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/* A reader for Crystal's geometry files */
/* Copyright (c) 2018 MJ Rutter
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3
* of the Licence, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, see http://www.gnu.org/licenses/
*/
#include<stdio.h>
#include<stdlib.h> /* malloc */
#include<string.h>
#include<math.h>
#include "c2xsf.h"
#ifdef SPGLIB
#include "spglib.h"
#endif
struct sym_op *sym_frac2abs(int spg_rot[][3][3],double spg_tr[][3],
struct unit_cell *c,int nsym);
#define LINE_SIZE 2049
void crystal_read(FILE* infile, struct unit_cell *c, struct contents *m,
struct symmetry *s){
int i,j,natoms;
int iflag,ifhr,ifso,igr,hall;
int ishift[3];
char buffer[LINE_SIZE+1];
double *ptr,abc[6],junk;
buffer[0]=0;
i=0;
while(fgets(buffer,LINE_SIZE,infile)){
if (!strncmp(buffer,"CRYSTAL",7)) break;
if (!strncmp(buffer,"SLAB",4))
error_exit("Reading of 2D Crystal systems not supported");
if (!strncmp(buffer,"POLYMER",7))
error_exit("Reading of 1D Crystal systems not supported");
if (!strncmp(buffer,"HELIX",5))
error_exit("Reading of 1D Crystal systems not supported");
if (!strncmp(buffer,"MOLECULE",8))
error_exit("Reading of 0D Crystal systems not supported");
if (!strncmp(buffer,"EXTERNAL",8))
error_exit("EXTERNAL keyword not supported. Read fort.34 directly");
if (!strncmp(buffer,"DLVINPUT",8))
error_exit("DLVINPUT keyword not supported");
}
fprintf(stderr,"Warning: using little-tested Crystal fort.12 reader - "
"check output!\n");
fgets(buffer,LINE_SIZE,infile);
if (sscanf(buffer,"%d %d %d",&iflag,&ifhr,&ifso)!=3)
error_exit("Error reading flags in CRYSTAL file");
if ((iflag<0)||(iflag>1)||(ifhr<0)||(ifhr>1)||(ifso<0)||(ifso>24))
error_exit("Invalid value for flags in CRYSTAL file");
if (iflag==1)
error_exit("H-M codes unsupported by c2x");
fgets(buffer,LINE_SIZE,infile);
if (sscanf(buffer,"%d",&igr)!=1)
error_exit("Error reading spacegroup in CRYSTAL file");
if ((igr<1)||(igr>230))
error_exit("Invalid value for space group in CRYSTAL file");
hall=igr2hall[igr];
if (ifhr==1){ /*ifhr=0 is hexagonal, 1 is rhombohedral */
if ((igr==146)||(igr==148)||(igr==155)||(igr==160)||(igr==161)||
(igr==166)||(igr==167))
hall+=1;
else
fprintf(stderr,"Unexpected value of ifhr ignored\n");
}
if (spgr_is_double(igr)){
if (debug>1) {
fprintf(stderr,"Two origins for space group, ");
if (ifso==1) fprintf(stderr,"first used\n");
else if (ifso==0) fprintf(stderr,"second used\n");
}
if (ifso==0) hall+=1;
}
else if (ifso==1){
fprintf(stderr,"Problem: input file says two origins possible, "
"but only one known to c2x\n"
"Result may be wrong\n");
}
if (ifso>1){
fgets(buffer,LINE_SIZE,infile);
if (sscanf(buffer,"%d %d %d",ishift,ishift+1,ishift+2)!=3)
error_exit("Error reading non-standard shift in CRYSTAL file");
