140 lines
5.0 KiB
Plaintext
140 lines
5.0 KiB
Plaintext
/*
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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) 2020 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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#include <stdlib.h>
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#include <stdio.h>
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//---
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extern "C" {
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#include <allocate.h>
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#include <atom.h>
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#include <cuda_atom.h>
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#include <pbc.h>
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#include <util.h>
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}
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extern int NmaxGhost;
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extern int *PBCx, *PBCy, *PBCz;
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static int c_NmaxGhost;
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static int *c_PBCx, *c_PBCy, *c_PBCz;
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__global__ void computeAtomsPbcUpdate(Atom a, MD_FLOAT xprd, MD_FLOAT yprd, MD_FLOAT zprd) {
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const int i = blockIdx.x * blockDim.x + threadIdx.x;
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Atom* atom = &a;
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if(i >= atom->Nlocal) {
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return;
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}
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if (atom_x(i) < 0.0) {
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atom_x(i) += xprd;
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} else if (atom_x(i) >= xprd) {
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atom_x(i) -= xprd;
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}
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if (atom_y(i) < 0.0) {
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atom_y(i) += yprd;
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} else if (atom_y(i) >= yprd) {
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atom_y(i) -= yprd;
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}
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if (atom_z(i) < 0.0) {
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atom_z(i) += zprd;
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} else if (atom_z(i) >= zprd) {
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atom_z(i) -= zprd;
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}
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}
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__global__ void computePbcUpdate(Atom a, int* PBCx, int* PBCy, int* PBCz, MD_FLOAT xprd, MD_FLOAT yprd, MD_FLOAT zprd){
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const int i = blockIdx.x * blockDim.x + threadIdx.x;
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const int Nghost = a.Nghost;
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if(i >= Nghost) {
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return;
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}
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Atom* atom = &a;
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int *border_map = atom->border_map;
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int nlocal = atom->Nlocal;
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atom_x(nlocal + i) = atom_x(border_map[i]) + PBCx[i] * xprd;
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atom_y(nlocal + i) = atom_y(border_map[i]) + PBCy[i] * yprd;
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atom_z(nlocal + i) = atom_z(border_map[i]) + PBCz[i] * zprd;
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}
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/* update coordinates of ghost atoms */
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/* uses mapping created in setupPbc */
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void updatePbc_cuda(Atom *atom, Atom *c_atom, Parameter *param, bool doReneighbor) {
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const int num_threads_per_block = get_num_threads();
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if (doReneighbor) {
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c_atom->Natoms = atom->Natoms;
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c_atom->Nlocal = atom->Nlocal;
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c_atom->Nghost = atom->Nghost;
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c_atom->ntypes = atom->ntypes;
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if (atom->Nmax > c_atom->Nmax){ // the number of ghost atoms has increased -> more space is needed
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c_atom->Nmax = atom->Nmax;
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c_atom->x = (MD_FLOAT *) reallocateGPU(c_atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3);
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c_atom->type = (int *) reallocateGPU(c_atom->type, sizeof(int) * atom->Nmax);
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}
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memcpyToGPU(c_atom->x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3);
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memcpyToGPU(c_atom->type, atom->type, sizeof(int) * atom->Nmax);
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if(c_NmaxGhost < NmaxGhost) {
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c_NmaxGhost = NmaxGhost;
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c_PBCx = (int *) reallocateGPU(c_PBCx, NmaxGhost * sizeof(int));
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c_PBCy = (int *) reallocateGPU(c_PBCy, NmaxGhost * sizeof(int));
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c_PBCz = (int *) reallocateGPU(c_PBCz, NmaxGhost * sizeof(int));
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c_atom->border_map = (int *) reallocateGPU(c_atom->border_map, NmaxGhost * sizeof(int));
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}
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memcpyToGPU(c_PBCx, PBCx, NmaxGhost * sizeof(int));
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memcpyToGPU(c_PBCy, PBCy, NmaxGhost * sizeof(int));
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memcpyToGPU(c_PBCz, PBCz, NmaxGhost * sizeof(int));
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memcpyToGPU(c_atom->border_map, atom->border_map, NmaxGhost * sizeof(int));
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}
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MD_FLOAT xprd = param->xprd;
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MD_FLOAT yprd = param->yprd;
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MD_FLOAT zprd = param->zprd;
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const int num_blocks = ceil((float)atom->Nghost / (float)num_threads_per_block);
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computePbcUpdate<<<num_blocks, num_threads_per_block>>>(*c_atom, c_PBCx, c_PBCy, c_PBCz, xprd, yprd, zprd);
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cuda_assert("computePbcUpdate", cudaPeekAtLastError());
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cuda_assert("computePbcUpdate", cudaDeviceSynchronize());
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}
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void updateAtomsPbc_cuda(Atom* atom, Atom *c_atom, Parameter *param) {
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const int num_threads_per_block = get_num_threads();
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MD_FLOAT xprd = param->xprd;
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MD_FLOAT yprd = param->yprd;
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MD_FLOAT zprd = param->zprd;
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const int num_blocks = ceil((float)atom->Nlocal / (float)num_threads_per_block);
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computeAtomsPbcUpdate<<<num_blocks, num_threads_per_block>>>(*c_atom, xprd, yprd, zprd);
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cuda_assert("computeAtomsPbcUpdate", cudaPeekAtLastError());
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cuda_assert("computeAtomsPbcUpdate", cudaDeviceSynchronize());
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memcpyFromGPU(atom->x, c_atom->x, sizeof(MD_FLOAT) * atom->Nlocal * 3);
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}
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