/
neighbor.cpp
1139 lines (958 loc) · 37.3 KB
/
neighbor.cpp
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#include "modsystem.h"
#include <iostream>
#include <iomanip>
#include <algorithm>
#include <stdio.h>
#include "string.h"
#include <chrono>
#include <pybind11/pybind11.h>
#include <pybind11/numpy.h>
#include <pybind11/stl.h>
#include <pybind11/complex.h>
#include <pybind11/functional.h>
#include <pybind11/chrono.h>
#include <map>
#include <string>
#include <any>
double get_abs_distance(vector<double> pos1, vector<double> pos2,
const int& triclinic,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box,
double& diffx,
double& diffy,
double& diffz){
/*
Get absolute distance between two atoms
*/
double abs, ax, ay, az;
diffx = pos1[0] - pos2[0];
diffy = pos1[1] - pos2[1];
diffz = pos1[2] - pos2[2];
if (triclinic == 1){
//convert to the triclinic system
ax = rotinv[0][0]*diffx + rotinv[0][1]*diffy + rotinv[0][2]*diffz;
ay = rotinv[1][0]*diffx + rotinv[1][1]*diffy + rotinv[1][2]*diffz;
az = rotinv[2][0]*diffx + rotinv[2][1]*diffy + rotinv[2][2]*diffz;
//scale to match the triclinic box size
diffx = ax*box[0];
diffy = ay*box[1];
diffz = az*box[2];
//now check pbc
//nearest image
if (diffx> box[0]/2.0) {diffx-=box[0];};
if (diffx<-box[0]/2.0) {diffx+=box[0];};
if (diffy> box[1]/2.0) {diffy-=box[1];};
if (diffy<-box[1]/2.0) {diffy+=box[1];};
if (diffz> box[2]/2.0) {diffz-=box[2];};
if (diffz<-box[2]/2.0) {diffz+=box[2];};
//now divide by box vals - scale down the size
diffx = diffx/box[0];
diffy = diffy/box[1];
diffz = diffz/box[2];
//now transform back to normal system
ax = rot[0][0]*diffx + rot[0][1]*diffy + rot[0][2]*diffz;
ay = rot[1][0]*diffx + rot[1][1]*diffy + rot[1][2]*diffz;
az = rot[2][0]*diffx + rot[2][1]*diffy + rot[2][2]*diffz;
//now assign to diffs and calculate distnace
diffx = ax;
diffy = ay;
diffz = az;
//finally distance
abs = sqrt(diffx*diffx + diffy*diffy + diffz*diffz);
}
else{
//nearest image
if (diffx> box[0]/2.0) {diffx-=box[0];};
if (diffx<-box[0]/2.0) {diffx+=box[0];};
if (diffy> box[1]/2.0) {diffy-=box[1];};
if (diffy<-box[1]/2.0) {diffy+=box[1];};
if (diffz> box[2]/2.0) {diffz-=box[2];};
if (diffz<-box[2]/2.0) {diffz+=box[2];};
abs = sqrt(diffx*diffx + diffy*diffy + diffz*diffz);
}
return abs;
}
vector<double> get_distance_vector(vector<double> pos1,
vector<double> pos2,
const int& triclinic,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box){
double diffx, diffy, diffz, dist;
dist = get_abs_distance(pos1, pos2, triclinic, rot, rotinv, box, diffx, diffy, diffz);
vector<double> dvec;
dvec.emplace_back(diffx);
dvec.emplace_back(diffy);
dvec.emplace_back(diffz);
return dvec;
}
vector<double> remap_atom_into_box(vector<double> pos,
const int& triclinic,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box){
double dx, dy, dz;
double abs, ax, ay, az;
dx = pos[0];
dy = pos[1];
dz = pos[2];
if (triclinic == 1){
//convert to the triclinic system
ax = rotinv[0][0]*dx + rotinv[0][1]*dy + rotinv[0][2]*dz;
ay = rotinv[1][0]*dx + rotinv[1][1]*dy + rotinv[1][2]*dz;
