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"platforms/hip/tests/TestHipHarmonicAngleForce.cpp" did not exist on "03a5288d3eabdbf478cc069ebf49e47f50734915"
Commit b880b5d9 authored by Peter Eastman's avatar Peter Eastman
Browse files

Fixed bug in PME when atoms were far outside the periodic box (see bug 1144)

parent a8a36d75
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Showing with 51 additions and 29 deletions
platforms/cuda/src/kernels/kCalculatePME.cu
View file @ b880b5d9
......@@ -108,9 +108,12 @@ void kUpdateGridIndexAndFraction_kernel()
for (int i = tid; i < cSim.atoms; i += tnb)
{
float4 posq = cSim.pPosq[i];
float3 t = make_float3((posq.x*cSim.invPeriodicBoxSizeX+1.0f)*cSim.pmeGridSize.x,
(posq.y*cSim.invPeriodicBoxSizeY+1.0f)*cSim.pmeGridSize.y,
(posq.z*cSim.invPeriodicBoxSizeZ+1.0f)*cSim.pmeGridSize.z);
posq.x -= floor(posq.x*cSim.invPeriodicBoxSizeX)*cSim.periodicBoxSizeX;
posq.y -= floor(posq.y*cSim.invPeriodicBoxSizeY)*cSim.periodicBoxSizeY;
posq.z -= floor(posq.z*cSim.invPeriodicBoxSizeZ)*cSim.periodicBoxSizeZ;
float3 t = make_float3((posq.x*cSim.invPeriodicBoxSizeX)*cSim.pmeGridSize.x,
(posq.y*cSim.invPeriodicBoxSizeY)*cSim.pmeGridSize.y,
(posq.z*cSim.invPeriodicBoxSizeZ)*cSim.pmeGridSize.z);
int3 gridIndex = make_int3(((int) t.x) % cSim.pmeGridSize.x,
((int) t.y) % cSim.pmeGridSize.y,
((int) t.z) % cSim.pmeGridSize.z);
......@@ -192,9 +195,12 @@ void kUpdateBsplines_kernel()
}
float4 posq = cSim.pPosq[i];
float3 t = make_float3((posq.x*cSim.invPeriodicBoxSizeX+1.0f)*cSim.pmeGridSize.x,
(posq.y*cSim.invPeriodicBoxSizeY+1.0f)*cSim.pmeGridSize.y,
(posq.z*cSim.invPeriodicBoxSizeZ+1.0f)*cSim.pmeGridSize.z);
posq.x -= floor(posq.x*cSim.invPeriodicBoxSizeX)*cSim.periodicBoxSizeX;
posq.y -= floor(posq.y*cSim.invPeriodicBoxSizeY)*cSim.periodicBoxSizeY;
posq.z -= floor(posq.z*cSim.invPeriodicBoxSizeZ)*cSim.periodicBoxSizeZ;
float3 t = make_float3((posq.x*cSim.invPeriodicBoxSizeX)*cSim.pmeGridSize.x,
(posq.y*cSim.invPeriodicBoxSizeY)*cSim.pmeGridSize.y,
(posq.z*cSim.invPeriodicBoxSizeZ)*cSim.pmeGridSize.z);
float4 dr = make_float4(t.x-(int) t.x, t.y-(int) t.y, t.z-(int) t.z, 0.0f);
data[PME_ORDER - 1] = make_float4(0.0f);
......@@ -341,9 +347,12 @@ void kGridInterpolateForce_kernel()
{
float3 force = make_float3(0.0f, 0.0f, 0.0f);
float4 posq = cSim.pPosq[atom];
float3 t = make_float3((posq.x*cSim.invPeriodicBoxSizeX+1.0f)*cSim.pmeGridSize.x,
(posq.y*cSim.invPeriodicBoxSizeY+1.0f)*cSim.pmeGridSize.y,
(posq.z*cSim.invPeriodicBoxSizeZ+1.0f)*cSim.pmeGridSize.z);
posq.x -= floor(posq.x*cSim.invPeriodicBoxSizeX)*cSim.periodicBoxSizeX;
posq.y -= floor(posq.y*cSim.invPeriodicBoxSizeY)*cSim.periodicBoxSizeY;
posq.z -= floor(posq.z*cSim.invPeriodicBoxSizeZ)*cSim.periodicBoxSizeZ;
float3 t = make_float3((posq.x*cSim.invPeriodicBoxSizeX)*cSim.pmeGridSize.x,
(posq.y*cSim.invPeriodicBoxSizeY)*cSim.pmeGridSize.y,
(posq.z*cSim.invPeriodicBoxSizeZ)*cSim.pmeGridSize.z);
int3 gridIndex = make_int3(((int) t.x) % cSim.pmeGridSize.x,
((int) t.y) % cSim.pmeGridSize.y,
((int) t.z) % cSim.pmeGridSize.z);
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ b880b5d9
......@@ -1296,9 +1296,8 @@ void OpenCLCalcNonbondedForceKernel::executeForces(ContextImpl& context) {
pmeInterpolateForceKernel = cl::Kernel(program, "gridInterpolateForce");
pmeGridIndexKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
pmeGridIndexKernel.setArg<cl::Buffer>(1, pmeAtomGridIndex->getDeviceBuffer());
pmeAtomRangeKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
pmeAtomRangeKernel.setArg<cl::Buffer>(1, pmeAtomGridIndex->getDeviceBuffer());
pmeAtomRangeKernel.setArg<cl::Buffer>(2, pmeAtomRange->getDeviceBuffer());
pmeAtomRangeKernel.setArg<cl::Buffer>(0, pmeAtomGridIndex->getDeviceBuffer());
pmeAtomRangeKernel.setArg<cl::Buffer>(1, pmeAtomRange->getDeviceBuffer());
pmeUpdateBsplinesKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
pmeUpdateBsplinesKernel.setArg<cl::Buffer>(1, pmeBsplineTheta->getDeviceBuffer());
pmeUpdateBsplinesKernel.setArg<cl::Buffer>(2, pmeBsplineDtheta->getDeviceBuffer());
......@@ -1336,11 +1335,13 @@ void OpenCLCalcNonbondedForceKernel::executeForces(ContextImpl& context) {
if (pmeGrid != NULL) {
mm_float4 boxSize = cl.getPeriodicBoxSize();
mm_float4 invBoxSize = cl.getInvPeriodicBoxSize();
pmeGridIndexKernel.setArg<mm_float4>(2, invBoxSize);
pmeGridIndexKernel.setArg<mm_float4>(2, boxSize);
pmeGridIndexKernel.setArg<mm_float4>(3, invBoxSize);
cl.executeKernel(pmeGridIndexKernel, cl.getNumAtoms());
sort->sort(*pmeAtomGridIndex);
cl.executeKernel(pmeAtomRangeKernel, cl.getNumAtoms());
pmeUpdateBsplinesKernel.setArg<mm_float4>(5, invBoxSize);
pmeUpdateBsplinesKernel.setArg<mm_float4>(5, boxSize);
pmeUpdateBsplinesKernel.setArg<mm_float4>(6, invBoxSize);
cl.executeKernel(pmeUpdateBsplinesKernel, cl.getNumAtoms());
cl.executeKernel(pmeSpreadChargeKernel, cl.getNumAtoms());
fft->execFFT(*pmeGrid, true);
......@@ -1348,7 +1349,8 @@ void OpenCLCalcNonbondedForceKernel::executeForces(ContextImpl& context) {
pmeConvolutionKernel.setArg<cl_float>(6, (float) (1.0/(M_PI*boxSize.x*boxSize.y*boxSize.z)));
cl.executeKernel(pmeConvolutionKernel, cl.getNumAtoms());
fft->execFFT(*pmeGrid, false);
pmeInterpolateForceKernel.setArg<mm_float4>(5, invBoxSize);
pmeInterpolateForceKernel.setArg<mm_float4>(5, boxSize);
pmeInterpolateForceKernel.setArg<mm_float4>(6, invBoxSize);
cl.executeKernel(pmeInterpolateForceKernel, cl.getNumAtoms());
}
}
......
platforms/opencl/src/kernels/pme.cl
View file @ b880b5d9
__kernel void updateGridIndexAndFraction(__global float4* posq, __global float2* pmeAtomGridIndex, float4 invPeriodicBoxSize) {
__kernel void updateGridIndexAndFraction(__global float4* posq, __global float2* pmeAtomGridIndex, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
float4 pos = posq[i];
float4 t = (float4) ((pos.x*invPeriodicBoxSize.x+1.0f)*GRID_SIZE_X,
(pos.y*invPeriodicBoxSize.y+1.0f)*GRID_SIZE_Y,
(pos.z*invPeriodicBoxSize.z+1.0f)*GRID_SIZE_Z, 0.0f);
pos.x -= floor(pos.x*invPeriodicBoxSize.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*invPeriodicBoxSize.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*invPeriodicBoxSize.z)*periodicBoxSize.z;
float4 t = (float4) ((pos.x*invPeriodicBoxSize.x)*GRID_SIZE_X,
(pos.y*invPeriodicBoxSize.y)*GRID_SIZE_Y,
(pos.z*invPeriodicBoxSize.z)*GRID_SIZE_Z, 0.0f);
int4 gridIndex = (int4) (((int) t.x) % GRID_SIZE_X,
((int) t.y) % GRID_SIZE_Y,
((int) t.z) % GRID_SIZE_Z, 0);
......@@ -15,7 +18,7 @@ __kernel void updateGridIndexAndFraction(__global float4* posq, __global float2*
* For each grid point, find the range of sorted atoms associated with that point.