}
if(hall>=489){ /* Cubic */
fgets(buffer,LINE_SIZE,infile);
if (sscanf(buffer,"%lf %lf",abc,&junk)!=1)
error_exit("Error reading abc in CRYSTAL file");
abc[1]=abc[0];
abc[2]=abc[0];
abc[3]=abc[4]=abc[5]=90;
}
else if (hall>=430){ /* Hexagonal or trigonal */
fgets(buffer,LINE_SIZE,infile);
if (ifhr==0){
if (sscanf(buffer,"%lf %lf %lf",abc,abc+2,&junk)!=2)
error_exit("Error reading abc in CRYSTAL file");
abc[1]=abc[0];
abc[3]=abc[4]=90;
abc[5]=120;
}
else{
if (sscanf(buffer,"%lf %lf %lf",abc,abc+3,&junk)!=2)
error_exit("Error reading abc in CRYSTAL file");
abc[1]=abc[0];
abc[2]=abc[0];
abc[4]=abc[3];
abc[5]=abc[3];
}
}
else if (hall>=349){ /* Tetragonal */
if (sscanf(buffer,"%lf %lf %lf",abc,abc+2,&junk)!=2)
error_exit("Error reading abc in CRYSTAL file");
abc[1]=abc[0];
abc[3]=abc[4]=abc[5]=90;
}
else if (hall>=108){ /* Orthorhombic */
if (sscanf(buffer,"%lf %lf %lf %lf",abc,abc+1,abc+2,&junk)!=3)
error_exit("Error reading abc in CRYSTAL file");
abc[3]=abc[4]=abc[5]=90;
}
else if (hall>=3){ /* Monoclinic */
if (sscanf(buffer,"%lf %lf %lf %lf %lf",abc,abc+1,abc+2,abc+4,&junk)!=4)
error_exit("Error reading abc in CRYSTAL file");
abc[3]=abc[5]=90;
}
else { /* Triclinic */
if (sscanf(buffer,"%lf %lf %lf %lf %lf %lf %lf",abc,abc+1,abc+2,
abc+3,abc+4,abc+4,&junk)!=6)
error_exit("Error reading abc in CRYSTAL file");
abc[3]=abc[5]=90;
}
if (!(c->basis=malloc(9*sizeof(double))))
error_exit("Malloc error in crystal_read for c->basis");
abc2cart(abc,c);
if (debug) fprintf(stderr,"Using Hall number of %d from IGR=%d\n",hall,igr);
cspg_hall2sym(hall,c,s);
if (debug) fprintf(stderr,"%d symops returned\n",s->n);
natoms=0;
fgets(buffer,LINE_SIZE,infile);
if (sscanf(buffer,"%d",&natoms)!=1)
error_exit("Error reading number of atoms in CRYSTAL file");
m->atoms=malloc(natoms*sizeof(struct atom));
if (!m->atoms) error_exit("Malloc error for atoms");
m->n=natoms;
init_atoms(m->atoms,m->n);
for(i=0;i<natoms;i++){
fgets(buffer,LINE_SIZE,infile);
ptr=m->atoms[i].frac;
if (sscanf(buffer,"%d %lf %lf %lf",&m->atoms[i].atno,ptr,ptr+1,ptr+2)!=4)
error_exit("Error parsing atom in CRYSTAL file");
m->atoms[i].atno=m->atoms[i].atno%100;
}
addabs(m->atoms,natoms,c->basis);
#ifdef SPGLIB
if (ifso>1){
for(i=0;i<m->n;i++)
for(j=0;j<3;j++){
m->atoms[i].frac[j]+=ishift[j]/24.0;
m->atoms[i].frac[j]=fmod(m->atoms[i].frac[j],1.0);
if (m->atoms[i].frac[j]<0) m->atoms[i].frac[j]+=1.0;
}
addabs(m->atoms,m->n,c->basis);
}
sym_expand(c,m,s);
if (ifso>1){
for(i=0;i<m->n;i++)
for(j=0;j<3;j++){
m->atoms[i].frac[j]-=ishift[j]/24.0;
m->atoms[i].frac[j]=fmod(m->atoms[i].frac[j],1.0);
if (m->atoms[i].frac[j]<0) m->atoms[i].frac[j]+=1.0;
}
addabs(m->atoms,m->n,c->basis);
}
#endif
}
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