az = rotinv[2][0]*dx + rotinv[2][1]*dy + rotinv[2][2]*dz;
//scale to match the triclinic box size
dx = ax*box[0];
dy = ay*box[1];
dz = az*box[2];
//now check pbc
//nearest image
if (dx < 0) {dx+=box[0];};
if (dx >= box[0]) {dx-=box[0];};
if (dy < 0) {dy+=box[1];};
if (dy >= box[1]) {dy-=box[1];};
if (dz < 0) {dz+=box[2];};
if (dz >= box[2]) {dz-=box[2];};
//now divide by box vals - scale down the size
dx = dx/box[0];
dy = dy/box[1];
dz = dz/box[2];
//now transform back to normal system
ax = rot[0][0]*dx + rot[0][1]*dy + rot[0][2]*dz;
ay = rot[1][0]*dx + rot[1][1]*dy + rot[1][2]*dz;
az = rot[2][0]*dx + rot[2][1]*dy + rot[2][2]*dz;
//now assign to diffs and calculate distnace
dx = ax;
dy = ay;
dz = az;
}
else{
//nearest image
if (dx < 0) {dx+=box[0];};
if (dx >= box[0]) {dx-=box[0];};
if (dy < 0) {dy+=box[1];};
if (dy >= box[1]) {dy-=box[1];};
if (dz < 0) {dz+=box[2];};
if (dz >= box[2]) {dz-=box[2];};
}
vector<double> rpos;
rpos.emplace_back(dx);
rpos.emplace_back(dy);
rpos.emplace_back(dz);
return rpos;
}
vector<double> remap_and_displace_atom(vector<double> pos,
const int& triclinic,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box,
const vector<double>& perturbation){
double dx, dy, dz;
double abs, ax, ay, az;
dx = pos[0];
dy = pos[1];
dz = pos[2];
if (triclinic == 1){
//convert to the triclinic system
ax = rotinv[0][0]*dx + rotinv[0][1]*dy + rotinv[0][2]*dz;
ay = rotinv[1][0]*dx + rotinv[1][1]*dy + rotinv[1][2]*dz;
az = rotinv[2][0]*dx + rotinv[2][1]*dy + rotinv[2][2]*dz;
//scale to match the triclinic box size
dx = ax*box[0];
dy = ay*box[1];
dz = az*box[2];
//now check pbc
//nearest image
if (dx < 0) {dx+=box[0];};
if (dx >= box[0]) {dx-=box[0];};
if (dy < 0) {dy+=box[1];};
if (dy >= box[1]) {dy-=box[1];};
if (dz < 0) {dz+=box[2];};
if (dz >= box[2]) {dz-=box[2];};
//now divide by box vals - scale down the size
dx = dx/box[0];
dy = dy/box[1];
dz = dz/box[2];
dx += perturbation[0];
dy += perturbation[1];
dz += perturbation[2];
//now transform back to normal system
ax = rot[0][0]*dx + rot[0][1]*dy + rot[0][2]*dz;
ay = rot[1][0]*dx + rot[1][1]*dy + rot[1][2]*dz;
az = rot[2][0]*dx + rot[2][1]*dy + rot[2][2]*dz;
//now assign to diffs and calculate distnace
dx = ax;
dy = ay;
dz = az;
}
else{
//nearest image
if (dx < 0) {dx+=box[0];};
if (dx >= box[0]) {dx-=box[0];};
if (dy < 0) {dy+=box[1];};
if (dy >= box[1]) {dy-=box[1];};
if (dz < 0) {dz+=box[2];};
if (dz >= box[2]) {dz-=box[2];};
dx = dx/box[0];
dy = dy/box[1];
dz = dz/box[2];
dx += perturbation[0];
dy += perturbation[1];
dz += perturbation[2];
dx = dx*box[0];
dy = dy*box[1];
dz = dz*box[2];
}
vector<double> rpos;
rpos.emplace_back(dx);
rpos.emplace_back(dy);
rpos.emplace_back(dz);
return rpos;
}
void reset_all_neighbors(py::dict& atoms){
/*
Reset all neighbors
*/
vector<vector<int>> temp2int;
vector<double> tempdouble;
vector<vector<double>> temp2double;
vector<vector<vector<double>>> temp3double;
for(unsigned int ti=0; ti<atoms.size(); ti++){
atoms[py::str("neighbors")] = temp2int;
atoms[py::str("neighbordist")] = temp2double;
atoms[py::str("temp_neighbors")] = temp2int;
