117 lines
3.9 KiB
C++
117 lines
3.9 KiB
C++
#include <fstream.h>
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#include <sys/stat.h>
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#include "phonlib.h"
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#include "getvalue.h"
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#include "parse.h"
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#include "version.h"
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#include "lattype.h"
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#include "arraylist.h"
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void find_distinct_sites(Array<int> *pwhich_atom,
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const Structure &str,
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const SpaceGroup &spacegroup) {
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LinkedList<int> which_atom_list;
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LinkedList<Array<rVector3d> > pointlist;
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for (int at=0; at<str.atom_pos.get_size(); at++) {
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Array<rVector3d> p(1);
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p(0)=str.atom_pos(at);
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if (add_unique(&pointlist,p,spacegroup)) {
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which_atom_list << new int(at);
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}
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}
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LinkedList_to_Array(pwhich_atom,which_atom_list);
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}
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// extern char *helpstring;
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char *helpstring="";
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int main(int argc, char *argv[]) {
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// cerr.setf(ios::fixed | ios::showpos);
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cerr.setf(ios::fixed);
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cerr.precision(5);
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char *latfilename="lat.in";
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char *strfilename="str.out";
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char *strprefix="pdef";
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Real enclosed_radius=0.;
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int dohelp=0;
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int sigdig=5;
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AskStruct options[]={
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{"","Point DEFect generator " MAPS_VERSION ", by Axel van de Walle",TITLEVAL,NULL},
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{"-l","Input file defining the lattice (default: lat.in)",STRINGVAL,&latfilename},
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{"-s","Input file defining the lattice (default: str.out)",STRINGVAL,&strfilename},
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{"-p","Prefix of the directories that will contain the defected structures (Default pdef)",STRINGVAL,&strprefix},
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{"-er","Minimum distance between point defects",REALVAL,&enclosed_radius},
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{"-sig","Number of significant digits printed (default: 5)",INTVAL,&sigdig},
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{"-h","Display more help",BOOLVAL,&dohelp}
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};
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if (!get_values(argc,argv,countof(options),options)) {
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display_help(countof(options),options);
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return 1;
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}
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if (dohelp) {
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cout << helpstring;
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return 1;
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}
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if (enclosed_radius==0) {
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ERRORQUIT("You need to specify at least the -er parameter.");
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}
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Structure lat;
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Array<Arrayint> site_type_list;
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Array<AutoString> atom_label;
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rMatrix3d axes;
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{
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ifstream file(latfilename);
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if (!file) ERRORQUIT("Unable to open lattice file.");
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parse_lattice_file(&lat.cell, &lat.atom_pos, &lat.atom_type, &site_type_list, &atom_label, file, &axes);
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if (fabs(det(lat.cell))<zero_tolerance) ERRORQUIT("Lattice vectors are coplanar.");
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wrap_inside_cell(&lat.atom_pos,lat.atom_pos,lat.cell);
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}
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Structure str;
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{
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ifstream file(strfilename);
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if (!file) ERRORQUIT("Unable to open structure file.");
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parse_structure_file(&str.cell,&str.atom_pos,&str.atom_type,atom_label,file);
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wrap_inside_cell(&str.atom_pos,str.atom_pos,str.cell);
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fix_atom_type(&str, lat,site_type_list,0);
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}
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Array<int> atoms;
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SpaceGroup str_spacegroup;
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str_spacegroup.cell=str.cell;
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find_spacegroup(&str_spacegroup.point_op,&str_spacegroup.trans,str.cell,str.atom_pos,str.atom_type);
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find_distinct_sites(&atoms,str,str_spacegroup);
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Structure ideal_supercell;
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find_smallest_supercell_enclosing_sphere(&(ideal_supercell.cell),str.cell,enclosed_radius);
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find_all_atom_in_supercell(&(ideal_supercell.atom_pos), &(ideal_supercell.atom_type), str.atom_pos, str.atom_type, str.cell, ideal_supercell.cell);
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int pert=0;
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for (int at=0; at<atoms.get_size(); at++) {
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int i_in_lat=which_atom(lat.atom_pos,str.atom_pos(atoms(at)),!(lat.cell));
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int i_in_supstr=which_atom(ideal_supercell.atom_pos,str.atom_pos(atoms(at)),!(ideal_supercell.cell));
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for (int s=0; s<site_type_list(lat.atom_type(i_in_lat)).get_size(); s++) {
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Structure supstr(ideal_supercell);
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if (s!=ideal_supercell.atom_type(i_in_supstr)) {
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supstr.atom_type(i_in_supstr)=s;
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ostrstream line;
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line << strprefix << "_" << pert << '\0';
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mkdir(line.str(),S_IRWXU | S_IRWXG | S_IRWXO);
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chdir_robust(line.str());
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{
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ofstream file("str.out");
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file.setf(ios::fixed);
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file.precision(sigdig);
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if (!file) ERRORQUIT("Unable to open output file.");
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write_structure(supstr,lat,site_type_list,atom_label,axes,file);
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ofstream waitfile("wait");
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}
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chdir_robust("..");
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pert++;
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}
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}
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}
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}
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