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Commit ba2503b5 authored by Peter Eastman's avatar Peter Eastman
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Fixed bugs in CustomGBForce

parent 454f9c52
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Showing with 317 additions and 118 deletions
platforms/opencl/src/OpenCLKernels.cpp
View file @ ba2503b5
......@@ -1812,7 +1812,7 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
// Record derivatives of expressions needed for the chain rule terms.
vector<vector<Lepton::ParsedExpression> > valueGradientExpressions(force.getNumComputedValues());
bool needParameterGradient = false;
needParameterGradient = false;
for (int i = 1; i < force.getNumComputedValues(); i++) {
Lepton::ParsedExpression ex = Lepton::Parser::parse(computedValueExpressions[i], functions).optimize();
valueGradientExpressions[i].push_back(ex.differentiate("x").optimize());
......@@ -2116,8 +2116,58 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customGBEnergyPerParticle, replacements), defines);
perParticleEnergyKernel = cl::Kernel(program, "computePerParticleEnergy");
}
if (needParameterGradient) {
// Create the kernel to compute chain rule terms for computed values that depend explicitly on particle coordinates.
stringstream compute, extraArgs;
if (force.getNumGlobalParameters() > 0)
extraArgs << ", __constant float* globals";
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
string paramName = "params"+intToString(i+1);
extraArgs << ", __global " << buffer.getType() << "* " << paramName;
}
for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
string valueName = "values"+intToString(i+1);
extraArgs << ", __global " << buffer.getType() << "* " << valueName;
}
for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
string index = intToString(i+1);
extraArgs << ", __global " << buffer.getType() << "* derivBuffers" << index;
compute << buffer.getType() << " deriv" << index << " = derivBuffers" << index << "[index];\n";
}
map<string, string> variables;
variables["x"] = "pos.x";
variables["y"] = "pos.y";
variables["z"] = "pos.z";
for (int i = 0; i < force.getNumPerParticleParameters(); i++)
variables[force.getPerParticleParameterName(i)] = "params"+params->getParameterSuffix(i, "[index]");
for (int i = 0; i < force.getNumGlobalParameters(); i++)
variables[force.getGlobalParameterName(i)] = "globals["+intToString(i)+"]";
for (int i = 0; i < force.getNumComputedValues(); i++)
variables[computedValueNames[i]] = "values"+computedValues->getParameterSuffix(i, "[index]");
map<string, Lepton::ParsedExpression> gradientExpressions;
for (int i = 1; i < force.getNumComputedValues(); i++) {
if (!isZeroExpression(valueGradientExpressions[i][0]))
gradientExpressions["force.x -= deriv"+energyDerivs->getParameterSuffix(i)+"*"] = valueGradientExpressions[i][0];
if (!isZeroExpression(valueGradientExpressions[i][1]))
gradientExpressions["force.y -= deriv"+energyDerivs->getParameterSuffix(i)+"*"] = valueGradientExpressions[i][1];
if (!isZeroExpression(valueGradientExpressions[i][2]))
gradientExpressions["force.z -= deriv"+energyDerivs->getParameterSuffix(i)+"*"] = valueGradientExpressions[i][2];
}
compute << OpenCLExpressionUtilities::createExpressions(gradientExpressions, variables, functionDefinitions, "temp", prefix+"functionParams");
map<string, string> replacements;
replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
replacements["COMPUTE_FORCES"] = compute.str();
map<string, string> defines;
defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customGBGradientChainRule, replacements), defines);
gradientChainRuleKernel = cl::Kernel(program, "computeGradientChainRuleTerms");
}
{
// Create the code to calculate chain rules terms (possibly as part of the default nonbonded kernel).
