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Commit f1ca1e6d authored by Peter Eastman's avatar Peter Eastman
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Continuing to implement OpenCL version of GayBerneForce

parent 3250fb43
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Showing with 100 additions and 58 deletions
openmmapi/src/GayBerneForceImpl.cpp
View file @ f1ca1e6d
......@@ -115,6 +115,7 @@ void GayBerneForceImpl::initialize(ContextImpl& context) {
double GayBerneForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
if ((groups&(1<<owner.getForceGroup())) != 0)
return kernel.getAs<CalcGayBerneForceKernel>().execute(context, includeForces, includeEnergy);
return 0.0;
}
std::vector<std::string> GayBerneForceImpl::getKernelNames() {
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ f1ca1e6d
......@@ -6154,9 +6154,7 @@ void OpenCLCalcGayBerneForceKernel::initialize(const System& system, const GayBe
defines["SWITCH_C5"] = cl.doubleToString(6/pow(force.getSwitchingDistance()-cutoff, 5.0));
}
}
if (!cl.getSupports64BitGlobalAtomics()) {
defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
}
defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
cl::Program program = cl.createProgram(OpenCLKernelSources::gayBerne, defines);
framesKernel = cl::Kernel(program, "computeEllipsoidFrames");
blockBoundsKernel = cl::Kernel(program, "findBlockBounds");
......@@ -6234,12 +6232,37 @@ double OpenCLCalcGayBerneForceKernel::execute(ContextImpl& context, bool include
cl.executeKernel(framesKernel, numRealParticles);
setPeriodicBoxArgs(cl, blockBoundsKernel, 1);
cl.executeKernel(blockBoundsKernel, (numRealParticles+31)/32);
if (nonbondedMethod != GayBerneForce::NoCutoff) {
setPeriodicBoxArgs(cl, neighborsKernel, 2);
cl.executeKernel(neighborsKernel, numRealParticles);
setPeriodicBoxArgs(cl, forceKernel, 20);
if (nonbondedMethod == GayBerneForce::NoCutoff) {
cl.executeKernel(forceKernel, cl.getNonbondedUtilities().getNumForceThreadBlocks()*cl.getNonbondedUtilities().getForceThreadBlockSize());
}
else {
while (true) {
setPeriodicBoxArgs(cl, neighborsKernel, 2);
cl.executeKernel(neighborsKernel, numRealParticles);
cl_int* count = (cl_int*) cl.getPinnedBuffer();
cl::Event event;
cl.getQueue().enqueueReadBuffer(neighborBlockCount->getDeviceBuffer(), CL_FALSE, 0, neighborBlockCount->getSize()*neighborBlockCount->getElementSize(), count, NULL, &event);
setPeriodicBoxArgs(cl, forceKernel, 20);
cl.executeKernel(forceKernel, cl.getNonbondedUtilities().getNumForceThreadBlocks()*cl.getNonbondedUtilities().getForceThreadBlockSize());
event.wait();
if (*count <= maxNeighborBlocks)
break;
// There wasn't enough room for the neighbor list, so we need to recreate it.