atoms[py::str("temp_neighbordist")] = temp2double;
atoms[py::str("neighborweight")] = temp2double;
atoms[py::str("diff")] = temp3double;
atoms[py::str("r")] = temp2double;
atoms[py::str("phi")] = temp2double;
atoms[py::str("theta")] = temp2double;
atoms[py::str("cutoff")] = tempdouble;
}
}
void convert_to_spherical_coordinates(double x,
double y,
double z,
double &r,
double &phi,
double &theta){
r = sqrt(x*x+y*y+z*z);
theta = acos(z/r);
phi = atan2(y,x);
}
void get_all_neighbors_normal(py::dict& atoms,
const double neighbordistance,
const int triclinic,
const vector<vector<double>> rot,
const vector<vector<double>> rotinv,
const vector<double> box)
{
double d;
double diffx,diffy,diffz;
double tempr,temptheta,tempphi;
vector<double> diffi, diffj;
//access positions and put it in an array
vector<vector<double>> positions = atoms[py::str("positions")].cast<vector<vector<double>>>();
vector<bool> mask_1 = atoms[py::str("mask_1")].cast<vector<bool>>();
vector<bool> mask_2 = atoms[py::str("mask_2")].cast<vector<bool>>();
//auto positions = atoms[py::str("positions")].cast<py::array_t<double>>();
int nop = positions.size();
vector<vector<int>> neighbors(nop);
vector<vector<double>> neighbordist(nop);
vector<vector<double>> neighborweight(nop);
vector<vector<vector<double>>> diff(nop);
vector<vector<double>> r(nop);
vector<vector<double>> phi(nop);
vector<vector<double>> theta(nop);
vector<double> cutoff(nop);
//now loop and calculate things
for (int ti=0; ti<nop; ti++){
//only consider ti if mask_1 is false
if (mask_1[ti]) continue;
for (int tj=ti+1; tj<nop; tj++){
//mask 2 is applied here
if (mask_2[tj]) continue;
d = get_abs_distance(positions[ti], positions[tj],
triclinic, rot, rotinv, box,
diffx, diffy, diffz);
if (d < neighbordistance){
neighbors[ti].emplace_back(tj);
neighbors[tj].emplace_back(ti);
neighbordist[ti].emplace_back(d);
neighbordist[tj].emplace_back(d);
neighborweight[ti].emplace_back(1.00);
neighborweight[tj].emplace_back(1.00);
diffi.clear();
diffi.emplace_back(diffx);
diffi.emplace_back(diffy);
diffi.emplace_back(diffz);
diffj.clear();
diffj.emplace_back(-diffx);
diffj.emplace_back(-diffy);
diffj.emplace_back(-diffz);
diff[ti].emplace_back(diffi);
diff[tj].emplace_back(diffj);
convert_to_spherical_coordinates(diffx, diffy, diffz, tempr, tempphi, temptheta);
r[ti].emplace_back(tempr);
phi[ti].emplace_back(tempphi);
theta[ti].emplace_back(temptheta);
//n_neighbors += 1;
cutoff[ti] = neighbordistance;
convert_to_spherical_coordinates(-diffx, -diffy, -diffz, tempr, tempphi, temptheta);
r[tj].emplace_back(tempr);
phi[tj].emplace_back(tempphi);
theta[tj].emplace_back(temptheta);
//atoms[tj].n_neighbors += 1;
cutoff[tj] = neighbordistance;
}
}
}
//calculation over lets assign
atoms[py::str("neighbors")] = neighbors;
atoms[py::str("neighbordist")] = neighbordist;
atoms[py::str("neighborweight")] = neighborweight;
atoms[py::str("diff")] = diff;
atoms[py::str("r")] = r;
atoms[py::str("theta")] = theta;
atoms[py::str("phi")] = phi;
atoms[py::str("cutoff")] = cutoff;
}
int cell_index(int cx, int cy, int cz, int nx, int ny, int nz){
