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Commit 1b9ab82b authored by Rossen Apostolov's avatar Rossen Apostolov
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Real space Ewald (direct summation) is now in kCalculateCDLJForces.h,... 

Real space Ewald (direct summation) is now in kCalculateCDLJForces.h, reciprocal summation is done in a separate kernel
parent d3b512ad
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Showing with 295 additions and 9 deletions
platforms/cuda/src/kernels/kCalculateCDLJForces.cu
View file @ 1b9ab82b
......@@ -108,7 +108,23 @@ void GetCalculateCDLJForcesSim(gpuContext gpu)
#include "kCalculateCDLJForces.h"
// Include version of the kernel with Ewald method
#include "kCalculateEwald.h"
// Real Space Ewald uses almost the same kernels as Periodic
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_PERIODIC
#define USE_EWALD
#define METHOD_NAME(a, b) a##EwaldDirect##b
#include "kCalculateCDLJForces.h"
#include "kFindInteractingBlocks.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##EwaldDirectByWarp##b
#include "kCalculateCDLJForces.h"
// Reciprocal Space Ewald summation is in a separate kernel
//#include "kCalculateEwaldReciprocal.h"
__global__ extern void kCalculateCDLJCutoffForces_12_kernel();
......@@ -177,10 +193,10 @@ void kCalculateCDLJForces(gpuContext gpu)
LAUNCHERROR("kCalculateCDLJPeriodicForces");
break;
case EWALD:
kFindBlockBoundsPeriodic_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
LAUNCHERROR("kFindBlockBoundsPeriodic");
kFindBlocksWithInteractionsPeriodic_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
LAUNCHERROR("kFindBlocksWithInteractionsPeriodic");
kFindBlockBoundsEwaldDirect_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
LAUNCHERROR("kFindBlockBoundsEwaldDirect");
kFindBlocksWithInteractionsEwaldDirect_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
LAUNCHERROR("kFindBlocksWithInteractionsEwaldDirect");
result = cudppCompact(gpu->cudpp, gpu->sim.pInteractingWorkUnit, gpu->sim.pInteractionCount,
gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits);
if (result != CUDPP_SUCCESS)
......@@ -190,15 +206,15 @@ void kCalculateCDLJForces(gpuContext gpu)
}
gpu->psInteractionCount->Download();
numWithInteractions = gpu->psInteractionCount->_pSysData[0];
kFindInteractionsWithinBlocksPeriodic_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kFindInteractionsWithinBlocksEwaldDirect_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, numWithInteractions);
if (gpu->bOutputBufferPerWarp)
kCalculateCDLJPeriodicByWarpForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateCDLJEwaldDirectByWarpForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, numWithInteractions);
else
kCalculateCDLJEwaldForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
kCalculateCDLJEwaldDirectForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit, numWithInteractions);
LAUNCHERROR("kCalculateCDLJPeriodicForces");
LAUNCHERROR("kCalculateCDLJEwaldDirectForces");
}
}
platforms/cuda/src/kernels/kCalculateCDLJForces.h
View file @ 1b9ab82b
......@@ -46,6 +46,12 @@ __global__ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUni
float3* tempBuffer = (float3*) &sA[cSim.nonbond_threads_per_block];
#endif
#ifdef USE_EWALD
float alphaEwald = 3.123413;
float PI = 3.14159265358979323846f;
float SQRT_PI = sqrt(PI);
#endif
unsigned int lasty = 0xFFFFFFFF;
while (pos < end)
{
......@@ -108,7 +114,13 @@ __global__ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUni
eps = a.y * psA[j].eps;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = alphaEwald * r;
dEdR += apos.w * psA[tj].q * invR * invR * invR * (erfc(alphaR) + 2.0 * alphaR * exp ( - alphaR * alphaR) / SQRT_PI );
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
#endif
#else
dEdR += apos.w * psA[j].q * invR;
#endif
......@@ -151,7 +163,13 @@ __global__ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUni
eps = a.y * psA[j].eps;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = alphaEwald * r;
dEdR += apos.w * psA[tj].q * invR * invR * invR * (erfc(alphaR) + 2.0 * alphaR * exp ( - alphaR * alphaR) / SQRT_PI );
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
#endif
#else
dEdR += apos.w * psA[j].q * invR;
#endif
......@@ -243,7 +261,13 @@ __global__ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUni
eps = a.y * psA[tj].eps;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = alphaEwald * r;
dEdR += apos.w * psA[tj].q * invR * invR * invR * (erfc(alphaR) + 2.0 * alphaR * exp ( - alphaR * alphaR) / SQRT_PI );
#else
dEdR += apos.w * psA[tj].q * (invR - 2.0f * cSim.reactionFieldK * r2);
#endif
#else
dEdR += apos.w * psA[tj].q * invR;
#endif
......@@ -292,7 +316,13 @@ __global__ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUni
eps = a.y * psA[j].eps;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = alphaEwald * r;
dEdR += apos.w * psA[tj].q * invR * invR * invR * (erfc(alphaR) + 2.0 * alphaR * exp ( - alphaR * alphaR) / SQRT_PI );
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
#endif
#else
dEdR += apos.w * psA[j].q * invR;
#endif
......@@ -377,7 +407,13 @@ __global__ void METHOD_NAME(kCalculateCDLJ, Forces_kernel)(unsigned int* workUni
eps = a.y * psA[tj].eps;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = alphaEwald * r;
dEdR += apos.w * psA[tj].q * invR * invR * invR * (erfc(alphaR) + 2.0 * alphaR * exp ( - alphaR * alphaR) / SQRT_PI );
#else
dEdR += apos.w * psA[tj].q * (invR - 2.0f * cSim.reactionFieldK * r2);
#endif
#else
dEdR += apos.w * psA[tj].q * invR;
#endif
......
platforms/cuda/src/kernels/kCalculateEwald.h → platforms/cuda/src/kernels/kCalculateEwaldReciprocal.h
View file @ 1b9ab82b
......@@ -71,17 +71,6 @@ __device__ cuComplex FloatComplexMul(float r, cuComplex a)
__global__ void kCalculateCDLJEwaldForces_kernel(unsigned int* workUnit, int numWorkUnits)
{
/*
extern __shared__ Atom sA[];
unsigned int totalWarps = cSim.nonbond_blocks*cSim.nonbond_threads_per_block/GRID;
unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID;
int pos = warp*numWorkUnits/totalWarps;
int end = (warp+1)*numWorkUnits/totalWarps;
//###########################################################################
// EWALD RECIP SPACE
//###########################################################################
// *******************************************************************
float alphaEwald = 3.123413f;