delete neighbors;
neighbors = NULL;
delete neighborIndex;
neighborIndex = NULL;
maxNeighborBlocks = (int) ceil((*count)*1.1);
neighbors = OpenCLArray::create<cl_int>(cl, maxNeighborBlocks*32, "neighbors");
neighborIndex = OpenCLArray::create<cl_int>(cl, maxNeighborBlocks, "neighbors");
neighborsKernel.setArg<cl::Buffer>(10, neighbors->getDeviceBuffer());
neighborsKernel.setArg<cl::Buffer>(11, neighborIndex->getDeviceBuffer());
forceKernel.setArg<cl::Buffer>(17, neighbors->getDeviceBuffer());
forceKernel.setArg<cl::Buffer>(18, neighborIndex->getDeviceBuffer());
}
}
cl.executeKernel(forceKernel, cl.getNonbondedUtilities().getNumForceThreadBlocks()*cl.getNonbondedUtilities().getForceThreadBlockSize());
cl.executeKernel(torqueKernel, numRealParticles);
return 0.0;
}
......@@ -6266,20 +6289,15 @@ void OpenCLCalcGayBerneForceKernel::copyParametersToContext(ContextImpl& context
vector<mm_float4> sigParamsVector(cl.getPaddedNumAtoms(), mm_float4(0, 0, 0, 0));
vector<mm_float2> epsParamsVector(cl.getPaddedNumAtoms(), mm_float2(0, 0));
vector<mm_float4> scaleVector(cl.getPaddedNumAtoms(), mm_float4(0, 0, 0, 0));
numRealParticles = 0;
for (int i = 0; i < force.getNumParticles(); i++) {
int xparticle, yparticle;
double sigma, epsilon, sx, sy, sz, ex, ey, ez;
force.getParticleParameters(i, sigma, epsilon, xparticle, yparticle, sx, sy, sz, ex, ey, ez);
sigParamsVector[i] = mm_float4((float) (0.5*sigma), (float) (0.5*sx), (float) (0.5*sy), (float) (0.5*sz));
sigParamsVector[i] = mm_float4((float) (0.5*sigma), (float) (0.25*sx*sx), (float) (0.25*sy*sy), (float) (0.25*sz*sz));
epsParamsVector[i] = mm_float2((float) sqrt(epsilon), (float) (0.125*(sx*sy + sz*sz)*sqrt(sx*sy)));
scaleVector[i] = mm_float4((float) (1/sqrt(ex)), (float) (1/sqrt(ey)), (float) (1/sqrt(ez)), 0);
if (epsilon != 0.0) {
numRealParticles++;
isRealParticle[i] = true;
}
else
isRealParticle[i] = false;
if (epsilon != 0.0 && !isRealParticle[i])
throw OpenMMException("updateParametersInContext: The set of ignored particles (ones with epsilon=0) has changed");
}
sigParams->upload(sigParamsVector);
epsParams->upload(epsParamsVector);
......
platforms/opencl/src/kernels/gayBerne.cl
View file @ f1ca1e6d
#pragma OPENCL EXTENSION cl_khr_global_int32_base_atomics : enable
#ifdef SUPPORTS_64_BIT_ATOMICS
#pragma OPENCL EXTENSION cl_khr_int64_base_atomics : enable
#endif
#define TILE_SIZE 32
#define NEIGHBOR_BLOCK_SIZE 32
......@@ -55,14 +58,8 @@ __kernel void computeEllipsoidFrames(int numParticles, __global const real4* res
float3 e2 = scale[originalIndex].xyz;
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++) {
real belem = 0;
real gelem = 0;
for (int k = 0; k < 3; k++) {
belem += a[k][i]*e2[k]*a[k][j];
gelem += a[k][i]*r2[k]*a[k][j];
}
b[i][j] = belem;
g[i][j] = gelem;
