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Commit 4d823b0a authored by peastman's avatar peastman
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Began CUDA version of CustomCentroidBondForce

parent 56d95193
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Showing with 858 additions and 4 deletions
platforms/cuda/include/CudaKernels.h
View file @ 4d823b0a
...@@ -922,6 +922,58 @@ private: ...@@ -922,6 +922,58 @@ private:
CUfunction donorKernel, acceptorKernel; CUfunction donorKernel, acceptorKernel;
}; };
/**
* This kernel is invoked by CustomCentroidBondForce to calculate the forces acting on the system.
*/
class CudaCalcCustomCentroidBondForceKernel : public CalcCustomCentroidBondForceKernel {
public:
CudaCalcCustomCentroidBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomCentroidBondForceKernel(name, platform),
cu(cu), params(NULL), globals(NULL), groupParticles(NULL), groupWeights(NULL), groupOffsets(NULL), groupForces(NULL), bondGroups(NULL), centerPositions(NULL), system(system) {
}
~CudaCalcCustomCentroidBondForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the CustomCentroidBondForce this kernel will be used for
*/
void initialize(const System& system, const CustomCentroidBondForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomCentroidBondForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force);
private:
int numGroups, numBonds;
CudaContext& cu;
CudaParameterSet* params;
CudaArray* globals;
CudaArray* groupParticles;
CudaArray* groupWeights;
CudaArray* groupOffsets;
CudaArray* groupForces;
CudaArray* bondGroups;
CudaArray* centerPositions;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
std::vector<CudaArray*> tabulatedFunctions;
std::vector<void*> groupForcesArgs;
CUfunction computeCentersKernel, groupForcesKernel, applyForcesKernel;
const System& system;
};
/** /**
* This kernel is invoked by CustomCompoundBondForce to calculate the forces acting on the system. * This kernel is invoked by CustomCompoundBondForce to calculate the forces acting on the system.
*/ */
......
platforms/cuda/src/CudaKernelFactory.cpp
View file @ 4d823b0a
...@@ -104,6 +104,8 @@ KernelImpl* CudaKernelFactory::createKernelImpl(std::string name, const Platform ...@@ -104,6 +104,8 @@ KernelImpl* CudaKernelFactory::createKernelImpl(std::string name, const Platform
return new CudaCalcCustomExternalForceKernel(name, platform, cu, context.getSystem()); return new CudaCalcCustomExternalForceKernel(name, platform, cu, context.getSystem());
if (name == CalcCustomHbondForceKernel::Name()) if (name == CalcCustomHbondForceKernel::Name())
return new CudaCalcCustomHbondForceKernel(name, platform, cu, context.getSystem()); return new CudaCalcCustomHbondForceKernel(name, platform, cu, context.getSystem());
if (name == CalcCustomCentroidBondForceKernel::Name())
return new CudaCalcCustomCentroidBondForceKernel(name, platform, cu, context.getSystem());
if (name == CalcCustomCompoundBondForceKernel::Name()) if (name == CalcCustomCompoundBondForceKernel::Name())
return new CudaCalcCustomCompoundBondForceKernel(name, platform, cu, context.getSystem()); return new CudaCalcCustomCompoundBondForceKernel(name, platform, cu, context.getSystem());
if (name == CalcCustomManyParticleForceKernel::Name()) if (name == CalcCustomManyParticleForceKernel::Name())
......
platforms/cuda/src/CudaKernels.cpp
View file @ 4d823b0a
...@@ -31,6 +31,7 @@ ...@@ -31,6 +31,7 @@
#include "openmm/internal/AndersenThermostatImpl.h" #include "openmm/internal/AndersenThermostatImpl.h"
#include "openmm/internal/CMAPTorsionForceImpl.h" #include "openmm/internal/CMAPTorsionForceImpl.h"
#include "openmm/internal/ContextImpl.h" #include "openmm/internal/ContextImpl.h"
#include "openmm/internal/CustomCentroidBondForceImpl.h"
#include "openmm/internal/CustomCompoundBondForceImpl.h" #include "openmm/internal/CustomCompoundBondForceImpl.h"
#include "openmm/internal/CustomHbondForceImpl.h" #include "openmm/internal/CustomHbondForceImpl.h"
#include "openmm/internal/CustomManyParticleForceImpl.h" #include "openmm/internal/CustomManyParticleForceImpl.h"
...@@ -2570,8 +2571,8 @@ void CudaCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCF ...@@ -2570,8 +2571,8 @@ void CudaCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCF
cutoff = force.getCutoffDistance(); cutoff = force.getCutoffDistance();
string source = CudaKernelSources::gbsaObc2; string source = CudaKernelSources::gbsaObc2;