return cx*ny*nz + cy*nz + cz;
}
vector<int> cell_periodic(int i, int j, int k, int nx, int ny, int nz){
vector<int> ci;
//apply periodic conditions
if (i<0) i = i + nx;
else if (i>nx-1) i = i -nx;
ci.emplace_back(i);
if (j<0) j = j + ny;
else if (j>ny-1) j = j -ny;
ci.emplace_back(j);
if (k<0) k = k + nz;
else if (k>nz-1) k = k -nz;
ci.emplace_back(k);
return ci;
}
vector<cell> set_up_cells(const vector<vector<double>>& positions,
const vector<double>& box,
const double neighbordistance){
int maincell, subcell, total_cells;
int nx, ny, nz;
double lx, ly, lz;
vector<int> cc;
vector<cell> cells;
//find of all find the number of cells in each direction
nx = box[0]/neighbordistance;
ny = box[1]/neighbordistance;
nz = box[2]/neighbordistance;
//now use this to find length of cell in each direction
lx = box[0]/nx;
ly = box[1]/ny;
lz = box[2]/nz;
//find the total number of cells
total_cells = nx*ny*nz;
cells.resize(total_cells);
//all neighbor cells are also added
for(int i=0; i<nx; i++){
for(int j=0; j<ny; j++){
for(int k=0; k<nz; k++){
maincell = cell_index(i, j, k, nx, ny, nz);
for(int si=i-1; si<=i+1; si++){
for(int sj=j-1; sj<=j+1; sj++){
for(int sk=k-1; sk<=k+1; sk++){
cc = cell_periodic(si, sj, sk, nx, ny, nz);
subcell = cell_index(cc[0], cc[1], cc[2], nx, ny, nz);
//add this to the list of neighbors
cells[maincell].neighbor_cells.emplace_back(subcell);
}
}
}
}
}
}
int cx, cy, cz;
double dx, dy, dz;
int ind;
int nop = positions.size();
//now loop over all atoms and assign cells
for(int ti=0; ti<nop; ti++){
//calculate c indices for the atom
dx = positions[ti][0];
dy = positions[ti][1];
dz = positions[ti][2];
//now apply boxdims
if( abs(dx-0) < 1E-6)
dx = 0;
if( abs(dy-0) < 1E-6)
dy = 0;
if( abs(dz-0) < 1E-6)
dz = 0;
if (dx < 0) dx+=box[0];
else if (dx >= box[0]) dx-=box[0];
if (dy < 0) dy+=box[1];
else if (dy >= box[1]) dy-=box[1];
if (dz < 0) dz+=box[2];
else if (dz >= box[2]) dz-=box[2];
//now find c vals
cx = dx/lx;
cy = dy/ly;
cz = dz/lz;
//now get cell index
ind = cell_index(cx, cy, cz, nx, ny, nz);
//now add the atom to the corresponding cells
cells[ind].members.emplace_back(ti);
}
return cells;
}
void get_all_neighbors_cells(py::dict& atoms,
const double neighbordistance,
const int triclinic,
const vector<vector<double>> rot,
const vector<vector<double>> rotinv,
const vector<double> box){
double d;
double diffx,diffy,diffz;
double tempr,temptheta,tempphi;
vector<double> diffi, diffj;
int ti, tj;
//access positions and put it in an array
vector<vector<double>> positions = atoms[py::str("positions")].cast<vector<vector<double>>>();
vector<bool> mask_1 = atoms[py::str("mask_1")].cast<vector<bool>>();
vector<bool> mask_2 = atoms[py::str("mask_2")].cast<vector<bool>>();
int nop = positions.size();
vector<vector<int>> neighbors(nop);
vector<vector<double>> neighbordist(nop);
vector<vector<double>> neighborweight(nop);
vector<vector<vector<double>>> diff(nop);
vector<vector<double>> r(nop);
vector<vector<double>> phi(nop);
vector<vector<double>> theta(nop);
vector<double> cutoff(nop);