// Create the code to calculate chain rules terms as part of the default nonbonded kernel.
map<string, string> globalVariables;
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
......@@ -2141,32 +2191,12 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
derivExpressions["float dV0dR1 = "] = dVdR;
derivExpressions["float dV0dR2 = "] = dVdR.renameVariables(rename);
chainSource << OpenCLExpressionUtilities::createExpressions(derivExpressions, variables, functionDefinitions, prefix+"temp0_", prefix+"functionParams");
if (needParameterGradient) {
chainSource << "float4 grad1_0_1 = (float4) 0;\n";
chainSource << "float4 grad1_0_2 = (float4) 0;\n";
chainSource << "float4 grad2_0_1 = (float4) 0;\n";
chainSource << "float4 grad2_0_2 = (float4) 0;\n";
if (useExclusionsForValue)
chainSource << "if (!isExcluded) {\n";
chainSource << "grad1_0_1 = dV0dR1*delta*invR;\n";
chainSource << "grad1_0_2 = dV0dR2*delta*invR;\n";
chainSource << "grad2_0_1 = grad1_0_1;\n";
chainSource << "grad2_0_2 = grad1_0_2;\n";
chainSource << "tempForce1 -= grad1_0_1*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(0, "1") << ";\n";
chainSource << "tempForce1 -= grad1_0_2*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(0, "2") << ";\n";
chainSource << "tempForce2 -= grad2_0_1*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(0, "1") << ";\n";
chainSource << "tempForce2 -= grad2_0_2*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(0, "2") << ";\n";
if (useExclusionsForValue)
chainSource << "}\n";
}
else {
if (useExclusionsForValue)
chainSource << "if (!isExcluded) {\n";
chainSource << "tempForce -= dV0dR1*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(0, "1") << ";\n";
chainSource << "tempForce -= dV0dR2*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(0, "2") << ";\n";
if (useExclusionsForValue)
chainSource << "}\n";
}
if (useExclusionsForValue)
chainSource << "if (!isExcluded) {\n";
chainSource << "tempForce -= dV0dR1*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(0, "1") << ";\n";
chainSource << "tempForce -= dV0dR2*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(0, "2") << ";\n";
if (useExclusionsForValue)
chainSource << "}\n";
variables = globalVariables;
map<string, string> rename1;
map<string, string> rename2;
......@@ -2198,56 +2228,18 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
if (i == 0)
continue;
string is = intToString(i);
if (needParameterGradient) {
chainSource << "float4 grad1_"+is+"_1 = (float4) 0;\n";
chainSource << "float4 grad1_"+is+"_2 = (float4) 0;\n";
chainSource << "float4 grad2_"+is+"_1 = (float4) 0;\n";
chainSource << "float4 grad2_"+is+"_2 = (float4) 0;\n";
for (int j = 0; j < i; j++) {
string js = intToString(j);
Lepton::ParsedExpression dVdV = Lepton::Parser::parse(computedValueExpressions[i], functions).differentiate(computedValueNames[j]).optimize();
derivExpressions.clear();
derivExpressions["float dV"+is+"dV"+js+"_1 = "] = dVdV.renameVariables(rename1);
derivExpressions["float dV"+is+"dV"+js+"_2 = "] = dVdV.renameVariables(rename2);
chainSource << OpenCLExpressionUtilities::createExpressions(derivExpressions, variables, functionDefinitions, prefix+"temp"+is+"_"+js+"_", prefix+"functionParams");
chainSource << "grad1_"+is+"_1 += dV"+is+"dV"+js+"_1*grad1_"+js+"_1;\n";
chainSource << "grad2_"+is+"_1 += dV"+is+"dV"+js+"_1*grad2_"+js+"_1;\n";
chainSource << "grad1_"+is+"_2 += dV"+is+"dV"+js+"_2*grad1_"+js+"_2;\n";
chainSource << "grad2_"+is+"_2 += dV"+is+"dV"+js+"_2*grad2_"+js+"_2;\n";
}
chainSource << "float dV"+is+"dR1 = 0;\n";
chainSource << "float dV"+is+"dR2 = 0;\n";
for (int j = 0; j < i; j++) {
string js = intToString(j);
Lepton::ParsedExpression dVdV = Lepton::Parser::parse(computedValueExpressions[i], functions).differentiate(computedValueNames[j]).optimize();
derivExpressions.clear();
if (!isZeroExpression(valueGradientExpressions[i][0])) {
