forked from lijiext/lammps
314 lines
9.3 KiB
Plaintext
314 lines
9.3 KiB
Plaintext
// **************************************************************************
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// neighbor_gpu.cu
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// -------------------
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// Peng Wang (Nvidia)
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// W. Michael Brown (ORNL)
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//
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// Device code for handling GPU generated neighbor lists
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//
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// __________________________________________________________________________
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// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
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// __________________________________________________________________________
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//
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// begin :
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// email : penwang@nvidia.com, brownw@ornl.gov
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// ***************************************************************************/
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#ifdef NV_KERNEL
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#include "lal_preprocessor.h"
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#ifdef LAMMPS_SMALLBIG
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#define tagint int
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#endif
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#ifdef LAMMPS_BIGBIG
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#include "inttypes.h"
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#define tagint int64_t
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#endif
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#ifdef LAMMPS_SMALLSMALL
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#define tagint int
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#endif
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#ifndef _DOUBLE_DOUBLE
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texture<float4> pos_tex;
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#else
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texture<int4,1> pos_tex;
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#endif
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__kernel void calc_cell_id(const numtyp4 *restrict pos,
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unsigned *restrict cell_id,
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int *restrict particle_id,
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numtyp boxlo0, numtyp boxlo1, numtyp boxlo2,
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numtyp i_cell_size, int ncellx, int ncelly,
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int ncellz, int inum, int nall,
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int cells_in_cutoff) {
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int i = threadIdx.x + blockIdx.x*blockDim.x;
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if (i < nall) {
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numtyp4 p;
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fetch4(p,i,pos_tex); //pos[i];
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p.x -= boxlo0;
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p.y -= boxlo1;
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p.z -= boxlo2;
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int ix = int(p.x*i_cell_size+cells_in_cutoff);
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int iy = int(p.y*i_cell_size+cells_in_cutoff);
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int iz = int(p.z*i_cell_size+cells_in_cutoff);
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int offset_lo, offset_hi;
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if (i<inum) {
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offset_lo=cells_in_cutoff;
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offset_hi=cells_in_cutoff+1;
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} else {
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offset_lo=0;
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offset_hi=1;
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}
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ix = max(ix,offset_lo);
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ix = min(ix,ncellx-offset_hi);
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iy = max(iy,offset_lo);
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iy = min(iy,ncelly-offset_hi);
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iz = max(iz,offset_lo);
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iz = min(iz,ncellz-offset_hi);
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cell_id[i] = ix+iy*ncellx+iz*ncellx*ncelly;
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particle_id[i] = i;
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}
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}
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__kernel void kernel_calc_cell_counts(const unsigned *restrict cell_id,
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int *restrict cell_counts,
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int nall, int ncell) {
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int idx = threadIdx.x + blockIdx.x * blockDim.x;
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if (idx < nall) {
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int id = cell_id[idx];
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// handle boundary cases
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if (idx == 0) {
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for (int i = 0; i < id + 1; i++)
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cell_counts[i] = 0;
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}
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if (idx == nall - 1) {
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for (int i = id+1; i <= ncell; i++)
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cell_counts[i] = nall;
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}
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if (idx > 0 && idx < nall) {
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int id_l = cell_id[idx-1];
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if (id != id_l) {
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for (int i = id_l+1; i <= id; i++)
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cell_counts[i] = idx;
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}
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}
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}
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}
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#else
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#define pos_tex x_
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#ifdef LAMMPS_SMALLBIG
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#define tagint int
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#endif
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#ifdef LAMMPS_BIGBIG
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#define tagint long long int
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#endif
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#ifdef LAMMPS_SMALLSMALL
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#define tagint int
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#endif
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#endif
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__kernel void transpose(__global tagint *restrict out,
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const __global tagint *restrict in,
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int columns_in, int rows_in)
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{
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__local tagint block[BLOCK_CELL_2D][BLOCK_CELL_2D+1];
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unsigned ti=THREAD_ID_X;
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unsigned tj=THREAD_ID_Y;
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unsigned bi=BLOCK_ID_X;
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unsigned bj=BLOCK_ID_Y;
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unsigned i=bi*BLOCK_CELL_2D+ti;
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unsigned j=bj*BLOCK_CELL_2D+tj;
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if ((i<columns_in) && (j<rows_in))
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block[tj][ti]=in[j*columns_in+i];
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__syncthreads();
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i=bj*BLOCK_CELL_2D+ti;
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j=bi*BLOCK_CELL_2D+tj;
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if ((i<rows_in) && (j<columns_in))
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out[j*rows_in+i] = block[ti][tj];
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}
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__kernel void calc_neigh_list_cell(const __global numtyp4 *restrict x_,
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const __global int *restrict cell_particle_id,
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const __global int *restrict cell_counts,
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__global int *nbor_list,
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__global int *host_nbor_list,
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__global int *host_numj,
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int neigh_bin_size, numtyp cell_size,
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int ncellx, int ncelly, int ncellz,
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int inum, int nt, int nall, int t_per_atom,
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int cells_in_cutoff)
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{
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int tid = THREAD_ID_X;
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int ix = BLOCK_ID_X + cells_in_cutoff;
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int iy = BLOCK_ID_Y % (ncelly - cells_in_cutoff*2) + cells_in_cutoff;