vector<cell> cells = set_up_cells(positions, box, neighbordistance);
int total_cells = cells.size();
int subcell;
//now loop to find distance
for(int i=0; i<total_cells; i++){
//for each member in cell i
for(size_t mi=0; mi<cells[i].members.size(); mi++){
//now go through the neighbors
ti = cells[i].members[mi];
if (mask_1[ti]) continue;
for(size_t j=0 ; j<cells[i].neighbor_cells.size(); j++){
//loop through members of j
subcell = cells[i].neighbor_cells[j];
for(size_t mj=0; mj<cells[subcell].members.size(); mj++){
//now we have mj -> members/compare with
tj = cells[subcell].members[mj];
if (mask_2[tj]) continue;
//compare ti and tj and add
if (ti < tj){
d = get_abs_distance(positions[ti], positions[tj],
triclinic, rot, rotinv, box,
diffx, diffy, diffz);
if (d < neighbordistance){
neighbors[ti].emplace_back(tj);
neighbors[tj].emplace_back(ti);
neighbordist[ti].emplace_back(d);
neighbordist[tj].emplace_back(d);
neighborweight[ti].emplace_back(1.00);
neighborweight[tj].emplace_back(1.00);
diffi.clear();
diffi.emplace_back(diffx);
diffi.emplace_back(diffy);
diffi.emplace_back(diffz);
diffj.clear();
diffj.emplace_back(-diffx);
diffj.emplace_back(-diffy);
diffj.emplace_back(-diffz);
diff[ti].emplace_back(diffi);
diff[tj].emplace_back(diffj);
convert_to_spherical_coordinates(diffx, diffy, diffz, tempr, tempphi, temptheta);
r[ti].emplace_back(tempr);
phi[ti].emplace_back(tempphi);
theta[ti].emplace_back(temptheta);
//n_neighbors += 1;
cutoff[ti] = neighbordistance;
convert_to_spherical_coordinates(-diffx, -diffy, -diffz, tempr, tempphi, temptheta);
r[tj].emplace_back(tempr);
phi[tj].emplace_back(tempphi);
theta[tj].emplace_back(temptheta);
//atoms[tj].n_neighbors += 1;
cutoff[tj] = neighbordistance;
}
}
}
}
}
}
//calculation over lets assign
atoms[py::str("neighbors")] = neighbors;
atoms[py::str("neighbordist")] = neighbordist;
atoms[py::str("neighborweight")] = neighborweight;
atoms[py::str("diff")] = diff;
atoms[py::str("r")] = r;
atoms[py::str("theta")] = theta;
atoms[py::str("phi")] = phi;
atoms[py::str("cutoff")] = cutoff;
}
void get_temp_neighbors_brute(const vector<vector<double>>& positions,
const vector<bool>& mask_1,
const vector<bool>& mask_2,
vector<vector<datom>>& temp_neighbors,
const int& triclinic,
const double neighbordistance,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box)
{
double d;
double diffx,diffy,diffz;
int nop = positions.size();
temp_neighbors.resize(nop);
for (int ti=0; ti<nop; ti++){
if (mask_1[ti]) continue;
for (int tj=ti+1; tj<nop; tj++){
if (mask_2[tj]) continue;
d = get_abs_distance(positions[ti], positions[tj],
triclinic, rot, rotinv, box,
diffx, diffy, diffz);
if (d <= neighbordistance){
datom x = {d, tj};
temp_neighbors[ti].emplace_back(x);
datom y = {d, ti};
temp_neighbors[tj].emplace_back(y);
}
}
}
}
void get_temp_neighbors_cells(const vector<vector<double>>& positions,
const vector<bool>& mask_1,
const vector<bool>& mask_2,
vector<vector<datom>>& temp_neighbors,
const int& triclinic,
const double neighbordistance,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box){
//first create cells
