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Commit b21e3182 authored by Jason Swails's avatar Jason Swails
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Merge branch 'master' into psfinscode

parents 7b30da6e 3946c025
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Showing with 322 additions and 71 deletions
platforms/opencl/src/kernels/fft.cl
View file @ b21e3182
......@@ -2,26 +2,57 @@ real2 multiplyComplex(real2 c1, real2 c2) {
return (real2) (c1.x*c2.x-c1.y*c2.y, c1.x*c2.y+c1.y*c2.x);
}
/**
* Load a value from the half-complex grid produces by a real-to-complex transform.
*/
real2 loadComplexValue(__global const real2* restrict in, int x, int y, int z) {
const int inputZSize = ZSIZE/2+1;
if (z < inputZSize)
return in[x*YSIZE*inputZSize+y*inputZSize+z];
int xp = (x == 0 ? 0 : XSIZE-x);
int yp = (y == 0 ? 0 : YSIZE-y);
real2 value = in[xp*YSIZE*inputZSize+yp*inputZSize+(ZSIZE-z)];
return (real2) (value.x, -value.y);
}
/**
* Perform a 1D FFT on each row along one axis.
*/
__kernel void execFFT(__global const real2* restrict in, __global real2* restrict out, int sign, __local real2* restrict w,
__kernel void execFFT(__global const INPUT_TYPE* restrict in, __global OUTPUT_TYPE* restrict out, __local real2* restrict w,
__local real2* restrict data0, __local real2* restrict data1) {
for (int i = get_local_id(0); i < ZSIZE; i += get_local_size(0))
w[i] = (real2) (cos(-sign*i*2*M_PI/ZSIZE), sin(-sign*i*2*M_PI/ZSIZE));
w[i] = (real2) (cos(-(SIGN)*i*2*M_PI/ZSIZE), sin(-(SIGN)*i*2*M_PI/ZSIZE));
barrier(CLK_LOCAL_MEM_FENCE);
for (int baseIndex = get_group_id(0)*BLOCKS_PER_GROUP; baseIndex < XSIZE*YSIZE; baseIndex += get_num_groups(0)*BLOCKS_PER_GROUP) {
int index = baseIndex+get_local_id(0)/ZSIZE;
int x = index/YSIZE;
int y = index-x*YSIZE;
#if OUTPUT_IS_PACKED
if (x < XSIZE/2+1) {
#endif
#if LOOP_REQUIRED
for (int z = get_local_id(0); z < ZSIZE; z += get_local_size(0))
#if INPUT_IS_REAL
data0[z] = (real2) (in[x*(YSIZE*ZSIZE)+y*ZSIZE+z], 0);
#elif INPUT_IS_PACKED
data0[z] = loadComplexValue(in, x, y, z);
#else
data0[z] = in[x*(YSIZE*ZSIZE)+y*ZSIZE+z];
#endif
#else
if (index < XSIZE*YSIZE)
#if INPUT_IS_REAL
data0[get_local_id(0)] = (real2) (in[x*(YSIZE*ZSIZE)+y*ZSIZE+get_local_id(0)%ZSIZE], 0);
#elif INPUT_IS_PACKED
data0[get_local_id(0)] = loadComplexValue(in, x, y, get_local_id(0)%ZSIZE);
#else
data0[get_local_id(0)] = in[x*(YSIZE*ZSIZE)+y*ZSIZE+get_local_id(0)%ZSIZE];
#endif
#endif
#if OUTPUT_IS_PACKED
}
#endif
barrier(CLK_LOCAL_MEM_FENCE);
COMPUTE_FFT
......
platforms/opencl/src/kernels/fftR2C.cl 0 → 100644
View file @ b21e3182
/**
* Combine the two halves of a real grid into a complex grid that is half as large.
*/
__kernel void packForwardData(__global const real* restrict in, __global real2* restrict out) {
const int gridSize = PACKED_XSIZE*PACKED_YSIZE*PACKED_ZSIZE;
for (int index = get_global_id(0); index < gridSize; index += get_global_size(0)) {
int x = index/(PACKED_YSIZE*PACKED_ZSIZE);
int remainder = index-x*(PACKED_YSIZE*PACKED_ZSIZE);
int y = remainder/PACKED_ZSIZE;
int z = remainder-y*PACKED_ZSIZE;
#if PACKED_AXIS == 0
real2 value = (real2) (in[2*x*YSIZE*ZSIZE+y*ZSIZE+z], in[(2*x+1)*YSIZE*ZSIZE+y*ZSIZE+z]);
#elif PACKED_AXIS == 1
real2 value = (real2) (in[x*YSIZE*ZSIZE+2*y*ZSIZE+z], in[x*YSIZE*ZSIZE+(2*y+1)*ZSIZE+z]);
#else
real2 value = (real2) (in[x*YSIZE*ZSIZE+y*ZSIZE+2*z], in[x*YSIZE*ZSIZE+y*ZSIZE+(2*z+1)]);
#endif
out[index] = value;
}
}
/**
* Split the transformed data back into a full sized, symmetric grid.