b[i][j] = a[0][i]*e2.x*a[0][j] + a[1][i]*e2.y*a[1][j] + a[2][i]*e2.z*a[2][j];
g[i][j] = a[0][i]*r2.x*a[0][j] + a[1][i]*r2.y*a[1][j] + a[2][i]*r2.z*a[2][j];
}
}
}
......@@ -201,15 +198,15 @@ void loadAtomData(AtomData* data, int sortedIndex, int originalIndex, __global c
}
real3 matrixVectorProduct(real (*m)[3], real3 v) {
return (real3) (m[0][0]*v[0] + m[0][1]*v[1] + m[0][2]*v[2],
m[1][0]*v[0] + m[1][1]*v[1] + m[1][2]*v[2],
m[2][0]*v[0] + m[2][1]*v[1] + m[2][2]*v[2]);
return (real3) (m[0][0]*v.x + m[0][1]*v.y + m[0][2]*v.z,
m[1][0]*v.x + m[1][1]*v.y + m[1][2]*v.z,
m[2][0]*v.x + m[2][1]*v.y + m[2][2]*v.z);
}
real3 vectorMatrixProduct(real3 v, real (*m)[3]) {
return (real3) (m[0][0]*v[0] + m[1][0]*v[1] + m[2][0]*v[2],
m[0][1]*v[0] + m[1][1]*v[1] + m[2][1]*v[2],
m[0][2]*v[0] + m[1][2]*v[1] + m[2][2]*v[2]);
return (real3) (m[0][0]*v.x + m[1][0]*v.y + m[2][0]*v.z,
m[0][1]*v.x + m[1][1]*v.y + m[2][1]*v.z,
m[0][2]*v.x + m[1][2]*v.y + m[2][2]*v.z);
}
......@@ -306,33 +303,33 @@ void computeOneInteraction(AtomData* data1, AtomData* data2, real sigma, real ep
real3 dchidq = cross(vectorMatrixProduct(iota, b), iota)*(-4*rInv2);
real3 scale = (real3) (sig.y, sig.z, sig.w)*(-0.5f*eta/detG12);
real d[3][3];
d[0][0] = scale[0]*(2*a[0][0]*(G12[1][1]*G12[2][2] - G12[1][2]*G12[2][1]) +
a[0][2]*(G12[1][2]*G12[0][1] + G12[1][0]*G12[2][1] - G12[1][1]*(G12[0][2] + G12[2][0])) +
a[0][1]*(G12[0][2]*G12[2][1] + G12[2][0]*G12[1][2] - G12[2][2]*(G12[0][1] + G12[1][0])));
d[0][1] = scale[0]*( a[0][0]*(G12[0][2]*G12[2][1] + G12[2][0]*G12[1][2] - G12[2][2]*(G12[0][1] + G12[1][0])) +
2*a[0][1]*(G12[0][0]*G12[2][2] - G12[2][0]*G12[0][2]) +
a[0][2]*(G12[1][0]*G12[0][2] + G12[2][0]*G12[0][1] - G12[0][0]*(G12[1][2] + G12[2][1])));
d[0][2] = scale[0]*( a[0][0]*(G12[0][1]*G12[1][2] + G12[1][0]*G12[2][1] - G12[1][1]*(G12[0][2] + G12[2][0])) +
a[0][1]*(G12[1][0]*G12[0][2] + G12[2][0]*G12[0][1] - G12[0][0]*(G12[1][2] + G12[2][1])) +
2*a[0][2]*(G12[1][1]*G12[0][0] - G12[1][0]*G12[0][1]));
d[1][0] = scale[1]*(2*a[1][0]*(G12[1][1]*G12[2][2] - G12[1][2]*G12[2][1]) +
a[1][1]*(G12[0][2]*G12[2][1] + G12[2][0]*G12[1][2] - G12[2][2]*(G12[0][1] + G12[1][0])) +
a[1][2]*(G12[1][2]*G12[0][1] + G12[1][0]*G12[2][1] - G12[1][1]*(G12[0][2] + G12[2][0])));
d[1][1] = scale[1]*( a[1][0]*(G12[0][2]*G12[2][1] + G12[2][0]*G12[1][2] - G12[2][2]*(G12[0][1] + G12[1][0])) +
2*a[1][1]*(G12[2][2]*G12[0][0] - G12[2][0]*G12[0][2]) +
a[1][2]*(G12[1][0]*G12[0][2] + G12[0][1]*G12[2][0] - G12[0][0]*(G12[1][2] + G12[2][1])));
d[1][2] = scale[1]*( a[1][0]*(G12[0][1]*G12[1][2] + G12[1][0]*G12[2][1] - G12[1][1]*(G12[0][2] + G12[2][0])) +
a[1][1]*(G12[1][0]*G12[0][2] + G12[0][1]*G12[2][0] - G12[0][0]*(G12[1][2] + G12[2][1])) +
2*a[1][2]*(G12[1][1]*G12[0][0] - G12[1][0]*G12[0][1]));
d[2][0] = scale[2]*(2*a[2][0]*(G12[1][1]*G12[2][2] - G12[2][1]*G12[1][2]) +
