87 lines
2.8 KiB
C++
87 lines
2.8 KiB
C++
#include <fstream.h>
|
|
#include "xtalutil.h"
|
|
#include "getvalue.h"
|
|
#include "parse.h"
|
|
#include "version.h"
|
|
|
|
|
|
void list_atom(ostream &file, const Array<Arrayint> &labellookup, const Array<AutoString> &label, int thetype) {
|
|
for (int i=0; i<labellookup(thetype).get_size(); i++) {
|
|
if (i>0) {cout << ",";}
|
|
cout << label(labellookup(thetype)(i));
|
|
}
|
|
}
|
|
|
|
|
|
int main(int argc, char *argv[]) {
|
|
char *latfilename="lat.in";
|
|
int listbond=0;
|
|
Real user_rad=0.0;
|
|
int sigdig=5;
|
|
int dummy;
|
|
AskStruct options[]={
|
|
{"","Nearest Neighbor Shell " MAPS_VERSION ", by Axel van de Walle and Paul Dalach",TITLEVAL,NULL},
|
|
{"-l","Input file defining the lattice (default: lat.in)",STRINGVAL,&latfilename},
|
|
{"-lb","List bond types in given structures",BOOLVAL,&listbond},
|
|
{"-sig","Number of significant digits to print in output files",INTVAL,&sigdig},
|
|
{"-r","Define a max radius for neighbor search",REALVAL,&user_rad},
|
|
{"-d","Use all default values",BOOLVAL,&dummy}
|
|
};
|
|
if (!get_values(argc,argv,countof(options),options)) {
|
|
display_help(countof(options),options);
|
|
return 1;
|
|
}
|
|
Structure lat;
|
|
Array<Arrayint> labellookup;
|
|
Array<AutoString> label;
|
|
rMatrix3d axes;
|
|
if (strcmp(latfilename,"-")==0) {
|
|
parse_lattice_file(&lat.cell, &lat.atom_pos, &lat.atom_type, &labellookup, &label, cin, &axes);
|
|
}
|
|
else {
|
|
ifstream latfile(latfilename);
|
|
if (!latfile) ERRORQUIT("Unable to open lattice file");
|
|
parse_lattice_file(&lat.cell, &lat.atom_pos, &lat.atom_type, &labellookup, &label, latfile, &axes);
|
|
}
|
|
wrap_inside_cell(&lat.atom_pos,lat.atom_pos,lat.cell);
|
|
|
|
cout.setf(ios::fixed);
|
|
cout.precision(sigdig);
|
|
if (listbond) {
|
|
for (int at=0; at<lat.atom_type.get_size(); at++) {
|
|
Real rnn=find_1nn_radius(lat,at);
|
|
AtomPairIterator p(lat.cell,lat.atom_pos(at),lat.atom_pos);
|
|
for ( ; p.length()<=rnn+zero_tolerance; p++) {
|
|
for (int i=0; i<2; i++) {
|
|
if (i>0) {cout <<"-";}
|
|
int thetype=lat.atom_type(which_atom(lat.atom_pos,p(i),!lat.cell));
|
|
list_atom(cout,labellookup,label,thetype);
|
|
}
|
|
cout << endl;
|
|
}
|
|
}
|
|
}
|
|
else {
|
|
for (int at=0; at<lat.atom_type.get_size(); at++) {
|
|
int nbnn=0;
|
|
cout << (!axes)*lat.atom_pos(at) << endl;
|
|
Real rnn;
|
|
if(user_rad>0) {rnn=user_rad;}
|
|
else {rnn=find_1nn_radius(lat,at);}
|
|
cout << rnn << endl;
|
|
list_atom(cout,labellookup,label,lat.atom_type(at));
|
|
cout << endl;
|
|
AtomPairIterator p(lat.cell,lat.atom_pos(at),lat.atom_pos);
|
|
while (p.length()<=rnn+zero_tolerance) {
|
|
cout << " " << (!axes)*(p(1)-p(0)) << " " << norm(p(1)-p(0)) << " ";
|
|
int thetype=lat.atom_type(which_atom(lat.atom_pos,p(1),!lat.cell));
|
|
list_atom(cout,labellookup,label,thetype);
|
|
cout << endl;
|
|
nbnn++;
|
|
p++;
|
|
}
|
|
cout << " " << nbnn << endl << endl;
|
|
}
|
|
}
|
|
}
|