nb.addInteraction(useCutoff, usePeriodic, false, cutoff, vector<vector<int> >(), source, force.getForceGroup()); nb.addInteraction(useCutoff, usePeriodic, false, cutoff, vector<vector<int> >(), source, force.getForceGroup());
nb.addParameter(CudaNonbondedUtilities::ParameterInfo("obcParams", "float", 2, sizeof(float2), params->getDevicePointer()));; nb.addParameter(CudaNonbondedUtilities::ParameterInfo("obcParams", "float", 2, sizeof(float2), params->getDevicePointer()));
nb.addParameter(CudaNonbondedUtilities::ParameterInfo("bornForce", "long long", 1, sizeof(long long), bornForce->getDevicePointer()));; nb.addParameter(CudaNonbondedUtilities::ParameterInfo("bornForce", "long long", 1, sizeof(long long), bornForce->getDevicePointer()));
cu.addForce(new CudaGBSAOBCForceInfo(force)); cu.addForce(new CudaGBSAOBCForceInfo(force));
} }
...@@ -4242,6 +4243,418 @@ void CudaCalcCustomHbondForceKernel::copyParametersToContext(ContextImpl& contex ...@@ -4242,6 +4243,418 @@ void CudaCalcCustomHbondForceKernel::copyParametersToContext(ContextImpl& contex
cu.invalidateMolecules(); cu.invalidateMolecules();
} }
class CudaCustomCentroidBondForceInfo : public CudaForceInfo {
public:
CudaCustomCentroidBondForceInfo(const CustomCentroidBondForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
}
void getParticlesInGroup(int index, vector<int>& particles) {
vector<double> parameters;
force.getBondParameters(index, particles, parameters);
}
bool areGroupsIdentical(int group1, int group2) {
vector<int> particles;
vector<double> parameters1, parameters2;
force.getBondParameters(group1, particles, parameters1);
force.getBondParameters(group2, particles, parameters2);
for (int i = 0; i < (int) parameters1.size(); i++)
if (parameters1[i] != parameters2[i])
return false;
return true;
}
private:
const CustomCentroidBondForce& force;
};
CudaCalcCustomCentroidBondForceKernel::~CudaCalcCustomCentroidBondForceKernel() {
cu.setAsCurrent();
if (params != NULL)
delete params;
if (globals != NULL)
delete globals;
if (groupParticles != NULL)
delete groupParticles;
if (groupWeights != NULL)
delete groupWeights;
if (groupOffsets != NULL)
delete groupOffsets;
if (groupForces != NULL)
delete groupForces;
if (bondGroups != NULL)
delete bondGroups;
if (centerPositions != NULL)
delete centerPositions;
for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
delete tabulatedFunctions[i];
}
void CudaCalcCustomCentroidBondForceKernel::initialize(const System& system, const CustomCentroidBondForce& force) {
cu.setAsCurrent();
numBonds = force.getNumBonds();
if (numBonds == 0)
return;
cu.addForce(new CudaCustomCentroidBondForceInfo(force));
// Record the groups.
numGroups = force.getNumGroups();
vector<int> groupParticleVec;
vector<float> groupWeightVecFloat;
vector<double> groupWeightVecDouble;
vector<int> groupOffsetVec;
groupOffsetVec.push_back(0);
for (int i = 0; i < numGroups; i++) {
vector<int> particles;
vector<double> weights;
force.getGroupParameters(i, particles, weights);
groupParticleVec.insert(groupParticleVec.end(), particles.begin(), particles.end());
groupOffsetVec.push_back(groupParticleVec.size());
}
vector<vector<double> > normalizedWeights;
CustomCentroidBondForceImpl::computeNormalizedWeights(force, system, normalizedWeights);
if (cu.getUseDoublePrecision()) {
for (int i = 0; i < numGroups; i++)
groupWeightVecDouble.insert(groupWeightVecDouble.end(), normalizedWeights[i].begin(), normalizedWeights[i].end());
}
else {
for (int i = 0; i < numGroups; i++)
for (int j = 0; j < normalizedWeights[i].size(); j++)
groupWeightVecFloat.push_back((float) normalizedWeights[i][j]);
}
groupParticles = CudaArray::create<int>(cu, groupParticleVec.size(), "groupParticles");
groupParticles->upload(groupParticleVec);
if (cu.getUseDoublePrecision()) {
groupWeights = CudaArray::create<double>(cu, groupParticleVec.size(), "groupWeights");
groupWeights->upload(groupWeightVecDouble);
centerPositions = CudaArray::create<double4>(cu, numGroups, "centerPositions");
}
else {
groupWeights = CudaArray::create<float>(cu, groupParticleVec.size(), "groupWeights");
groupWeights->upload(groupWeightVecFloat);
centerPositions = CudaArray::create<float4>(cu, numGroups, "centerPositions");
}
groupOffsets = CudaArray::create<int>(cu, groupOffsetVec.size(), "groupOffsets");
groupOffsets->upload(groupOffsetVec);
groupForces = CudaArray::create<long long>(cu, numGroups*3, "groupForces");
cu.addAutoclearBuffer(*groupForces);
// Record the bonds.