a[2][1]*(G12[0][2]*G12[2][1] + G12[1][2]*G12[2][0] - G12[2][2]*(G12[0][1] + G12[1][0])) +
a[2][2]*(G12[0][1]*G12[1][2] + G12[2][1]*G12[1][0] - G12[1][1]*(G12[0][2] + G12[2][0])));
d[2][1] = scale[2]*( a[2][0]*(G12[0][2]*G12[2][1] + G12[1][2]*G12[2][0] - G12[2][2]*(G12[0][1] + G12[1][0])) +
2*a[2][1]*(G12[0][0]*G12[2][2] - G12[0][2]*G12[2][0]) +
a[2][2]*(G12[1][0]*G12[0][2] + G12[0][1]*G12[2][0] - G12[0][0]*(G12[1][2] + G12[2][1])));
d[2][2] = scale[2]*( a[2][0]*(G12[0][1]*G12[1][2] + G12[2][1]*G12[1][0] - G12[1][1]*(G12[0][2] + G12[2][0])) +
a[2][1]*(G12[1][0]*G12[0][2] + G12[2][0]*G12[0][1] - G12[0][0]*(G12[1][2] + G12[2][1])) +
2*a[2][2]*(G12[1][1]*G12[0][0] - G12[1][0]*G12[0][1]));
d[0][0] = scale.x*(2*a[0][0]*(G12[1][1]*G12[2][2] - G12[1][2]*G12[2][1]) +
a[0][2]*(G12[1][2]*G12[0][1] + G12[1][0]*G12[2][1] - G12[1][1]*(G12[0][2] + G12[2][0])) +
a[0][1]*(G12[0][2]*G12[2][1] + G12[2][0]*G12[1][2] - G12[2][2]*(G12[0][1] + G12[1][0])));
d[0][1] = scale.x*( a[0][0]*(G12[0][2]*G12[2][1] + G12[2][0]*G12[1][2] - G12[2][2]*(G12[0][1] + G12[1][0])) +
2*a[0][1]*(G12[0][0]*G12[2][2] - G12[2][0]*G12[0][2]) +
a[0][2]*(G12[1][0]*G12[0][2] + G12[2][0]*G12[0][1] - G12[0][0]*(G12[1][2] + G12[2][1])));
d[0][2] = scale.x*( a[0][0]*(G12[0][1]*G12[1][2] + G12[1][0]*G12[2][1] - G12[1][1]*(G12[0][2] + G12[2][0])) +
a[0][1]*(G12[1][0]*G12[0][2] + G12[2][0]*G12[0][1] - G12[0][0]*(G12[1][2] + G12[2][1])) +
2*a[0][2]*(G12[1][1]*G12[0][0] - G12[1][0]*G12[0][1]));
d[1][0] = scale.y*(2*a[1][0]*(G12[1][1]*G12[2][2] - G12[1][2]*G12[2][1]) +
a[1][1]*(G12[0][2]*G12[2][1] + G12[2][0]*G12[1][2] - G12[2][2]*(G12[0][1] + G12[1][0])) +
a[1][2]*(G12[1][2]*G12[0][1] + G12[1][0]*G12[2][1] - G12[1][1]*(G12[0][2] + G12[2][0])));
d[1][1] = scale.y*( a[1][0]*(G12[0][2]*G12[2][1] + G12[2][0]*G12[1][2] - G12[2][2]*(G12[0][1] + G12[1][0])) +
2*a[1][1]*(G12[2][2]*G12[0][0] - G12[2][0]*G12[0][2]) +
a[1][2]*(G12[1][0]*G12[0][2] + G12[0][1]*G12[2][0] - G12[0][0]*(G12[1][2] + G12[2][1])));
d[1][2] = scale.y*( a[1][0]*(G12[0][1]*G12[1][2] + G12[1][0]*G12[2][1] - G12[1][1]*(G12[0][2] + G12[2][0])) +
a[1][1]*(G12[1][0]*G12[0][2] + G12[0][1]*G12[2][0] - G12[0][0]*(G12[1][2] + G12[2][1])) +
2*a[1][2]*(G12[1][1]*G12[0][0] - G12[1][0]*G12[0][1]));
d[2][0] = scale.z*(2*a[2][0]*(G12[1][1]*G12[2][2] - G12[2][1]*G12[1][2]) +
a[2][1]*(G12[0][2]*G12[2][1] + G12[1][2]*G12[2][0] - G12[2][2]*(G12[0][1] + G12[1][0])) +
a[2][2]*(G12[0][1]*G12[1][2] + G12[2][1]*G12[1][0] - G12[1][1]*(G12[0][2] + G12[2][0])));
d[2][1] = scale.z*( a[2][0]*(G12[0][2]*G12[2][1] + G12[1][2]*G12[2][0] - G12[2][2]*(G12[0][1] + G12[1][0])) +
2*a[2][1]*(G12[0][0]*G12[2][2] - G12[0][2]*G12[2][0]) +
a[2][2]*(G12[1][0]*G12[0][2] + G12[0][1]*G12[2][0] - G12[0][0]*(G12[1][2] + G12[2][1])));
