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neighbor_list.cc
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#include "neighbor_list.h"
#include "device.h"
#include <iostream>
#include <limits>
// #include <iomanip>
// using namespace std;
enum {
MAX_WARN_IDX_OUT_OF_BOUND = 10,
};
bool
is_loc (const std::vector<int> & idx,
const std::vector<int> & nat_stt,
const std::vector<int> & nat_end)
{
bool ret = true;
for (int dd = 0; dd < 3; ++dd) ret = ret && idx[dd] >= nat_stt[dd];
for (int dd = 0; dd < 3; ++dd) ret = ret && idx[dd] < nat_end[dd];
return ret;
}
int
collapse_index (const std::vector<int> & idx,
const std::vector<int> & size)
{
return (idx[0] * size[1] + idx[1]) * size[2] + idx[2];
}
void
expand_index (std::vector<int > & o_idx,
const int & i_idx,
const std::vector<int> & size)
{
int tmp1 = i_idx / size[2];
o_idx[2] = i_idx - tmp1 * size[2];
o_idx[0] = tmp1 / size[1];
o_idx[1] = tmp1 - o_idx[0] * size[1];
}
void
build_clist (std::vector<std::vector<int > > & clist,
const std::vector<double > & coord,
const int & nloc,
const std::vector<int > & nat_stt,
const std::vector<int > & nat_end,
const std::vector<int > & ext_stt,
const std::vector<int > & ext_end,
const SimulationRegion<double> & region,
const std::vector<int > & global_grid)
{
static int count_warning_loc_idx_lower = 0;
static int count_warning_loc_idx_upper = 0;
static int count_warning_ghost_idx_lower = 0;
static int count_warning_ghost_idx_upper = 0;
// compute region info, in terms of internal coord
int nall = coord.size() / 3;
std::vector<int> ext_ncell(3);
for (int dd = 0; dd < 3; ++dd) ext_ncell[dd] = ext_end[dd] - ext_stt[dd];
int ncell = ext_ncell[0] * ext_ncell[1] * ext_ncell[2];
std::vector<double > cell_size (3);
for (int dd = 0; dd < 3; ++dd) cell_size[dd] = 1./global_grid[dd];
std::vector<double > nat_orig(3);
for (int dd = 0; dd < 3; ++dd) nat_orig[dd] = nat_stt[dd] * cell_size[dd];
std::vector<int> idx_orig_shift(3);
for (int dd = 0; dd < 3; ++dd) idx_orig_shift[dd] = nat_stt[dd] - ext_stt[dd];
// allocate the reserve the cell list
clist.resize (ncell);
int esti_natom_per_cell = nall / ncell + 10;
for (unsigned ii = 0; ii < clist.size(); ++ii){
clist[ii].clear();
clist[ii].reserve (esti_natom_per_cell);
}
// build the cell list
for (int ii = 0; ii < nloc; ++ii){
double inter[3];
region.phys2Inter (inter, &(coord[ii*3]));
std::vector<int > idx(3);
for (int dd = 0; dd < 3; ++dd){
idx[dd] = (inter[dd] - nat_orig[dd]) / cell_size[dd];
if (inter[dd] - nat_orig[dd] < 0.) idx[dd] --;
if (idx[dd] < nat_stt[dd]) {
if (count_warning_loc_idx_lower < MAX_WARN_IDX_OUT_OF_BOUND) {
std::cerr << "# warning: loc idx out of lower bound (ignored if warned for more than " << MAX_WARN_IDX_OUT_OF_BOUND << " times) " << std::endl;
count_warning_loc_idx_lower ++;
}
idx[dd] = nat_stt[dd];
}
else if (idx[dd] >= nat_end[dd]) {
if (count_warning_loc_idx_upper < MAX_WARN_IDX_OUT_OF_BOUND) {
std::cerr << "# warning: loc idx out of upper bound (ignored if warned for more than " << MAX_WARN_IDX_OUT_OF_BOUND << " times) " << std::endl;
count_warning_loc_idx_upper ++;
}
idx[dd] = nat_end[dd] - 1;
}
idx[dd] += idx_orig_shift[dd];
}
clist[collapse_index(idx, ext_ncell)].push_back (ii);
}
for (int ii = nloc; ii < nall; ++ii){
double inter[3];
region.phys2Inter (inter, &(coord[ii*3]));
std::vector<int > idx(3);
for (int dd = 0; dd < 3; ++dd){
idx[dd] = (inter[dd] - nat_orig[dd]) / cell_size[dd];
if (inter[dd] - nat_orig[dd] < 0.) idx[dd] --;
if (idx[dd] < ext_stt[dd]) {
if (count_warning_ghost_idx_lower < MAX_WARN_IDX_OUT_OF_BOUND &&
fabs((inter[dd] - nat_orig[dd]) - (ext_stt[dd] * cell_size[dd]))
> fabs(ext_stt[dd] * cell_size[dd]) * std::numeric_limits<double>::epsilon() * 5.