vector<cell> cells = set_up_cells(positions, box, neighbordistance);
int total_cells = cells.size();
int subcell;
int ti, tj;
double d;
double diffx,diffy,diffz;
int nop = positions.size();
temp_neighbors.resize(nop);
//now loop to find distance
for(int i=0; i<total_cells; i++){
//now go over the neighbor cells
//for each member in cell i
for(size_t mi=0; mi<cells[i].members.size(); mi++){
//now go through the neighbors
ti = cells[i].members[mi];
if (mask_1[ti]) continue;
for(size_t j=0 ; j<cells[i].neighbor_cells.size(); j++){
//loop through members of j
subcell = cells[i].neighbor_cells[j];
for(size_t mj=0; mj<cells[subcell].members.size(); mj++){
//now we have mj -> members/compare with
tj = cells[subcell].members[mj];
if (mask_2[tj]) continue;
//compare ti and tj and add
if (ti < tj){
d = get_abs_distance(positions[ti], positions[tj],
triclinic, rot, rotinv, box,
diffx, diffy, diffz);
if (d <= neighbordistance){
datom x = {d, tj};
temp_neighbors[ti].emplace_back(x);
datom y = {d, ti};
temp_neighbors[tj].emplace_back(y);
}
}
}
}
}
}
}
int get_all_neighbors_bynumber(py::dict& atoms,
double& neighbordistance,
const int& triclinic,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box,
double prefactor,
int nns,
int usecells,
int assign){
double d;
double diffx,diffy,diffz;
double tempr,temptheta,tempphi;
vector<double> diffi, diffj;
int finished;
finished = 1;
//access positions and put it in an array
vector<vector<double>> positions = atoms[py::str("positions")].cast<vector<vector<double>>>();
vector<bool> mask_1 = atoms[py::str("mask_1")].cast<vector<bool>>();
vector<bool> mask_2 = atoms[py::str("mask_2")].cast<vector<bool>>();
int nop = positions.size();
vector<vector<int>> neighbors(nop);
vector<vector<double>> neighbordist(nop);
vector<vector<double>> neighborweight(nop);
vector<vector<vector<double>>> diff(nop);
vector<vector<double>> r(nop);
vector<vector<double>> phi(nop);
vector<vector<double>> theta(nop);
vector<double> cutoff(nop);
vector<vector<int>> atom_temp_neighbors(nop);
vector<vector<double>> atom_temp_neighbordist(nop);
vector<int> nids;
vector<double> dists, sorted_dists;
double boxvol;
if (triclinic==1){
double a1, a2, a3, b1, b2, b3, c1, c2, c3;
//rot is the cell vectors transposed
a1 = rot[0][0];
a2 = rot[1][0];
a3 = rot[2][0];
b1 = rot[0][1];
b2 = rot[1][1];
b3 = rot[2][1];
c1 = rot[0][2];
c2 = rot[1][2];
c3 = rot[2][2];
boxvol = c1*(a2*b3-a3*b2) - c2*(a1*b3-b1*a3) + c3*(a1*b2-a2*b1);
}
else{
boxvol = box[0]*box[1]*box[2];
}
//now find the volume per particle
double guessvol = boxvol/float(nop);
//guess the side of a cube that is occupied by an atom - this is a guess distance
double guessdist = cbrt(guessvol);
//now add some safe padding - this is the prefactor which we will read in
guessdist = prefactor*guessdist;
neighbordistance = guessdist;
vector<vector<datom>> temp_neighbors;
if (usecells){
get_temp_neighbors_cells(positions, mask_1, mask_2, temp_neighbors, triclinic, neighbordistance, rot, rotinv, box);
}
else{
get_temp_neighbors_brute(positions, mask_1, mask_2, temp_neighbors, triclinic, neighbordistance, rot, rotinv, box);