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int iz = BLOCK_ID_Y / (ncelly - cells_in_cutoff*2) + cells_in_cutoff;
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int bsx = BLOCK_SIZE_X;
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int icell = ix + iy*ncellx + iz*ncellx*ncelly;
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__local int cell_list_sh[BLOCK_NBOR_BUILD];
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__local numtyp4 pos_sh[BLOCK_NBOR_BUILD];
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int icell_begin = cell_counts[icell];
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int icell_end = cell_counts[icell+1];
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int nborz0 = iz-cells_in_cutoff, nborz1 = iz+cells_in_cutoff,
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nbory0 = iy-cells_in_cutoff, nbory1 = iy+cells_in_cutoff,
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nborx0 = ix-cells_in_cutoff, nborx1 = ix+cells_in_cutoff;
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numtyp4 diff;
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numtyp r2;
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int cap=ucl_ceil((numtyp)(icell_end - icell_begin)/bsx);
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for (int ii = 0; ii < cap; ii++) {
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int i = icell_begin + tid + ii*bsx;
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int pid_i = nall, pid_j, stride;
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numtyp4 atom_i, atom_j;
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int cnt = 0;
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__global int *neigh_counts, *neigh_list;
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if (i < icell_end)
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pid_i = cell_particle_id[i];
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if (pid_i < nt) {
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fetch4(atom_i,pid_i,pos_tex); //pos[i];
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}
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if (pid_i < inum) {
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stride=inum;
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neigh_counts=nbor_list+stride+pid_i;
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neigh_list=neigh_counts+stride+pid_i*(t_per_atom-1);
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stride=stride*t_per_atom-t_per_atom;
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nbor_list[pid_i]=pid_i;
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} else {
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stride=0;
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neigh_counts=host_numj+pid_i-inum;
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neigh_list=host_nbor_list+(pid_i-inum)*neigh_bin_size;
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}
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// loop through neighbors
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for (int nborz = nborz0; nborz <= nborz1; nborz++) {
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for (int nbory = nbory0; nbory <= nbory1; nbory++) {
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for (int nborx = nborx0; nborx <= nborx1; nborx++) {
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int jcell = nborx + nbory*ncellx + nborz*ncellx*ncelly;
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int jcell_begin = cell_counts[jcell];
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int jcell_end = cell_counts[jcell+1];
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int num_atom_cell = jcell_end - jcell_begin;
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// load jcell to shared memory
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int num_iter = ucl_ceil((numtyp)num_atom_cell/bsx);
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for (int k = 0; k < num_iter; k++) {
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int end_idx = min(bsx, num_atom_cell-k*bsx);
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if (tid < end_idx) {
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pid_j = cell_particle_id[tid+k*bsx+jcell_begin];
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cell_list_sh[tid] = pid_j;
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fetch4(atom_j,pid_j,pos_tex); //[pid_j];
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pos_sh[tid].x = atom_j.x;
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pos_sh[tid].y = atom_j.y;
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pos_sh[tid].z = atom_j.z;
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}
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__syncthreads();
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if (pid_i < nt) {
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for (int j = 0; j < end_idx; j++) {
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int pid_j = cell_list_sh[j]; // gather from shared memory
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diff.x = atom_i.x - pos_sh[j].x;
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diff.y = atom_i.y - pos_sh[j].y;
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diff.z = atom_i.z - pos_sh[j].z;
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r2 = diff.x*diff.x + diff.y*diff.y + diff.z*diff.z;
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if (r2 < cell_size*cell_size && r2 > 1e-5) {
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cnt++;
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if (cnt <= neigh_bin_size) {
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*neigh_list = pid_j;
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neigh_list++;
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if ((cnt & (t_per_atom-1))==0)
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neigh_list=neigh_list+stride;
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}
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}
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}
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}
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__syncthreads();
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} // for (k)
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}
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}
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}
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if (pid_i < nt)
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*neigh_counts = cnt;
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} // for (i)
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}
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__kernel void kernel_special(__global int *dev_nbor,
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__global int *host_nbor_list,
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const __global int *host_numj,
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const __global tagint *restrict tag,
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const __global int *restrict nspecial,
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const __global tagint *restrict special,
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int inum, int nt, int max_nbors, int t_per_atom) {
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int tid=THREAD_ID_X;
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int ii=fast_mul((int)BLOCK_ID_X,(int)(BLOCK_SIZE_X)/t_per_atom);
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ii+=tid/t_per_atom;
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int offset=tid & (t_per_atom-1);
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if (ii<nt) {
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int stride;
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__global int *list, *list_end;
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int n1=nspecial[ii*3];
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int n2=nspecial[ii*3+1];
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int n3=nspecial[ii*3+2];
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int numj;
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if (ii < inum) {
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stride=inum;
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list=dev_nbor+stride+ii;
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numj=*list;
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list+=stride+fast_mul(ii,t_per_atom-1);
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stride=fast_mul(inum,t_per_atom);
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int njt=numj/t_per_atom;
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list_end=list+fast_mul(njt,stride)+(numj & (t_per_atom-1));
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list+=offset;
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} else {
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stride=1;
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list=host_nbor_list+(ii-inum)*max_nbors;
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numj=host_numj[ii-inum];
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list_end=list+fast_mul(numj,stride);
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}
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for ( ; list<list_end; list+=stride) {
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int nbor=*list;
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tagint jtag=tag[nbor];
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int offset=ii;
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for (int i=0; i<n3; i++) {
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if (special[offset]==jtag) {
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int which = 1;
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if (i>=n1)
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which++;
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if (i>=n2)
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which++;
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nbor=nbor ^ (which << SBBITS);
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*list=nbor;
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}
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offset+=nt;
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}
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}
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} // if ii
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}
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