2021-03-25 06:49:28 +01:00
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/*
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* =======================================================================================
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*
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* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
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* Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
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*
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* This file is part of MD-Bench.
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*
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* MD-Bench is free software: you can redistribute it and/or modify it
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* under the terms of the GNU Lesser General Public License as published
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* by the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* MD-Bench is distributed in the hope that it will be useful, but WITHOUT ANY
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* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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* PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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* details.
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*
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* You should have received a copy of the GNU Lesser General Public License along
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* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
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* =======================================================================================
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*/
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2021-11-09 08:37:37 +01:00
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#include <stdio.h>
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#include <stdlib.h>
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2021-11-10 16:02:05 +01:00
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#include <stddef.h>
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2021-11-08 20:32:12 +01:00
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#include <cuda_runtime.h>
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2021-11-10 16:02:05 +01:00
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#include <device_launch_parameters.h>
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2021-11-11 14:49:29 +01:00
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extern "C" {
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#include <likwid-marker.h>
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2021-03-25 06:49:28 +01:00
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2021-11-11 14:49:29 +01:00
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#include <timing.h>
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#include <neighbor.h>
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#include <parameter.h>
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#include <atom.h>
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}
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2021-03-25 06:49:28 +01:00
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2021-11-10 16:02:05 +01:00
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// cuda kernel
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__global__ void calc_force(
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Atom *atom,
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MD_FLOAT xtmp, MD_FLOAT ytmp, MD_FLOAT ztmp,
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MD_FLOAT *fix, MD_FLOAT *fiy, MD_FLOAT *fiz,
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int i, int numneighs, int *neighs) {
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// Calculate idx k from thread information
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const long long k = blockIdx.x * blockDim.x + threadIdx.x;
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if( k >= numneighs ) {
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return;
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}
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int j = neighs[k];
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MD_FLOAT delx = xtmp - atom_x(j);
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MD_FLOAT dely = ytmp - atom_y(j);
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MD_FLOAT delz = ztmp - atom_z(j);
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MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
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const int type_i = atom->type[i];
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const int type_j = atom->type[j];
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const int type_ij = type_i * atom->ntypes + type_j;
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const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
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const MD_FLOAT sigma6 = atom->sigma6[type_ij];
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const MD_FLOAT epsilon = atom->epsilon[type_ij];
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if(rsq < cutforcesq) {
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MD_FLOAT sr2 = 1.0 / rsq;
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MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
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MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
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fix[j] = delx * force;
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fiy[j] = dely * force;
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fiz[j] = delz * force;
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}
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}
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2021-11-11 14:49:29 +01:00
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extern "C" {
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2021-10-26 09:11:17 +02:00
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double computeForce(
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Parameter *param,
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Atom *atom,
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Neighbor *neighbor
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)
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{
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2021-03-25 06:49:28 +01:00
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int Nlocal = atom->Nlocal;
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int* neighs;
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2021-10-26 09:11:17 +02:00
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MD_FLOAT* fx = atom->fx;
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MD_FLOAT* fy = atom->fy;
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MD_FLOAT* fz = atom->fz;
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#ifndef EXPLICIT_TYPES
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2021-03-25 06:49:28 +01:00
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MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
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2021-10-26 09:11:17 +02:00
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#endif
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2021-03-25 06:49:28 +01:00
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for(int i = 0; i < Nlocal; i++) {
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fx[i] = 0.0;
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fy[i] = 0.0;
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fz[i] = 0.0;
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}
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2021-11-11 14:49:29 +01:00
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double S = getTimeStamp();
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2021-06-30 13:44:02 +02:00
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LIKWID_MARKER_START("force");
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2021-10-12 22:39:54 +02:00
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2021-10-26 09:11:17 +02:00
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#pragma omp parallel for
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for(int i = 0; i < Nlocal; i++) {
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neighs = &neighbor->neighbors[i * neighbor->maxneighs];
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int numneighs = neighbor->numneigh[i];
