KERNEL void findAtomGridIndex(GLOBAL const real4* RESTRICT posq, GLOBAL int2* RESTRICT pmeAtomGridIndex, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ #ifndef SUPPORTS_64_BIT_ATOMICS , GLOBAL real4* RESTRICT pmeBsplineTheta, LOCAL real4* RESTRICT bsplinesCache, #ifdef CHARGE_FROM_SIGEPS GLOBAL const float2* RESTRICT sigmaEpsilon #else GLOBAL const real* RESTRICT charges #endif #endif ) { // Compute the index of the grid point each atom is associated with. for (int atom = GLOBAL_ID; atom < NUM_ATOMS; atom += GLOBAL_SIZE) { real4 pos = posq[atom]; APPLY_PERIODIC_TO_POS(pos) real3 t = make_real3(pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x, pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y, pos.z*recipBoxVecZ.z); t.x = (t.x-floor(t.x))*GRID_SIZE_X; t.y = (t.y-floor(t.y))*GRID_SIZE_Y; t.z = (t.z-floor(t.z))*GRID_SIZE_Z; int3 gridIndex = make_int3(((int) t.x) % GRID_SIZE_X, ((int) t.y) % GRID_SIZE_Y, ((int) t.z) % GRID_SIZE_Z); pmeAtomGridIndex[atom] = make_int2(atom, gridIndex.x*GRID_SIZE_Y*GRID_SIZE_Z+gridIndex.y*GRID_SIZE_Z+gridIndex.z); #ifndef SUPPORTS_64_BIT_ATOMICS // Compute B-splines here for use in the charge spreading kernel. const real4 scale = 1/(real) (PME_ORDER-1); LOCAL real4* data = &bsplinesCache[LOCAL_ID*PME_ORDER]; real4 dr = (real4) (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; data[0] = 1.0f-dr; for (int j = 3; j < PME_ORDER; j++) { real div = RECIP(j-1.0f); data[j-1] = div*dr*data[j-2]; for (int k = 1; k < (j-1); k++) data[j-k-1] = div*((dr+make_real4(k))*data[j-k-2] + (-dr+make_real4(j-k))*data[j-k-1]); data[0] = div*(- dr+1.0f)*data[0]; } data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2]; for (int j = 1; j < (PME_ORDER-1); j++) data[PME_ORDER-j-1] = scale*((dr+make_real4(j))*data[PME_ORDER-j-2] + (-dr+make_real4(PME_ORDER-j))*data[PME_ORDER-j-1]); data[0] = scale*(-dr+1.0f)*data[0]; for (int j = 0; j < PME_ORDER; j++) { #ifdef CHARGE_FROM_SIGEPS const float2 sigEps = sigmaEpsilon[atom]; const real charge = 8*sigEps.x*sigEps.x*sigEps.x*sigEps.y; #else const real charge = CHARGE; #endif data[j].w = charge; // Storing the charge here improves cache coherency in the charge spreading kernel pmeBsplineTheta[atom+j*NUM_ATOMS] = data[j]; } #endif } } #ifdef SUPPORTS_64_BIT_ATOMICS #pragma OPENCL EXTENSION cl_khr_int64_base_atomics : enable #if defined(USE_HIP) && !defined(AMD_RDNA) LAUNCH_BOUNDS_EXACT(128, 1) #endif KERNEL void gridSpreadCharge(GLOBAL const real4* RESTRICT posq, #ifdef USE_FIXED_POINT_CHARGE_SPREADING GLOBAL mm_ulong* RESTRICT pmeGrid, #else GLOBAL real* RESTRICT pmeGrid, #endif real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ, GLOBAL const int2* RESTRICT pmeAtomGridIndex, #ifdef CHARGE_FROM_SIGEPS GLOBAL const float2* RESTRICT sigmaEpsilon #else GLOBAL const real* RESTRICT charges #endif ) { // HIP-TODO: Workaround for RDNA, remove it when the compiler issue is fixed #if defined(USE_HIP) (void)GLOBAL_ID; #endif // To improve memory