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/*
Copyright (C) 2005 by Marcin Wojdyr
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 2
of the License, 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, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
The GNU GPL can also be found at http://www.gnu.org
*/
/* PowderCell structure data format - read-only
*
* example:
*
* cell 5.64009 5.64009 5.64009 90 90 90
* Na 11 0 0 0
* Cl 17 0.5 0 0
* rgnr 225
*
* For detailed description of file format see:
* http://users.omskreg.ru/~kolosov/bam/a_v/v_1/powder/details/strucdat.htm
* or mirror:
* http://www.ccp14.ac.uk/ccp/web-mirrors/powdcell/a_v/v_1/powder/details/powcell.htm
*
*/
#include <stdio.h>
#include <string.h>
#include "gdis.h"
#include "coords.h"
#include "model.h"
#include "file.h"
#include "parse.h"
/****************/
/* file reading */
/****************/
gint read_cel(gchar *filename, struct model_pak *model)
{
gchar *line;
FILE *fp;
int i;
gint num_tokens, natom=0;
gchar **buff;
struct core_pak *core;
/* checks */
g_return_val_if_fail(model != NULL, 1);
g_return_val_if_fail(filename != NULL, 2);
fp = fopen(filename, "rt");
if (!fp)
return 3;
/* 1st line - cell parameters */
line = file_read_line(fp);
if (!line || strlen(line) < 5 || g_ascii_strncasecmp("cell", line, 4) != 0)
{
printf("The first line should start with the keyword CELL.\n");
return 4;
}
buff = tokenize(line+4, &num_tokens);
g_free(line);
if (num_tokens < 6)
{
g_strfreev(buff);
printf("Keyword CELL should be followed by six numbers.\n");
return 5;
}
for (i=0; i<3; ++i)
model->pbc[i] = str_to_float(buff[i]);
for (i=3; i<6; ++i)
model->pbc[i] = str_to_float(buff[i]) * D2R;
g_strfreev(buff);
/* next lines - atomic positions */
for (;;)
{
line = file_read_line(fp);
if (!line) /*the end of file*/
{
printf("No 'rgnr' symmetry line found.\n");
return 6;
}
else if (g_ascii_strncasecmp("rgnr", line, 4) == 0) /*no more atomic pos.*/
{
break;
}
else if (g_ascii_strncasecmp("natom", line, 5) == 0)/*number of atoms */
/*some old .cel files have second line with number of atoms eg. "natom 6"*/
{
buff = tokenize(line, &num_tokens);
if (num_tokens > 1)
natom = str_to_float(buff[1]);
else
printf("Warning: ignoring `natom' line:\n%s\n", line);
g_free(line);
g_strfreev(buff);
}
else if (strncmp(" ", line, 4) != 0) /* atomic position */
{
buff = tokenize(line, &num_tokens);
g_free(line);
if (num_tokens < 5)
{
g_strfreev(buff);
continue;
}
core = new_core(*buff, model);
core->atom_label = g_strdup(buff[0]);
/* in second column there is either atomic number
* or something like "Mg2+" or "K+". The second form is for
* " the use of different bonding states of one and the same
* element (e.g. Fe2+ and Fe3+ in Fe3O4)"
* FIXME how these bonding states can be interpreted in GDIS */
if (g_ascii_isdigit(buff[1][0]))
core->atom_code = str_to_float(buff[1]);
else
{
core->atom_code = elem_symbol_test(buff[1]);
}
for (i=0; i<3; ++i)
core->x[i] = str_to_float(buff[2+i]);
/* TODO interpret 2 next optional numbers:
* so-called multiplied substitution and replacement factor (SOF)
* and isotropic Debye-Waller factor
* FIXME can they be interpreted by GDIS? -MW */
model->cores = g_slist_prepend(model->cores, core);
g_strfreev(buff);
}
else /* replacement atom */
{
/*FIXME replacement atoms are now silently ignored
* how can I use this information in GDIS? - MW*/
g_free(line);
}
}
/* last line - symmetry */
buff = tokenize(line, &num_tokens);
model->sginfo.spacenum = str_to_float(buff[1]);
/* FIXME/TODO how to interpret the second (optional) number?
* From fileformat docs:
* "sometimes there exists more than one setting of a space-group type.
* Thus, a further number must be given if the structure hasn't been described
* using a conventional setting (standard setting)."
* http://users.omskreg.ru/~kolosov/bam/a_v/v_1/powder/details/strucdat.htm
* http://users.omskreg.ru/~kolosov/bam/a_v/v_1/powder/details/setting.htm
* Unfortunatelly I'm ignorant about space-groups - MW
*/
g_free(line);
g_strfreev(buff);
if (natom>0 && natom != g_slist_length(model->cores))
printf("Warning: expected %i atoms, have %i.", natom,
g_slist_length(model->cores));
/* model setup */
model->fractional = TRUE;
model->periodic = 3;
strcpy(model->filename, filename);
g_free(model->basename);
model->basename = parse_strip(filename);
model_prep(model);
return 0;
}
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