) {
std::cerr << "# warning: ghost idx out of lower bound (ignored if warned for more than " << MAX_WARN_IDX_OUT_OF_BOUND << " times) " << std::endl;
count_warning_ghost_idx_lower ++;
}
idx[dd] = ext_stt[dd];
}
else if (idx[dd] >= ext_end[dd]) {
if (count_warning_ghost_idx_upper < MAX_WARN_IDX_OUT_OF_BOUND) {
std::cerr << "# warning: ghost idx out of upper bound (ignored if warned for more than " << MAX_WARN_IDX_OUT_OF_BOUND << " times) " << std::endl;
count_warning_ghost_idx_upper ++;
}
idx[dd] = ext_end[dd] - 1;
}
idx[dd] += idx_orig_shift[dd];
}
clist[collapse_index(idx, ext_ncell)].push_back (ii);
}
}
void
build_clist (std::vector<std::vector<int > > & clist,
const std::vector<double > & coord,
const std::vector<int> & sel,
const std::vector<int > & nat_stt,
const std::vector<int > & nat_end,
const SimulationRegion<double> & region)
{
static int count_warning_loc_idx_lower = 0;
static int count_warning_loc_idx_upper = 0;
// compute region info, in terms of internal coord
int nall = coord.size() / 3;
std::vector<int> nat_ncell(3);
for (int dd = 0; dd < 3; ++dd) nat_ncell[dd] = nat_end[dd] - nat_stt[dd];
int ncell = nat_ncell[0] * nat_ncell[1] * nat_ncell[2];
std::vector<double > cell_size (3);
for (int dd = 0; dd < 3; ++dd) cell_size[dd] = 1./nat_end[dd];
std::vector<double > nat_orig(3);
for (int dd = 0; dd < 3; ++dd) nat_orig[dd] = nat_stt[dd] * cell_size[dd];
// allocate the reserve the cell list
clist.resize (ncell);
int esti_natom_per_cell = nall / ncell + 10;
for (unsigned ii = 0; ii < clist.size(); ++ii){
clist[ii].clear();
clist[ii].reserve (esti_natom_per_cell);
}
// build the cell list
for (unsigned _ = 0; _ < sel.size(); ++_){
int ii = sel[_];
double inter[3];
region.phys2Inter (inter, &(coord[ii*3]));
std::vector<int > idx(3);
for (int dd = 0; dd < 3; ++dd){
idx[dd] = (inter[dd] - nat_orig[dd]) / cell_size[dd];
if (inter[dd] - nat_orig[dd] < 0.) idx[dd] --;
if (idx[dd] < nat_stt[dd]) {
if (count_warning_loc_idx_lower < MAX_WARN_IDX_OUT_OF_BOUND) {
std::cerr << "# warning: loc idx out of lower bound (ignored if warned for more than " << MAX_WARN_IDX_OUT_OF_BOUND << " times) " << std::endl;
count_warning_loc_idx_lower ++;
}
idx[dd] = nat_stt[dd];
}
else if (idx[dd] >= nat_end[dd]) {
if (count_warning_loc_idx_upper < MAX_WARN_IDX_OUT_OF_BOUND) {
std::cerr << "# warning: loc idx out of upper bound (ignored if warned for more than " << MAX_WARN_IDX_OUT_OF_BOUND << " times) " << std::endl;
count_warning_loc_idx_upper ++;
}
idx[dd] = nat_end[dd] - 1;
}
}
clist[collapse_index(idx, nat_ncell)].push_back (ii);
}
}
void
build_nlist_cell (std::vector<std::vector<int> > & nlist0,
std::vector<std::vector<int> > & nlist1,
const int & cidx,
const int & tidx,
const std::vector<std::vector<int > > & clist,
const std::vector<double > & coord,
const double & rc02,
const double & rc12,
const std::vector<int> & shift = {0, 0, 0},
const std::vector<double > & boxt = {0., 0., 0., 0., 0., 0., 0., 0., 0.})
{
int nloc = nlist0.size();
// loop over c (current) cell
for (unsigned ii = 0; ii < clist[cidx].size(); ++ii){
int i_idx = clist[cidx][ii];
// assert (i_idx < nloc);
// loop over t (target) cell
for (unsigned jj = 0; jj < clist[tidx].size(); ++jj){