*/
__kernel void findAtomRangeForGrid(__global float4* posq, __global float2* pmeAtomGridIndex, __global int* pmeAtomRange) {
__kernel void findAtomRangeForGrid(__global float2* pmeAtomGridIndex, __global int* pmeAtomRange) {
int start = (NUM_ATOMS*get_global_id(0))/get_global_size(0);
int end = (NUM_ATOMS*(get_global_id(0)+1))/get_global_size(0);
int last = (start == 0 ? -1 : pmeAtomGridIndex[start-1].y);
......@@ -38,7 +41,7 @@ __kernel void findAtomRangeForGrid(__global float4* posq, __global float2* pmeAt
}
}
__kernel void updateBsplines(__global float4* posq, __global float4* pmeBsplineTheta, __global float4* pmeBsplineDTheta, __local float4* bsplinesCache, __global float2* pmeAtomGridIndex, float4 invPeriodicBoxSize) {
__kernel void updateBsplines(__global float4* posq, __global float4* pmeBsplineTheta, __global float4* pmeBsplineDTheta, __local float4* bsplinesCache, __global float2* pmeAtomGridIndex, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
const float4 scale = 1.0f/(PME_ORDER-1);
for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
__local float4* data = &bsplinesCache[get_local_id(0)*PME_ORDER];
......@@ -48,9 +51,12 @@ __kernel void updateBsplines(__global float4* posq, __global float4* pmeBsplineT
ddata[j] = 0.0f;
}
float4 pos = posq[i];
float4 t = (float4) ((pos.x*invPeriodicBoxSize.x+1.0f)*GRID_SIZE_X,
(pos.y*invPeriodicBoxSize.y+1.0f)*GRID_SIZE_Y,
(pos.z*invPeriodicBoxSize.z+1.0f)*GRID_SIZE_Z, 0.0f);
pos.x -= floor(pos.x*invPeriodicBoxSize.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*invPeriodicBoxSize.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*invPeriodicBoxSize.z)*periodicBoxSize.z;
float4 t = (float4) ((pos.x*invPeriodicBoxSize.x)*GRID_SIZE_X,
(pos.y*invPeriodicBoxSize.y)*GRID_SIZE_Y,
(pos.z*invPeriodicBoxSize.z)*GRID_SIZE_Z, 0.0f);
float4 dr = (float4) (t.x-(int) t.x, t.y-(int) t.y, t.z-(int) t.z, 0.0f);
data[PME_ORDER-1] = 0.0f;
data[1] = dr;
......@@ -148,13 +154,16 @@ __kernel void reciprocalConvolution(__global float2* pmeGrid, __global float* en
energyBuffer[get_global_id(0)] += 0.5f*energy;
}
__kernel void gridInterpolateForce(__global float4* posq, __global float4* forceBuffers, __global float4* pmeBsplineTheta, __global float4* pmeBsplineDTheta, __global float2* pmeGrid, float4 invPeriodicBoxSize) {
__kernel void gridInterpolateForce(__global float4* posq, __global float4* forceBuffers, __global float4* pmeBsplineTheta, __global float4* pmeBsplineDTheta, __global float2* pmeGrid, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
for (int atom = get_global_id(0); atom < NUM_ATOMS; atom += get_global_size(0)) {
float4 force = 0.0f;
float4 pos = posq[atom];
float4 t = (float4) ((pos.x*invPeriodicBoxSize.x+1.0f)*GRID_SIZE_X,
(pos.y*invPeriodicBoxSize.y+1.0f)*GRID_SIZE_Y,
(pos.z*invPeriodicBoxSize.z+1.0f)*GRID_SIZE_Z, 0.0f);
pos.x -= floor(pos.x*invPeriodicBoxSize.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*invPeriodicBoxSize.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*invPeriodicBoxSize.z)*periodicBoxSize.z;
float4 t = (float4) ((pos.x*invPeriodicBoxSize.x)*GRID_SIZE_X,
(pos.y*invPeriodicBoxSize.y)*GRID_SIZE_Y,
(pos.z*invPeriodicBoxSize.z)*GRID_SIZE_Z, 0.0f);
int4 gridIndex = (int4) (((int) t.x) % GRID_SIZE_X,
((int) t.y) % GRID_SIZE_Y,
((int) t.z) % GRID_SIZE_Z, 0);
......
platforms/reference/src/SimTKReference/PME.cpp
View file @ b880b5d9
......@@ -241,7 +241,9 @@ pme_update_grid_index_and_fraction(pme_t pme,
* numerical problems, so this shouldnt cause any problems.
* (And, by adding 100.0 box lengths, we would lose a bit of numerical accuracy here!)
*/
t = (atomCoordinates[i][d] / periodicBoxSize[d] + 1)*pme->ngrid[d];
RealOpenMM coord = atomCoordinates[i][d];
coord -= floor(coord/periodicBoxSize[d])*periodicBoxSize[d];
t = (coord / periodicBoxSize[d])*pme->ngrid[d];
ti = (int) t;
pme->particlefraction[i][d] = t - ti;
......
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