int groupsPerBond = force.getNumGroupsPerBond();
vector<int> bondGroupVec(numBonds*groupsPerBond);
params = new CudaParameterSet(cu, force.getNumPerBondParameters(), numBonds, "customCentroidBondParams");
vector<vector<float> > paramVector(numBonds);
for (int i = 0; i < numBonds; i++) {
vector<int> groups;
vector<double> parameters;
force.getBondParameters(i, groups, parameters);
for (int j = 0; j < groups.size(); j++)
bondGroupVec[i+j*numBonds] = groups[j];
paramVector[i].resize(parameters.size());
for (int j = 0; j < (int) parameters.size(); j++)
paramVector[i][j] = (float) parameters[j];
}
params->setParameterValues(paramVector);
bondGroups = CudaArray::create<int>(cu, bondGroupVec.size(), "bondGroups");
bondGroups->upload(bondGroupVec);
// Record the arguments to the force kernel.
groupForcesArgs.push_back(&groupForces->getDevicePointer());
groupForcesArgs.push_back(NULL); // Energy buffer hasn't been created yet
groupForcesArgs.push_back(&centerPositions->getDevicePointer());
groupForcesArgs.push_back(&bondGroups->getDevicePointer());
// Record the tabulated functions.
map<string, Lepton::CustomFunction*> functions;
vector<pair<string, string> > functionDefinitions;
vector<const TabulatedFunction*> functionList;
stringstream extraArgs;
for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i);
string arrayName = "table"+cu.intToString(i);
functionDefinitions.push_back(make_pair(name, arrayName));
functions[name] = cu.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
int width;
vector<float> f = cu.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
tabulatedFunctions.push_back(CudaArray::create<float>(cu, f.size(), "TabulatedFunction"));
tabulatedFunctions.back()->upload(f);
extraArgs << ", const float";
if (width > 1)
extraArgs << width;
extraArgs << "* __restrict__ " << arrayName;
groupForcesArgs.push_back(&tabulatedFunctions.back()->getDevicePointer());
}
// Record information about parameters.
globalParamNames.resize(force.getNumGlobalParameters());
globalParamValues.resize(force.getNumGlobalParameters());
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
globalParamNames[i] = force.getGlobalParameterName(i);
globalParamValues[i] = (float) force.getGlobalParameterDefaultValue(i);
}
map<string, string> variables;
for (int i = 0; i < groupsPerBond; i++) {
string index = cu.intToString(i+1);
variables["x"+index] = "pos"+index+".x";
variables["y"+index] = "pos"+index+".y";
variables["z"+index] = "pos"+index+".z";
}
for (int i = 0; i < force.getNumPerBondParameters(); i++) {
const string& name = force.getPerBondParameterName(i);
variables[name] = "bondParams"+params->getParameterSuffix(i);
}
if (force.getNumGlobalParameters() > 0) {
globals = CudaArray::create<float>(cu, force.getNumGlobalParameters(), "customCentroidBondGlobals");
globals->upload(globalParamValues);
extraArgs << ", const float* __restrict__ globals";
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
const string& name = force.getGlobalParameterName(i);
string value = "globals["+cu.intToString(i)+"]";
variables[name] = value;
}
groupForcesArgs.push_back(&globals->getDevicePointer());
}
// Now to generate the kernel. First, it needs to calculate all distances, angles,
// and dihedrals the expression depends on.
map<string, vector<int> > distances;
map<string, vector<int> > angles;
map<string, vector<int> > dihedrals;
Lepton::ParsedExpression energyExpression = CustomCentroidBondForceImpl::prepareExpression(force, functions, distances, angles, dihedrals);
map<string, Lepton::ParsedExpression> forceExpressions;
set<string> computedDeltas;
vector<string> atomNames, posNames;
for (int i = 0; i < groupsPerBond; i++) {
string index = cu.intToString(i+1);
atomNames.push_back("P"+index);
posNames.push_back("pos"+index);
}
stringstream compute;
for (int i = 0; i < groupsPerBond; i++) {
compute<<"int group"<<(i+1)<<" = bondGroups[index+"<<(i*numBonds)<<"];\n";
compute<<"real4 pos"<<(i+1)<<" = centerPositions[group"<<(i+1)<<"];\n";
}
int index = 0;
for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
const vector<int>& groups = iter->second;
string deltaName = atomNames[groups[0]]+atomNames[groups[1]];
if (computedDeltas.count(deltaName) == 0) {
compute<<"real4 delta"<<deltaName<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<");\n";
computedDeltas.insert(deltaName);
}
compute<<"real r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
variables[iter->first] = "r_"+deltaName;
forceExpressions["real dEdDistance"+cu.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
}
index = 0;
for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
const vector<int>& groups = iter->second;
string deltaName1 = atomNames[groups[1]]+atomNames[groups[0]];