int j_idx = clist[tidx][jj];
if (cidx == tidx && j_idx <= i_idx) continue;
double diff[3];
for (int dd0 = 0; dd0 < 3; ++dd0) {
diff[dd0] = coord[i_idx*3 + dd0] - coord[j_idx*3 + dd0];
for (int dd1 = 0; dd1 < 3; ++dd1) {
diff[dd0] += shift[dd1] * boxt[3*dd1+dd0];
}
}
double r2 = deepmd::dot3(diff, diff);
if (r2 < rc02) {
if (i_idx < nloc) nlist0[i_idx].push_back (j_idx);
if (j_idx < nloc) nlist0[j_idx].push_back (i_idx);
}
else if (r2 < rc12) {
if (i_idx < nloc) nlist1[i_idx].push_back (j_idx);
if (j_idx < nloc) nlist1[j_idx].push_back (i_idx);
}
}
}
}
void
build_nlist_cell (std::vector<std::vector<int> > & nlist0,
std::vector<std::vector<int> > & nlist1,
const int & cidx,
const int & tidx,
const std::vector<std::vector<int > > & clist0,
const std::vector<std::vector<int > > & clist1,
const std::vector<double > & coord,
const double & rc02,
const double & rc12,
const std::vector<int> & shift = {0, 0, 0},
const std::vector<double > & boxt = {0., 0., 0., 0., 0., 0., 0., 0., 0.})
{
// loop over c (current) cell
for (unsigned ii = 0; ii < clist0[cidx].size(); ++ii){
int i_idx = clist0[cidx][ii];
if (i_idx >= nlist0.size()) continue;
// loop over t (target) cell
for (unsigned jj = 0; jj < clist1[tidx].size(); ++jj){
int j_idx = clist1[tidx][jj];
if (cidx == tidx && j_idx == i_idx) continue;
double diff[3];
for (int dd0 = 0; dd0 < 3; ++dd0) {
diff[dd0] = coord[i_idx*3 + dd0] - coord[j_idx*3 + dd0];
for (int dd1 = 0; dd1 < 3; ++dd1) {
diff[dd0] += shift[dd1] * boxt[3*dd1+dd0];
}
}
double r2 = deepmd::dot3(diff, diff);
if (r2 < rc02) {
nlist0[i_idx].push_back (j_idx);
}
else if (r2 < rc12) {
nlist1[i_idx].push_back (j_idx);
}
}
}
}
void
build_nlist (std::vector<std::vector<int > > & nlist0,
std::vector<std::vector<int > > & nlist1,
const std::vector<double > & coord,
const int & nloc,
const double & rc0,
const double & rc1,
const std::vector<int > & nat_stt_,
const std::vector<int > & nat_end_,
const std::vector<int > & ext_stt_,
const std::vector<int > & ext_end_,
const SimulationRegion<double> & region,
const std::vector<int > & global_grid)
{
// normalize the index
// i require that the ext_stt = {0, 0, 0}
std::vector<int > nat_stt (nat_stt_);
std::vector<int > nat_end (nat_end_);
std::vector<int > ext_stt (ext_stt_);
std::vector<int > ext_end (ext_end_);
// compute the clist
std::vector<std::vector<int > > clist;
build_clist (clist, coord, nloc, nat_stt, nat_end, ext_stt, ext_end, region, global_grid);
// compute the region info
int nall = coord.size() / 3;
std::vector<int> ext_ncell(3);
for (int dd = 0; dd < 3; ++dd) ext_ncell[dd] = ext_end[dd] - ext_stt[dd];
// compute number of iter according to the cut-off
assert (rc0 <= rc1);
std::vector<int> niter (3);
double to_face [3];
region.toFaceDistance (to_face);
for (int dd = 0; dd < 3; ++dd){
double cell_size = to_face[dd] / nat_end[dd];
niter[dd] = rc1 / cell_size;
if (niter[dd] * cell_size < rc1) niter[dd] += 1;
assert (niter[dd] * cell_size >= rc1);
}
// check the validity of the iters
for (int dd = 0; dd < 3; ++dd){
assert (nat_stt[dd] - niter[dd] >= ext_stt[dd]);
assert (nat_end[dd] + niter[dd] <= ext_end[dd]);
}
// allocate the nlists
double density = nloc / region.getVolume();
