(system.getNumParticles(), 0);
vector<vector<int> > atoms(numTorsions, vector<int>(8));
vector<cl_int> torsionMapsVec(numTorsions);
vector<mm_int16> torsionIndicesVec(numTorsions);
for (int i = 0; i < numTorsions; i++) {
mm_int16& ind = torsionIndicesVec[i];
force.getTorsionParameters(startIndex+i, torsionMapsVec[i], ind.s0, ind.s1, ind.s2, ind.s3, ind.s4, ind.s5, ind.s6, ind.s7);
ind.s8 = forceBufferCounter[ind.s0]++;
ind.s9 = forceBufferCounter[ind.s1]++;
ind.s10 = forceBufferCounter[ind.s2]++;
ind.s11 = forceBufferCounter[ind.s3]++;
ind.s12 = forceBufferCounter[ind.s4]++;
ind.s13 = forceBufferCounter[ind.s5]++;
ind.s14 = forceBufferCounter[ind.s6]++;
ind.s15 = forceBufferCounter[ind.s7]++;
}
for (int i = 0; i < numTorsions; i++)
force.getTorsionParameters(startIndex+i, torsionMapsVec[i], atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], atoms[i][4], atoms[i][5], atoms[i][6], atoms[i][7]);
coefficients = new OpenCLArray<mm_float4>(cl, coeffVec.size(), "cmapTorsionCoefficients");
mapPositions = new OpenCLArray<mm_int2>(cl, numMaps, "cmapTorsionMapPositions");
torsionMaps = new OpenCLArray<cl_int>(cl, numTorsions, "cmapTorsionMaps");
torsionIndices = new OpenCLArray<mm_int16>(cl, numTorsions, "cmapTorsionIndices");
coefficients->upload(coeffVec);
mapPositions->upload(mapPositionsVec);
torsionMaps->upload(torsionMapsVec);
torsionIndices->upload(torsionIndicesVec);
int maxBuffers = 1;
for (int i = 0; i < (int) forceBufferCounter.size(); i++)
maxBuffers = max(maxBuffers, forceBufferCounter[i]);
cl.addForce(new OpenCLCMAPTorsionForceInfo(maxBuffers, force));
cl::Program program = cl.createProgram(OpenCLKernelSources::cmapTorsionForce);
kernel = cl::Kernel(program, "computeCMAPTorsionForces");
map<string, string> replacements;
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");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::cmapTorsionForce, replacements));
cl.addForce(new OpenCLCMAPTorsionForceInfo(0, force));
}
double OpenCLCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numTorsions == 0)
return 0.0;
if (!hasInitializedKernel) {
hasInitializedKernel = true;
kernel.setArg<cl_int>(0, cl.getPaddedNumAtoms());
kernel.setArg<cl_int>(1, numTorsions);
kernel.setArg<cl::Buffer>(2, cl.getForceBuffers().getDeviceBuffer());
kernel.setArg<cl::Buffer>(3, cl.getEnergyBuffer().getDeviceBuffer());
kernel.setArg<cl::Buffer>(4, cl.getPosq().getDeviceBuffer());
kernel.setArg<cl::Buffer>(5, coefficients->getDeviceBuffer());
kernel.setArg<cl::Buffer>(6, mapPositions->getDeviceBuffer());
kernel.setArg<cl::Buffer>(7, torsionIndices->getDeviceBuffer());
kernel.setArg<cl::Buffer>(8, torsionMaps->getDeviceBuffer());
}
cl.executeKernel(kernel, numTorsions);
return 0.0;
}
......@@ -889,8 +792,6 @@ private:
OpenCLCalcCustomTorsionForceKernel::~OpenCLCalcCustomTorsionForceKernel() {
if (params != NULL)
delete params;
if (indices != NULL)
delete indices;
if (globals != NULL)
delete globals;
}
......@@ -902,32 +803,18 @@ void OpenCLCalcCustomTorsionForceKernel::initialize(const System& system, const
numTorsions = endIndex-startIndex;
if (numTorsions == 0)
return;
vector<vector<int> > atoms(numTorsions, vector<int>(4));
params = new OpenCLParameterSet(cl, force.getNumPerTorsionParameters(), numTorsions, "customTorsionParams");
indices = new OpenCLArray<mm_int8>(cl, numTorsions, "customTorsionIndices");
string extraArguments;
if (force.getNumGlobalParameters() > 0) {
globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customTorsionGlobals", false, CL_MEM_READ_ONLY);
extraArguments += ", __constant float* globals";
}
vector<int> forceBufferCounter(system.getNumParticles(), 0);
vector<vector<cl_float> > paramVector(numTorsions);
vector<mm_int8> indicesVector(numTorsions);
for (int i = 0; i < numTorsions; i++) {
int particle1, particle2, particle3, particle4;
vector<double> parameters;
force.getTorsionParameters(startIndex+i, particle1, particle2, particle3, particle4, parameters);
force.getTorsionParameters(startIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], parameters);
paramVector[i].resize(parameters.size());
for (int j = 0; j < (int) parameters.size(); j++)
paramVector[i][j] = (cl_float) parameters[j];
indicesVector[i] = mm_int8(particle1, particle2, particle3, particle4, forceBufferCounter[particle1]++,
forceBufferCounter[particle2]++, forceBufferCounter[particle3]++, forceBufferCounter[particle4]++);
}
params->setParameterValues(paramVector);
indices->upload(indicesVector);
int maxBuffers = 1;
for (int i = 0; i < (int) forceBufferCounter.size(); i++)
maxBuffers = max(maxBuffers, forceBufferCounter[i]);
cl.addForce(new OpenCLCustomTorsionForceInfo(maxBuffers, force));
cl.addForce(new OpenCLCustomTorsionForceInfo(0, force));
// Record information for the expressions.