string deltaName2 = atomNames[groups[1]]+atomNames[groups[2]];
string angleName = "angle_"+atomNames[groups[0]]+atomNames[groups[1]]+atomNames[groups[2]];
if (computedDeltas.count(deltaName1) == 0) {
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[0]]<<");\n";
computedDeltas.insert(deltaName1);
}
if (computedDeltas.count(deltaName2) == 0) {
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[2]]<<");\n";
computedDeltas.insert(deltaName2);
}
compute<<"real "<<angleName<<" = computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
variables[iter->first] = angleName;
forceExpressions["real dEdAngle"+cu.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
}
index = 0;
for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
const vector<int>& groups = iter->second;
string deltaName1 = atomNames[groups[0]]+atomNames[groups[1]];
string deltaName2 = atomNames[groups[2]]+atomNames[groups[1]];
string deltaName3 = atomNames[groups[2]]+atomNames[groups[3]];
string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
string dihedralName = "dihedral_"+atomNames[groups[0]]+atomNames[groups[1]]+atomNames[groups[2]]+atomNames[groups[3]];
if (computedDeltas.count(deltaName1) == 0) {
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<");\n";
computedDeltas.insert(deltaName1);
}
if (computedDeltas.count(deltaName2) == 0) {
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[1]]<<");\n";
computedDeltas.insert(deltaName2);
}
if (computedDeltas.count(deltaName3) == 0) {
compute<<"real4 delta"<<deltaName3<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[3]]<<");\n";
computedDeltas.insert(deltaName3);
}
compute<<"real4 "<<crossName1<<" = computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
compute<<"real4 "<<crossName2<<" = computeCross(delta"<<deltaName2<<", delta"<<deltaName3<<");\n";
compute<<"real "<<dihedralName<<" = computeAngle("<<crossName1<<", "<<crossName2<<");\n";
compute<<dihedralName<<" *= (delta"<<deltaName1<<".x*"<<crossName2<<".x + delta"<<deltaName1<<".y*"<<crossName2<<".y + delta"<<deltaName1<<".z*"<<crossName2<<".z < 0 ? -1 : 1);\n";
variables[iter->first] = dihedralName;
forceExpressions["real dEdDihedral"+cu.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
}
// Now evaluate the expressions.
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
CudaNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
extraArgs<<", const "<<buffer.getType()<<"* __restrict__ globalParams"<<i;
compute<<buffer.getType()<<" bondParams"<<(i+1)<<" = globalParams"<<i<<"[index];\n";
groupForcesArgs.push_back(&buffer.getMemory());
}
forceExpressions["energy += "] = energyExpression;
compute << cu.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, "temp");
// Finally, apply forces to groups.
vector<string> forceNames;
for (int i = 0; i < groupsPerBond; i++) {
string istr = cu.intToString(i+1);
string forceName = "force"+istr;
forceNames.push_back(forceName);
compute<<"real3 "<<forceName<<" = make_real3(0);\n";
compute<<"{\n";
Lepton::ParsedExpression forceExpressionX = energyExpression.differentiate("x"+istr).optimize();
Lepton::ParsedExpression forceExpressionY = energyExpression.differentiate("y"+istr).optimize();
Lepton::ParsedExpression forceExpressionZ = energyExpression.differentiate("z"+istr).optimize();
map<string, Lepton::ParsedExpression> expressions;
if (!isZeroExpression(forceExpressionX))
expressions[forceName+".x -= "] = forceExpressionX;
if (!isZeroExpression(forceExpressionY))
expressions[forceName+".y -= "] = forceExpressionY;
if (!isZeroExpression(forceExpressionZ))
expressions[forceName+".z -= "] = forceExpressionZ;
if (expressions.size() > 0)
compute<<cu.getExpressionUtilities().createExpressions(expressions, variables, functionList, functionDefinitions, "coordtemp");
compute<<"}\n";
}
index = 0;
for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
const vector<int>& groups = iter->second;
string deltaName = atomNames[groups[0]]+atomNames[groups[1]];
string value = "(dEdDistance"+cu.intToString(index)+"/r_"+deltaName+")*trim(delta"+deltaName+")";
compute<<forceNames[groups[0]]<<" += "<<"-"<<value<<";\n";
compute<<forceNames[groups[1]]<<" += "<<value<<";\n";
}
index = 0;
for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
const vector<int>& groups = iter->second;
string deltaName1 = atomNames[groups[1]]+atomNames[groups[0]];
string deltaName2 = atomNames[groups[1]]+atomNames[groups[2]];
compute<<"{\n";
compute<<"real3 crossProd = cross(delta"<<deltaName2<<", delta"<<deltaName1<<");\n";
compute<<"real lengthCross = max(SQRT(dot(crossProd, crossProd)), 1e-6f);\n";
compute<<"real3 deltaCross0 = -cross(trim(delta"<<deltaName1<<"), crossProd)*dEdAngle"<<cu.intToString(index)<<"/(delta"<<deltaName1<<".w*lengthCross);\n";