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MD_FLOAT xtmp = atom_x(i);
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MD_FLOAT ytmp = atom_y(i);
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MD_FLOAT ztmp = atom_z(i);
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#ifdef EXPLICIT_TYPES
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const int type_i = atom->type[i];
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#endif
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2021-10-12 22:39:54 +02:00
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2021-11-09 16:40:25 +01:00
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Atom *c_atom;
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cudaMalloc((void**)&c_atom, sizeof(Atom));
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cudaMemcpy(c_atom, atom, sizeof(Atom), cudaMemcpyHostToDevice);
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2021-11-09 08:37:37 +01:00
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2021-11-09 16:40:25 +01:00
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cudaMalloc((void**)&c_atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3);
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cudaMemcpy(c_atom->x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice);
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2021-11-09 08:37:37 +01:00
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2021-11-09 16:40:25 +01:00
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cudaMalloc((void**)&c_atom->y, sizeof(MD_FLOAT) * atom->Nmax * 3);
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cudaMemcpy(c_atom->y, atom->y, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice);
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2021-11-09 08:37:37 +01:00
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2021-11-09 16:40:25 +01:00
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cudaMalloc((void**)&c_atom->z, sizeof(MD_FLOAT) * atom->Nmax * 3);
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cudaMemcpy(c_atom->z, atom->z, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice);
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2021-11-09 08:37:37 +01:00
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2021-11-09 16:40:25 +01:00
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cudaMalloc((void**)&c_atom->type, sizeof(int) * atom->Nmax);
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cudaMemcpy(c_atom->type, atom->type, sizeof(int) * atom->Nmax, cudaMemcpyHostToDevice);
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2021-11-09 08:37:37 +01:00
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2021-11-09 16:40:25 +01:00
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cudaMalloc((void**)&c_atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes);
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cudaMemcpy(c_atom->epsilon, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice);
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2021-11-09 08:37:37 +01:00
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2021-11-09 16:40:25 +01:00
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cudaMalloc((void**)&c_atom->sigma6, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes);
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cudaMemcpy(c_atom->sigma6, atom->sigma6, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice);
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2021-11-09 08:37:37 +01:00
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2021-11-09 16:40:25 +01:00
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cudaMalloc((void**)&c_atom->cutforcesq, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes);
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cudaMemcpy(c_atom->cutforcesq, atom->cutforcesq, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice);
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2021-11-09 08:37:37 +01:00
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2021-11-09 16:40:25 +01:00
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int *c_neighs;
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cudaMalloc((void**)&c_neighs, sizeof(int) * numneighs);
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cudaMemcpy(c_neighs, neighs, sizeof(int) * numneighs, cudaMemcpyHostToDevice);
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2021-11-09 08:37:37 +01:00
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2021-11-09 16:40:25 +01:00
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MD_FLOAT *c_fix, *c_fiy, *c_fiz;
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2021-11-10 16:02:05 +01:00
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cudaMalloc((void**)&c_fix, sizeof(MD_FLOAT) * numneighs);
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cudaMalloc((void**)&c_fiy, sizeof(MD_FLOAT) * numneighs);
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cudaMalloc((void**)&c_fiz, sizeof(MD_FLOAT) * numneighs);
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const int num_blocks = 64;
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const int num_threads_per_block = numneighs / num_blocks;
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printf("numneighs: %d => num-blocks: %d, num_threads => %d\r\n", numneighs, num_blocks, num_threads_per_block);
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// launch cuda kernel
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calc_force <<< num_blocks, num_threads_per_block >>> (c_atom, xtmp, ytmp, ztmp, c_fix, c_fiy, c_fiz, i, numneighs, c_neighs);
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cudaDeviceSynchronize();
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// sum result
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MD_FLOAT *d_fix, *d_fiy, *d_fiz;
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d_fix = (MD_FLOAT*)malloc(sizeof(MD_FLOAT) * numneighs);
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d_fiy = (MD_FLOAT*)malloc(sizeof(MD_FLOAT) * numneighs);
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d_fiz = (MD_FLOAT*)malloc(sizeof(MD_FLOAT) * numneighs);
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cudaMemcpy((void**)d_fix, c_fix, sizeof(MD_FLOAT) * numneighs, cudaMemcpyDeviceToHost);
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cudaMemcpy((void**)d_fiy, c_fiy, sizeof(MD_FLOAT) * numneighs, cudaMemcpyDeviceToHost);
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cudaMemcpy((void**)d_fiz, c_fiz, sizeof(MD_FLOAT) * numneighs, cudaMemcpyDeviceToHost);
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2021-10-12 22:39:54 +02:00
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2021-10-26 09:11:17 +02:00
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for(int k = 0; k < numneighs; k++) {
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2021-11-10 16:02:05 +01:00
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fx[i] += d_fix[k];
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fy[i] += d_fiy[k];
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fz[i] += d_fiz[k];
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2021-04-07 00:46:51 +02:00
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}
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2021-10-26 09:11:17 +02:00
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2021-11-10 16:02:05 +01:00
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cudaFree(c_fix); cudaFree(c_fiy); cudaFree(c_fiz);
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cudaFree(c_atom); cudaFree(c_neighs);
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2021-03-25 06:49:28 +01:00
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}
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2021-10-12 22:39:54 +02:00
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2021-06-30 13:44:02 +02:00
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LIKWID_MARKER_STOP("force");
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2021-11-11 14:49:29 +01:00
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double E = getTimeStamp();
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2021-10-11 16:57:02 +02:00
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2021-11-11 14:49:29 +01:00
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return E-S;
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2021-11-11 08:03:56 +01:00
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return 0;
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2021-03-25 06:49:28 +01:00
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}
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2021-11-11 14:49:29 +01:00
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}
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