......@@ -937,8 +824,6 @@ void OpenCLCalcCustomTorsionForceKernel::initialize(const System& system, const
globalParamNames[i] = force.getGlobalParameterName(i);
globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
}
if (globals != NULL)
globals->upload(globalParamValues);
Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
Lepton::ParsedExpression forceExpression = energyExpression.differentiate("theta").optimize();
map<string, Lepton::ParsedExpression> expressions;
......@@ -953,30 +838,31 @@ void OpenCLCalcCustomTorsionForceKernel::initialize(const System& system, const
const string& name = force.getPerTorsionParameterName(i);
variables[name] = "torsionParams"+params->getParameterSuffix(i);
}
if (force.getNumGlobalParameters() > 0) {
globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customTorsionGlobals", false, CL_MEM_READ_ONLY);
globals->upload(globalParamValues);
string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
const string& name = force.getGlobalParameterName(i);
string value = "globals["+intToString(i)+"]";
string value = argName+"["+intToString(i)+"]";
variables[name] = value;
}
}
stringstream compute;
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
extraArguments += ", __global "+buffer.getType()+"* "+buffer.getName();
compute<<buffer.getType()<<" torsionParams"<<(i+1)<<" = "<<buffer.getName()<<"[index];\n";
string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
compute<<buffer.getType()<<" torsionParams"<<(i+1)<<" = "<<argName<<"[index];\n";
}
vector<pair<string, string> > functions;
compute << OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "temp", "");
map<string, string> replacements;
replacements["COMPUTE_FORCE"] = compute.str();
replacements["EXTRA_ARGUMENTS"] = extraArguments;
replacements["M_PI"] = doubleToString(M_PI);
cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customTorsionForce, replacements));
kernel = cl::Kernel(program, "computeCustomTorsionForces");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::customTorsionForce, replacements));
}
double OpenCLCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numTorsions == 0)
return 0.0;
if (globals != NULL) {
bool changed = false;
for (int i = 0; i < (int) globalParamNames.size(); i++) {
......@@ -988,23 +874,6 @@ double OpenCLCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool in
if (changed)
globals->upload(globalParamValues);
}
if (!hasInitializedKernel) {
hasInitializedKernel = true;
kernel.setArg<cl_int>(0, cl.getPaddedNumAtoms());
kernel.setArg<cl_int>(1, numTorsions);
kernel.setArg<cl::Buffer>(2, cl.getForceBuffers().getDeviceBuffer());
kernel.setArg<cl::Buffer>(3, cl.getEnergyBuffer().getDeviceBuffer());
kernel.setArg<cl::Buffer>(4, cl.getPosq().getDeviceBuffer());
kernel.setArg<cl::Buffer>(5, indices->getDeviceBuffer());
int nextIndex = 6;
if (globals != NULL)
kernel.setArg<cl::Buffer>(nextIndex++, globals->getDeviceBuffer());
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
kernel.setArg<cl::Memory>(nextIndex++, buffer.getMemory());
}
}
cl.executeKernel(kernel, numTorsions);
return 0.0;
}
......@@ -2632,8 +2501,6 @@ private:
OpenCLCalcCustomExternalForceKernel::~OpenCLCalcCustomExternalForceKernel() {
if (params != NULL)
delete params;
if (indices != NULL)
delete indices;
if (globals != NULL)
delete globals;
}
......@@ -2645,24 +2512,17 @@ void OpenCLCalcCustomExternalForceKernel::initialize(const System& system, const
numParticles = endIndex-startIndex;
if (numParticles == 0)
return;
vector<vector<int> > atoms(numParticles, vector<int>(1));
params = new OpenCLParameterSet(cl, force.getNumPerParticleParameters(), numParticles, "customExternalParams");
indices = new OpenCLArray<cl_int>(cl, numParticles, "customExternalIndices");
string extraArguments;
if (force.getNumGlobalParameters() > 0) {
globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customExternalGlobals", false, CL_MEM_READ_ONLY);
extraArguments += ", __constant float* globals";
}
vector<vector<cl_float> > paramVector(numParticles);
vector<cl_int> indicesVector(numParticles);
for (int i = 0; i < numParticles; i++) {
vector<double> parameters;
force.getParticleParameters(startIndex+i, indicesVector[i], parameters);
force.getParticleParameters(startIndex+i, atoms[i][0], parameters);
paramVector[i].resize(parameters.size());
for (int j = 0; j < (int) parameters.size(); j++)
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
indices->upload(indicesVector);
cl.addForce(new OpenCLCustomExternalForceInfo(force, system.getNumParticles()));
// Record information for the expressions.