derivExpressions["grad1_"+is+"_1.x -= "] = valueGradientExpressions[i][0].renameVariables(rename1);
derivExpressions["grad2_"+is+"_2.x -= "] = valueGradientExpressions[i][0].renameVariables(rename2);
}
if (!isZeroExpression(valueGradientExpressions[i][1])) {
derivExpressions["grad1_"+is+"_1.y -= "] = valueGradientExpressions[i][1].renameVariables(rename1);
derivExpressions["grad2_"+is+"_2.y -= "] = valueGradientExpressions[i][1].renameVariables(rename2);
}
if (!isZeroExpression(valueGradientExpressions[i][2])) {
derivExpressions["grad1_"+is+"_1.z -= "] = valueGradientExpressions[i][2].renameVariables(rename1);
derivExpressions["grad2_"+is+"_2.z -= "] = valueGradientExpressions[i][2].renameVariables(rename2);
}
chainSource << OpenCLExpressionUtilities::createExpressions(derivExpressions, variables, functionDefinitions, prefix+"temp"+is+"_", prefix+"functionParams");
chainSource << "tempForce1 -= grad1_"<<is<<"_1*"<<prefix<<"dEdV"<<energyDerivs->getParameterSuffix(i, "1")<<";\n";
chainSource << "tempForce2 -= grad2_"<<is<<"_1*"<<prefix<<"dEdV"<<energyDerivs->getParameterSuffix(i, "1")<<";\n";
chainSource << "tempForce1 -= grad1_"<<is<<"_2*"<<prefix<<"dEdV"<<energyDerivs->getParameterSuffix(i, "2")<<";\n";
chainSource << "tempForce2 -= grad2_"<<is<<"_2*"<<prefix<<"dEdV"<<energyDerivs->getParameterSuffix(i, "2")<<";\n";
}
else {
chainSource << "float dV"+is+"dR1 = 0;\n";
chainSource << "float dV"+is+"dR2 = 0;\n";
for (int j = 0; j < i; j++) {
string js = intToString(j);
Lepton::ParsedExpression dVdV = Lepton::Parser::parse(computedValueExpressions[i], functions).differentiate(computedValueNames[j]).optimize();
derivExpressions.clear();
derivExpressions["dV"+is+"dR1 += dV"+js+"dR1*"] = dVdV.renameVariables(rename1);
derivExpressions["dV"+is+"dR2 += dV"+js+"dR2*"] = dVdV.renameVariables(rename2);
chainSource << OpenCLExpressionUtilities::createExpressions(derivExpressions, variables, functionDefinitions, prefix+"temp"+is+"_"+js+"_", prefix+"functionParams");
}
chainSource << "tempForce -= dV"<< is << "dR1*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(i, "1") << ";\n";
chainSource << "tempForce -= dV"<< is << "dR2*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(i, "2") << ";\n";
derivExpressions["dV"+is+"dR1 += dV"+js+"dR1*"] = dVdV.renameVariables(rename1);
derivExpressions["dV"+is+"dR2 += dV"+js+"dR2*"] = dVdV.renameVariables(rename2);
chainSource << OpenCLExpressionUtilities::createExpressions(derivExpressions, variables, functionDefinitions, prefix+"temp"+is+"_"+js+"_", prefix+"functionParams");
}
chainSource << "tempForce -= dV"<< is << "dR1*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(i, "1") << ";\n";
chainSource << "tempForce -= dV"<< is << "dR2*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(i, "2") << ";\n";
}
map<string, string> replacements;
replacements["COMPUTE_FORCE"] = chainSource.str();
......@@ -2273,21 +2265,11 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
globals->upload(globalParamValues);
arguments.push_back(OpenCLNonbondedUtilities::ParameterInfo(prefix+"globals", "float", 1, sizeof(cl_float), globals->getDeviceBuffer()));
}
if (needParameterGradient) {
chainRuleParameters = parameters;
chainRuleArguments = arguments;
chainRuleSource = source;
separateChainRuleKernel = true;
cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, force.getNumExclusions() > 0, force.getCutoffDistance(), exclusionList, "");
}
else {
cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, force.getNumExclusions() > 0, force.getCutoffDistance(), exclusionList, source);
for (int i = 0; i < (int) parameters.size(); i++)
cl.getNonbondedUtilities().addParameter(parameters[i]);
for (int i = 0; i < (int) arguments.size(); i++)
cl.getNonbondedUtilities().addArgument(arguments[i]);
separateChainRuleKernel = false;
}
cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, force.getNumExclusions() > 0, force.getCutoffDistance(), exclusionList, source);
for (int i = 0; i < (int) parameters.size(); i++)
cl.getNonbondedUtilities().addParameter(parameters[i]);
for (int i = 0; i < (int) arguments.size(); i++)
cl.getNonbondedUtilities().addArgument(arguments[i]);
}
cl.addForce(new OpenCLCustomGBForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force));
for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
......@@ -2409,7 +2391,19 @@ void OpenCLCalcCustomGBForceKernel::executeForces(ContextImpl& context) {
perParticleEnergyKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
perParticleEnergyKernel.setArg<cl::Buffer>(index++, tabulatedFunctionParams->getDeviceBuffer());
}
chainRuleKernel = nb.createInteractionKernel(chainRuleSource, chainRuleParameters, chainRuleArguments, true, false);
if (needParameterGradient) {
index = 0;
gradientChainRuleKernel.setArg<cl::Buffer>(index++, cl.getForceBuffers().getDeviceBuffer());
gradientChainRuleKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
if (globals != NULL)
gradientChainRuleKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
for (int i = 0; i < (int) params->getBuffers().size(); i++)
gradientChainRuleKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
for (int i = 0; i < (int) computedValues->getBuffers().size(); i++)
gradientChainRuleKernel.setArg<cl::Memory>(index++, computedValues->getBuffers()[i].getMemory());
for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++)
gradientChainRuleKernel.setArg<cl::Memory>(index++, energyDerivs->getBuffers()[i].getMemory());
}
}
if (globals != NULL) {
bool changed = false;
......@@ -2427,17 +2421,13 @@ void OpenCLCalcCustomGBForceKernel::executeForces(ContextImpl& context) {
pairValueKernel.setArg<mm_float4>(11, cl.getInvPeriodicBoxSize());
pairEnergyKernel.setArg<mm_float4>(11, cl.getPeriodicBoxSize());
pairEnergyKernel.setArg<mm_float4>(12, cl.getInvPeriodicBoxSize());
if (separateChainRuleKernel) {
chainRuleKernel.setArg<mm_float4>(10, cl.getPeriodicBoxSize());
chainRuleKernel.setArg<mm_float4>(11, cl.getInvPeriodicBoxSize());
}
}
cl.executeKernel(pairValueKernel, nb.getTiles().getSize()*OpenCLContext::TileSize);
cl.executeKernel(perParticleValueKernel, cl.getPaddedNumAtoms());
cl.executeKernel(pairEnergyKernel, nb.getTiles().getSize()*OpenCLContext::TileSize);
cl.executeKernel(perParticleEnergyKernel, cl.getPaddedNumAtoms());
if (separateChainRuleKernel)
cl.executeKernel(chainRuleKernel, nb.getTiles().getSize()*OpenCLContext::TileSize);
if (needParameterGradient)
cl.executeKernel(gradientChainRuleKernel, cl.getPaddedNumAtoms());
}
double OpenCLCalcCustomGBForceKernel::executeEnergy(ContextImpl& context) {
......
platforms/opencl/src/OpenCLKernels.h
View file @ ba2503b5
......@@ -624,7 +624,7 @@ public:
*/
double executeEnergy(ContextImpl& context);
private:
bool hasInitializedKernels, separateChainRuleKernel;
bool hasInitializedKernels, needParameterGradient;
OpenCLContext& cl;
OpenCLParameterSet* params;
OpenCLParameterSet* computedValues;
......@@ -635,11 +635,8 @@ private:
std::vector<std::string> globalParamNames;
std::vector<cl_float> globalParamValues;
std::vector<OpenCLArray<mm_float4>*> tabulatedFunctions;
std::vector<OpenCLNonbondedUtilities::ParameterInfo> chainRuleParameters;
std::vector<OpenCLNonbondedUtilities::ParameterInfo> chainRuleArguments;
std::string chainRuleSource;
System& system;
cl::Kernel pairValueKernel, perParticleValueKernel, pairEnergyKernel, perParticleEnergyKernel, chainRuleKernel;
cl::Kernel pairValueKernel, perParticleValueKernel, pairEnergyKernel, perParticleEnergyKernel, gradientChainRuleKernel;
};
/**
......
platforms/opencl/src/kernels/customGBGradientChainRule.cl 0 → 100644
View file @ ba2503b5
/**
* Compute chain rule terms for computed values that depend explicitly on particle coordinates.
