/* -------------------------------------------------------------------------- * * OpenMM * * -------------------------------------------------------------------------- * * This is part of the OpenMM molecular simulation toolkit originating from * * Simbios, the NIH National Center for Physics-Based Simulation of * * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * * Portions copyright (c) 2009 Stanford University and the Authors. * * Authors: Scott Le Grand, Peter Eastman * * Contributors: * * * * Permission is hereby granted, free of charge, to any person obtaining a * * copy of this software and associated documentation files (the "Software"), * * to deal in the Software without restriction, including without limitation * * the rights to use, copy, modify, merge, publish, distribute, sublicense, * * and/or sell copies of the Software, and to permit persons to whom the * * Software is furnished to do so, subject to the following conditions: * * * * The above copyright notice and this permission notice shall be included in * * all copies or substantial portions of the Software. * * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL * * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, * * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR * * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE * * USE OR OTHER DEALINGS IN THE SOFTWARE. * * -------------------------------------------------------------------------- */ #include "kCalculateGBVIAux.h" /** * This file contains the kernel for evalauating the second stage of GBSA. It is included * several times in kCalculateGBVIForces2.cu with different #defines to generate * different versions of the kernels. */ __global__ void #if (__CUDA_ARCH__ >= 200) __launch_bounds__(GF1XX_BORNFORCE2_THREADS_PER_BLOCK, 1) #elif (__CUDA_ARCH__ >= 130) __launch_bounds__(GT2XX_BORNFORCE2_THREADS_PER_BLOCK, 1) #else __launch_bounds__(G8X_BORNFORCE2_THREADS_PER_BLOCK, 1) #endif METHOD_NAME(kCalculateGBVI, Forces2_kernel)(unsigned int* workUnit, unsigned int numWorkUnits) { extern __shared__ Atom sA[]; unsigned int totalWarps = cSim.bornForce2_blocks*cSim.bornForce2_threads_per_block/GRID; unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID; unsigned int pos = warp*numWorkUnits/totalWarps; unsigned int end = (warp+1)*numWorkUnits/totalWarps; #ifdef USE_CUTOFF float3* tempBuffer = (float3*) &sA[cSim.bornForce2_threads_per_block]; #endif unsigned int lasty = -0xFFFFFFFF; while (pos < end) { // Extract cell coordinates from appropriate work unit unsigned int x = workUnit[pos]; unsigned int y = ((x >> 2) & 0x7fff) << GRIDBITS; x = (x >> 17) << GRIDBITS; unsigned int tgx = threadIdx.x & (GRID - 1); unsigned int i = x + tgx; float4 apos = cSim.pPosq[i]; float4 ar = cSim.pGBVIData[i]; float fb = cSim.pBornForce[i]; unsigned int tbx = threadIdx.x - tgx; unsigned int tj = tgx; Atom* psA = &sA[tbx]; float3 af; sA[threadIdx.x].fx = af.x = 0.0f; sA[threadIdx.x].fy = af.y = 0.0f; sA[threadIdx.x].fz = af.z = 0.0f; if (x == y) // Handle diagonals uniquely at 50% efficiency { // Read fixed atom data into registers and GRF sA[threadIdx.x].x = apos.x; sA[threadIdx.x].y = apos.y; sA[threadIdx.x].z = apos.z; sA[threadIdx.x].r = ar.x; sA[threadIdx.x].sr = ar.y; sA[threadIdx.x].fb = fb; for (unsigned int j = (tgx+1)&(GRID-1); j != tgx; j = (j+1)&(GRID-1)) { float dx = psA[j].x - apos.x; float dy = psA[j].y - apos.y; float dz = psA[j].z - apos.z; #ifdef USE_PERIODIC 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; #endif float r2 = dx * dx + dy * dy + dz * dz; float r = sqrt(r2); // Atom I Born forces and sum float dE = getGBVI_dE2( r, ar.x, psA[j].sr, fb ); #if defined USE_PERIODIC if (i >= cSim.atoms || x+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr) { dE = 0.0f; } #endif #if defined USE_CUTOFF if (r2 > cSim.nonbondedCutoffSqr) { dE = 0.0f; } #endif float d = dx * dE; af.x -= d; psA[j].fx += d; d = dy * dE; af.y -= d; psA[j].fy += d; d = dz * dE; af.z -= d; psA[j].fz += d; } // Write results float4 of; #ifdef USE_OUTPUT_BUFFER_PER_WARP unsigned int offset = x + tgx + warp*cSim.stride; of = cSim.pForce4b[offset]; of.x += af.x + sA[threadIdx.x].fx; of.y += af.y + sA[threadIdx.x].fy; of.z += af.z + sA[threadIdx.x].fz; cSim.pForce4b[offset] = of; #else unsigned int offset = x + tgx + (x >> GRIDBITS) * cSim.stride; of = cSim.pForce4b[offset]; of.x += af.x + sA[threadIdx.x].fx; of.y += af.y + sA[threadIdx.x].fy; of.z += af.z + sA[threadIdx.x].fz; of.w = 0.0f; cSim.pForce4b[offset] = of; #endif } else { // Read fixed atom data into registers and GRF if (lasty != y) { unsigned int j = y + tgx; float4 temp = cSim.pPosq[j]; float4 temp1 = cSim.pGBVIData[j]; float fb = cSim.pBornForce[j]; sA[threadIdx.x].fb = fb; sA[threadIdx.x].x = temp.x; sA[threadIdx.x].y = temp.y; sA[threadIdx.x].z = temp.z; sA[threadIdx.x].r = temp1.x; sA[threadIdx.x].sr = temp1.y; } #ifdef USE_CUTOFF unsigned int flags = cSim.pInteractionFlag[pos]; if (flags == 0) { // No interactions in this block. } else if (flags == 0xFFFFFFFF) #endif { // Compute all interactions within this block. for (unsigned int j = 0; j < GRID; j++) { float dx = psA[tj].x - apos.x; float dy = psA[tj].y - apos.y; float dz = psA[tj].z - apos.z; #ifdef USE_PERIODIC 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; #endif float r2 = dx * dx + dy * dy + dz * dz; float r = sqrt(r2); float dE = getGBVI_dE2( r, ar.x, psA[tj].sr, fb ); #if defined USE_PERIODIC if (i >= cSim.atoms || y+tj >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr) { dE = 0.0f; } #endif #if defined USE_CUTOFF if (r2 > cSim.nonbondedCutoffSqr) { dE = 0.0f; } #endif float d = dx * dE; af.x -= d; psA[tj].fx += d; d = dy * dE; af.y -= d; psA[tj].fy += d; d = dz * dE; af.z -= d; psA[tj].fz += d; // Atom J Born sum term dE = getGBVI_dE2( r, psA[tj].r, ar.y, psA[tj].fb ); #ifdef USE_PERIODIC if (i >= cSim.atoms || y+tj >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr) { dE = 0.0f; } #endif #if defined USE_CUTOFF if (r2 > cSim.nonbondedCutoffSqr) { dE = 0.0f; } #endif dx *= dE; dy *= dE; dz *= dE; psA[tj].fx += dx; psA[tj].fy += dy; psA[tj].fz += dz; af.x -= dx; af.y -= dy; af.z -= dz; tj = (tj + 1) & (GRID - 1); } } #ifdef USE_CUTOFF else { // Compute only a subset of the interactions in this block. for (unsigned int j = 0; j < GRID; j++) { if ((flags&(1<= cSim.atoms || y+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr) { dE = 0.0f; } #endif #if defined USE_CUTOFF if (r2 > cSim.nonbondedCutoffSqr) { dE = 0.0f; } #endif float d = dx * dE; af.x -= d; tempBuffer[threadIdx.x].x = d; d = dy * dE; af.y -= d; tempBuffer[threadIdx.x].y = d; d = dz * dE; af.z -= d; tempBuffer[threadIdx.x].z = d; // Atom J Born sum term dE = getGBVI_dE2( r, psA[j].r, ar.y, psA[j].fb ); #ifdef USE_PERIODIC if (i >= cSim.atoms || y+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr) { dE = 0.0f; } #endif #if defined USE_CUTOFF if (r2 > cSim.nonbondedCutoffSqr) { dE = 0.0f; } #endif dx *= dE; dy *= dE; dz *= dE; tempBuffer[threadIdx.x].x += dx; tempBuffer[threadIdx.x].y += dy; tempBuffer[threadIdx.x].z += dz; af.x -= dx; af.y -= dy; af.z -= dz; // Sum the forces on atom j. if (tgx % 2 == 0) { tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+1].x; tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+1].y; tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+1].z; } if (tgx % 4 == 0) { tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+2].x; tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+2].y; tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+2].z; } if (tgx % 8 == 0) { tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+4].x; tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+4].y; tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+4].z; } if (tgx % 16 == 0) { tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+8].x; tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+8].y; tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+8].z; } if (tgx == 0) { psA[j].fx += tempBuffer[threadIdx.x].x + tempBuffer[threadIdx.x+16].x; psA[j].fy += tempBuffer[threadIdx.x].y + tempBuffer[threadIdx.x+16].y; psA[j].fz += tempBuffer[threadIdx.x].z + tempBuffer[threadIdx.x+16].z; } } } } #endif // Write results float4 of; #ifdef USE_OUTPUT_BUFFER_PER_WARP unsigned int offset = x + tgx + warp*cSim.stride; of = cSim.pForce4b[offset]; of.x += af.x; of.y += af.y; of.z += af.z; cSim.pForce4b[offset] = of; offset = y + tgx + warp*cSim.stride; of = cSim.pForce4b[offset]; of.x += sA[threadIdx.x].fx; of.y += sA[threadIdx.x].fy; of.z += sA[threadIdx.x].fz; cSim.pForce4b[offset] = of; #else unsigned int offset = x + tgx + (y >> GRIDBITS) * cSim.stride; of = cSim.pForce4b[offset]; of.x += af.x; of.y += af.y; of.z += af.z; of.w = 0.0f; cSim.pForce4b[offset] = of; offset = y + tgx + (x >> GRIDBITS) * cSim.stride; of = cSim.pForce4b[offset]; of.x += sA[threadIdx.x].fx; of.y += sA[threadIdx.x].fy; of.z += sA[threadIdx.x].fz; cSim.pForce4b[offset] = of; #endif } lasty = y; pos++; } }