nlist0.resize (nloc);
for (int ii = 0; ii < nloc; ++ii){
nlist0[ii].clear();
int esti = 4./3. * 3.14 * (rc0*rc0*rc0) * density * 1.5 + 20;
if (esti < 0) esti = 10;
nlist0[ii].reserve ( esti );
}
nlist1.resize (nloc);
for (int ii = 0; ii < nloc; ++ii){
nlist1[ii].clear();
int esti = 4./3. * 3.14 * (rc1*rc1*rc1 - rc0*rc0*rc0) * density * 1.5 + 20;
if (esti < 0) esti = 10;
nlist1[ii].reserve ( esti );
}
// shift of the idx origin
std::vector<int> idx_orig_shift(3);
for (int dd = 0; dd < 3; ++dd) idx_orig_shift[dd] = nat_stt[dd] - ext_stt[dd];
// compute the nlists
double rc02 = 0;
if (rc0 > 0) rc02 = rc0 * rc0;
double rc12 = rc1 * rc1;
std::vector<int> cidx(3);
for (cidx[0] = nat_stt[0]; cidx[0] < nat_end[0]; ++cidx[0]){
for (cidx[1] = nat_stt[1]; cidx[1] < nat_end[1]; ++cidx[1]){
for (cidx[2] = nat_stt[2]; cidx[2] < nat_end[2]; ++cidx[2]){
std::vector<int> mcidx(3);
for (int dd = 0; dd < 3; ++dd) mcidx[dd] = cidx[dd] + idx_orig_shift[dd];
int clp_cidx = collapse_index (mcidx, ext_ncell);
std::vector<int> tidx(3);
for (tidx[0] = cidx[0] - niter[0]; tidx[0] < cidx[0] + niter[0] + 1; ++tidx[0]) {
for (tidx[1] = cidx[1] - niter[1]; tidx[1] < cidx[1] + niter[1] + 1; ++tidx[1]) {
for (tidx[2] = cidx[2] - niter[2]; tidx[2] < cidx[2] + niter[2] + 1; ++tidx[2]) {
std::vector<int> mtidx(3);
for (int dd = 0; dd < 3; ++dd) mtidx[dd] = tidx[dd] + idx_orig_shift[dd];
int clp_tidx = collapse_index (mtidx, ext_ncell);
if (is_loc(tidx, nat_stt, nat_end) && clp_tidx < clp_cidx) continue;
build_nlist_cell (nlist0, nlist1, clp_cidx, clp_tidx, clist, coord, rc02, rc12);
}
}
}
}
}
}
}
// assume nat grid is the global grid. only used for serial simulations
void
build_nlist (std::vector<std::vector<int > > & nlist0,
std::vector<std::vector<int > > & nlist1,
const std::vector<double > & coord,
const double & rc0,
const double & rc1,
const std::vector<int > & grid,
const SimulationRegion<double> & region)
{
// assuming nloc == nall
int nloc = coord.size() / 3;
// compute the clist
std::vector<int> nat_stt(3, 0);
std::vector<int> nat_end(grid);
std::vector<std::vector<int > > clist;
build_clist (clist, coord, nloc, nat_stt, nat_end, nat_stt, nat_end, region, nat_end);
// compute the region info
int nall = coord.size() / 3;
std::vector<int> nat_ncell(3);
for (int dd = 0; dd < 3; ++dd) nat_ncell[dd] = nat_end[dd] - nat_stt[dd];
// compute number of iter according to the cut-off
assert (rc0 <= rc1);
std::vector<int> niter (3);
double to_face [3];
region.toFaceDistance (to_face);
for (int dd = 0; dd < 3; ++dd){
double cell_size = to_face[dd] / nat_end[dd];
niter[dd] = rc1 / cell_size;
if (niter[dd] * cell_size < rc1) niter[dd] += 1;
assert (niter[dd] * cell_size >= rc1);
}
// check the validity of the iters
for (int dd = 0; dd < 3; ++dd){
assert (niter[dd] <= (nat_end[dd] - nat_stt[dd]) / 2);
}
// allocate the nlists
double density = nall / region.getVolume();
nlist0.resize (nloc);
for (int ii = 0; ii < nloc; ++ii){
nlist0[ii].clear();
nlist0[ii].reserve ( 4./3. * 3.14 * (rc0*rc0*rc0) * density * 1.5 + 20);
}
nlist1.resize (nloc);
for (int ii = 0; ii < nloc; ++ii){
nlist1[ii].clear();
nlist1[ii].reserve ( 4./3. * 3.14 * (rc1*rc1*rc1 - rc0*rc0*rc0) * density * 1.5 + 20);
