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neighbor_gpu.cu
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rLAMMPS lammps
neighbor_gpu.cu
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// **************************************************************************
// atom.cu
// -------------------
// Peng Wang (Nvidia)
// W. Michael Brown (ORNL)
//
// Device code for handling GPU generated neighbor lists
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin :
// email : penwang@nvidia.com, brownw@ornl.gov
// ***************************************************************************/
#ifdef NV_KERNEL
#include "nv_kernel_def.h"
texture<float4> neigh_tex;
#ifdef _DOUBLE_DOUBLE
__inline double4 fetch_pos(const int i, const double4 *pos)
{
return pos[i];
}
#else
__inline float4 fetch_pos(const int& i, const float4 *pos)
{
return tex1Dfetch(neigh_tex, i);
}
#endif
#else
#define fetch_pos(i,y) x_[i]
#define BLOCK_NBOR_BUILD 64
#endif
#ifdef _DOUBLE_DOUBLE
#define numtyp double
#define numtyp4 double4
#endif
#ifdef _SINGLE_DOUBLE
#define numtyp float
#define numtyp4 float4
#endif
#ifndef numtyp
#define numtyp float
#define numtyp4 float4
#endif
#define BLOCK_CELL_2D 8
#define SBBITS 30
#define SBBITS 30
__kernel void transpose(int *out, int *in, int columns_in, int rows_in)
{
__local float block[BLOCK_CELL_2D][BLOCK_CELL_2D+1];
unsigned ti=THREAD_ID_X;
unsigned tj=THREAD_ID_Y;
unsigned bi=BLOCK_ID_X;
unsigned bj=BLOCK_ID_Y;
unsigned i=bi*BLOCK_CELL_2D+ti;
unsigned j=bj*BLOCK_CELL_2D+tj;
if ((i<columns_in) && (j<rows_in))
block[tj][ti]=in[j*columns_in+i];
__syncthreads();
i=bj*BLOCK_CELL_2D+ti;
j=bi*BLOCK_CELL_2D+tj;
if ((i<rows_in) && (j<columns_in))
out[j*rows_in+i] = block[ti][tj];
}
__kernel void calc_cell_id(numtyp4 *pos, unsigned *cell_id, int *particle_id,
numtyp boxlo0,
numtyp boxlo1, numtyp boxlo2, numtyp boxhi0,
numtyp boxhi1, numtyp boxhi2, numtyp cell_size,
int ncellx, int ncelly, int nall) {
int i = threadIdx.x + blockIdx.x*blockDim.x;
if (i < nall) {
numtyp4 p = fetch_pos(i,pos); //pos[i];
p.x -= boxlo0;
p.y -= boxlo1;
p.z -= boxlo2;
p.x = fmaxf(p.x, -cell_size);
p.x = fminf(p.x, boxhi0-boxlo0+cell_size);
p.y = fmaxf(p.y, -cell_size);
p.y = fminf(p.y, boxhi1-boxlo1+cell_size);
p.z = fmaxf(p.z, -cell_size);
p.z = fminf(p.z, boxhi2-boxlo2+cell_size);
unsigned int id = (unsigned int)(p.x/cell_size + 1.0)
+ (unsigned int)(p.y/cell_size + 1.0) * ncellx
+ (unsigned int)(p.z/cell_size + 1.0) * ncellx * ncelly;
cell_id[i] = id;
particle_id[i] = i;
}
}
__kernel void kernel_calc_cell_counts(unsigned *cell_id,
int *cell_counts, int nall, int ncell) {
int idx = threadIdx.x + blockIdx.x * blockDim.x;
if (idx < nall) {
int id = cell_id[idx];
// handle boundary cases
if (idx == 0) {
for (int i = 0; i < id + 1; i++)
cell_counts[i] = 0;
}
if (idx == nall - 1) {
for (int i = id+1; i <= ncell; i++)
cell_counts[i] = nall;
}
if (idx > 0 && idx < nall) {
int id_l = cell_id[idx-1];
if (id != id_l) {
for (int i = id_l+1; i <= id; i++)
cell_counts[i] = idx;
}
}
}
}
__kernel void calc_neigh_list_cell(numtyp4 *pos,
int *cell_particle_id,
int *cell_counts,
int *nbor_list,
int *host_nbor_list,
int *host_numj,
int neigh_bin_size,
numtyp cell_size,
int ncellx, int ncelly, int ncellz,
int inum, int nt, int nall)
{
int tid = threadIdx.x;