......@@ -110,32 +99,40 @@ __global__ void kCalculateCDLJEwaldForces_kernel(unsigned int* workUnit, int nu
unsigned int numRz = 60+1;
const int kmax = 61;
cuComplex eir[kmax][numberOfAtoms][3];
cuComplex tab_xy[numberOfAtoms];
cuComplex tab_qxyz[numberOfAtoms];
unsigned int pos = threadIdx.x + blockIdx.x * blockDim.x;
cuComplex eir[kmax][cSim.atoms][3];
cuComplex tab_xy[cSim.atoms];
cuComplex tab_qxyz[cSim.atoms];
for(unsigned int i = 0; i < numberOfAtoms; i++) {
while (pos < cSim.atoms)
{
float4 apos = cSim.pPosq[pos];
for(unsigned int m = 0; (m < 3); m++) {
eir[0][i][m].x = 1;
eir[0][i][m].y = 0;
eir[0][pos][m].x = 1;
eir[0][pos][m].y = 0;
}
eir[1][i][0].x = cos(apos.x*recipBoxSizeX);
eir[1][i][0].y = sin(apos.x*recipBoxSizeX);
eir[1][pos][0].x = cos(apos.x*recipBoxSizeX);
eir[1][pos][0].y = sin(apos.x*recipBoxSizeX);
eir[1][i][1].x = cos(apos.y*recipBoxSizeY);
eir[1][i][1].y = sin(apos.y*recipBoxSizeY);
eir[1][pos][1].x = cos(apos.y*recipBoxSizeY);
eir[1][pos][1].y = sin(apos.y*recipBoxSizeY);
eir[1][i][2].x = cos(apos.z*recipBoxSizeZ);
eir[1][i][2].y = sin(apos.z*recipBoxSizeZ);
eir[1][pos][2].x = cos(apos.z*recipBoxSizeZ);
eir[1][pos][2].y = sin(apos.z*recipBoxSizeZ);
for(unsigned int j=2; (j<kmax); j++) {
for(unsigned int m=0; (m<3); m++) {
eir[j][i][m] = ComplexMul (eir[j-1][i][m] , eir[1][i][m]);
eir[j][pos][m] = ComplexMul (eir[j-1][pos][m] , eir[1][pos][m]);
}
}
pos += blockDim.x * gridDim.x;
}
// *******************************************************************
......@@ -153,14 +150,18 @@ __global__ void kCalculateCDLJEwaldForces_kernel(unsigned int* workUnit, int nu
float ky = ry * recipBoxSizeY;
if(ry >= 0) {
for(int n = 0; n < numberOfAtoms; n++) {
tab_xy[n] = ComplexMul (eir[rx][n][0] , eir[ry][n][1]);
while (pos < cSim.atoms)
{
tab_xy[pos] = ComplexMul (eir[rx][pos][0] , eir[ry][pos][1]);
pos += blockDim.x * gridDim.x;
}
}
else {
for(int n = 0; n < numberOfAtoms; n++) {
tab_xy[n]= ComplexConjMul (eir[rx][n][0] , (eir[-ry][n][1]));
while (pos < cSim.atoms)
{
tab_xy[pos]= ComplexConjMul (eir[rx][pos][0] , (eir[-ry][pos][1]));
pos += blockDim.x * gridDim.x;
}
}
......@@ -173,34 +174,47 @@ __global__ void kCalculateCDLJEwaldForces_kernel(unsigned int* workUnit, int nu
if( rz >= 0) {
for( int n = 0; n < numberOfAtoms; n++) {
tab_qxyz[n] = FloatComplexMul ( Charge[n] * ComplexMul (tab_xy[n] , eir[rz][n][2]));
while (pos < cSim.atoms)
{
float4 apos = cSim.pPosq[pos];
apos.w *= cSim.epsfac;
tab_qxyz[pos] = FloatComplexMul ( apos.w * ComplexMul (tab_xy[pos] , eir[rz][pos][2]));
pos += blockDim.x * gridDim.x;
}
}
else {
for( int n = 0; n < numberOfAtoms; n++) {
tab_qxyz[n] = FloatComplexMul( Charge[n] * ComplexConjMul (tab_xy[n] , conj(eir[-rz][n][2])) );
while (pos < cSim.atoms)
{
float4 apos = cSim.pPosq[pos];
apos.w *= cSim.epsfac;
tab_qxyz[pos] = FloatComplexMul( apos.w * ComplexConjMul (tab_xy[pos] , conj(eir[-rz][pos][2])) );
pos += blockDim.x * gridDim.x;
}
}
float cs = 0.0f;
float ss = 0.0f;
for( int n = 0; n < numberOfAtoms; n++) {
cs += tab_qxyz[n].x;
ss += tab_qxyz[n].y;
while (pos < cSim.atoms)
{
cs += tab_qxyz[pos].x;
ss += tab_qxyz[pos].y;
pos += blockDim.x * gridDim.x;
}
recipEnergy += ak * ( cs * cs + ss * ss);