compute<<"real3 deltaCross2 = cross(trim(delta"<<deltaName2<<"), crossProd)*dEdAngle"<<cu.intToString(index)<<"/(delta"<<deltaName2<<".w*lengthCross);\n";
compute<<"real3 deltaCross1 = -(deltaCross0+deltaCross2);\n";
compute<<forceNames[groups[0]]<<" += deltaCross0;\n";
compute<<forceNames[groups[1]]<<" += deltaCross1;\n";
compute<<forceNames[groups[2]]<<" += deltaCross2;\n";
compute<<"}\n";
}
index = 0;
for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
const vector<int>& groups = iter->second;
string deltaName1 = atomNames[groups[0]]+atomNames[groups[1]];
string deltaName2 = atomNames[groups[2]]+atomNames[groups[1]];
string deltaName3 = atomNames[groups[2]]+atomNames[groups[3]];
string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
compute<<"{\n";
compute<<"real r = sqrt(delta"<<deltaName2<<".w);\n";
compute<<"real4 ff;\n";
compute<<"ff.x = (-dEdDihedral"<<cu.intToString(index)<<"*r)/"<<crossName1<<".w;\n";
compute<<"ff.y = (delta"<<deltaName1<<".x*delta"<<deltaName2<<".x + delta"<<deltaName1<<".y*delta"<<deltaName2<<".y + delta"<<deltaName1<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
compute<<"ff.z = (delta"<<deltaName3<<".x*delta"<<deltaName2<<".x + delta"<<deltaName3<<".y*delta"<<deltaName2<<".y + delta"<<deltaName3<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
compute<<"ff.w = (dEdDihedral"<<cu.intToString(index)<<"*r)/"<<crossName2<<".w;\n";
compute<<"real3 internalF0 = ff.x*trim("<<crossName1<<");\n";
compute<<"real3 internalF3 = ff.w*trim("<<crossName2<<");\n";
compute<<"real3 s = ff.y*internalF0 - ff.z*internalF3;\n";
compute<<forceNames[groups[0]]<<" += internalF0;\n";
compute<<forceNames[groups[1]]<<" += s-internalF0;\n";
compute<<forceNames[groups[2]]<<" += -s-internalF3;\n";
compute<<forceNames[groups[3]]<<" += internalF3;\n";
compute<<"}\n";
}
// Save the forces to global memory.
for (int i = 0; i < groupsPerBond; i++) {
compute<<"atomicAdd(&groupForce[group"<<(i+1)<<"], static_cast<unsigned long long>((long long) (force"<<(i+1)<<".x*0x100000000)));\n";
compute<<"atomicAdd(&groupForce[group"<<(i+1)<<"+NUM_GROUPS], static_cast<unsigned long long>((long long) (force"<<(i+1)<<".y*0x100000000)));\n";
compute<<"atomicAdd(&groupForce[group"<<(i+1)<<"+NUM_GROUPS*2], static_cast<unsigned long long>((long long) (force"<<(i+1)<<".z*0x100000000)));\n";
compute<<"__threadfence_block();\n";
}
map<string, string> replacements;
replacements["M_PI"] = cu.doubleToString(M_PI);
replacements["NUM_GROUPS"] = cu.intToString(numGroups);
replacements["NUM_BONDS"] = cu.intToString(numBonds);
replacements["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms());
replacements["EXTRA_ARGS"] = extraArgs.str();
replacements["COMPUTE_FORCE"] = compute.str();
CUmodule module = cu.createModule(CudaKernelSources::vectorOps+cu.replaceStrings(CudaKernelSources::customCentroidBond, replacements));
computeCentersKernel = cu.getKernel(module, "computeGroupCenters");
groupForcesKernel = cu.getKernel(module, "computeGroupForces");
applyForcesKernel = cu.getKernel(module, "applyForcesToAtoms");
}
double CudaCalcCustomCentroidBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if (globals != NULL) {
bool changed = false;
for (int i = 0; i < (int) globalParamNames.size(); i++) {
float value = (float) context.getParameter(globalParamNames[i]);
if (value != globalParamValues[i])
changed = true;
globalParamValues[i] = value;
}
if (changed)
globals->upload(globalParamValues);
}
void* computeCentersArgs[] = {&cu.getPosq().getDevicePointer(), &groupParticles->getDevicePointer(), &groupWeights->getDevicePointer(),
&groupOffsets->getDevicePointer(), &centerPositions->getDevicePointer()};
cu.executeKernel(computeCentersKernel, computeCentersArgs, CudaContext::TileSize*numGroups);
groupForcesArgs[1] = &cu.getEnergyBuffer().getDevicePointer();
cu.executeKernel(groupForcesKernel, &groupForcesArgs[0], numBonds);
void* applyForcesArgs[] = {&groupParticles->getDevicePointer(), &groupWeights->getDevicePointer(), &groupOffsets->getDevicePointer(),
&groupForces->getDevicePointer(), &cu.getForce().getDevicePointer()};
cu.executeKernel(applyForcesKernel, applyForcesArgs, CudaContext::TileSize*numGroups);
return 0.0;
}
void CudaCalcCustomCentroidBondForceKernel::copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force) {
cu.setAsCurrent();
int numContexts = cu.getPlatformData().contexts.size();
int startIndex = cu.getContextIndex()*force.getNumBonds()/numContexts;
int endIndex = (cu.getContextIndex()+1)*force.getNumBonds()/numContexts;
if (numBonds != endIndex-startIndex)
throw OpenMMException("updateParametersInContext: The number of bonds has changed");
if (numBonds == 0)
return;
// Record the per-bond parameters.