......@@ -2673,8 +2533,6 @@ void OpenCLCalcCustomExternalForceKernel::initialize(const System& system, const
globalParamNames[i] = force.getGlobalParameterName(i);
globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
}
if (globals != NULL)
globals->upload(globalParamValues);
Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
Lepton::ParsedExpression forceExpressionX = energyExpression.differentiate("x").optimize();
Lepton::ParsedExpression forceExpressionY = energyExpression.differentiate("y").optimize();
......@@ -2688,36 +2546,37 @@ void OpenCLCalcCustomExternalForceKernel::initialize(const System& system, const
// Create the kernels.
map<string, string> variables;
variables["x"] = "pos.x";
variables["y"] = "pos.y";
variables["z"] = "pos.z";
variables["x"] = "pos1.x";
variables["y"] = "pos1.y";
variables["z"] = "pos1.z";
for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
const string& name = force.getPerParticleParameterName(i);
variables[name] = "particleParams"+params->getParameterSuffix(i);
}
if (force.getNumGlobalParameters() > 0) {
globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customExternalGlobals", false, CL_MEM_READ_ONLY);
globals->upload(globalParamValues);
string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
const string& name = force.getGlobalParameterName(i);
string value = "globals["+intToString(i)+"]";
string value = argName+"["+intToString(i)+"]";
variables[name] = value;
}
}
stringstream compute;
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
extraArguments += ", __global "+buffer.getType()+"* "+buffer.getName();
compute<<buffer.getType()<<" particleParams"<<(i+1)<<" = "<<buffer.getName()<<"[index];\n";
string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
compute<<buffer.getType()<<" particleParams"<<(i+1)<<" = "<<argName<<"[index];\n";
}
vector<pair<string, string> > functions;
compute << OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "temp", "");
map<string, string> replacements;
replacements["COMPUTE_FORCE"] = compute.str();
replacements["EXTRA_ARGUMENTS"] = extraArguments;
cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customExternalForce, replacements));
kernel = cl::Kernel(program, "computeCustomExternalForces");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::customExternalForce, replacements));
}
double OpenCLCalcCustomExternalForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (numParticles == 0)
return 0.0;
if (globals != NULL) {
bool changed = false;
for (int i = 0; i < (int) globalParamNames.size(); i++) {
......@@ -2729,22 +2588,6 @@ double OpenCLCalcCustomExternalForceKernel::execute(ContextImpl& context, bool i
if (changed)
globals->upload(globalParamValues);
}
if (!hasInitializedKernel) {
hasInitializedKernel = true;
kernel.setArg<cl_int>(0, numParticles);
kernel.setArg<cl::Buffer>(1, cl.getForceBuffers().getDeviceBuffer());
kernel.setArg<cl::Buffer>(2, cl.getEnergyBuffer().getDeviceBuffer());
kernel.setArg<cl::Buffer>(3, cl.getPosq().getDeviceBuffer());
kernel.setArg<cl::Buffer>(4, indices->getDeviceBuffer());
int nextIndex = 5;
if (globals != NULL)
kernel.setArg<cl::Buffer>(nextIndex++, globals->getDeviceBuffer());
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
kernel.setArg<cl::Memory>(nextIndex++, buffer.getMemory());
}
}
cl.executeKernel(kernel, numParticles);
return 0.0;
}
......
platforms/opencl/src/OpenCLKernels.h
View file @ f51a85b9
......@@ -217,7 +217,7 @@ private:
class OpenCLCalcCustomBondForceKernel : public CalcCustomBondForceKernel {
public:
OpenCLCalcCustomBondForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomBondForceKernel(name, platform),
hasInitializedKernel(false), cl(cl), system(system), params(NULL), indices(NULL), globals(NULL) {
hasInitializedKernel(false), cl(cl), system(system), params(NULL), globals(NULL) {
}
~OpenCLCalcCustomBondForceKernel();
/**
......@@ -242,11 +242,9 @@ private:
OpenCLContext& cl;
System& system;
OpenCLParameterSet* params;
OpenCLArray<mm_int4>* indices;
OpenCLArray<cl_float>* globals;
std::vector<std::string> globalParamNames;
std::vector<cl_float> globalParamValues;
cl::Kernel kernel;
};
/**
......@@ -288,7 +286,7 @@ private:
class OpenCLCalcCustomAngleForceKernel : public CalcCustomAngleForceKernel {
public:
OpenCLCalcCustomAngleForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomAngleForceKernel(name, platform),
hasInitializedKernel(false), cl(cl), system(system), params(NULL), indices(NULL), globals(NULL) {
hasInitializedKernel(false), cl(cl), system(system), params(NULL), globals(NULL) {
}
~OpenCLCalcCustomAngleForceKernel();
/**