*/
__kernel void unpackForwardData(__global const real2* restrict in, __global real2* restrict out, __local real2* restrict w) {
// Compute the phase factors.
#if PACKED_AXIS == 0
for (int i = get_local_id(0); i < PACKED_XSIZE; i += get_local_size(0))
w[i] = (real2) (sin(i*2*M_PI/XSIZE), cos(i*2*M_PI/XSIZE));
#elif PACKED_AXIS == 1
for (int i = get_local_id(0); i < PACKED_YSIZE; i += get_local_size(0))
w[i] = (real2) (sin(i*2*M_PI/YSIZE), cos(i*2*M_PI/YSIZE));
#else
for (int i = get_local_id(0); i < PACKED_ZSIZE; i += get_local_size(0))
w[i] = (real2) (sin(i*2*M_PI/ZSIZE), cos(i*2*M_PI/ZSIZE));
#endif
barrier(CLK_LOCAL_MEM_FENCE);
// Transform the data.
const int gridSize = PACKED_XSIZE*PACKED_YSIZE*PACKED_ZSIZE;
const int outputZSize = ZSIZE/2+1;
for (int index = get_global_id(0); index < gridSize; index += get_global_size(0)) {
int x = index/(PACKED_YSIZE*PACKED_ZSIZE);
int remainder = index-x*(PACKED_YSIZE*PACKED_ZSIZE);
int y = remainder/PACKED_ZSIZE;
int z = remainder-y*PACKED_ZSIZE;
int xp = (x == 0 ? 0 : PACKED_XSIZE-x);
int yp = (y == 0 ? 0 : PACKED_YSIZE-y);
int zp = (z == 0 ? 0 : PACKED_ZSIZE-z);
real2 z1 = in[x*PACKED_YSIZE*PACKED_ZSIZE+y*PACKED_ZSIZE+z];
real2 z2 = in[xp*PACKED_YSIZE*PACKED_ZSIZE+yp*PACKED_ZSIZE+zp];
#if PACKED_AXIS == 0
real2 wfac = w[x];
#elif PACKED_AXIS == 1
real2 wfac = w[y];
#else
real2 wfac = w[z];
#endif
real2 output = (real2) ((z1.x+z2.x - wfac.x*(z1.x-z2.x) + wfac.y*(z1.y+z2.y))/2, (z1.y-z2.y - wfac.y*(z1.x-z2.x) - wfac.x*(z1.y+z2.y))/2);
if (z < outputZSize)
out[x*YSIZE*outputZSize+y*outputZSize+z] = output;
xp = (x == 0 ? 0 : XSIZE-x);
yp = (y == 0 ? 0 : YSIZE-y);
zp = (z == 0 ? 0 : ZSIZE-z);
if (zp < outputZSize) {
#if PACKED_AXIS == 0
if (x == 0)
out[PACKED_XSIZE*YSIZE*outputZSize+yp*outputZSize+zp] = (real2) ((z1.x-z1.y+z2.x-z2.y)/2, (-z1.x-z1.y+z2.x+z2.y)/2);
#elif PACKED_AXIS == 1
if (y == 0)
out[xp*YSIZE*outputZSize+PACKED_YSIZE*outputZSize+zp] = (real2) ((z1.x-z1.y+z2.x-z2.y)/2, (-z1.x-z1.y+z2.x+z2.y)/2);
#else
if (z == 0)
out[xp*YSIZE*outputZSize+yp*outputZSize+PACKED_ZSIZE] = (real2) ((z1.x-z1.y+z2.x-z2.y)/2, (-z1.x-z1.y+z2.x+z2.y)/2);
#endif
else
out[xp*YSIZE*outputZSize+yp*outputZSize+zp] = (real2) (output.x, -output.y);
}
}
}
/**
* Load a value from the half-complex grid produced by a real-to-complex transform.