}
// physical cell size
std::vector<double> phys_cs(9);
for (int dd = 0; dd < 9; ++dd) phys_cs[dd] = region.getBoxTensor()[dd];
// compute the nlists
double rc02 = 0;
if (rc0 > 0) rc02 = rc0 * rc0;
double rc12 = rc1 * rc1;
#ifdef HALF_NEIGHBOR_LIST
std::vector<int> cidx(3);
for (cidx[0] = nat_stt[0]; cidx[0] < nat_end[0]; ++cidx[0]){
for (cidx[1] = nat_stt[1]; cidx[1] < nat_end[1]; ++cidx[1]){
for (cidx[2] = nat_stt[2]; cidx[2] < nat_end[2]; ++cidx[2]){
#else
int idx_range[3];
idx_range[0] = nat_end[0] - nat_stt[0];
idx_range[1] = nat_end[1] - nat_stt[1];
idx_range[2] = nat_end[2] - nat_stt[2];
int idx_total = idx_range[0] * idx_range[1] * idx_range[2];
#pragma omp parallel for
for (int tmpidx = 0; tmpidx < idx_total; ++tmpidx) {
std::vector<int> cidx(3);
cidx[0] = nat_stt[0] + tmpidx / (idx_range[1] * idx_range[2]);
int tmpidx1 = tmpidx - cidx[0] * idx_range[1] * idx_range[2];
cidx[1] = nat_stt[1] + tmpidx1 / idx_range[2];
cidx[2] = nat_stt[2] + tmpidx1 - cidx[1] * idx_range[2];
{
{
#endif
int clp_cidx = collapse_index (cidx, nat_ncell);
std::vector<int> tidx(3);
std::vector<int> stidx(3);
std::vector<int> shift(3);
for (tidx[0] = cidx[0] - niter[0]; tidx[0] < cidx[0] + niter[0] + 1; ++tidx[0]) {
shift[0] = 0;
if (tidx[0] < 0) shift[0] += 1;
else if (tidx[0] >= nat_ncell[0]) shift[0] -= 1;
stidx[0] = tidx[0] + shift[0] * nat_ncell[0];
for (tidx[1] = cidx[1] - niter[1]; tidx[1] < cidx[1] + niter[1] + 1; ++tidx[1]) {
shift[1] = 0;
if (tidx[1] < 0) shift[1] += 1;
else if (tidx[1] >= nat_ncell[1]) shift[1] -= 1;
stidx[1] = tidx[1] + shift[1] * nat_ncell[1];
for (tidx[2] = cidx[2] - niter[2]; tidx[2] < cidx[2] + niter[2] + 1; ++tidx[2]) {
shift[2] = 0;
if (tidx[2] < 0) shift[2] += 1;
else if (tidx[2] >= nat_ncell[2]) shift[2] -= 1;
stidx[2] = tidx[2] + shift[2] * nat_ncell[2];
int clp_tidx = collapse_index (stidx, nat_ncell);
#ifdef HALF_NEIGHBOR_LIST
if (clp_tidx < clp_cidx) continue;
build_nlist_cell (nlist0, nlist1, clp_cidx, clp_tidx, clist, coord, rc02, rc12, shift, phys_cs);
#else
build_nlist_cell (nlist0, nlist1, clp_cidx, clp_tidx, clist, clist, coord, rc02, rc12, shift, phys_cs);
#endif
}
}
}
}
}
}
}
void
build_nlist (std::vector<std::vector<int > > & nlist0,
std::vector<std::vector<int > > & nlist1,
const std::vector<double > & coord,
const std::vector<int> & sel0,
const std::vector<int> & sel1,
const double & rc0,
const double & rc1,
const std::vector<int > & grid,
const SimulationRegion<double> & region)
{
int nloc = coord.size() / 3;
// compute the clist
std::vector<int> nat_stt(3, 0);
std::vector<int> nat_end(grid);
std::vector<std::vector<int > > clist0, clist1;
build_clist (clist0, coord, sel0, nat_stt, nat_end, region);
build_clist (clist1, coord, sel1, nat_stt, nat_end, region);
// compute the region info
int nall = coord.size() / 3;
std::vector<int> nat_ncell(3);
for (int dd = 0; dd < 3; ++dd) nat_ncell[dd] = nat_end[dd] - nat_stt[dd];
// compute number of iter according to the cut-off
assert (rc0 <= rc1);
std::vector<int> niter (3);
double to_face [3];
region.toFaceDistance (to_face);
for (int dd = 0; dd < 3; ++dd){
double cell_size = to_face[dd] / nat_end[dd];