}
for (int ti=0; ti<nop; ti++){
if (int(temp_neighbors[ti].size()) < nns){
return 0;
}
sort(temp_neighbors[ti].begin(), temp_neighbors[ti].end(), by_dist());
for(size_t i=0; i<temp_neighbors[ti].size(); i++){
atom_temp_neighbors[ti].emplace_back(temp_neighbors[ti][i].index);
atom_temp_neighbordist[ti].emplace_back(temp_neighbors[ti][i].dist);
}
if(assign == 1){
//assign the neighbors
for(int i=0; i<nns; i++){
int tj = temp_neighbors[ti][i].index;
d = get_abs_distance(positions[ti], positions[tj],
triclinic, rot, rotinv, box,
diffx, diffy, diffz);
neighbors[ti].emplace_back(tj);
neighbordist[ti].emplace_back(d);
neighborweight[ti].emplace_back(1.00);
diffi.clear();
diffi.emplace_back(diffx);
diffi.emplace_back(diffy);
diffi.emplace_back(diffz);
diff[ti].emplace_back(diffi);
convert_to_spherical_coordinates(diffx, diffy, diffz, tempr, tempphi, temptheta);
r[ti].emplace_back(tempr);
phi[ti].emplace_back(tempphi);
theta[ti].emplace_back(temptheta);
//n_neighbors += 1;
cutoff[ti] = neighbordistance;
}
}
finished = 1;
}
if (assign==1){
atoms[py::str("neighbors")] = neighbors;
atoms[py::str("neighbordist")] = neighbordist;
atoms[py::str("neighborweight")] = neighborweight;
atoms[py::str("diff")] = diff;
atoms[py::str("r")] = r;
atoms[py::str("theta")] = theta;
atoms[py::str("phi")] = phi;
atoms[py::str("cutoff")] = cutoff;
}
//in any case add the temp neighbors
atoms[py::str("temp_neighbors")] = atom_temp_neighbors;
atoms[py::str("temp_neighbordist")] = atom_temp_neighbordist;
return finished;
}
int get_all_neighbors_sann(py::dict& atoms,
double& neighbordistance,
const int& triclinic,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box,
double prefactor,
int usecells){
double d, dcut;
double diffx,diffy,diffz;
double tempr,temptheta,tempphi;
vector<double> diffi, diffj;
int m, maxneighs, finished;
finished = 1;
//access positions and put it in an array
vector<vector<double>> positions = atoms[py::str("positions")].cast<vector<vector<double>>>();
vector<bool> mask_1 = atoms[py::str("mask_1")].cast<vector<bool>>();
vector<bool> mask_2 = atoms[py::str("mask_2")].cast<vector<bool>>();
int nop = positions.size();
vector<vector<int>> neighbors(nop);
vector<vector<double>> neighbordist(nop);
vector<vector<double>> neighborweight(nop);
vector<vector<vector<double>>> diff(nop);
vector<vector<double>> r(nop);
vector<vector<double>> phi(nop);
vector<vector<double>> theta(nop);
vector<double> cutoff(nop);
vector<vector<int>> atom_temp_neighbors(nop);
vector<vector<double>> atom_temp_neighbordist(nop);
vector<int> nids;
vector<double> dists, sorted_dists;
double summ;
double boxvol;
if (triclinic==1){
double a1, a2, a3, b1, b2, b3, c1, c2, c3;
//rot is the cell vectors transposed
a1 = rot[0][0];
a2 = rot[1][0];
a3 = rot[2][0];
b1 = rot[0][1];
b2 = rot[1][1];
b3 = rot[2][1];
c1 = rot[0][2];
c2 = rot[1][2];
c3 = rot[2][2];
boxvol = c1*(a2*b3-a3*b2) - c2*(a1*b3-b1*a3) + c3*(a1*b2-a2*b1);
}
else{
boxvol = box[0]*box[1]*box[2];
}
//now find the volume per particle
double guessvol = boxvol/float(nop);
