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"platforms/cuda2/tests/TestCudaRBTorsionForce.cpp" did not exist on "ad75a3907915beba16c0f81c0b129a4b98f2f106"
Commit 402e01b2 authored by peastman's avatar peastman
Browse files

CPU platform supports multiple NonbondedForces

parent 9c5efe5d
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Showing with 41 additions and 11 deletions
platforms/cpu/include/CpuKernels.h
View file @ 402e01b2
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013-2016 Stanford University and the Authors. *
* Portions copyright (c) 2013-2018 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -268,7 +268,7 @@ public:
private:
class PmeIO;
CpuPlatform::PlatformData& data;
int numParticles, num14;
int numParticles, num14, posqIndex;
int **bonded14IndexArray;
double **bonded14ParamArray;
double nonbondedCutoff, switchingDistance, rfDielectric, ewaldAlpha, ewaldDispersionAlpha, ewaldSelfEnergy, dispersionCoefficient;
......@@ -277,6 +277,7 @@ private:
std::vector<std::set<int> > exclusions;
std::vector<std::pair<float, float> > particleParams;
std::vector<float> C6params;
std::vector<float> charges;
NonbondedMethod nonbondedMethod;
CpuNonbondedForce* nonbonded;
Kernel optimizedPme, optimizedDispersionPme;
......@@ -363,7 +364,9 @@ public:
void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force);
private:
CpuPlatform::PlatformData& data;
int posqIndex;
std::vector<std::pair<float, float> > particleParams;
std::vector<float> charges;
CpuGBSAOBCForce obc;
};
......
platforms/cpu/include/CpuPlatform.h
View file @ 402e01b2
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013-2016 Stanford University and the Authors. *
* Portions copyright (c) 2013-2018 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -92,6 +92,7 @@ public:
PlatformData(int numParticles, int numThreads, bool deterministicForces);
~PlatformData();
void requestNeighborList(double cutoffDistance, double padding, bool useExclusions, const std::vector<std::set<int> >& exclusionList);
int requestPosqIndex();
AlignedArray<float> posq;
std::vector<AlignedArray<float> > threadForce;
ThreadPool threads;
......@@ -101,6 +102,7 @@ public:
CpuNeighborList* neighborList;
double cutoff, paddedCutoff;
bool anyExclusions, deterministicForces;
int currentPosqIndex, nextPosqIndex;
std::vector<std::set<int> > exclusions;
};
......
platforms/cpu/src/CpuKernels.cpp
View file @ 402e01b2
......@@ -138,6 +138,19 @@ static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>&
return 0.5*energy;
}
/**
* Copy particle charges into the fourth element of the posq array.
*/
static void copyChargesToPosq(ContextImpl& context, const vector<float>& charges, int index) {
CpuPlatform::PlatformData& data = CpuPlatform::getPlatformData(context);
if (index == data.currentPosqIndex)
return;
data.currentPosqIndex = index;
AlignedArray<float>& posq = data.posq;
for (int i = 0; i < charges.size(); i++)
posq[4*i+3] = charges[i];
}
CpuCalcForcesAndEnergyKernel::CpuCalcForcesAndEnergyKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data, ContextImpl& context) :
CalcForcesAndEnergyKernel(name, platform), data(data) {
// Create a Reference platform version of this kernel.
......@@ -530,6 +543,7 @@ CpuCalcNonbondedForceKernel::~CpuCalcNonbondedForceKernel() {
}
void CpuCalcNonbondedForceKernel::initialize(const System& system, const NonbondedForce& force) {
posqIndex = data.requestPosqIndex();
// Identify which exceptions are 1-4 interactions.
......@@ -556,12 +570,13 @@ void CpuCalcNonbondedForceKernel::initialize(const System& system, const Nonbond
for (int i = 0; i < num14; i++)
bonded14ParamArray[i] = new double[3];
particleParams.resize(numParticles);
charges.resize(numParticles);
C6params.resize(numParticles);
double sumSquaredCharges = 0.0;
for (int i = 0; i < numParticles; ++i) {
double charge, radius, depth;
force.getParticleParameters(i, charge, radius, depth);
data.posq[4*i+3] = (float) charge;
charges[i] = (float) charge;
particleParams[i] = make_pair((float) (0.5*radius), (float) (2.0*sqrt(depth)));
C6params[i] = 8.0*pow(particleParams[i].first, 3.0) * particleParams[i].second;
sumSquaredCharges += charge*charge;
......@@ -660,6 +675,7 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
}
}
}
copyChargesToPosq(context, charges, posqIndex);
AlignedArray<float>& posq = data.posq;
vector<Vec3>& posData = extractPositions(context);
vector<Vec3>& forceData = extractForces(context);
......@@ -726,11 +742,12 @@ void CpuCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context,
// Record the values.