niter[dd] = rc1 / cell_size;
if (niter[dd] * cell_size < rc1) niter[dd] += 1;
assert (niter[dd] * cell_size >= rc1);
}
// check the validity of the iters
for (int dd = 0; dd < 3; ++dd){
assert (niter[dd] <= (nat_end[dd] - nat_stt[dd]) / 2);
}
// allocate the nlists
double density = nall / region.getVolume();
nlist0.resize (nloc);
for (int ii = 0; ii < nloc; ++ii){
nlist0[ii].clear();
nlist0[ii].reserve ( 4./3. * 3.14 * (rc0*rc0*rc0) * density * 1.5 + 20);
}
nlist1.resize (nloc);
for (int ii = 0; ii < nloc; ++ii){
nlist1[ii].clear();
nlist1[ii].reserve ( 4./3. * 3.14 * (rc1*rc1*rc1 - rc0*rc0*rc0) * density * 1.5 + 20);
}
// physical cell size
std::vector<double> phys_cs(9);
for (int dd = 0; dd < 9; ++dd) phys_cs[dd] = region.getBoxTensor()[dd];
// compute the nlists
double rc02 = 0;
if (rc0 > 0) rc02 = rc0 * rc0;
double rc12 = rc1 * rc1;
std::vector<int> cidx(3);
for (cidx[0] = nat_stt[0]; cidx[0] < nat_end[0]; ++cidx[0]){
for (cidx[1] = nat_stt[1]; cidx[1] < nat_end[1]; ++cidx[1]){
for (cidx[2] = nat_stt[2]; cidx[2] < nat_end[2]; ++cidx[2]){
int clp_cidx = collapse_index (cidx, nat_ncell);
std::vector<int> tidx(3);
std::vector<int> stidx(3);
std::vector<int> shift(3);
for (tidx[0] = cidx[0] - niter[0]; tidx[0] < cidx[0] + niter[0] + 1; ++tidx[0]) {
shift[0] = 0;
if (tidx[0] < 0) shift[0] += 1;
else if (tidx[0] >= nat_ncell[0]) shift[0] -= 1;
stidx[0] = tidx[0] + shift[0] * nat_ncell[0];
for (tidx[1] = cidx[1] - niter[1]; tidx[1] < cidx[1] + niter[1] + 1; ++tidx[1]) {
shift[1] = 0;
if (tidx[1] < 0) shift[1] += 1;
else if (tidx[1] >= nat_ncell[1]) shift[1] -= 1;
stidx[1] = tidx[1] + shift[1] * nat_ncell[1];
for (tidx[2] = cidx[2] - niter[2]; tidx[2] < cidx[2] + niter[2] + 1; ++tidx[2]) {
shift[2] = 0;
if (tidx[2] < 0) shift[2] += 1;
else if (tidx[2] >= nat_ncell[2]) shift[2] -= 1;
stidx[2] = tidx[2] + shift[2] * nat_ncell[2];
int clp_tidx = collapse_index (stidx, nat_ncell);
build_nlist_cell (nlist0, nlist1, clp_cidx, clp_tidx, clist0, clist1, coord, rc02, rc12, shift, phys_cs);
}
}
}
}
}
}
}
void
build_nlist (std::vector<std::vector<int > > & nlist0,
std::vector<std::vector<int > > & nlist1,
const std::vector<double > & posi3,
const double & rc0_,
const double & rc1_,
const SimulationRegion<double > * region)
{
double rc0 (rc0_);
double rc1 (rc1_);
assert (rc0 <= rc1);
double rc02 = rc0 * rc0;
// negative rc0 means not applying rc0
if (rc0 < 0) rc02 = 0;
double rc12 = rc1 * rc1;
unsigned natoms = posi3.size()/3;
nlist0.clear();
nlist1.clear();
nlist0.resize(natoms);
nlist1.resize(natoms);
for (unsigned ii = 0; ii < natoms; ++ii){
nlist0[ii].reserve (60);
nlist1[ii].reserve (60);
}
for (unsigned ii = 0; ii < natoms; ++ii){
for (unsigned jj = ii+1; jj < natoms; ++jj){
double diff[3];
if (region != NULL) {
region->diffNearestNeighbor (posi3[jj*3+0], posi3[jj*3+1], posi3[jj*3+2],
posi3[ii*3+0], posi3[ii*3+1], posi3[ii*3+2],
diff[0], diff[1], diff[2]);
}
else {
diff[0] = posi3[jj*3+0] - posi3[ii*3+0];
diff[1] = posi3[jj*3+1] - posi3[ii*3+1];
diff[2] = posi3[jj*3+2] - posi3[ii*3+2];
}
double r2 = deepmd::dot3(diff, diff);
if (r2 < rc02) {
nlist0[ii].push_back (jj);
nlist0[jj].push_back (ii);
}
else if (r2 < rc12) {
nlist1[ii].push_back (jj);