int ix = blockIdx.x;
int iy = blockIdx.y % ncelly;
int iz = blockIdx.y / ncelly;
int icell = ix + iy*ncellx + iz*ncellx*ncelly;
__shared__ int cell_list_sh[BLOCK_NBOR_BUILD];
__shared__ numtyp4 pos_sh[BLOCK_NBOR_BUILD];
int icell_begin = cell_counts[icell];
int icell_end = cell_counts[icell+1];
int nborz0 = max(iz-1,0), nborz1 = min(iz+1, ncellz-1),
nbory0 = max(iy-1,0), nbory1 = min(iy+1, ncelly-1),
nborx0 = max(ix-1,0), nborx1 = min(ix+1, ncellx-1);
numtyp4 diff;
numtyp r2;
for (int ii = 0; ii < ceil((numtyp)(icell_end - icell_begin)/blockDim.x); ii++) {
int i = icell_begin + tid + ii*blockDim.x;
int pid_i = nall, pid_j, stride;
numtyp4 atom_i, atom_j;
int cnt = 0;
int *neigh_counts, *neigh_list;
if (i < icell_end)
pid_i = cell_particle_id[i];
if (pid_i < nt) {
atom_i = fetch_pos(pid_i,pos); //pos[pid_i];
}
if (pid_i < inum) {
stride=inum;
neigh_counts=nbor_list+stride+pid_i;
neigh_list=neigh_counts+stride;
nbor_list[pid_i]=pid_i;
} else {
stride=1;
neigh_counts=host_numj+pid_i-inum;
neigh_list=host_nbor_list+(pid_i-inum)*neigh_bin_size;
}
// loop through neighbors
for (int nborz = nborz0; nborz <= nborz1; nborz++) {
for (int nbory = nbory0; nbory <= nbory1; nbory++) {
for (int nborx = nborx0; nborx <= nborx1; nborx++) {
int jcell = nborx + nbory*ncellx + nborz*ncellx*ncelly;
int jcell_begin = cell_counts[jcell];
int jcell_end = cell_counts[jcell+1];
int num_atom_cell = jcell_end - jcell_begin;
// load jcell to shared memory
int num_iter = (int)ceil((numtyp)num_atom_cell/BLOCK_NBOR_BUILD);
for (int k = 0; k < num_iter; k++) {
int end_idx = min(BLOCK_NBOR_BUILD, num_atom_cell-k*BLOCK_NBOR_BUILD);
if (tid < end_idx) {
pid_j = cell_particle_id[tid+k*BLOCK_NBOR_BUILD+jcell_begin];
cell_list_sh[tid] = pid_j;
atom_j = fetch_pos(pid_j,pos); //[pid_j];
pos_sh[tid].x = atom_j.x;
pos_sh[tid].y = atom_j.y;
pos_sh[tid].z = atom_j.z;
}
__syncthreads();
if (pid_i < nt) {
for (int j = 0; j < end_idx; j++) {
int pid_j = cell_list_sh[j]; // gather from shared memory
diff.x = atom_i.x - pos_sh[j].x;
diff.y = atom_i.y - pos_sh[j].y;
diff.z = atom_i.z - pos_sh[j].z;
r2 = diff.x*diff.x + diff.y*diff.y + diff.z*diff.z;
if (r2 < cell_size*cell_size && r2 > 1e-5) {
if (cnt < neigh_bin_size) {
*neigh_list = pid_j;
neigh_list+=stride;
}
cnt++;
}
}
}
__syncthreads();
} // for (k)
}
}
}
if (pid_i < nt)
*neigh_counts = cnt;
} // for (i)
}
__kernel void kernel_special(__global int *dev_nbor,
__global int *host_nbor_list,
__global int *host_numj, __global int *tag,
__global int *nspecial, __global int *special,
int inum, int nt, int max_nbors) {
// ii indexes the two interacting particles in gi
int ii=GLOBAL_ID_X;
if (ii<nt) {
int stride;
__global int *list, *list_end;
int n1=nspecial[ii*3];
int n2=nspecial[ii*3+1];
int n3=nspecial[ii*3+2];
int numj;
if (ii < inum) {
stride=inum;
list=dev_nbor+stride+ii;
numj=*list;
list+=stride;
} else {
stride=1;
list=host_nbor_list+(ii-inum)*max_nbors;
numj=host_numj[ii-inum];
}
list_end=list+numj*stride;
for ( ; list<list_end; list+=stride) {
int nbor=*list;
int jtag=tag[nbor];
int offset=ii;
for (int i=0; i<n3; i++) {
if (special[offset]==jtag) {
int which = 1;
if (i>=n1)
which++;
if (i>=n2)
which++;
nbor=nbor ^ (which << SBBITS);
*list=nbor;
}
offset+=nt;
}
}
} // if ii
}
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