*/
real2 loadComplexValue(__global const real2* restrict in, int x, int y, int z) {
const int inputZSize = ZSIZE/2+1;
if (z < inputZSize)
return in[x*YSIZE*inputZSize+y*inputZSize+z];
int xp = (x == 0 ? 0 : XSIZE-x);
int yp = (y == 0 ? 0 : YSIZE-y);
real2 value = in[xp*YSIZE*inputZSize+yp*inputZSize+(ZSIZE-z)];
return (real2) (value.x, -value.y);
}
/**
* Repack the symmetric complex grid into one half as large in preparation for doing an inverse complex-to-real transform.
*/
__kernel void packBackwardData(__global const real2* restrict in, __global real2* restrict out, __local real2* restrict w) {
// Compute the phase factors.
#if PACKED_AXIS == 0
for (int i = get_local_id(0); i < PACKED_XSIZE; i += get_local_size(0))
w[i] = (real2) (cos(i*2*M_PI/XSIZE), sin(i*2*M_PI/XSIZE));
#elif PACKED_AXIS == 1
for (int i = get_local_id(0); i < PACKED_YSIZE; i += get_local_size(0))
w[i] = (real2) (cos(i*2*M_PI/YSIZE), sin(i*2*M_PI/YSIZE));
#else
for (int i = get_local_id(0); i < PACKED_ZSIZE; i += get_local_size(0))
w[i] = (real2) (cos(i*2*M_PI/ZSIZE), sin(i*2*M_PI/ZSIZE));
#endif
barrier(CLK_LOCAL_MEM_FENCE);
// Transform the data.
const int gridSize = PACKED_XSIZE*PACKED_YSIZE*PACKED_ZSIZE;
for (int index = get_global_id(0); index < gridSize; index += get_global_size(0)) {
int x = index/(PACKED_YSIZE*PACKED_ZSIZE);
int remainder = index-x*(PACKED_YSIZE*PACKED_ZSIZE);
int y = remainder/PACKED_ZSIZE;
int z = remainder-y*PACKED_ZSIZE;
int xp = (x == 0 ? 0 : PACKED_XSIZE-x);
int yp = (y == 0 ? 0 : PACKED_YSIZE-y);
int zp = (z == 0 ? 0 : PACKED_ZSIZE-z);
real2 z1 = loadComplexValue(in, x, y, z);
#if PACKED_AXIS == 0
real2 wfac = w[x];
real2 z2 = loadComplexValue(in, PACKED_XSIZE-x, yp, zp);
#elif PACKED_AXIS == 1
real2 wfac = w[y];
real2 z2 = loadComplexValue(in, xp, PACKED_YSIZE-y, zp);
#else
real2 wfac = w[z];
real2 z2 = loadComplexValue(in, xp, yp, PACKED_ZSIZE-z);
#endif
real2 even = (real2) ((z1.x+z2.x)/2, (z1.y-z2.y)/2);
real2 odd = (real2) ((z1.x-z2.x)/2, (z1.y+z2.y)/2);
odd = (real2) (odd.x*wfac.x-odd.y*wfac.y, odd.y*wfac.x+odd.x*wfac.y);
out[x*PACKED_YSIZE*PACKED_ZSIZE+y*PACKED_ZSIZE+z] = (real2) (even.x-odd.y, even.y+odd.x);
}
}
/**
* Split the data back into a full sized, real grid after an inverse transform.