float vir = akv * ( cs * cs + ss * ss);
for(int n = 0; n < numberOfAtoms; n++) {
float force = ak * (cs * tab_qxyz[n].y - ss * tab_qxyz[n].x);
forces[n][0] += 2.0 * recipCoeff * force * kx ;
forces[n][1] += 2.0 * recipCoeff * force * ky ;
forces[n][2] += 2.0 * recipCoeff * force * kz ;
while (pos < cSim.atoms)
{
float4 force = cSim.pForce4[pos];
float dEdR = ak * (cs * tab_qxyz[pos].y - ss * tab_qxyz[pos].x);
force.x += 2.0 * recipCoeff * dEdR * kx ;
force.y += 2.0 * recipCoeff * dEdR * ky ;
force.z += 2.0 * recipCoeff * dEdR * kz ;
}
lowrz = 1 - numRz;
......@@ -217,120 +231,4 @@ __global__ void kCalculateCDLJEwaldForces_kernel(unsigned int* workUnit, int nu
// END EWALD RECIP SPACE
//###########################################################################
while (pos < end)
{
// Extract cell coordinates from appropriate work unit
unsigned int x = workUnit[pos];
unsigned int y = ((x >> 2) & 0x7fff) << GRIDBITS;
bool bExclusionFlag = (x & 0x1);
x = (x >> 17) << GRIDBITS;
float4 apos; // Local atom x, y, z, q
float3 af; // Local atom fx, fy, fz
float dx;
float dy;
float dz;
float r2;
float r;
float invR;
float sig;
float sig2;
float sig6;
float eps;
float dEdR;
unsigned int tgx = threadIdx.x & (GRID - 1);
unsigned int tbx = threadIdx.x - tgx;
int tj = tgx;
Atom* psA = &sA[tbx];
unsigned int i = x + tgx;
apos = cSim.pPosq[i];
float2 a = cSim.pAttr[i];
af.x = 0.0f;
af.y = 0.0f;
af.z = 0.0f;
int j = y + tgx;
float4 temp = cSim.pPosq[j];
float2 temp1 = cSim.pAttr[j];
sA[threadIdx.x].x = temp.x;
sA[threadIdx.x].y = temp.y;
sA[threadIdx.x].z = temp.z;
sA[threadIdx.x].q = temp.w;
sA[threadIdx.x].sig = temp1.x;
sA[threadIdx.x].eps = temp1.y;
sA[threadIdx.x].fx = 0.0f;
sA[threadIdx.x].fy = 0.0f;
sA[threadIdx.x].fz = 0.0f;
apos.w *= cSim.epsfac;
// Read fixed atom data into registers and GRF
unsigned int excl = cSim.pExclusion[x * cSim.exclusionStride + y + tgx];
excl = (excl >> tgx) | (excl << (GRID - tgx));
for (unsigned int j = 0; j < GRID; j++)
{
dx = psA[tj].x - apos.x;
dy = psA[tj].y - apos.y;
dz = psA[tj].z - apos.z;
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
r2 = dx * dx + dy * dy + dz * dz;
r = sqrt(r2);
invR = 1.0f / sqrt(r2);
sig = a.x + psA[tj].sig;
sig2 = invR * sig;
sig2 *= sig2;
sig6 = sig2 * sig2 * sig2;
eps = a.y * psA[tj].eps;
// ##### LJ
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
// ##### SHORT RANGE EWALD
float alphaR = alphaEwald * r;
dEdR += apos.w * psA[tj].q * invR * invR * invR * (erfc(alphaR) + 2.0 * alphaR * exp ( - alphaR * alphaR) / SQRT_PI );
if (!(excl & 0x1) || r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
}
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
af.x -= dx;
af.y -= dy;
af.z -= dz;
psA[tj].fx += dx;
psA[tj].fy += dy;
psA[tj].fz += dz;
excl >>= 1;
tj = (tj + 1) & (GRID - 1);
}
// Write results
float4 of;
of.x = af.x;
of.y = af.y;
of.z = af.z;
of.w = 0.0f;
int offset = x + tgx + (y >> GRIDBITS) * cSim.stride;
cSim.pForce4a[offset] = of;
of.x = sA[threadIdx.x].fx;
of.y = sA[threadIdx.x].fy;
of.z = sA[threadIdx.x].fz;
offset = y + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pForce4a[offset] = of;
pos++;
}
*/
}
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