efficiency, we divide indices along the z axis into // PME_ORDER blocks, where the data for each block is stored together. We // can ensure that all threads write to the same block at the same time, // which leads to better coalescing of writes. LOCAL int zindexTable[GRID_SIZE_Z+PME_ORDER]; int blockSize = (int) ceil(GRID_SIZE_Z/(real) PME_ORDER); for (int i = LOCAL_ID; i < GRID_SIZE_Z+PME_ORDER; i += LOCAL_SIZE) { int zindex = i % GRID_SIZE_Z; int block = zindex % PME_ORDER; zindexTable[i] = zindex/PME_ORDER + block*GRID_SIZE_X*GRID_SIZE_Y*blockSize; } SYNC_THREADS; // Process the atoms in spatially sorted order. This improves efficiency when writing // the grid values. real3 data[PME_ORDER]; const real scale = RECIP((real) (PME_ORDER-1)); for (int i = GLOBAL_ID; i < NUM_ATOMS; i += GLOBAL_SIZE) { int atom = pmeAtomGridIndex[i].x; real4 pos = posq[atom]; #ifdef CHARGE_FROM_SIGEPS const float2 sigEps = sigmaEpsilon[atom]; const real charge = 8*sigEps.x*sigEps.x*sigEps.x*sigEps.y; #else const real charge = (CHARGE)*EPSILON_FACTOR; #endif APPLY_PERIODIC_TO_POS(pos) real3 t = make_real3(pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x, pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y, pos.z*recipBoxVecZ.z); t.x = (t.x-floor(t.x))*GRID_SIZE_X; t.y = (t.y-floor(t.y))*GRID_SIZE_Y; t.z = (t.z-floor(t.z))*GRID_SIZE_Z; int3 gridIndex = make_int3(((int) t.x) % GRID_SIZE_X, ((int) t.y) % GRID_SIZE_Y, ((int) t.z) % GRID_SIZE_Z); if (charge == 0) continue; // Since we need the full set of thetas, it's faster to compute them here than load them // from global memory. real3 dr = make_real3(t.x-(int) t.x, t.y-(int) t.y, t.z-(int) t.z); data[PME_ORDER-1] = make_real3(0); data[1] = dr; data[0] = make_real3(1)-dr; for (int j = 3; j < PME_ORDER; j++) { real div = RECIP((real) (j-1)); data[j-1] = div*dr*data[j-2]; for (int k = 1; k < (j-1); k++) data[j-k-1] = div*((dr+make_real3(k))*data[j-k-2] + (make_real3(j-k)-dr)*data[j-k-1]); data[0] = div*(make_real3(1)-dr)*data[0]; } data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2]; for (int j = 1; j < (PME_ORDER-1); j++) data[PME_ORDER-j-1] = scale*((dr+make_real3(j))*data[PME_ORDER-j-2] + (make_real3(PME_ORDER-j)-dr)*data[PME_ORDER-j-1]); data[0] = scale*(make_real3(1)-dr)*data[0]; // Spread the charge from this atom onto each grid point. int izoffset = (PME_ORDER-(gridIndex.z%PME_ORDER)) % PME_ORDER; for (int ix = 0; ix < PME_ORDER; ix++) { int xbase = gridIndex.x+ix; xbase -= (xbase >= GRID_SIZE_X ? GRID_SIZE_X : 0); xbase = xbase*GRID_SIZE_Y; real dx = charge*data[ix].x; for (int iy = 0; iy < PME_ORDER; iy++) { int ybase = gridIndex.y+iy; ybase -= (ybase >= GRID_SIZE_Y ? GRID_SIZE_Y : 0); ybase = (xbase+ybase)*blockSize; real dxdy = dx*data[iy].y; for (int i = 0; i < PME_ORDER; i++) { int iz = (i+izoffset) % PME_ORDER; int zindex = gridIndex.z+iz; int index = ybase + zindexTable[zindex]; real add = dxdy*data[iz].z; #ifdef USE_FIXED_POINT_CHARGE_SPREADING