*/
__kernel void unpackBackwardData(__global const real2* restrict in, __global real* restrict out) {
const int gridSize = PACKED_XSIZE*PACKED_YSIZE*PACKED_ZSIZE;
for (int index = get_global_id(0); index < gridSize; index += get_global_size(0)) {
int x = index/(PACKED_YSIZE*PACKED_ZSIZE);
int remainder = index-x*(PACKED_YSIZE*PACKED_ZSIZE);
int y = remainder/PACKED_ZSIZE;
int z = remainder-y*PACKED_ZSIZE;
real2 value = 2*in[index];
#if PACKED_AXIS == 0
out[2*x*YSIZE*ZSIZE+y*ZSIZE+z] = value.x;
out[(2*x+1)*YSIZE*ZSIZE+y*ZSIZE+z] = value.y;
#elif PACKED_AXIS == 1
out[x*YSIZE*ZSIZE+2*y*ZSIZE+z] = value.x;
out[x*YSIZE*ZSIZE+(2*y+1)*ZSIZE+z] = value.y;
#else
out[x*YSIZE*ZSIZE+y*ZSIZE+2*z] = value.x;
out[x*YSIZE*ZSIZE+y*ZSIZE+(2*z+1)] = value.y;
#endif
}
}
platforms/opencl/src/kernels/gbsaObc_cpu.cl
View file @ b21e3182
......@@ -21,7 +21,8 @@ __kernel void computeBornSum(
__global const real4* restrict posq, __global const float2* restrict global_params,
#ifdef USE_CUTOFF
__global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize,
unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, __global const real4* restrict blockCenter,
__global const real4* restrict blockSize, __global const int* restrict interactingAtoms,
#else
unsigned int numTiles,
#endif
......@@ -62,7 +63,7 @@ __kernel void computeBornSum(
real4 posq2 = (real4) (localData[j].x, localData[j].y, localData[j].z, localData[j].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = dot(delta.xyz, delta.xyz);
#ifdef USE_CUTOFF
......@@ -111,7 +112,7 @@ __kernel void computeBornSum(
real4 posq2 = (real4) (localData[j].x, localData[j].y, localData[j].z, localData[j].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
#ifdef USE_CUTOFF
......@@ -253,14 +254,13 @@ __kernel void computeBornSum(
real4 blockCenterX = blockCenter[x];
for (unsigned int tgx = 0; tgx < TILE_SIZE; tgx++) {
localData[tgx].x -= floor((localData[tgx].x-blockCenterX.x)*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
localData[tgx].y -= floor((localData[tgx].y-blockCenterX.y)*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
localData[tgx].z -= floor((localData[tgx].z-blockCenterX.z)*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
APPLY_PERIODIC_TO_POS_WITH_CENTER(localData[tgx], blockCenterX)
}
for (unsigned int tgx = 0; tgx < TILE_SIZE; tgx++) {
unsigned int atom1 = x*TILE_SIZE+tgx;
real bornSum = 0;
real4 posq1 = posq[atom1];
APPLY_PERIODIC_TO_POS_WITH_CENTER(posq1, blockCenterX)
float2 params1 = global_params[atom1];
for (unsigned int j = 0; j < TILE_SIZE; j++) {
real4 posq2 = (real4) (localData[j].x, localData[j].y, localData[j].z, localData[j].q);
......@@ -321,7 +321,7 @@ __kernel void computeBornSum(
real4 posq2 = (real4) (localData[j].x, localData[j].y, localData[j].z, localData[j].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
int atom2 = atomIndices[j];
......@@ -412,7 +412,8 @@ __kernel void computeGBSAForce1(
__global real* restrict energyBuffer, __global const real4* restrict posq, __global const real* restrict global_bornRadii,
#ifdef USE_CUTOFF
__global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize,
unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, __global const real4* restrict blockCenter,
__global const real4* restrict blockSize, __global const int* restrict interactingAtoms,
#else
unsigned int numTiles,
#endif
......@@ -452,7 +453,7 @@ __kernel void computeGBSAForce1(
real4 posq2 = (real4) (localData[j].x, localData[j].y, localData[j].z, localData[j].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
#ifdef USE_CUTOFF
......@@ -516,7 +517,7 @@ __kernel void computeGBSAForce1(
real4 posq2 = (real4) (localData[j].x, localData[j].y, localData[j].z, localData[j].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
#ifdef USE_CUTOFF
......@@ -669,15 +670,13 @@ __kernel void computeGBSAForce1(
real4 blockCenterX = blockCenter[x];
for (unsigned int tgx = 0; tgx < TILE_SIZE; tgx++) {
localData[tgx].x -= floor((localData[tgx].x-blockCenterX.x)*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
localData[tgx].y -= floor((localData[tgx].y-blockCenterX.y)*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
localData[tgx].z -= floor((localData[tgx].z-blockCenterX.z)*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
APPLY_PERIODIC_TO_POS_WITH_CENTER(localData[tgx], blockCenterX)
}
for (unsigned int tgx = 0; tgx < TILE_SIZE; tgx++) {
unsigned int atom1 = x*TILE_SIZE+tgx;
real4 force = 0;
real4 posq1 = posq[atom1];
posq1.xyz -= floor((posq1.xyz-blockCenterX.xyz)*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_POS_WITH_CENTER(posq1, blockCenterX)
float bornRadius1 = global_bornRadii[atom1];
for (unsigned int j = 0; j < TILE_SIZE; j++) {
real4 posq2 = (real4) (localData[j].x, localData[j].y, localData[j].z, localData[j].q);
......@@ -740,7 +739,7 @@ __kernel void computeGBSAForce1(
real4 posq2 = (real4) (localData[j].x, localData[j].y, localData[j].z, localData[j].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
int atom2 = atomIndices[j];
......