......@@ -313,11 +311,9 @@ private:
OpenCLContext& cl;
System& system;
OpenCLParameterSet* params;
OpenCLArray<mm_int8>* indices;
OpenCLArray<cl_float>* globals;
std::vector<std::string> globalParamNames;
std::vector<cl_float> globalParamValues;
cl::Kernel kernel;
};
/**
......@@ -392,7 +388,7 @@ private:
class OpenCLCalcCMAPTorsionForceKernel : public CalcCMAPTorsionForceKernel {
public:
OpenCLCalcCMAPTorsionForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCMAPTorsionForceKernel(name, platform),
hasInitializedKernel(false), cl(cl), system(system), coefficients(NULL), mapPositions(NULL), torsionIndices(NULL), torsionMaps(NULL) {
hasInitializedKernel(false), cl(cl), system(system), coefficients(NULL), mapPositions(NULL), torsionMaps(NULL) {
}
~OpenCLCalcCMAPTorsionForceKernel();
/**
......@@ -418,9 +414,7 @@ private:
System& system;
OpenCLArray<mm_float4>* coefficients;
OpenCLArray<mm_int2>* mapPositions;
OpenCLArray<mm_int16>* torsionIndices;
OpenCLArray<cl_int>* torsionMaps;
cl::Kernel kernel;
};
/**
......@@ -429,7 +423,7 @@ private:
class OpenCLCalcCustomTorsionForceKernel : public CalcCustomTorsionForceKernel {
public:
OpenCLCalcCustomTorsionForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomTorsionForceKernel(name, platform),
hasInitializedKernel(false), cl(cl), system(system), params(NULL), indices(NULL), globals(NULL) {
hasInitializedKernel(false), cl(cl), system(system), params(NULL), globals(NULL) {
}
~OpenCLCalcCustomTorsionForceKernel();
/**
......@@ -454,11 +448,9 @@ private:
OpenCLContext& cl;
System& system;
OpenCLParameterSet* params;
OpenCLArray<mm_int8>* indices;
OpenCLArray<cl_float>* globals;
std::vector<std::string> globalParamNames;
std::vector<cl_float> globalParamValues;
cl::Kernel kernel;
};
/**
......@@ -651,7 +643,7 @@ private:
class OpenCLCalcCustomExternalForceKernel : public CalcCustomExternalForceKernel {
public:
OpenCLCalcCustomExternalForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomExternalForceKernel(name, platform),
hasInitializedKernel(false), cl(cl), system(system), params(NULL), indices(NULL), globals(NULL) {
hasInitializedKernel(false), cl(cl), system(system), params(NULL), globals(NULL) {
}
~OpenCLCalcCustomExternalForceKernel();
/**
......@@ -676,11 +668,9 @@ private:
OpenCLContext& cl;
System& system;
OpenCLParameterSet* params;
OpenCLArray<cl_int>* indices;
OpenCLArray<cl_float>* globals;
std::vector<std::string> globalParamNames;
std::vector<cl_float> globalParamValues;
cl::Kernel kernel;
};
/**
......
platforms/opencl/src/kernels/cmapTorsionForce.cl
View file @ f51a85b9
/**
* Compute CNAP torsion forces.
*/
const float PI = 3.14159265358979323846f;
__kernel void computeCMAPTorsionForces(int numAtoms, int numTorsions, __global float4* forceBuffers, __global float* energyBuffer,
__global float4* posq, __global float4* coeff, __global int2* mapPositions, __global int16* indices, __global int* maps) {
const float PI = 3.14159265358979323846f;
float energy = 0.0f;
for (int index = get_global_id(0); index < numTorsions; index += get_global_size(0)) {
int16 atoms = indices[index];
float4 a1 = posq[atoms.s0];
float4 a2 = posq[atoms.s1];
float4 a3 = posq[atoms.s2];
float4 a4 = posq[atoms.s3];
float4 b1 = posq[atoms.s4];
float4 b2 = posq[atoms.s5];
float4 b3 = posq[atoms.s6];
float4 b4 = posq[atoms.s7];
// Compute the first angle.
// Compute the first angle.
float4 v0a = (float4) (a1.xyz-a2.xyz, 0.0f);
float4 v1a = (float4) (a3.xyz-a2.xyz, 0.0f);
float4 v2a = (float4) (a3.xyz-a4.xyz, 0.0f);
float4 cp0a = cross(v0a, v1a);
float4 cp1a = cross(v1a, v2a);
float cosangle = dot(normalize(cp0a), normalize(cp1a));
float angleA;
if (cosangle > 0.99f || cosangle < -0.99f) {
float4 v0a = (float4) (pos1.xyz-pos2.xyz, 0.0f);
float4 v1a = (float4) (pos3.xyz-pos2.xyz, 0.0f);
float4 v2a = (float4) (pos3.xyz-pos4.xyz, 0.0f);
float4 cp0a = cross(v0a, v1a);
float4 cp1a = cross(v1a, v2a);
float cosangle = dot(normalize(cp0a), normalize(cp1a));
float angleA;
if (cosangle > 0.99f || cosangle < -0.99f) {
// We're close to the singularity in acos(), so take the cross product and use asin() instead.
float4 cross_prod = cross(cp0a, cp1a);
......@@ -34,22 +17,22 @@ __kernel void computeCMAPTorsionForces(int numAtoms, int numTorsions, __global f
angleA = asin(SQRT(dot(cross_prod, cross_prod)/scale));
if (cosangle < 0.0f)
angleA = PI-angleA;
}
else
}
else
angleA = acos(cosangle);
angleA = (dot(v0a, cp1a) >= 0 ? angleA : -angleA);
angleA = fmod(angleA+2.0f*PI, 2.0f*PI);
angleA = (dot(v0a, cp1a) >= 0 ? angleA : -angleA);
angleA = fmod(angleA+2.0f*PI, 2.0f*PI);
// Compute the second angle.