d[2][2] = scale.z*( a[2][0]*(G12[0][1]*G12[1][2] + G12[2][1]*G12[1][0] - G12[1][1]*(G12[0][2] + G12[2][0])) +
a[2][1]*(G12[1][0]*G12[0][2] + G12[2][0]*G12[0][1] - G12[0][0]*(G12[1][2] + G12[2][1])) +
2*a[2][2]*(G12[1][1]*G12[0][0] - G12[1][0]*G12[0][1]));
real3 detadq = 0;
for (int i = 0; i < 3; i++)
detadq += cross((real3) (a[i][0], a[i][1], a[i][2]), (real3) (d[i][0], d[i][1], d[i][2]));
......@@ -365,6 +362,8 @@ __kernel void computeForce(
mixed energy = 0;
#ifdef USE_CUTOFF
const int numBlocks = *neighborBlockCount;
if (numBlocks > maxNeighborBlocks)
return; // There wasn't enough memory for the neighbor list.
for (int block = get_global_id(0); block < numBlocks; block += get_global_size(0)) {
// Load parameters for atom1.
......@@ -597,4 +596,4 @@ __kernel void applyTorques(
#endif
}
}
}
\ No newline at end of file
}
tests/TestGayBerneForce.h
View file @ f1ca1e6d
......@@ -133,6 +133,20 @@ void testEnergyScales() {
state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(expectedEnergy*expectedScale, state.getPotentialEnergy(), 1e-5);
ASSERT_EQUAL_VEC(Vec3(0, expectedForce*expectedScale, 0), state.getForces()[3], 1e-5);
// Modify their parameters and see if the result is still correct.
double newSigma = 1.1*sigma;
gb->setParticleParameters(0, newSigma, 1.5*epsilon, 1, 2, newSigma, newSigma, newSigma, 1.2, 1.6, 1.9);
gb->setParticleParameters(3, newSigma, epsilon, 4, 5, newSigma, newSigma, newSigma, 1.3, 1.7, 1.8);
gb->updateParametersInContext(context);
double combinedEpsilon = sqrt(1.5)*epsilon;
expectedEnergy = 4*combinedEpsilon*(pow(newSigma, 12.0)-pow(newSigma, 6.0));
expectedForce = 4*combinedEpsilon*(12*pow(newSigma, 12.0)-6*pow(newSigma, 6.0));
expectedScale = pow(2.0/(1/sqrt(1.6) + 1/sqrt(1.8)), 2.0);
state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(expectedEnergy*expectedScale, state.getPotentialEnergy(), 1e-5);
ASSERT_EQUAL_VEC(Vec3(0, expectedForce*expectedScale, 0), state.getForces()[3], 1e-5);
}
void testEnergyConservation() {
......@@ -218,6 +232,16 @@ void testExceptions() {
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(expectedEnergy*expectedScale, state.getPotentialEnergy(), 1e-5);
ASSERT_EQUAL_VEC(Vec3(expectedForce*expectedScale, 0, 0), state.getForces()[3], 1e-5);
// Modify the exception and see if the results are still correct.
gb->setExceptionParameters(0, 0, 3, sigma, 3.1*epsilon);
gb->updateParametersInContext(context);
expectedEnergy = 3.1*4*epsilon*(pow(sigma, 12.0)-pow(sigma, 6.0));
expectedForce = 3.1*4*epsilon*(12*pow(sigma, 12.0)-6*pow(sigma, 6.0));
state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(expectedEnergy*expectedScale, state.getPotentialEnergy(), 1e-5);
ASSERT_EQUAL_VEC(Vec3(expectedForce*expectedScale, 0, 0), state.getForces()[3], 1e-5);
}
void runPlatformTests();
......
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