platforms/opencl/src/kernels/pme.cl
View file @ b21e3182
......@@ -138,35 +138,34 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
zindex -= (zindex >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
int index = xindex*GRID_SIZE_Y*GRID_SIZE_Z + yindex*GRID_SIZE_Z + zindex;
real add = pos.w*data[ix].x*data[iy].y*data[iz].z;
#ifdef USE_DOUBLE_PRECISION
atom_add(&pmeGrid[2*index], (long) (add*0x100000000));
#ifdef USE_ALTERNATE_MEMORY_ACCESS_PATTERN
// On Nvidia devices (at least Maxwell anyway), this split ordering produces much higher performance. Why?
// I have no idea! And of course on AMD it produces slower performance. GPUs are not meant to be understood.
atom_add(&pmeGrid[index%2 == 0 ? index/2 : (index+GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z)/2], (long) (add*0x100000000));
#else
atom_add(&pmeGrid[index], (long) (add*0x100000000));
#endif
}
}
}
}
}
__kernel void finishSpreadCharge(__global long* restrict pmeGrid) {
__global real2* realGrid = (__global real2*) pmeGrid;
__kernel void finishSpreadCharge(__global long* restrict fixedGrid, __global real* restrict realGrid) {
const unsigned int gridSize = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z;
real scale = EPSILON_FACTOR/(real) 0x100000000;
for (int index = get_global_id(0); index < gridSize; index += get_global_size(0)) {
#ifdef USE_DOUBLE_PRECISION
long value = pmeGrid[2*index];
#ifdef USE_ALTERNATE_MEMORY_ACCESS_PATTERN
long value = fixedGrid[index%2 == 0 ? index/2 : (index+gridSize)/2];
#else
long value = pmeGrid[index];
long value = fixedGrid[index];
#endif
real2 realValue = (real2) ((real) (value*scale), 0);
realGrid[index] = realValue;
realGrid[index] = (real) (value*scale);
}
}
#elif defined(DEVICE_IS_CPU)
__kernel void gridSpreadCharge(__global const real4* restrict posq, __global const int2* restrict pmeAtomGridIndex, __global const int* restrict pmeAtomRange,
__global real2* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
__global real* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
const int firstx = get_global_id(0)*GRID_SIZE_X/get_global_size(0);
const int lastx = (get_global_id(0)+1)*GRID_SIZE_X/get_global_size(0);
if (firstx == lastx)
......@@ -230,7 +229,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
int zindex = gridIndex.z+iz;
zindex -= (zindex >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
int index = xindex*GRID_SIZE_Y*GRID_SIZE_Z + yindex*GRID_SIZE_Z + zindex;
pmeGrid[index].x += EPSILON_FACTOR*pos.w*data[ix].x*data[iy].y*data[iz].z;
pmeGrid[index] += EPSILON_FACTOR*pos.w*data[ix].x*data[iy].y*data[iz].z;
}
}
}
......@@ -238,7 +237,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
}
#else
__kernel void gridSpreadCharge(__global const real4* restrict posq, __global const int2* restrict pmeAtomGridIndex, __global const int* restrict pmeAtomRange,
__global real2* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta) {
__global real* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta) {
unsigned int numGridPoints = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z;
for (int gridIndex = get_global_id(0); gridIndex < numGridPoints; gridIndex += get_global_size(0)) {
// Compute the charge on a grid point.