//guess the side of a cube that is occupied by an atom - this is a guess distance
double guessdist = cbrt(guessvol);
//now add some safe padding - this is the prefactor which we will read in
guessdist = prefactor*guessdist;
neighbordistance = guessdist;
vector<vector<datom>> temp_neighbors;
if (usecells){
get_temp_neighbors_cells(positions, mask_1, mask_2, temp_neighbors, triclinic, neighbordistance, rot, rotinv, box);
}
else{
get_temp_neighbors_brute(positions, mask_1, mask_2, temp_neighbors, triclinic, neighbordistance, rot, rotinv, box);
}
for (int ti=0; ti<nop; ti++){
if (temp_neighbors[ti].size() < 3){
return 0;
}
sort(temp_neighbors[ti].begin(), temp_neighbors[ti].end(), by_dist());
for(size_t i=0; i<temp_neighbors[ti].size(); i++){
atom_temp_neighbors[ti].emplace_back(temp_neighbors[ti][i].index);
atom_temp_neighbordist[ti].emplace_back(temp_neighbors[ti][i].dist);
}
m = 3;
summ = 0;
for(int i=0; i<m; i++){
summ += temp_neighbors[ti][i].dist;
int tj = temp_neighbors[ti][i].index;
d = get_abs_distance(positions[ti], positions[tj],
triclinic, rot, rotinv, box,
diffx, diffy, diffz);
neighbors[ti].emplace_back(tj);
neighbordist[ti].emplace_back(d);
neighborweight[ti].emplace_back(1.00);
diffi.clear();
diffi.emplace_back(diffx);
diffi.emplace_back(diffy);
diffi.emplace_back(diffz);
diff[ti].emplace_back(diffi);
convert_to_spherical_coordinates(diffx, diffy, diffz, tempr, tempphi, temptheta);
r[ti].emplace_back(tempr);
phi[ti].emplace_back(tempphi);
theta[ti].emplace_back(temptheta);
//n_neighbors += 1;
}
dcut = summ/float(m-2);
maxneighs = temp_neighbors[ti].size();
while( (m < maxneighs) && (dcut >= temp_neighbors[ti][m].dist)){
//increase m
m = m+1;
//here now we can add this to the list neighbors and process things
int tj = temp_neighbors[ti][m].index;
d = get_abs_distance(positions[ti], positions[tj],
triclinic, rot, rotinv, box,
diffx, diffy, diffz);
neighbors[ti].emplace_back(tj);
neighbordist[ti].emplace_back(d);
neighborweight[ti].emplace_back(1.00);
diffi.clear();
diffi.emplace_back(diffx);
diffi.emplace_back(diffy);
diffi.emplace_back(diffz);
diff[ti].emplace_back(diffi);
convert_to_spherical_coordinates(diffx, diffy, diffz, tempr, tempphi, temptheta);
r[ti].emplace_back(tempr);
phi[ti].emplace_back(tempphi);
theta[ti].emplace_back(temptheta);
//n_neighbors += 1;
//find new dcut
summ = summ + temp_neighbors[ti][m].dist;
dcut = summ/float(m-2);
cutoff[ti] = dcut;
}
//find if there was an error
if (m==maxneighs){
finished = 0;
break;
}
else{
finished = 1;
}
}
atoms[py::str("neighbors")] = neighbors;
atoms[py::str("neighbordist")] = neighbordist;
atoms[py::str("neighborweight")] = neighborweight;
atoms[py::str("diff")] = diff;
atoms[py::str("r")] = r;
atoms[py::str("theta")] = theta;
atoms[py::str("phi")] = phi;
atoms[py::str("cutoff")] = cutoff;
//in any case add the temp neighbors
atoms[py::str("temp_neighbors")] = atom_temp_neighbors;
atoms[py::str("temp_neighbordist")] = atom_temp_neighbordist;
return finished;
}
int get_all_neighbors_adaptive(py::dict& atoms,
double& neighbordistance,
const int& triclinic,