ATOMIC_ADD(&pmeGrid[index], (mm_ulong) realToFixedPoint(add)); #else ATOMIC_ADD(&pmeGrid[index], add); #endif } } } } } KERNEL void finishSpreadCharge( #ifdef USE_FIXED_POINT_CHARGE_SPREADING GLOBAL const mm_long* RESTRICT grid1, #else GLOBAL const real* RESTRICT grid1, #endif GLOBAL real* RESTRICT grid2) { // HIP-TODO: Workaround for RDNA, remove it when the compiler issue is fixed #if defined(USE_HIP) (void)GLOBAL_ID; #endif // During charge spreading, we shuffled the order of indices along the z // axis to make memory access more efficient. We now need to unshuffle // them. If the values were accumulated as fixed point, we also need to // convert them to floating point. LOCAL int zindexTable[GRID_SIZE_Z]; int blockSize = (int) ceil(GRID_SIZE_Z/(real) PME_ORDER); for (int i = LOCAL_ID; i < GRID_SIZE_Z; i += LOCAL_SIZE) { int block = i % PME_ORDER; zindexTable[i] = i/PME_ORDER + block*GRID_SIZE_X*GRID_SIZE_Y*blockSize; } SYNC_THREADS; const unsigned int gridSize = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z; real scale = 1/(real) 0x100000000; for (int index = GLOBAL_ID; index < gridSize; index += GLOBAL_SIZE) { int zindex = index%GRID_SIZE_Z; int loadIndex = zindexTable[zindex] + blockSize*(int) (index/GRID_SIZE_Z); #ifdef USE_FIXED_POINT_CHARGE_SPREADING grid2[index] = scale*grid1[loadIndex]; #else grid2[index] = grid1[loadIndex]; #endif } } #elif defined(DEVICE_IS_CPU) KERNEL void gridSpreadCharge(GLOBAL const real4* RESTRICT posq, GLOBAL real* RESTRICT pmeGrid, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ, #ifdef CHARGE_FROM_SIGEPS GLOBAL const float2* RESTRICT sigmaEpsilon #else GLOBAL const real* RESTRICT charges #endif ) { const int firstx = GLOBAL_ID*GRID_SIZE_X/GLOBAL_SIZE; const int lastx = (GLOBAL_ID+1)*GRID_SIZE_X/GLOBAL_SIZE; if (firstx == lastx) return; const real4 scale = 1/(real) (PME_ORDER-1); real4 data[PME_ORDER]; // Process the atoms in spatially sorted order. This improves efficiency when writing // the grid values. for (int i = 0; i < NUM_ATOMS; i++) { int atom = i; real4 pos = posq[atom]; APPLY_PERIODIC_TO_POS(pos) real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x, pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y, pos.z*recipBoxVecZ.z); t.x = (t.x-floor(t.x))*GRID_SIZE_X; t.y = (t.y-floor(t.y))*GRID_SIZE_Y; t.z = (t.z-floor(t.z))*GRID_SIZE_Z; int4 gridIndex = (int4) (((int) t.x) % GRID_SIZE_X, ((int) t.y) % GRID_SIZE_Y, ((int) t.z) % GRID_SIZE_Z, 0); // Spread the charge from this atom onto each grid point. #ifdef CHARGE_FROM_SIGEPS const float2 sigEps = sigmaEpsilon[atom]; const real charge = 8*sigEps.x*sigEps.x*sigEps.x*sigEps.y; #else const real charge = (CHARGE)*EPSILON_FACTOR; #endif if (charge == 0) continue; bool hasComputedThetas = false; for (int ix = 0; ix < PME_ORDER; ix++) { int xindex = gridIndex.x+ix; xindex -= (xindex >= GRID_SIZE_X ? GRID_SIZE_X : 0); if (xindex < firstx || xindex >= lastx) continue; if (!hasComputedThetas) { hasComputedThetas = true; // Since