nlist1[jj].push_back (ii);
}
}
}
}
static int compute_pbc_shift (int idx,
int ncell)
{
int shift = 0;
if (idx < 0) {
shift = 1;
while (idx + shift * ncell < 0) shift ++;
}
else if (idx >= ncell) {
shift = -1;
while (idx + shift * ncell >= ncell) shift --;
}
assert (idx + shift * ncell >= 0 && idx + shift * ncell < ncell);
return shift;
}
void
copy_coord (std::vector<double > & out_c,
std::vector<int > & out_t,
std::vector<int > & mapping,
std::vector<int> & ncell,
std::vector<int> & ngcell,
const std::vector<double > & in_c,
const std::vector<int > & in_t,
const double & rc,
const SimulationRegion<double > & region)
{
int nloc = in_c.size() / 3;
assert(nloc == in_t.size());
ncell.resize(3);
ngcell.resize(3);
double to_face [3];
double cell_size [3];
region.toFaceDistance (to_face);
for (int dd = 0; dd < 3; ++dd){
ncell[dd] = to_face[dd] / rc;
if (ncell[dd] == 0) ncell[dd] = 1;
cell_size[dd] = to_face[dd] / ncell[dd];
ngcell[dd] = int(rc / cell_size[dd]) + 1;
assert(cell_size[dd] * ngcell[dd] >= rc);
}
int total_ncell = (2 * ngcell[0] + ncell[0]) * (2 * ngcell[1] + ncell[1]) * (2 * ngcell[2] + ncell[2]);
int loc_ncell = (ncell[0]) * (ncell[1]) * (ncell[2]);
int esti_ntotal = total_ncell / loc_ncell * nloc + 10;
// alloc
out_c.reserve(esti_ntotal * 6);
out_t.reserve(esti_ntotal * 2);
mapping.reserve(esti_ntotal * 2);
// build cell list
std::vector<std::vector<int > > clist;
std::vector<int> nat_stt(3, 0);
build_clist (clist, in_c, nloc, nat_stt, ncell, nat_stt, ncell, region, ncell);
// copy local atoms
out_c.resize(nloc * 3);
out_t.resize(nloc);
mapping.resize(nloc);
copy(in_c.begin(), in_c.end(), out_c.begin());
copy(in_t.begin(), in_t.end(), out_t.begin());
for (int ii = 0; ii < nloc; ++ii) mapping[ii] = ii;
// push ghost
std::vector<int> ii(3), jj(3), pbc_shift(3, 0);
double pbc_shift_d[3];
for (ii[0] = -ngcell[0]; ii[0] < ncell[0] + ngcell[0]; ++ii[0]){
pbc_shift[0] = compute_pbc_shift(ii[0], ncell[0]);
pbc_shift_d[0] = pbc_shift[0];
jj[0] = ii[0] + pbc_shift[0] * ncell[0];
for (ii[1] = -ngcell[1]; ii[1] < ncell[1] + ngcell[1]; ++ii[1]){
pbc_shift[1] = compute_pbc_shift(ii[1], ncell[1]);
pbc_shift_d[1] = pbc_shift[1];
jj[1] = ii[1] + pbc_shift[1] * ncell[1];
for (ii[2] = -ngcell[2]; ii[2] < ncell[2] + ngcell[2]; ++ii[2]){
pbc_shift[2] = compute_pbc_shift(ii[2], ncell[2]);
pbc_shift_d[2] = pbc_shift[2];
jj[2] = ii[2] + pbc_shift[2] * ncell[2];
// local cell, continue
if (ii[0] >= 0 && ii[0] < ncell[0] &&
ii[1] >= 0 && ii[1] < ncell[1] &&
ii[2] >= 0 && ii[2] < ncell[2] ){
continue;
}
double shift_v [3];
region.inter2Phys(shift_v, pbc_shift_d);
int cell_idx = collapse_index(jj, ncell);
std::vector<int> & cur_clist = clist[cell_idx];
for (int kk = 0; kk < cur_clist.size(); ++kk){
int p_idx = cur_clist[kk];
double shifted_coord [3];
out_c.push_back(in_c[p_idx*3+0] - shift_v[0]);
out_c.push_back(in_c[p_idx*3+1] - shift_v[1]);
out_c.push_back(in_c[p_idx*3+2] - shift_v[2]);
out_t.push_back(in_t[p_idx]);
mapping.push_back(p_idx);
// double phys[3];
// for (int dd = 0; dd < 3; ++dd) phys[dd] = in_c[p_idx*3+dd] - shift_v[dd];
// double inter[3];
// region.phys2Inter(inter, phys);
// if ( inter[0] >= 0 && inter[0] < 1 &&