// Compute the second angle.
float4 v0b = (float4) (b1.xyz-b2.xyz, 0.0f);
float4 v1b = (float4) (b3.xyz-b2.xyz, 0.0f);
float4 v2b = (float4) (b3.xyz-b4.xyz, 0.0f);
float4 cp0b = cross(v0b, v1b);
float4 cp1b = cross(v1b, v2b);
cosangle = dot(normalize(cp0b), normalize(cp1b));
float angleB;
if (cosangle > 0.99f || cosangle < -0.99f) {
float4 v0b = (float4) (pos5.xyz-pos6.xyz, 0.0f);
float4 v1b = (float4) (pos7.xyz-pos6.xyz, 0.0f);
float4 v2b = (float4) (pos7.xyz-pos8.xyz, 0.0f);
float4 cp0b = cross(v0b, v1b);
float4 cp1b = cross(v1b, v2b);
cosangle = dot(normalize(cp0b), normalize(cp1b));
float angleB;
if (cosangle > 0.99f || cosangle < -0.99f) {
// We're close to the singularity in acos(), so take the cross product and use asin() instead.
float4 cross_prod = cross(cp0b, cp1b);
......@@ -57,98 +40,73 @@ __kernel void computeCMAPTorsionForces(int numAtoms, int numTorsions, __global f
angleB = asin(SQRT(dot(cross_prod, cross_prod)/scale));
if (cosangle < 0.0f)
angleB = PI-angleB;
}
else
}
else
angleB = acos(cosangle);
angleB = (dot(v0b, cp1b) >= 0 ? angleB : -angleB);
angleB = fmod(angleB+2.0f*PI, 2.0f*PI);
angleB = (dot(v0b, cp1b) >= 0 ? angleB : -angleB);
angleB = fmod(angleB+2.0f*PI, 2.0f*PI);
// Identify which patch this is in.
// Identify which patch this is in.
int2 pos = mapPositions[maps[index]];
int size = pos.y;
float delta = 2*PI/size;
int s = (int) (angleA/delta);
int t = (int) (angleB/delta);
float4 c[4];
int coeffIndex = pos.x+4*(s+size*t);
c[0] = coeff[coeffIndex];
c[1] = coeff[coeffIndex+1];
c[2] = coeff[coeffIndex+2];
c[3] = coeff[coeffIndex+3];
float da = angleA/delta-s;
float db = angleB/delta-t;
int2 pos = MAP_POS[MAPS[index]];
int size = pos.y;
float delta = 2*PI/size;
int s = (int) (angleA/delta);
int t = (int) (angleB/delta);
float4 c[4];
int coeffIndex = pos.x+4*(s+size*t);
c[0] = COEFF[coeffIndex];
c[1] = COEFF[coeffIndex+1];
c[2] = COEFF[coeffIndex+2];
c[3] = COEFF[coeffIndex+3];
float da = angleA/delta-s;
float db = angleB/delta-t;
// Evaluate the spline to determine the energy and gradients.
// Evaluate the spline to determine the energy and gradients.
float torsionEnergy = 0.0f;
float dEdA = 0.0f;
float dEdB = 0.0f;
torsionEnergy = da*torsionEnergy + ((c[3].w*db + c[3].z)*db + c[3].y)*db + c[3].x;
dEdA = db*dEdA + (3.0f*c[3].w*da + 2.0f*c[2].w)*da + c[1].w;
dEdB = da*dEdB + (3.0f*c[3].w*db + 2.0f*c[3].z)*db + c[3].y;
torsionEnergy = da*torsionEnergy + ((c[2].w*db + c[2].z)*db + c[2].y)*db + c[2].x;
dEdA = db*dEdA + (3.0f*c[3].z*da + 2.0f*c[2].z)*da + c[1].z;
dEdB = da*dEdB + (3.0f*c[2].w*db + 2.0f*c[2].z)*db + c[2].y;
torsionEnergy = da*torsionEnergy + ((c[1].w*db + c[1].z)*db + c[1].y)*db + c[1].x;
dEdA = db*dEdA + (3.0f*c[3].y*da + 2.0f*c[2].y)*da + c[1].y;
dEdB = da*dEdB + (3.0f*c[1].w*db + 2.0f*c[1].z)*db + c[1].y;
torsionEnergy = da*torsionEnergy + ((c[0].w*db + c[0].z)*db + c[0].y)*db + c[0].x;
dEdA = db*dEdA + (3.0f*c[3].x*da + 2.0f*c[2].x)*da + c[1].x;
dEdB = da*dEdB + (3.0f*c[0].w*db + 2.0f*c[0].z)*db + c[0].y;
dEdA /= delta;
dEdB /= delta;
energy += torsionEnergy;
float torsionEnergy = 0.0f;
float dEdA = 0.0f;
float dEdB = 0.0f;
torsionEnergy = da*torsionEnergy + ((c[3].w*db + c[3].z)*db + c[3].y)*db + c[3].x;
dEdA = db*dEdA + (3.0f*c[3].w*da + 2.0f*c[2].w)*da + c[1].w;
dEdB = da*dEdB + (3.0f*c[3].w*db + 2.0f*c[3].z)*db + c[3].y;
torsionEnergy = da*torsionEnergy + ((c[2].w*db + c[2].z)*db + c[2].y)*db + c[2].x;
dEdA = db*dEdA + (3.0f*c[3].z*da + 2.0f*c[2].z)*da + c[1].z;
dEdB = da*dEdB + (3.0f*c[2].w*db + 2.0f*c[2].z)*db + c[2].y;
torsionEnergy = da*torsionEnergy + ((c[1].w*db + c[1].z)*db + c[1].y)*db + c[1].x;
dEdA = db*dEdA + (3.0f*c[3].y*da + 2.0f*c[2].y)*da + c[1].y;
dEdB = da*dEdB + (3.0f*c[1].w*db + 2.0f*c[1].z)*db + c[1].y;
torsionEnergy = da*torsionEnergy + ((c[0].w*db + c[0].z)*db + c[0].y)*db + c[0].x;
dEdA = db*dEdA + (3.0f*c[3].x*da + 2.0f*c[2].x)*da + c[1].x;
dEdB = da*dEdB + (3.0f*c[0].w*db + 2.0f*c[0].z)*db + c[0].y;
dEdA /= delta;
dEdB /= delta;
energy += torsionEnergy;
// Apply the force to the first torsion.