we need the full set of thetas, it's faster to compute them here than load them // from global memory. real4 dr = (real4) (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; data[0] = 1.0f-dr; for (int j = 3; j < PME_ORDER; j++) { real div = RECIP(j-1.0f); data[j-1] = div*dr*data[j-2]; for (int k = 1; k < (j-1); k++) data[j-k-1] = div*((dr+(real4) k) *data[j-k-2] + (-dr+(real4) (j-k))*data[j-k-1]); data[0] = div*(- dr+1.0f)*data[0]; } data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2]; for (int j = 1; j < (PME_ORDER-1); j++) data[PME_ORDER-j-1] = scale*((dr+(real4) j)*data[PME_ORDER-j-2] + (-dr+(real4) (PME_ORDER-j))*data[PME_ORDER-j-1]); data[0] = scale*(-dr+1.0f)*data[0]; } for (int iy = 0; iy < PME_ORDER; iy++) { int yindex = gridIndex.y+iy; yindex -= (yindex >= GRID_SIZE_Y ? GRID_SIZE_Y : 0); for (int iz = 0; iz < PME_ORDER; iz++) { 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] += charge*data[ix].x*data[iy].y*data[iz].z; } } } } } #else /** * For each grid point, find the range of sorted atoms associated with that point. */ KERNEL void findAtomRangeForGrid(GLOBAL int2* RESTRICT pmeAtomGridIndex, GLOBAL int* RESTRICT pmeAtomRange, GLOBAL const real4* RESTRICT posq) { int start = (NUM_ATOMS*GLOBAL_ID)/GLOBAL_SIZE; int end = (NUM_ATOMS*(GLOBAL_ID+1))/GLOBAL_SIZE; int last = (start == 0 ? -1 : pmeAtomGridIndex[start-1].y); for (int i = start; i < end; ++i) { int2 atomData = pmeAtomGridIndex[i]; int gridIndex = atomData.y; if (gridIndex != last) { for (int j = last+1; j <= gridIndex; ++j) pmeAtomRange[j] = i; last = gridIndex; } } // Fill in values beyond the last atom. if (GLOBAL_ID == GLOBAL_SIZE-1) { int gridSize = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z; for (int j = last+1; j <= gridSize; ++j) pmeAtomRange[j] = NUM_ATOMS; } } /** * The grid index won't be needed again. Reuse that component to hold the z index, thus saving * some work in the charge spreading kernel. */ KERNEL void recordZIndex(GLOBAL int2* RESTRICT pmeAtomGridIndex, GLOBAL const real4* RESTRICT posq, real4 periodicBoxSize, real4 recipBoxVecZ) { int start = (NUM_ATOMS*GLOBAL_ID)/GLOBAL_SIZE; int end = (NUM_ATOMS*(GLOBAL_ID+1))/GLOBAL_SIZE; for (int i = start; i < end; ++i) { real posz = posq[pmeAtomGridIndex[i].x].z; posz -= floor(posz*recipBoxVecZ.z)*periodicBoxSize.z; int z = ((int) ((posz*recipBoxVecZ.z)*GRID_SIZE_Z)) % GRID_SIZE_Z; pmeAtomGridIndex[i].y = z; } } KERNEL void gridSpreadCharge(GLOBAL const real4* RESTRICT posq, GLOBAL real* RESTRICT pmeGrid, GLOBAL const int2* RESTRICT pmeAtomGridIndex, GLOBAL const int* RESTRICT pmeAtomRange, GLOBAL const real4* RESTRICT pmeBsplineTheta #ifdef CHARGE_FROM_SIGEPS , GLOBAL const float2* RESTRICT sigmaEpsilon #else , GLOBAL const real* RESTRICT charges #endif ) { unsigned int numGridPoints = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z; for (int gridIndex = GLOBAL_ID; gridIndex < numGridPoints; gridIndex += GLOBAL_SIZE) { // Compute the charge on a grid point. int4 gridPoint; gridPoint.x = gridIndex/(GRID_SIZE_Y*GRID_SIZE_Z); int remainder = gridIndex-gridPoint.x*GRID_SIZE_Y*GRID_SIZE_Z; gridPoint.y = remainder/GRID_SIZE_Z; gridPoint.z = remainder-gridPoint.y*GRID_SIZE_Z; real result = 0.0f; // Loop over all atoms that affect this grid point. for (int ix = 0; ix < PME_ORDER; ++ix) { int x = gridPoint.x-ix+(gridPoint.x >= ix ? 