MD-Bench/lammps/cuda/pbc.cu

/*
 * Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
 * All rights reserved. This file is part of MD-Bench.
 * Use of this source code is governed by a LGPL-3.0
 * license that can be found in the LICENSE file.
 */
#include <stdlib.h>
#include <stdio.h>
//---

extern "C" {

#include <allocate.h>
#include <atom.h>
#include <device.h>
#include <pbc.h>
#include <util.h>

}

extern int NmaxGhost;
extern int *PBCx, *PBCy, *PBCz;
static int c_NmaxGhost = 0;
static int *c_PBCx = NULL, *c_PBCy = NULL, *c_PBCz = NULL;

__global__ void computeAtomsPbcUpdate(DeviceAtom a, int nlocal, MD_FLOAT xprd, MD_FLOAT yprd, MD_FLOAT zprd) {
    const int i = blockIdx.x * blockDim.x + threadIdx.x;
    DeviceAtom *atom = &a;
    if(i >= nlocal) {
        return;
    }

    if (atom_x(i) < 0.0) {
        atom_x(i) += xprd;
    } else if (atom_x(i) >= xprd) {
        atom_x(i) -= xprd;
    }

    if (atom_y(i) < 0.0) {
        atom_y(i) += yprd;
    } else if (atom_y(i) >= yprd) {
        atom_y(i) -= yprd;
    }

    if (atom_z(i) < 0.0) {
        atom_z(i) += zprd;
    } else if (atom_z(i) >= zprd) {
        atom_z(i) -= zprd;
    }
}

__global__ void computePbcUpdate(DeviceAtom a, int nlocal, int nghost, int* PBCx, int* PBCy, int* PBCz, MD_FLOAT xprd, MD_FLOAT yprd, MD_FLOAT zprd){
    const int i = blockIdx.x * blockDim.x + threadIdx.x;
    if(i >= nghost) {
        return;
    }

    DeviceAtom* atom = &a;
    int *border_map = atom->border_map;
    atom_x(nlocal + i) = atom_x(border_map[i]) + PBCx[i] * xprd;
    atom_y(nlocal + i) = atom_y(border_map[i]) + PBCy[i] * yprd;
    atom_z(nlocal + i) = atom_z(border_map[i]) + PBCz[i] * zprd;
}

/* update coordinates of ghost atoms */
/* uses mapping created in setupPbc */
void updatePbc_cuda(Atom *atom, Parameter *param, bool reneigh) {
    const int num_threads_per_block = get_num_threads();

    if(reneigh) {
        memcpyToGPU(atom->d_atom.x,     atom->x,    sizeof(MD_FLOAT) * atom->Nmax * 3);
        memcpyToGPU(atom->d_atom.type,  atom->type, sizeof(int) * atom->Nmax);

        if(c_NmaxGhost < NmaxGhost) {
            c_NmaxGhost = NmaxGhost;
            c_PBCx = (int *) reallocateGPU(c_PBCx, NmaxGhost * sizeof(int));
            c_PBCy = (int *) reallocateGPU(c_PBCy, NmaxGhost * sizeof(int));
            c_PBCz = (int *) reallocateGPU(c_PBCz, NmaxGhost * sizeof(int));
            atom->d_atom.border_map = (int *) reallocateGPU(atom->d_atom.border_map, NmaxGhost * sizeof(int));
        }

        memcpyToGPU(c_PBCx, PBCx, NmaxGhost * sizeof(int));
        memcpyToGPU(c_PBCy, PBCy, NmaxGhost * sizeof(int));
        memcpyToGPU(c_PBCz, PBCz, NmaxGhost * sizeof(int));
        memcpyToGPU(atom->d_atom.border_map, atom->border_map, NmaxGhost * sizeof(int));
        cuda_assert("updatePbc.reneigh", cudaPeekAtLastError());
        cuda_assert("updatePbc.reneigh", cudaDeviceSynchronize());
    }

    MD_FLOAT xprd = param->xprd;
    MD_FLOAT yprd = param->yprd;
    MD_FLOAT zprd = param->zprd;

    const int num_blocks = ceil((float)atom->Nghost / (float)num_threads_per_block);
    computePbcUpdate<<<num_blocks, num_threads_per_block>>>(atom->d_atom, atom->Nlocal, atom->Nghost, c_PBCx, c_PBCy, c_PBCz, xprd, yprd, zprd);
    cuda_assert("updatePbc", cudaPeekAtLastError());
    cuda_assert("updatePbc", cudaDeviceSynchronize());
}

void updateAtomsPbc_cuda(Atom* atom, Parameter *param) {
    const int num_threads_per_block = get_num_threads();
    MD_FLOAT xprd = param->xprd;
    MD_FLOAT yprd = param->yprd;
    MD_FLOAT zprd = param->zprd;

    const int num_blocks = ceil((float)atom->Nlocal / (float)num_threads_per_block);
    computeAtomsPbcUpdate<<<num_blocks, num_threads_per_block>>>(atom->d_atom, atom->Nlocal, xprd, yprd, zprd);
    cuda_assert("computeAtomsPbcUpdate", cudaPeekAtLastError());
    cuda_assert("computeAtomsPbcUpdate", cudaDeviceSynchronize());
    memcpyFromGPU(atom->x, atom->d_atom.x, sizeof(MD_FLOAT) * atom->Nlocal * 3);
}