posqIndex = data.requestPosqIndex();
double sumSquaredCharges = 0.0;
for (int i = 0; i < numParticles; ++i) {
double charge, radius, depth;
force.getParticleParameters(i, charge, radius, depth);
data.posq[4*i+3] = (float) charge;
charges[i] = (float) charge;
particleParams[i] = make_pair((float) (0.5*radius), (float) (2.0*sqrt(depth)));
sumSquaredCharges += charge*charge;
}
......@@ -964,12 +981,14 @@ CpuCalcGBSAOBCForceKernel::~CpuCalcGBSAOBCForceKernel() {
}
void CpuCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCForce& force) {
posqIndex = data.requestPosqIndex();
int numParticles = system.getNumParticles();
particleParams.resize(numParticles);
charges.resize(numParticles);
for (int i = 0; i < numParticles; ++i) {
double charge, radius, scalingFactor;
force.getParticleParameters(i, charge, radius, scalingFactor);
data.posq[4*i+3] = (float) charge;
charges[i] = (float) charge;
radius -= 0.009;
particleParams[i] = make_pair((float) radius, (float) (scalingFactor*radius));
}
......@@ -983,6 +1002,7 @@ void CpuCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCFo
}
double CpuCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
copyChargesToPosq(context, charges, posqIndex);
if (data.isPeriodic) {
Vec3& boxSize = extractBoxSize(context);
float floatBoxSize[3] = {(float) boxSize[0], (float) boxSize[1], (float) boxSize[2]};
......@@ -1000,10 +1020,11 @@ void CpuCalcGBSAOBCForceKernel::copyParametersToContext(ContextImpl& context, co
// Record the values.
posqIndex = data.requestPosqIndex();
for (int i = 0; i < numParticles; ++i) {
double charge, radius, scalingFactor;
force.getParticleParameters(i, charge, radius, scalingFactor);
data.posq[4*i+3] = (float) charge;
charges[i] = (float) charge;
radius -= 0.009;
particleParams[i] = make_pair((float) radius, (float) (scalingFactor*radius));
}
......
platforms/cpu/src/CpuPlatform.cpp
View file @ 402e01b2
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013-2016 Stanford University and the Authors. *
* Portions copyright (c) 2013-2018 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -147,7 +147,7 @@ const CpuPlatform::PlatformData& CpuPlatform::getPlatformData(const ContextImpl&
}
CpuPlatform::PlatformData::PlatformData(int numParticles, int numThreads, bool deterministicForces) : posq(4*numParticles), threads(numThreads),
deterministicForces(deterministicForces), neighborList(NULL), cutoff(0.0), paddedCutoff(0.0), anyExclusions(false) {
deterministicForces(deterministicForces), neighborList(NULL), cutoff(0.0), paddedCutoff(0.0), anyExclusions(false), currentPosqIndex(-1), nextPosqIndex(0) {
numThreads = threads.getNumThreads();
threadForce.resize(numThreads);
for (int i = 0; i < numThreads; i++)
......@@ -184,3 +184,7 @@ void CpuPlatform::PlatformData::requestNeighborList(double cutoffDistance, doubl
else if (!anyExclusions)
exclusions = exclusionList;
}
int CpuPlatform::PlatformData::requestPosqIndex() {
return nextPosqIndex++;
}
\ No newline at end of file
platforms/cuda/src/CudaKernels.cpp
View file @ 402e01b2
......@@ -1716,7 +1716,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
map<string, string> replacements;
replacements["CHARGE"] = (usePosqCharges ? "pos.w" : "charges[atom]");
CUmodule module = cu.createModule(CudaKernelSources::vectorOps+cu.replaceStrings(CudaKernelSources::pme, replacements), pmeDefines);
if (cu.getPlatformData().useCpuPme && !doLJPME) {
if (cu.getPlatformData().useCpuPme && !doLJPME && usePosqCharges) {
// Create the CPU PME kernel.
try {
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 402e01b2
......@@ -1692,7 +1692,7 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
if (deviceIsCpu)
pmeDefines["DEVICE_IS_CPU"] = "1";
if (cl.getPlatformData().useCpuPme && !doLJPME) {
if (cl.getPlatformData().useCpuPme && !doLJPME && usePosqCharges) {
// Create the CPU PME kernel.
try {
......
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