vector<vector<float> > paramVector(numBonds);
vector<int> particles;
vector<double> parameters;
for (int i = 0; i < numBonds; i++) {
force.getBondParameters(startIndex+i, particles, parameters);
paramVector[i].resize(parameters.size());
for (int j = 0; j < (int) parameters.size(); j++)
paramVector[i][j] = (float) parameters[j];
}
params->setParameterValues(paramVector);
// Mark that the current reordering may be invalid.
cu.invalidateMolecules();
}
class CudaCustomCompoundBondForceInfo : public CudaForceInfo { class CudaCustomCompoundBondForceInfo : public CudaForceInfo {
public: public:
CudaCustomCompoundBondForceInfo(const CustomCompoundBondForce& force) : force(force) { CudaCustomCompoundBondForceInfo(const CustomCompoundBondForce& force) : force(force) {
...@@ -4304,7 +4717,6 @@ void CudaCalcCustomCompoundBondForceKernel::initialize(const System& system, con ...@@ -4304,7 +4717,6 @@ void CudaCalcCustomCompoundBondForceKernel::initialize(const System& system, con
map<string, Lepton::CustomFunction*> functions; map<string, Lepton::CustomFunction*> functions;
vector<pair<string, string> > functionDefinitions; vector<pair<string, string> > functionDefinitions;
vector<const TabulatedFunction*> functionList; vector<const TabulatedFunction*> functionList;
stringstream tableArgs;
for (int i = 0; i < force.getNumTabulatedFunctions(); i++) { for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
functionList.push_back(&force.getTabulatedFunction(i)); functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i); string name = force.getTabulatedFunctionName(i);
...@@ -4507,7 +4919,7 @@ void CudaCalcCustomCompoundBondForceKernel::initialize(const System& system, con ...@@ -4507,7 +4919,7 @@ void CudaCalcCustomCompoundBondForceKernel::initialize(const System& system, con
cu.getBondedUtilities().addInteraction(atoms, compute.str(), force.getForceGroup()); cu.getBondedUtilities().addInteraction(atoms, compute.str(), force.getForceGroup());
map<string, string> replacements; map<string, string> replacements;
replacements["M_PI"] = cu.doubleToString(M_PI); replacements["M_PI"] = cu.doubleToString(M_PI);
cu.getBondedUtilities().addPrefixCode(cu.replaceStrings(CudaKernelSources::customCompoundBond, replacements));; cu.getBondedUtilities().addPrefixCode(cu.replaceStrings(CudaKernelSources::customCompoundBond, replacements));
} }
double CudaCalcCustomCompoundBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) { double CudaCalcCustomCompoundBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......
platforms/cuda/src/CudaPlatform.cpp
View file @ 4d823b0a
...@@ -80,6 +80,7 @@ CudaPlatform::CudaPlatform() { ...@@ -80,6 +80,7 @@ CudaPlatform::CudaPlatform() {
registerKernelFactory(CalcCustomGBForceKernel::Name(), factory); registerKernelFactory(CalcCustomGBForceKernel::Name(), factory);
registerKernelFactory(CalcCustomExternalForceKernel::Name(), factory); registerKernelFactory(CalcCustomExternalForceKernel::Name(), factory);
registerKernelFactory(CalcCustomHbondForceKernel::Name(), factory); registerKernelFactory(CalcCustomHbondForceKernel::Name(), factory);
registerKernelFactory(CalcCustomCentroidBondForceKernel::Name(), factory);
registerKernelFactory(CalcCustomCompoundBondForceKernel::Name(), factory); registerKernelFactory(CalcCustomCompoundBondForceKernel::Name(), factory);
registerKernelFactory(CalcCustomManyParticleForceKernel::Name(), factory); registerKernelFactory(CalcCustomManyParticleForceKernel::Name(), factory);
registerKernelFactory(IntegrateVerletStepKernel::Name(), factory); registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
......
platforms/cuda/src/kernels/customCentroidBond.cu 0 → 100644
View file @ 4d823b0a
/**
* Compute the center of each group.
*/
extern "C" __global__ void computeGroupCenters(const real4* __restrict__ posq, const int* __restrict__ groupParticles,
const real* __restrict__ groupWeights, const int* __restrict__ groupOffsets, real4* __restrict__ centerPositions) {
__shared__ volatile real3 temp[64];
for (int group = blockIdx.x; group < NUM_GROUPS; group += gridDim.x) {
// The threads in this block work together to compute the center one group.
int firstIndex = groupOffsets[group];
int lastIndex = groupOffsets[group+1];
real3 center = make_real3(0, 0, 0);
for (int index = threadIdx.x; index < lastIndex-firstIndex; index += blockDim.x) {
int atom = groupParticles[firstIndex+index];
real weight = groupWeights[firstIndex+index];
real4 pos = posq[atom];
center.x += weight*pos.x;
center.y += weight*pos.y;
center.z += weight*pos.z;
}
// Sum the values.