*/
__kernel void computeGradientChainRuleTerms(__global float4* forceBuffers, __global float4* posq
PARAMETER_ARGUMENTS) {
unsigned int index = get_global_id(0);
while (index < NUM_ATOMS) {
float4 pos = posq[index];
float4 force = forceBuffers[index];
COMPUTE_FORCES
forceBuffers[index] = force;
index += get_global_size(0);
}
}
platforms/opencl/tests/TestOpenCLCustomGBForce.cpp
View file @ ba2503b5
......@@ -141,6 +141,95 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
}
}
void testMembrane() {
const int numMolecules = 70;
const int numParticles = numMolecules*2;
const double boxSize = 10.0;
OpenCLPlatform platform;
// Create a system with an implicit membrane.
System system;
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
}
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
CustomGBForce* custom = new CustomGBForce();
custom->setCutoffDistance(2.0);
custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale");
custom->addGlobalParameter("thickness", 3);
custom->addGlobalParameter("solventDielectric", 78.3);
custom->addGlobalParameter("soluteDielectric", 1);
custom->addComputedValue("Imol", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
"U=r+sr2;"
"C=2*(1/or1-1/L)*step(sr2-r-or1);"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
custom->addComputedValue("Imem", "(1/radius+2*log(2)/thickness)/(1+exp(7.2*(abs(z)+radius-0.5*thickness)))", CustomGBForce::SingleParticle);
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=max(Imol,Imem)*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.5;
custom->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
else {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.8;
custom->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
}
system.addForce(custom);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = stepSize/norm;
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/stepSize, 1e-2);
}
void testTabulatedFunction(bool interpolating) {
OpenCLPlatform platform;
System system;
......@@ -334,6 +423,7 @@ int main() {
testOBC(GBSAOBCForce::NoCutoff, CustomGBForce::NoCutoff);
testOBC(GBSAOBCForce::CutoffNonPeriodic, CustomGBForce::CutoffNonPeriodic);
testOBC(GBSAOBCForce::CutoffPeriodic, CustomGBForce::CutoffPeriodic);
testMembrane();
testTabulatedFunction(true);
testTabulatedFunction(false);
testMultipleChainRules();
......
platforms/reference/src/SimTKReference/ReferenceCustomGBIxn.cpp
View file @ ba2503b5
......@@ -349,6 +349,24 @@ void ReferenceCustomGBIxn::calculateChainRuleForces(int numAtoms, RealOpenMM** a
}
}
}
// Compute chain rule terms for computed values that depend explicitly on particle coordinates.
map<string, double> variables = globalParameters;
for (int i = 0; i < numAtoms; i++) {
variables["x"] = atomCoordinates[i][0];
variables["y"] = atomCoordinates[i][1];
variables["z"] = atomCoordinates[i][2];
for (int j = 0; j < (int) paramNames.size(); j++)
variables[paramNames[j]] = atomParameters[i][j];
for (int j = 1; j < (int) valueNames.size(); j++) {
variables[valueNames[j-1]] = values[j-1][i];
for (int k = 0; k < 3; k++) {
RealOpenMM gradient = (RealOpenMM) valueGradientExpressions[j][k].evaluate(variables);
forces[i][k] -= dEdV[j][i]*gradient;
}
}
}
}
void ReferenceCustomGBIxn::calculateOnePairChainRule(int atom1, int atom2, RealOpenMM** atomCoordinates, RealOpenMM** atomParameters,
......@@ -378,16 +396,18 @@ void ReferenceCustomGBIxn::calculateOnePairChainRule(int atom1, int atom2, RealO
// Evaluate the derivative of each parameter with respect to position and apply forces.