// inter[1] >= 0 && inter[1] < 1 &&
// inter[2] >= 0 && inter[2] < 1 ){
// std::cout << out_c.size() / 3 << " "
// << inter[0] << " "
// << inter[1] << " "
// << inter[2] << " "
// << std::endl;
// std::cout << "err here inner" << std::endl;
// exit(1);
// }
}
}
}
}
}
using namespace deepmd;
void
deepmd::
convert_nlist(
InputNlist & to_nlist,
std::vector<std::vector<int> > & from_nlist
)
{
to_nlist.inum = from_nlist.size();
for(int ii = 0; ii < to_nlist.inum; ++ii){
to_nlist.ilist[ii] = ii;
to_nlist.numneigh[ii] = from_nlist[ii].size();
to_nlist.firstneigh[ii] = &from_nlist[ii][0];
}
}
int
deepmd::
max_numneigh(
const InputNlist & nlist
)
{
int max_num = 0;
for(int ii = 0; ii < nlist.inum; ++ii){
if(nlist.numneigh[ii] > max_num) max_num = nlist.numneigh[ii];
}
return max_num;
}
template <typename FPTYPE>
int
deepmd::
build_nlist_cpu(
InputNlist & nlist,
int * max_list_size,
const FPTYPE * c_cpy,
const int & nloc,
const int & nall,
const int & mem_size_,
const float & rcut)
{
const int mem_size = mem_size_;
*max_list_size = 0;
nlist.inum = nloc;
FPTYPE rcut2 = rcut * rcut;
std::vector<int> jlist;
jlist.reserve(mem_size);
for(int ii = 0; ii < nlist.inum; ++ii){
nlist.ilist[ii] = ii;
jlist.clear();
for(int jj = 0; jj < nall; ++jj){
if(jj == ii) continue;
FPTYPE diff[3];
for(int dd = 0; dd < 3; ++dd){
diff[dd] = c_cpy[ii*3+dd] - c_cpy[jj*3+dd];
}
FPTYPE diff2 = deepmd::dot3(diff, diff);
if(diff2 < rcut2){
jlist.push_back(jj);
}
}
if(jlist.size() > mem_size){
*max_list_size = jlist.size();
return 1;
}
else {
int list_size = jlist.size();
nlist.numneigh[ii] = list_size;
if(list_size > *max_list_size) *max_list_size = list_size;
std::copy(jlist.begin(), jlist.end(), nlist.firstneigh[ii]);
}
}
return 0;
}
template
int
deepmd::
build_nlist_cpu<double>(
InputNlist & nlist,
int * max_list_size,
const double * c_cpy,
const int & nloc,
const int & nall,
const int & mem_size,
const float & rcut);
template
int
deepmd::
build_nlist_cpu<float>(
InputNlist & nlist,
int * max_list_size,
const float * c_cpy,
const int & nloc,
const int & nall,
const int & mem_size,
const float & rcut);
#if GOOGLE_CUDA || TENSORFLOW_USE_ROCM
void deepmd::convert_nlist_gpu_device(
InputNlist & gpu_nlist,
InputNlist & cpu_nlist,
int* & gpu_memory,
const int & max_nbor_size)
{
const int inum = cpu_nlist.inum;
gpu_nlist.inum = inum;
malloc_device_memory(gpu_nlist.ilist, inum);
malloc_device_memory(gpu_nlist.numneigh, inum);
malloc_device_memory(gpu_nlist.firstneigh, inum);
memcpy_host_to_device(gpu_nlist.ilist, cpu_nlist.ilist, inum);
memcpy_host_to_device(gpu_nlist.numneigh, cpu_nlist.numneigh, inum);
int ** _firstneigh = NULL;
_firstneigh = (int**)malloc(sizeof(int*) * inum);
for (int ii = 0; ii < inum; ii++) {
memcpy_host_to_device(gpu_memory + ii * max_nbor_size, cpu_nlist.firstneigh[ii], cpu_nlist.numneigh[ii]);
_firstneigh[ii] = gpu_memory + ii * max_nbor_size;
}
memcpy_host_to_device(gpu_nlist.firstneigh, _firstneigh, inum);
free(_firstneigh);
}
void deepmd::free_nlist_gpu_device(
InputNlist & gpu_nlist)
{
delete_device_memory(gpu_nlist.ilist);
delete_device_memory(gpu_nlist.numneigh);
delete_device_memory(gpu_nlist.firstneigh);
}
#endif // GOOGLE_CUDA || TENSORFLOW_USE_ROCM