// Apply the force to the first torsion.
float normCross1 = dot(cp0a, cp0a);
float normSqrBC = dot(v1a, v1a);
float normBC = SQRT(normSqrBC);
float normCross2 = dot(cp1a, cp1a);
float dp = 1.0f/normSqrBC;
float4 ff = (float4) ((-dEdA*normBC)/normCross1, dot(v0a, v1a)*dp, dot(v2a, v1a)*dp, (dEdA*normBC)/normCross2);
float4 internalF0 = ff.x*cp0a;
float4 internalF3 = ff.w*cp1a;
float4 d = ff.y*internalF0 - ff.z*internalF3;
int4 offset = atoms.lo.lo + numAtoms*atoms.hi.lo;
float4 forceA = forceBuffers[offset.x];
float4 forceB = forceBuffers[offset.y];
float4 forceC = forceBuffers[offset.z];
float4 forceD = forceBuffers[offset.w];
forceA.xyz += internalF0.xyz;
forceB.xyz += d.xyz-internalF0.xyz;
forceC.xyz += -d.xyz-internalF3.xyz;
forceD.xyz += internalF3.xyz;
forceBuffers[offset.x] = forceA;
forceBuffers[offset.y] = forceB;
forceBuffers[offset.z] = forceC;
forceBuffers[offset.w] = forceD;
float normCross1 = dot(cp0a, cp0a);
float normSqrBC = dot(v1a, v1a);
float normBC = SQRT(normSqrBC);
float normCross2 = dot(cp1a, cp1a);
float dp = 1.0f/normSqrBC;
float4 ff = (float4) ((-dEdA*normBC)/normCross1, dot(v0a, v1a)*dp, dot(v2a, v1a)*dp, (dEdA*normBC)/normCross2);
float4 force1 = ff.x*cp0a;
float4 force4 = ff.w*cp1a;
float4 d = ff.y*force1 - ff.z*force4;
float4 force2 = d-force1;
float4 force3 = -d-force4;
// Apply the force to the second torsion.
// Apply the force to the second torsion.
normCross1 = dot(cp0b, cp0b);
normSqrBC = dot(v1b, v1b);
normBC = SQRT(normSqrBC);
normCross2 = dot(cp1b, cp1b);
dp = 1.0f/normSqrBC;
ff = (float4) ((-dEdB*normBC)/normCross1, dot(v0b, v1b)*dp, dot(v2b, v1b)*dp, (dEdB*normBC)/normCross2);
internalF0 = ff.x*cp0b;
internalF3 = ff.w*cp1b;
d = ff.y*internalF0 - ff.z*internalF3;
offset = atoms.lo.hi + numAtoms*atoms.hi.hi;
forceA = forceBuffers[offset.x];
forceB = forceBuffers[offset.y];
forceC = forceBuffers[offset.z];
forceD = forceBuffers[offset.w];
forceA.xyz += internalF0.xyz;
forceB.xyz += d.xyz-internalF0.xyz;
forceC.xyz += -d.xyz-internalF3.xyz;
forceD.xyz += internalF3.xyz;
forceBuffers[offset.x] = forceA;
forceBuffers[offset.y] = forceB;
forceBuffers[offset.z] = forceC;
forceBuffers[offset.w] = forceD;
}
energyBuffer[get_global_id(0)] += energy;
}
normCross1 = dot(cp0b, cp0b);
normSqrBC = dot(v1b, v1b);
normBC = SQRT(normSqrBC);
normCross2 = dot(cp1b, cp1b);
dp = 1.0f/normSqrBC;
ff = (float4) ((-dEdB*normBC)/normCross1, dot(v0b, v1b)*dp, dot(v2b, v1b)*dp, (dEdB*normBC)/normCross2);
float4 force5 = ff.x*cp0b;
float4 force8 = ff.w*cp1b;
d = ff.y*force5 - ff.z*force8;
float4 force6 = d-force5;
float4 force7 = -d-force8;
platforms/opencl/src/kernels/customAngleForce.cl
View file @ f51a85b9
/**
* Compute custom angle forces.