int thread = threadIdx.x;
temp[thread].x = center.x;
temp[thread].y = center.y;
temp[thread].z = center.z;
__syncthreads();
if (thread < 32) {
temp[thread].x += temp[thread+32].x;
temp[thread].y += temp[thread+32].y;
temp[thread].z += temp[thread+32].z;
if (thread < 16) {
temp[thread].x += temp[thread+16].x;
temp[thread].y += temp[thread+16].y;
temp[thread].z += temp[thread+16].z;
}
if (thread < 8) {
temp[thread].x += temp[thread+8].x;
temp[thread].y += temp[thread+8].y;
temp[thread].z += temp[thread+8].z;
}
if (thread < 4) {
temp[thread].x += temp[thread+4].x;
temp[thread].y += temp[thread+4].y;
temp[thread].z += temp[thread+4].z;
}
if (thread < 2) {
temp[thread].x += temp[thread+2].x;
temp[thread].y += temp[thread+2].y;
temp[thread].z += temp[thread+2].z;
}
}
if (thread == 0)
centerPositions[group] = make_real4(temp[0].x+temp[1].x, temp[0].y+temp[1].y, temp[0].z+temp[1].z, 0);
}
}
/**
* Convert a real4 to a real3 by removing its last element.
*/
inline __device__ real3 trim(real4 v) {
return make_real3(v.x, v.y, v.z);
}
/**
* Compute the difference between two vectors, setting the fourth component to the squared magnitude.
*/
inline __device__ real4 delta(real4 vec1, real4 vec2) {
real4 result = make_real4(vec1.x-vec2.x, vec1.y-vec2.y, vec1.z-vec2.z, 0);
result.w = result.x*result.x + result.y*result.y + result.z*result.z;
return result;
}
/**
* Compute the angle between two vectors. The w component of each vector should contain the squared magnitude.
*/
__device__ real computeAngle(real4 vec1, real4 vec2) {
real dotProduct = vec1.x*vec2.x + vec1.y*vec2.y + vec1.z*vec2.z;
real cosine = dotProduct*RSQRT(vec1.w*vec2.w);
real angle;
if (cosine > 0.99f || cosine < -0.99f) {
// We're close to the singularity in acos(), so take the cross product and use asin() instead.
real3 crossProduct = cross(vec1, vec2);
real scale = vec1.w*vec2.w;
angle = ASIN(SQRT(dot(crossProduct, crossProduct)/scale));
if (cosine < 0.0f)
angle = M_PI-angle;
}
else
angle = ACOS(cosine);
return angle;
}
/**
* Compute the cross product of two vectors, setting the fourth component to the squared magnitude.
*/
inline __device__ real4 computeCross(real4 vec1, real4 vec2) {
real3 cp = cross(vec1, vec2);
return make_real4(cp.x, cp.y, cp.z, cp.x*cp.x+cp.y*cp.y+cp.z*cp.z);
}
/**
* Compute the forces on groups based on the bonds.
*/
extern "C" __global__ void computeGroupForces(unsigned long long* __restrict__ groupForce, real* __restrict__ energyBuffer, const real4* __restrict__ centerPositions,
const int* __restrict__ bondGroups
EXTRA_ARGS) {
extern __shared__ real4 posBuffer[];
real energy = 0;
for (int index = blockIdx.x*blockDim.x+threadIdx.x; index < NUM_BONDS; index += blockDim.x*gridDim.x) {
COMPUTE_FORCE
}
energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += energy;
}
/**
* Apply the forces from the group centers to the individual atoms.
*/
extern "C" __global__ void applyForcesToAtoms(const int* __restrict__ groupParticles, const real* __restrict__ groupWeights, const int* __restrict__ groupOffsets,
const long long* __restrict__ groupForce, unsigned long long* __restrict__ atomForce) {
for (int group = blockIdx.x; group < NUM_GROUPS; group += gridDim.x) {
long long fx = groupForce[group];
long long fy = groupForce[group+NUM_GROUPS];
long long fz = groupForce[group+NUM_GROUPS*2];
int firstIndex = groupOffsets[group];
int lastIndex = groupOffsets[group+1];
for (int index = threadIdx.x; index < lastIndex-firstIndex; index += blockDim.x) {
int atom = groupParticles[firstIndex+index];
real weight = groupWeights[firstIndex+index];
atomicAdd(&atomForce[atom], static_cast<unsigned long long>((long long) (fx*weight)));
atomicAdd(&atomForce[atom+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (fy*weight)));
atomicAdd(&atomForce[atom+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (fz*weight)));
}
}
}
platforms/cuda/tests/TestCudaCustomCentroidBondForce.cpp 0 → 100644
View file @ 4d823b0a
/* -------------------------------------------------------------------------- *
* 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) 2015 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 reference implementation of CustomCompoundBondForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomCentroidBondForce.h"
#include "openmm/CustomCompoundBondForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
const double TOL = 1e-5;
void testHarmonicBond() {
System system;
system.addParticle(1.0);
system.addParticle(2.0);
system.addParticle(3.0);
system.addParticle(4.0);
system.addParticle(5.0);
CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "k*distance(g1,g2)^2");
force->addPerBondParameter("k");
vector<int> particles1;
particles1.push_back(0);
particles1.push_back(1);
vector<int> particles2;
particles2.push_back(2);
particles2.push_back(3);
particles2.push_back(4);
force->addGroup(particles1);
force->addGroup(particles2);
vector<int> groups;
groups.push_back(0);
groups.push_back(1);
vector<double> parameters;
parameters.push_back(1.0);
force->addBond(groups, parameters);
system.addForce(force);
ASSERT(!system.usesPeriodicBoundaryConditions());
// The center of mass of group 0 is (1.5, 0, 0).