......@@ -290,22 +289,23 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
}
}
}
pmeGrid[gridIndex] = (real2) (result*EPSILON_FACTOR, 0);
pmeGrid[gridIndex] = result*EPSILON_FACTOR;
}
}
#endif
__kernel void reciprocalConvolution(__global real2* restrict pmeGrid, __global real* restrict energyBuffer, __global const real* restrict pmeBsplineModuliX,
__global const real* restrict pmeBsplineModuliY, __global const real* restrict pmeBsplineModuliZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ, real recipScaleFactor) {
const unsigned int gridSize = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z;
real energy = 0.0f;
__kernel void reciprocalConvolution(__global real2* restrict pmeGrid, __global const real* restrict pmeBsplineModuliX,
__global const real* restrict pmeBsplineModuliY, __global const real* restrict pmeBsplineModuliZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
// R2C stores into a half complex matrix where the last dimension is cut by half
const unsigned int gridSize = GRID_SIZE_X*GRID_SIZE_Y*(GRID_SIZE_Z/2+1);
const real recipScaleFactor = (1.0f/M_PI)*recipBoxVecX.x*recipBoxVecY.y*recipBoxVecZ.z;
for (int index = get_global_id(0); index < gridSize; index += get_global_size(0)) {
int kx = index/(GRID_SIZE_Y*GRID_SIZE_Z);
int remainder = index-kx*GRID_SIZE_Y*GRID_SIZE_Z;
int ky = remainder/GRID_SIZE_Z;
int kz = remainder-ky*GRID_SIZE_Z;
if (kx == 0 && ky == 0 && kz == 0)
continue;
// real indices
int kx = index/(GRID_SIZE_Y*(GRID_SIZE_Z/2+1));
int remainder = index-kx*GRID_SIZE_Y*(GRID_SIZE_Z/2+1);
int ky = remainder/(GRID_SIZE_Z/2+1);
int kz = remainder-ky*(GRID_SIZE_Z/2+1);
int mx = (kx < (GRID_SIZE_X+1)/2) ? kx : (kx-GRID_SIZE_X);
int my = (ky < (GRID_SIZE_Y+1)/2) ? ky : (ky-GRID_SIZE_Y);
int mz = (kz < (GRID_SIZE_Z+1)/2) ? kz : (kz-GRID_SIZE_Z);
......@@ -319,13 +319,53 @@ __kernel void reciprocalConvolution(__global real2* restrict pmeGrid, __global r
real m2 = mhx*mhx+mhy*mhy+mhz*mhz;
real denom = m2*bx*by*bz;
real eterm = recipScaleFactor*EXP(-RECIP_EXP_FACTOR*m2)/denom;
if (kx != 0 || ky != 0 || kz != 0) {
pmeGrid[index] = (real2) (grid.x*eterm, grid.y*eterm);
}
}
}
__kernel void gridEvaluateEnergy(__global real2* restrict pmeGrid, __global real* restrict energyBuffer,
__global const real* restrict pmeBsplineModuliX, __global const real* restrict pmeBsplineModuliY, __global const real* restrict pmeBsplineModuliZ,
real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
// R2C stores into a half complex matrix where the last dimension is cut by half
const unsigned int gridSize = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z;
const real recipScaleFactor = (1.0f/M_PI)*recipBoxVecX.x*recipBoxVecY.y*recipBoxVecZ.z;
real energy = 0;
for (int index = get_global_id(0); index < gridSize; index += get_global_size(0)) {
// real indices
int kx = index/(GRID_SIZE_Y*(GRID_SIZE_Z));
int remainder = index-kx*GRID_SIZE_Y*(GRID_SIZE_Z);
int ky = remainder/(GRID_SIZE_Z);
int kz = remainder-ky*(GRID_SIZE_Z);
int mx = (kx < (GRID_SIZE_X+1)/2) ? kx : (kx-GRID_SIZE_X);
int my = (ky < (GRID_SIZE_Y+1)/2) ? ky : (ky-GRID_SIZE_Y);
int mz = (kz < (GRID_SIZE_Z+1)/2) ? kz : (kz-GRID_SIZE_Z);
real mhx = mx*recipBoxVecX.x;
real mhy = mx*recipBoxVecY.x+my*recipBoxVecY.y;
real mhz = mx*recipBoxVecZ.x+my*recipBoxVecZ.y+mz*recipBoxVecZ.z;
real m2 = mhx*mhx+mhy*mhy+mhz*mhz;
real bx = pmeBsplineModuliX[kx];
real by = pmeBsplineModuliY[ky];
real bz = pmeBsplineModuliZ[kz];
real denom = m2*bx*by*bz;
real eterm = recipScaleFactor*EXP(-RECIP_EXP_FACTOR*m2)/denom;
if (kz >= (GRID_SIZE_Z/2+1)) {
kx = ((kx == 0) ? kx : GRID_SIZE_X-kx);