*/
__kernel void computeCustomAngleForces(int numAtoms, int numAngles, __global float4* forceBuffers, __global float* energyBuffer,
__global float4* posq, __global int8* indices
EXTRA_ARGUMENTS) {
float energy = 0.0f;
for (int index = get_global_id(0); index < numAngles; index += get_global_size(0)) {
int8 atoms = indices[index];
float4 a1 = posq[atoms.s0];
float4 a2 = posq[atoms.s1];
float4 a3 = posq[atoms.s2];
// Compute the force.
float4 v0 = a2-a1;
float4 v1 = a2-a3;
float4 cp = cross(v0, v1);
float rp = cp.x*cp.x + cp.y*cp.y + cp.z*cp.z;
rp = max(sqrt(rp), 1.0e-06f);
float r21 = v0.x*v0.x + v0.y*v0.y + v0.z*v0.z;
float r23 = v1.x*v1.x + v1.y*v1.y + v1.z*v1.z;
float dot = v0.x*v1.x + v0.y*v1.y + v0.z*v1.z;
float cosine = clamp(dot/sqrt(r21*r23), -1.0f, 1.0f);
float theta = acos(cosine);
COMPUTE_FORCE
float4 c21 = cross(v0, cp)*(dEdAngle/(r21*rp));
float4 c23 = cross(cp, v1)*(dEdAngle/(r23*rp));
// Record the force on each of the three atoms.
unsigned int offsetA = atoms.s0+atoms.s3*numAtoms;
unsigned int offsetB = atoms.s1+atoms.s4*numAtoms;
unsigned int offsetC = atoms.s2+atoms.s5*numAtoms;
float4 forceA = forceBuffers[offsetA];
float4 forceB = forceBuffers[offsetB];
float4 forceC = forceBuffers[offsetC];
forceA.xyz += c21.xyz;
forceB.xyz -= c21.xyz+c23.xyz;
forceC.xyz += c23.xyz;
forceBuffers[offsetA] = forceA;
forceBuffers[offsetB] = forceB;
forceBuffers[offsetC] = forceC;
}
energyBuffer[get_global_id(0)] += energy;
}
float4 v0 = pos2-pos1;
float4 v1 = pos2-pos3;
float4 cp = cross(v0, v1);
float rp = cp.x*cp.x + cp.y*cp.y + cp.z*cp.z;
rp = max(sqrt(rp), 1.0e-06f);
float r21 = v0.x*v0.x + v0.y*v0.y + v0.z*v0.z;
float r23 = v1.x*v1.x + v1.y*v1.y + v1.z*v1.z;
float dot = v0.x*v1.x + v0.y*v1.y + v0.z*v1.z;
float cosine = clamp(dot/sqrt(r21*r23), -1.0f, 1.0f);
float theta = acos(cosine);
COMPUTE_FORCE
float4 force1 = cross(v0, cp)*(dEdAngle/(r21*rp));
float4 force3 = cross(cp, v1)*(dEdAngle/(r23*rp));
float4 force2 = -force1-force3;
platforms/opencl/src/kernels/customBondForce.cl
View file @ f51a85b9
/**
* Compute custom bond forces.
*/
__kernel void computeCustomBondForces(int numAtoms, int numBonds, __global float4* forceBuffers, __global float* energyBuffer,
__global float4* posq, __global int4* indices
EXTRA_ARGUMENTS) {
float energy = 0.0f;
for (int index = get_global_id(0); index < numBonds; index += get_global_size(0)) {
// Look up the data for this bond.
int4 atoms = indices[index];
float4 delta = posq[atoms.y]-posq[atoms.x];
// Compute the force.
float r = SQRT(delta.x*delta.x + delta.y*delta.y + delta.z*delta.z);
COMPUTE_FORCE
delta.xyz *= -dEdR/r;
// Record the force on each of the two atoms.
unsigned int offsetA = atoms.x+atoms.z*numAtoms;
unsigned int offsetB = atoms.y+atoms.w*numAtoms;
float4 forceA = forceBuffers[offsetA];
float4 forceB = forceBuffers[offsetB];
forceA.xyz -= delta.xyz;
forceB.xyz += delta.xyz;
forceBuffers[offsetA] = forceA;
forceBuffers[offsetB] = forceB;
}
energyBuffer[get_global_id(0)] += energy;
}
float4 delta = pos2-pos1;
float r = SQRT(delta.x*delta.x + delta.y*delta.y + delta.z*delta.z);
COMPUTE_FORCE
delta.xyz *= -dEdR/r;
float4 force1 = -delta;
float4 force2 = delta;
platforms/opencl/src/kernels/customExternalForce.cl
View file @ f51a85b9
/**
* Compute custom external forces.