0 : GRID_SIZE_X); for (int iy = 0; iy < PME_ORDER; ++iy) { int y = gridPoint.y-iy+(gridPoint.y >= iy ? 0 : GRID_SIZE_Y); int z1 = gridPoint.z-PME_ORDER+1; z1 += (z1 >= 0 ? 0 : GRID_SIZE_Z); int z2 = (z1 < gridPoint.z ? gridPoint.z : GRID_SIZE_Z-1); int gridIndex1 = x*GRID_SIZE_Y*GRID_SIZE_Z+y*GRID_SIZE_Z+z1; int gridIndex2 = x*GRID_SIZE_Y*GRID_SIZE_Z+y*GRID_SIZE_Z+z2; int firstAtom = pmeAtomRange[gridIndex1]; int lastAtom = pmeAtomRange[gridIndex2+1]; for (int i = firstAtom; i < lastAtom; ++i) { int2 atomData = pmeAtomGridIndex[i]; int atomIndex = atomData.x; int z = atomData.y; int iz = gridPoint.z-z+(gridPoint.z >= z ? 0 : GRID_SIZE_Z); real atomCharge = pmeBsplineTheta[atomIndex+ix*NUM_ATOMS].w; result += atomCharge*pmeBsplineTheta[atomIndex+ix*NUM_ATOMS].x*pmeBsplineTheta[atomIndex+iy*NUM_ATOMS].y*pmeBsplineTheta[atomIndex+iz*NUM_ATOMS].z; } if (z1 > gridPoint.z) { gridIndex1 = x*GRID_SIZE_Y*GRID_SIZE_Z+y*GRID_SIZE_Z; gridIndex2 = x*GRID_SIZE_Y*GRID_SIZE_Z+y*GRID_SIZE_Z+gridPoint.z; firstAtom = pmeAtomRange[gridIndex1]; lastAtom = pmeAtomRange[gridIndex2+1]; for (int i = firstAtom; i < lastAtom; ++i) { int2 atomData = pmeAtomGridIndex[i]; int atomIndex = atomData.x; int z = atomData.y; int iz = gridPoint.z-z+(gridPoint.z >= z ? 0 : GRID_SIZE_Z); real atomCharge = pmeBsplineTheta[atomIndex+ix*NUM_ATOMS].w; result += atomCharge*pmeBsplineTheta[atomIndex+ix*NUM_ATOMS].x*pmeBsplineTheta[atomIndex+iy*NUM_ATOMS].y*pmeBsplineTheta[atomIndex+iz*NUM_ATOMS].z; } } } } pmeGrid[gridIndex] = result*EPSILON_FACTOR; } } #endif 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); #ifdef USE_LJPME const real recipScaleFactor = -(2*M_PI/6)*SQRT(M_PI)*recipBoxVecX.x*recipBoxVecY.y*recipBoxVecZ.z; real bfac = M_PI / EWALD_ALPHA; real fac1 = 2*M_PI*M_PI*M_PI*SQRT(M_PI); real fac2 = EWALD_ALPHA*EWALD_ALPHA*EWALD_ALPHA; real fac3 = -2*EWALD_ALPHA*M_PI*M_PI; #else const real recipScaleFactor = RECIP(M_PI)*recipBoxVecX.x*recipBoxVecY.y*recipBoxVecZ.z; #endif for (int index = GLOBAL_ID; index < gridSize; index += GLOBAL_SIZE) { // 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); 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 bx = pmeBsplineModuliX[kx]; real by = pmeBsplineModuliY[ky]; real bz = pmeBsplineModuliZ[kz]; real2 grid = pmeGrid[index]; real m2 = mhx*mhx+mhy*mhy+mhz*mhz; #ifdef USE_LJPME real denom = recipScaleFactor/(bx*by*bz); real m = SQRT(m2); real m3 = m*m2; real b = bfac*m; real expfac = -b*b; real expterm = EXP(expfac); real erfcterm = ERFC(b); real eterm = (fac1*erfcterm*m3 + expterm*(fac2 + fac3*m2)) * denom; pmeGrid[index] = make_real2(grid.x*eterm, grid.y*eterm); #else real denom = m2*bx*by*bz; real eterm = recipScaleFactor*EXP(-RECIP_EXP_FACTOR*m2)/denom; if (kx != 0 || ky != 0 || kz != 0) { pmeGrid[index] = make_real2(grid.x*eterm, grid.y*eterm); } #endif } } KERNEL void gridEvaluateEnergy(GLOBAL real2* RESTRICT pmeGrid, GLOBAL mixed* 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; #ifdef USE_LJPME const real recipScaleFactor = -(2*M_PI/6)*SQRT(M_PI)*recipBoxVecX.x*recipBoxVecY.y*recipBoxVecZ.z; real bfac = M_PI / EWALD_ALPHA; real fac1 = 2*M_PI*M_PI*M_PI*SQRT(M_PI); real fac2 = EWALD_ALPHA*EWALD_ALPHA*EWALD_ALPHA; real fac3 = -2*EWALD_ALPHA*M_PI*M_PI; #else const real recipScaleFactor = RECIP(M_PI)*recipBoxVecX.x*recipBoxVecY.y*recipBoxVecZ.z; #endif mixed energy = 0; for (int index = GLOBAL_ID; index < gridSize; index += GLOBAL_SIZE) { // 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]; #ifdef USE_LJPME real denom = recipScaleFactor/(bx*by*bz); real m = SQRT(m2); real m3 = m*m2; real b = bfac*m; real expfac = -b*b; real expterm = EXP(expfac); real erfcterm = ERFC(b); real eterm = (fac1*erfcterm*m3 + expterm*(fac2 + fac3*m2)) * denom; #else real denom = m2*bx*by*bz; real eterm = recipScaleFactor*EXP(-RECIP_EXP_FACTOR*m2)/denom; #endif 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]; #ifndef USE_LJPME if (kx != 0 || ky != 0 || kz != 0) #endif energy += eterm*(grid.x*grid.x + grid.y*grid.y); } #if defined(USE_PME_STREAM) && !defined(USE_LJPME) energyBuffer[GLOBAL_ID] = 0.5f*energy; #else energyBuffer[GLOBAL_ID] += 0.5f*energy; #endif } #if defined(USE_HIP) && !defined(AMD_RDNA) && !defined(USE_DOUBLE_PRECISION) LAUNCH_BOUNDS_EXACT(128, 1) #endif KERNEL void gridInterpolateForce(GLOBAL const real4* RESTRICT posq, GLOBAL mm_ulong* RESTRICT forceBuffers, GLOBAL const real* RESTRICT pmeGrid, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ, GLOBAL const int2* RESTRICT pmeAtomGridIndex, #ifdef CHARGE_FROM_SIGEPS GLOBAL const float2* RESTRICT sigmaEpsilon #else GLOBAL const real* RESTRICT charges #endif ) { real3 data[PME_ORDER]; real3 ddata[PME_ORDER]; const real scale = RECIP((real) (PME_ORDER-1)); // Process the atoms in spatially sorted order. This improves cache performance when loading // the grid values. for (int i = GLOBAL_ID; i < NUM_ATOMS; i += GLOBAL_SIZE) { int atom = pmeAtomGridIndex[i].x; real3 force = make_real3(0); real4 pos = posq[atom]; APPLY_PERIODIC_TO_POS(pos) real3 t = make_real3(pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x, pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y, pos.z*recipBoxVecZ.z); t.x = (t.x-floor(t.x))*GRID_SIZE_X; t.y = (t.y-floor(t.y))*GRID_SIZE_Y; t.z = (t.z-floor(t.z))*GRID_SIZE_Z; int3 gridIndex = make_int3(((int) t.x) % GRID_SIZE_X, ((int) t.y) % GRID_SIZE_Y, ((int) t.z) % GRID_SIZE_Z); // Since we need the full set of thetas, it's faster to compute them here than load them // from global memory. real3 dr = make_real3(t.x-(int) t.x, t.y-(int) t.y, t.z-(int) t.z); data[PME_ORDER-1] = make_real3(0); data[1] = dr; data[0] = make_real3(1)-dr; for (int j = 3; j < PME_ORDER; j++) { real div = RECIP((real) (j-1)); data[j-1] = div*dr*data[j-2]; for (int k = 1; k < (j-1); k++) data[j-k-1] = div*((dr+make_real3(k))*data[j-k-2] + (make_real3(j-k)-dr)*data[j-k-1]); data[0] = div*(make_real3(1)-dr)*data[0]; } ddata[0] = -data[0]; for (int j = 1; j < PME_ORDER; j++) ddata[j] = data[j-1]-data[j]; data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2]; for (int j = 1; j < (PME_ORDER-1); j++) data[PME_ORDER-j-1] = scale*((dr+make_real3(j))*data[PME_ORDER-j-2] + (make_real3(PME_ORDER-j)-dr)*data[PME_ORDER-j-1]); data[0] = scale*(make_real3(1)-dr)*data[0]; // Compute the force on this atom. for (int ix = 0; ix < PME_ORDER; ix++) { int xbase = gridIndex.x+ix; xbase -= (xbase >= GRID_SIZE_X ? GRID_SIZE_X : 0); xbase = xbase*GRID_SIZE_Y*GRID_SIZE_Z; real dx = data[ix].x; real ddx = ddata[ix].x; for (int iy = 0; iy < PME_ORDER; iy++) { int ybase = gridIndex.y+iy; ybase -= (ybase >= GRID_SIZE_Y ? GRID_SIZE_Y : 0); ybase = xbase + ybase*GRID_SIZE_Z; real dy = data[iy].y; real ddy = ddata[iy].y; for (int iz = 0; iz < PME_ORDER; iz++) { int zindex = gridIndex.z+iz; zindex -= (zindex >= GRID_SIZE_Z ? GRID_SIZE_Z : 0); int index = ybase + zindex; real gridvalue = pmeGrid[index]; force.x += ddx*dy*data[iz].z*gridvalue; force.y += dx*ddy*data[iz].z*gridvalue; force.z += dx*dy*ddata[iz].z*gridvalue; } } } #ifdef CHARGE_FROM_SIGEPS const float2 sigEps = sigmaEpsilon[atom]; real q = 8*sigEps.x*sigEps.x*sigEps.x*sigEps.y; #else real q = CHARGE*EPSILON_FACTOR; #endif real forceX = -q*(force.x*GRID_SIZE_X*recipBoxVecX.x); real forceY = -q*(force.x*GRID_SIZE_X*recipBoxVecY.x+force.y*GRID_SIZE_Y*recipBoxVecY.y); real forceZ = -q*(force.x*GRID_SIZE_X*recipBoxVecZ.x+force.y*GRID_SIZE_Y*recipBoxVecZ.y+force.z*GRID_SIZE_Z*recipBoxVecZ.z); #ifdef USE_PME_STREAM ATOMIC_ADD(&forceBuffers[atom], (mm_ulong) realToFixedPoint(forceX)); ATOMIC_ADD(&forceBuffers[atom+PADDED_NUM_ATOMS], (mm_ulong) realToFixedPoint(forceY)); ATOMIC_ADD(&forceBuffers[atom+2*PADDED_NUM_ATOMS], (mm_ulong) realToFixedPoint(forceZ)); #else forceBuffers[atom] += (mm_ulong) realToFixedPoint(forceX); forceBuffers[atom+PADDED_NUM_ATOMS] += (mm_ulong) realToFixedPoint(forceY); forceBuffers[atom+2*PADDED_NUM_ATOMS] += (mm_ulong) realToFixedPoint(forceZ); #endif } } KERNEL void addForces(GLOBAL const real4* RESTRICT forces, GLOBAL mm_long* RESTRICT forceBuffers) { for (int atom = GLOBAL_ID; atom < NUM_ATOMS; atom += GLOBAL_SIZE) { real4 f = forces[atom]; forceBuffers[atom] += realToFixedPoint(f.x); forceBuffers[atom+PADDED_NUM_ATOMS] += realToFixedPoint(f.y); forceBuffers[atom+2*PADDED_NUM_ATOMS] += realToFixedPoint(f.z); } } KERNEL void addEnergy(GLOBAL const mixed* RESTRICT pmeEnergyBuffer, GLOBAL mixed* RESTRICT energyBuffer, int bufferSize) { for (int i = GLOBAL_ID; i < bufferSize; i += GLOBAL_SIZE) energyBuffer[i] += pmeEnergyBuffer[i]; }