ky = ((ky == 0) ? ky : GRID_SIZE_Y-ky);
kz = GRID_SIZE_Z-kz;
}
int indexInHalfComplexGrid = kz + ky*(GRID_SIZE_Z/2+1)+kx*(GRID_SIZE_Y*(GRID_SIZE_Z/2+1));
real2 grid = pmeGrid[indexInHalfComplexGrid];
if (kx != 0 || ky != 0 || kz != 0) {
energy += eterm*(grid.x*grid.x + grid.y*grid.y);
}
}
energyBuffer[get_global_id(0)] += 0.5f*energy;
}
__kernel void gridInterpolateForce(__global const real4* restrict posq, __global real4* restrict forceBuffers, __global const real2* restrict pmeGrid,
__kernel void gridInterpolateForce(__global const real4* restrict posq, __global real4* restrict forceBuffers, __global const real* restrict pmeGrid,
real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ, __global int2* restrict pmeAtomGridIndex) {
const real4 scale = 1/(real) (PME_ORDER-1);
real4 data[PME_ORDER];
......@@ -385,7 +425,7 @@ __kernel void gridInterpolateForce(__global const real4* restrict posq, __global
int zindex = gridIndex.z+iz;
zindex -= (zindex >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
int index = xindex*GRID_SIZE_Y*GRID_SIZE_Z + yindex*GRID_SIZE_Z + zindex;
real gridvalue = pmeGrid[index].x;
real gridvalue = pmeGrid[index];
force.x += ddata[ix].x*data[iy].y*data[iz].z*gridvalue;
force.y += data[ix].x*ddata[iy].y*data[iz].z*gridvalue;
force.z += data[ix].x*data[iy].y*ddata[iz].z*gridvalue;
......
platforms/opencl/src/kernels/sort.cl
View file @ b21e3182
......@@ -109,13 +109,7 @@ __kernel void assignElementsToBuckets(__global const DATA_TYPE* restrict data, u
float maxValue = (float) (range[1]);
float bucketWidth = (maxValue-minValue)/numBuckets;
for (uint index = get_global_id(0); index < length; index += get_global_size(0)) {
#if defined(MAC_AMD_WORKAROUND) && VALUE_IS_INT2
__global int* d = (__global int*) data;
int2 element = (int2) (d[2*index], d[2*index+1]);
float key = (float) getValue(element);
#else
float key = (float) getValue(data[index]);
#endif
uint bucketIndex = min((uint) ((key-minValue)/bucketWidth), numBuckets-1);
offsetInBucket[index] = atom_inc(&bucketOffset[bucketIndex]);
bucketOfElement[index] = bucketIndex;
......
platforms/opencl/tests/TestOpenCLFFT.cpp
View file @ b21e3182
......@@ -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) 2011 Stanford University and the Authors. *
* Portions copyright (c) 2011-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -51,7 +51,7 @@ using namespace std;
static OpenCLPlatform platform;
template <class Real2>
void testTransform() {
void testTransform(bool realToComplex, int xsize, int ysize, int zsize) {
System system;
system.addParticle(0.0);
OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"), "false");
......@@ -59,7 +59,6 @@ void testTransform() {
context.initialize();
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
int xsize = 28, ysize = 25, zsize = 30;
vector<Real2> original(xsize*ysize*zsize);
vector<t_complex> reference(original.size());
for (int i = 0; i < (int) original.size(); i++) {
......@@ -67,10 +66,16 @@ void testTransform() {
original[i] = value;
reference[i] = t_complex(value.x, value.y);
}
for (int i = 0; i < (int) reference.size(); i++) {
if (realToComplex)
reference[i] = t_complex(i%2 == 0 ? original[i/2].x : original[i/2].y, 0);
else
reference[i] = t_complex(original[i].x, original[i].y);
}
OpenCLArray grid1(context, original.size(), sizeof(Real2), "grid1");
OpenCLArray grid2(context, original.size(), sizeof(Real2), "grid2");
grid1.upload(original);
OpenCLFFT3D fft(context, xsize, ysize, zsize);
OpenCLFFT3D fft(context, xsize, ysize, zsize, realToComplex);
// Perform a forward FFT, then verify the result is correct.