*/
__kernel void computeCustomExternalForces(int numTerms, __global float4* forceBuffers, __global float* energyBuffer,
__global float4* posq, __global int* indices
EXTRA_ARGUMENTS) {
float energy = 0.0f;
for (int index = get_global_id(0); index < numTerms; index += get_global_size(0)) {
// Look up the data for this particle.
int atom = indices[index];
float4 pos = posq[atom];
// Compute the force.
COMPUTE_FORCE
// Record the force on the atom.
float4 force = forceBuffers[atom];
force.x -= dEdX;
force.y -= dEdY;
force.z -= dEdZ;
forceBuffers[atom] = force;
}
energyBuffer[get_global_id(0)] += energy;
}
COMPUTE_FORCE
float4 force1 = (float4) (-dEdX, -dEdY, -dEdZ, 0.0f);
platforms/opencl/src/kernels/customTorsionForce.cl
View file @ f51a85b9
/**
* Compute custom torsion forces.
*/
__kernel void computeCustomTorsionForces(int numAtoms, int numTorsions, __global float4* forceBuffers, __global float* energyBuffer,
__global float4* posq, __global int8* indices
EXTRA_ARGUMENTS) {
float energy = 0.0f;
for (int index = get_global_id(0); index < numTorsions; index += get_global_size(0)) {
int8 atoms = indices[index];
float4 a1 = posq[atoms.s0];
float4 a2 = posq[atoms.s1];
float4 a3 = posq[atoms.s2];
float4 a4 = posq[atoms.s3];
// Compute the force.
float4 v0 = (float4) (a1.xyz-a2.xyz, 0.0f);
float4 v1 = (float4) (a3.xyz-a2.xyz, 0.0f);
float4 v2 = (float4) (a3.xyz-a4.xyz, 0.0f);
float4 cp0 = cross(v0, v1);
float4 cp1 = cross(v1, v2);
float cosangle = dot(normalize(cp0), normalize(cp1));
float theta;
if (cosangle > 0.99f || cosangle < -0.99f) {
float4 v0 = (float4) (pos1.xyz-pos2.xyz, 0.0f);
float4 v1 = (float4) (pos3.xyz-pos2.xyz, 0.0f);
float4 v2 = (float4) (pos3.xyz-pos4.xyz, 0.0f);
float4 cp0 = cross(v0, v1);
float4 cp1 = cross(v1, v2);
float cosangle = dot(normalize(cp0), normalize(cp1));
float theta;
if (cosangle > 0.99f || cosangle < -0.99f) {
// We're close to the singularity in acos(), so take the cross product and use asin() instead.
float4 cross_prod = cross(cp0, cp1);
......@@ -30,39 +13,19 @@ __kernel void computeCustomTorsionForces(int numAtoms, int numTorsions, __global
theta = asin(sqrt(dot(cross_prod, cross_prod)/scale));
if (cosangle < 0.0f)
theta = M_PI-theta;
}
else
theta = acos(cosangle);
theta = (dot(v0, cp1) >= 0 ? theta : -theta);
COMPUTE_FORCE
float normCross1 = dot(cp0, cp0);
float normSqrBC = dot(v1, v1);
float normBC = sqrt(normSqrBC);
float normCross2 = dot(cp1, cp1);
float dp = 1.0f/normSqrBC;
float4 ff = (float4) ((-dEdAngle*normBC)/normCross1, dot(v0, v1)*dp, dot(v2, v1)*dp, (dEdAngle*normBC)/normCross2);
float4 internalF0 = ff.x*cp0;
float4 internalF3 = ff.w*cp1;
float4 s = ff.y*internalF0 - ff.z*internalF3;
// Record the force on each of the four atoms.
unsigned int offsetA = atoms.s0+atoms.s4*numAtoms;
unsigned int offsetB = atoms.s1+atoms.s5*numAtoms;
unsigned int offsetC = atoms.s2+atoms.s6*numAtoms;
unsigned int offsetD = atoms.s3+atoms.s7*numAtoms;
float4 forceA = forceBuffers[offsetA];
float4 forceB = forceBuffers[offsetB];
float4 forceC = forceBuffers[offsetC];
float4 forceD = forceBuffers[offsetD];
forceA.xyz += internalF0.xyz;
forceB.xyz += s.xyz-internalF0.xyz;
forceC.xyz += -s.xyz-internalF3.xyz;
forceD.xyz += internalF3.xyz;
forceBuffers[offsetA] = forceA;
forceBuffers[offsetB] = forceB;
forceBuffers[offsetC] = forceC;
forceBuffers[offsetD] = forceD;
}
energyBuffer[get_global_id(0)] += energy;
}
else
theta = acos(cosangle);
theta = (dot(v0, cp1) >= 0 ? theta : -theta);
COMPUTE_FORCE
float normCross1 = dot(cp0, cp0);
float normSqrBC = dot(v1, v1);
float normBC = sqrt(normSqrBC);
float normCross2 = dot(cp1, cp1);
float dp = 1.0f/normSqrBC;
float4 ff = (float4) ((-dEdAngle*normBC)/normCross1, dot(v0, v1)*dp, dot(v2, v1)*dp, (dEdAngle*normBC)/normCross2);
float4 force1 = ff.x*cp0;
float4 force4 = ff.w*cp1;
float4 s = ff.y*force1 - ff.z*force4;
float4 force2 = s-force1;
float4 force3 = -s-force4;
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