/* -------------------------------------------------------------------------- * * 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. * * -------------------------------------------------------------------------- */ /** * This file contains the kernel for calculating Born sums. It is included * several times in kCalculateGBVIBornSum.cu with different #defines to generate * different versions of the kernels. */ #include "kCalculateGBVIAux.h" __global__ #if (__CUDA_ARCH__ >= 200) __launch_bounds__(GF1XX_NONBOND_THREADS_PER_BLOCK, 1) #elif (__CUDA_ARCH__ >= 120) __launch_bounds__(GT2XX_NONBOND_THREADS_PER_BLOCK, 1) #else __launch_bounds__(G8X_NONBOND_THREADS_PER_BLOCK, 1) #endif void METHOD_NAME(kCalculateGBVI, BornSum_kernel)(unsigned int* workUnit) { extern __shared__ volatile Atom sA[]; unsigned int totalWarps = cSim.nonbond_blocks*cSim.nonbond_threads_per_block/GRID; unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID; unsigned int numWorkUnits = cSim.pInteractionCount[0]; unsigned int pos = warp*numWorkUnits/totalWarps; unsigned int end = (warp+1)*numWorkUnits/totalWarps; #ifdef USE_CUTOFF volatile float* tempBuffer = (volatile float*) &sA[cSim.nonbond_threads_per_block]; #endif 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; float dx; float dy; float dz; float r2; float r; // forces tgx into interval [0,31] // forces tbx 0 unsigned int tgx = threadIdx.x & (GRID - 1); unsigned int tbx = threadIdx.x - tgx; unsigned int tj = tgx; volatile Atom* psA = &sA[tbx]; if (x == y) // Handle diagonals uniquely at 50% efficiency { // Read fixed atom data into registers and GRF unsigned int i = x + tgx; float4 apos = cSim.pPosq[i]; // Local atom x, y, z, sum float4 ar = cSim.pGBVIData[i]; // Local atom vr, sr 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; apos.w = 0.0f; for (unsigned int j = 0; j < GRID; j++) { dx = psA[j].x - apos.x; dy = psA[j].y - apos.y; dz = psA[j].z - apos.z; #ifdef USE_PERIODIC dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; #endif r2 = dx * dx + dy * dy + dz * dz; #if defined USE_CUTOFF if (i < cSim.atoms && x+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr && j != tgx) #else if (i < cSim.atoms && x+j < cSim.atoms && j != tgx ) #endif { r = sqrtf(r2); apos.w += getGBVI_Volume( r, ar.x, psA[j].sr ); } } // Write results #ifdef USE_OUTPUT_BUFFER_PER_WARP unsigned int offset = x + tgx + warp*cSim.stride; cSim.pBornSum[offset] += apos.w; #else unsigned int offset = x + tgx + (x >> GRIDBITS) * cSim.stride; cSim.pBornSum[offset] = apos.w; #endif } else { // Read fixed atom data into registers and GRF unsigned int j = y + tgx; unsigned int i = x + tgx; float4 temp = cSim.pPosq[j]; float4 temp1 = cSim.pGBVIData[j]; float4 apos = cSim.pPosq[i]; // Local atom x, y, z, sum float4 ar = cSim.pGBVIData[i]; // Local atom vr, sr 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; sA[threadIdx.x].sum = 0.0f; apos.w = 0.0f; #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++) { dx = psA[tj].x - apos.x; dy = psA[tj].y - apos.y; dz = psA[tj].z - apos.z; #ifdef USE_PERIODIC dx -= floorf(dx*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX; dy -= floorf(dy*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY; dz -= floorf(dz*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ; #endif r2 = dx * dx + dy * dy + dz * dz; #ifdef USE_CUTOFF if (i < cSim.atoms && y+tj < cSim.atoms && r2 < cSim.nonbondedCutoffSqr) #else if (i < cSim.atoms && y+tj < cSim.atoms ) #endif { r = sqrtf(r2); apos.w += getGBVI_Volume( r, ar.x, psA[tj].sr ); psA[tj].sum += getGBVI_Volume( r, psA[tj].r, ar.y ); } 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<> GRIDBITS) * cSim.stride; cSim.pBornSum[offset] = apos.w; offset = y + tgx + (x >> GRIDBITS) * cSim.stride; cSim.pBornSum[offset] = sA[threadIdx.x].sum; #endif } pos++; } }