......@@ -80,9 +85,14 @@ void testTransform() {
fftpack_t plan;
fftpack_init_3d(&plan, xsize, ysize, zsize);
fftpack_exec_3d(plan, FFTPACK_FORWARD, &reference[0], &reference[0]);
for (int i = 0; i < (int) result.size(); ++i) {
ASSERT_EQUAL_TOL(reference[i].re, result[i].x, 1e-3);
ASSERT_EQUAL_TOL(reference[i].im, result[i].y, 1e-3);
int outputZSize = (realToComplex ? zsize/2+1 : zsize);
for (int x = 0; x < xsize; x++)
for (int y = 0; y < ysize; y++)
for (int z = 0; z < outputZSize; z++) {
int index1 = x*ysize*zsize + y*zsize + z;
int index2 = x*ysize*outputZSize + y*outputZSize + z;
ASSERT_EQUAL_TOL(reference[index1].re, result[index2].x, 1e-3);
ASSERT_EQUAL_TOL(reference[index1].im, result[index2].y, 1e-3);
}
fftpack_destroy(plan);
......@@ -91,7 +101,8 @@ void testTransform() {
fft.execFFT(grid2, grid1, false);
grid1.download(result);
double scale = 1.0/(xsize*ysize*zsize);
for (int i = 0; i < (int) result.size(); ++i) {
int valuesToCheck = (realToComplex ? original.size()/2 : original.size());
for (int i = 0; i < valuesToCheck; ++i) {
ASSERT_EQUAL_TOL(original[i].x, scale*result[i].x, 1e-4);
ASSERT_EQUAL_TOL(original[i].y, scale*result[i].y, 1e-4);
}
......@@ -101,10 +112,20 @@ int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
if (platform.getPropertyDefaultValue("OpenCLPrecision") == "double")
testTransform<mm_double2>();
else
testTransform<mm_float2>();
if (platform.getPropertyDefaultValue("OpenCLPrecision") == "double") {
testTransform<mm_double2>(false, 28, 25, 30);
testTransform<mm_double2>(true, 28, 25, 25);
testTransform<mm_double2>(true, 25, 28, 25);
testTransform<mm_double2>(true, 25, 25, 28);
testTransform<mm_double2>(true, 21, 25, 27);
}
else {
testTransform<mm_float2>(false, 28, 25, 30);
testTransform<mm_float2>(true, 28, 25, 25);
testTransform<mm_float2>(true, 25, 28, 25);
testTransform<mm_float2>(true, 25, 25, 28);
testTransform<mm_float2>(true, 21, 25, 27);
}
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/reference/src/SimTKReference/ObcParameters.cpp
View file @ b21e3182
......@@ -382,9 +382,9 @@ void ObcParameters::setPeriodic(OpenMM::RealVec* vectors) {
assert(_cutoff);
assert(boxSize[0][0] >= 2.0*_cutoffDistance);
assert(boxSize[1][1] >= 2.0*_cutoffDistance);
assert(boxSize[2][2] >= 2.0*_cutoffDistance);
assert(vectors[0][0] >= 2.0*_cutoffDistance);
assert(vectors[1][1] >= 2.0*_cutoffDistance);
assert(vectors[2][2] >= 2.0*_cutoffDistance);
_periodic = true;
_periodicBoxVectors[0] = vectors[0];
......
tests/TestVectorize.cpp
View file @ b21e3182
......@@ -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) 2014 Stanford University and the Authors. *
* Portions copyright (c) 2014-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -148,6 +148,7 @@ void testMathFunctions() {
ASSERT_VEC4_EQUAL(min(f1, f2), 0.4, 1.2, -1.2, -5.0);
ASSERT_VEC4_EQUAL(max(f1, f2), 1.1, 1.9, 1.3, -3.8);
ASSERT_VEC4_EQUAL(sqrt(fvec4(1.5, 3.1, 4.0, 15.0)), sqrt(1.5), sqrt(3.1), sqrt(4.0), sqrt(15.0));
ASSERT_VEC4_EQUAL(rsqrt(fvec4(1.5, 3.1, 4.0, 15.0)), 1.0/sqrt(1.5), 1.0/sqrt(3.1), 1.0/sqrt(4.0), 1.0/sqrt(15.0));
ASSERT_EQUAL_TOL(f1[0]*f2[0]+f1[1]*f2[1]+f1[2]*f2[2], dot3(f1, f2), 1e-6);
ASSERT_EQUAL_TOL(f1[0]*f2[0]+f1[1]*f2[1]+f1[2]*f2[2]+f1[3]*f2[3], dot4(f1, f2), 1e-6);
ASSERT(any(f1 > 0.5));
......
wrappers/python/src/swig_doxygen/swig_lib/python/extend.i
View file @ b21e3182
......@@ -417,7 +417,6 @@ Parameters:
@staticmethod
def deserialize(inputString):
"""Reconstruct an object that has been serialized as XML."""
# Look for the first tag to figure out what type of object it is.
import re
match = re.search("<([^?]\S*)", inputString)
if match is None:
......
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