vector<Vec3> positions(5);
positions[0] = Vec3(2.5, 0, 0);
positions[1] = Vec3(1, 0, 0);
// The center of mass of group 1 is (-1, 0, 0).
positions[2] = Vec3(-6, 0, 0);
positions[3] = Vec3(-1, 0, 0);
positions[4] = Vec3(2, 0, 0);
// Check the forces and energy.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(2.5*2.5, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(Vec3(-2*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-2*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_VEC(Vec3(2*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
ASSERT_EQUAL_VEC(Vec3(2*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
ASSERT_EQUAL_VEC(Vec3(2*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
// Update the per-bond parameter and see if the results change.
parameters[0] = 2.0;
force->setBondParameters(0, groups, parameters);
force->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(2*2.5*2.5, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(Vec3(-4*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-4*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
}
void testComplexFunction() {
int numParticles = 4;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(2.0);
// When every group contains only one particle, a CustomCentroidBondForce is identical to a
// CustomCompoundBondForce. Use that to test a complicated energy function with lots of terms.
CustomCompoundBondForce* compound = new CustomCompoundBondForce(4, "x1+y2+z4+distance(p1,p2)*angle(p3,p2,p4)+0.5*dihedral(p2,p1,p4,p3)");
CustomCentroidBondForce* centroid = new CustomCentroidBondForce(4, "x1+y2+z4+distance(g1,g2)*angle(g3,g2,g4)+0.5*dihedral(g2,g1,g4,g3)");
// Add a single bond to the CustomCompoundBondForce.
vector<int> particles(4);
vector<double> parameters;
particles[0] = 0;
particles[1] = 1;
particles[2] = 2;
particles[3] = 3;
compound->addBond(particles, parameters);
// Add an identical bond to the CustomCentroidBondForce. As a stronger test, make sure that
// group number is different from particle number.
vector<int> groupMembers(1);
groupMembers[0] = 3;
centroid->addGroup(groupMembers);
groupMembers[0] = 0;
centroid->addGroup(groupMembers);
groupMembers[0] = 1;
centroid->addGroup(groupMembers);
groupMembers[0] = 2;
centroid->addGroup(groupMembers);
vector<int> groups(4);
groups[0] = 1;
groups[1] = 2;
groups[2] = 3;
groups[3] = 0;
centroid->addBond(groups, parameters);
// Add both forces as different force groups, and create a context.
centroid->setForceGroup(1);
system.addForce(compound);
system.addForce(centroid);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
// Evaluate the force and energy for various positions and see if they match.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < numParticles; j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
context.setPositions(positions);
State state1 = context.getState(State::Forces | State::Energy, false, 1<<0);
State state2 = context.getState(State::Forces | State::Energy, false, 1<<1);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), TOL);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], TOL);
}
}
void testCustomWeights() {
System system;
system.addParticle(1.0);
system.addParticle(2.0);
system.addParticle(3.0);
system.addParticle(4.0);
CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "distance(g1,g2)^2");
vector<int> particles(2);
vector<double> weights(2);
particles[0] = 0;
particles[1] = 1;
weights[0] = 0.5;
weights[1] = 1.5;
force->addGroup(particles, weights);
particles[0] = 2;
particles[1] = 3;
weights[0] = 2.0;
weights[1] = 1.0;
force->addGroup(particles, weights);
vector<int> groups;
groups.push_back(0);
groups.push_back(1);
vector<double> parameters;
force->addBond(groups, parameters);
system.addForce(force);
// The center of mass of group 0 is (0, 1, 0).
vector<Vec3> positions(4);
positions[0] = Vec3(0, 4, 0);
positions[1] = Vec3(0, 0, 0);
// The center of mass of group 1 is (0, 10, 0).
positions[2] = Vec3(0, 9, 0);
positions[3] = Vec3(0, 12, 0);
// Check the forces and energy.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(9*9, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(Vec3(0, 2*9*(0.5/2.0), 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 2*9*(1.5/2.0), 0), state.getForces()[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -2*9*(2.0/3.0), 0), state.getForces()[2], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -2*9*(1.0/3.0), 0), state.getForces()[3], TOL);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testHarmonicBond();
testComplexFunction();
testCustomWeights();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
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