vector<vector<RealOpenMM> > gradient1(valueDerivExpressions.size(), vector<RealOpenMM>(3, 0.0));
vector<vector<RealOpenMM> > gradient2(valueDerivExpressions.size(), vector<RealOpenMM>(3, 0.0));
RealOpenMM rinv = 1/r;
deltaR[0] *= rinv;
deltaR[1] *= rinv;
deltaR[2] *= rinv;
vector<RealOpenMM> dVdR1(valueDerivExpressions.size(), 0.0);
vector<RealOpenMM> dVdR2(valueDerivExpressions.size(), 0.0);
if (!isExcluded || valueTypes[0] != OpenMM::CustomGBForce::ParticlePair) {
RealOpenMM dVdR = (RealOpenMM) valueDerivExpressions[0][0].evaluate(variables);
RealOpenMM rinv = 1/r;
dVdR1[0] = (RealOpenMM) valueDerivExpressions[0][0].evaluate(variables);;
dVdR2[0] = -dVdR1[0];
for (int i = 0; i < 3; i++) {
gradient1[0][i] = dVdR*deltaR[i]*rinv;
gradient2[0][i] = -gradient1[0][i];
forces[atom1][i] -= dEdV[0][atom1]*gradient1[0][i];
forces[atom2][i] -= dEdV[0][atom1]*gradient2[0][i];
forces[atom1][i] -= dEdV[0][atom1]*dVdR1[0]*deltaR[i];
forces[atom2][i] -= dEdV[0][atom1]*dVdR2[0]*deltaR[i];
}
}
variables = globalParameters;
......@@ -401,15 +421,12 @@ void ReferenceCustomGBIxn::calculateOnePairChainRule(int atom1, int atom2, RealO
variables["z"] = atomCoordinates[atom1][2];
for (int j = 0; j < i; j++) {
RealOpenMM dVdV = (RealOpenMM) valueDerivExpressions[i][j].evaluate(variables);
for (int k = 0; k < 3; k++) {
gradient1[i][k] += dVdV*gradient1[j][k];
gradient2[i][k] += dVdV*gradient2[j][k];
}
dVdR1[i] += dVdV*dVdR1[j];
dVdR2[i] += dVdV*dVdR2[j];
}
for (int k = 0; k < 3; k++) {
gradient1[i][k] += (RealOpenMM) valueGradientExpressions[i][k].evaluate(variables);
forces[atom1][k] -= dEdV[i][atom1]*gradient1[i][k];
forces[atom2][k] -= dEdV[i][atom1]*gradient2[i][k];
forces[atom1][k] -= dEdV[i][atom1]*dVdR1[i]*deltaR[k];
forces[atom2][k] -= dEdV[i][atom1]*dVdR2[i]*deltaR[k];
}
}
}
platforms/reference/tests/TestReferenceCustomGBForce.cpp
View file @ ba2503b5
......@@ -143,6 +143,95 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
}
}
void testMembrane() {
const int numMolecules = 70;
const int numParticles = numMolecules*2;
const double boxSize = 10.0;
ReferencePlatform platform;
// Create a system with an implicit membrane.
System system;
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
}
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
CustomGBForce* custom = new CustomGBForce();
custom->setCutoffDistance(2.0);
custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale");
custom->addGlobalParameter("thickness", 3);
custom->addGlobalParameter("solventDielectric", 78.3);
custom->addGlobalParameter("soluteDielectric", 1);
custom->addComputedValue("Imol", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
"U=r+sr2;"
"C=2*(1/or1-1/L)*step(sr2-r-or1);"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
custom->addComputedValue("Imem", "(1/radius+2*log(2)/thickness)/(1+exp(7.2*(abs(z)+radius-0.5*thickness)))", CustomGBForce::SingleParticle);
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=max(Imol,Imem)*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.5;
custom->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
else {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.8;
custom->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
}
system.addForce(custom);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = stepSize/norm;
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/stepSize, 1e-2);
}
void testTabulatedFunction(bool interpolating) {
ReferencePlatform platform;
System system;
......@@ -775,6 +864,7 @@ int main() {
testOBC(GBSAOBCForce::NoCutoff, CustomGBForce::NoCutoff);
testOBC(GBSAOBCForce::CutoffNonPeriodic, CustomGBForce::CutoffNonPeriodic);
testOBC(GBSAOBCForce::CutoffPeriodic, CustomGBForce::CutoffPeriodic);
testMembrane();
testTabulatedFunction(true);
testTabulatedFunction(false);
testMultipleChainRules();
......
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