gint core_match(const gchar *label, struct core_pak *core)
{
gint code;
#if DEBUG_ATOM_MATCH
printf("[%s] : [%s]\n", label, core->atom_label);
#endif
code = elem_symbol_test(label);
/* if input label doesnt match the element symbol length - it means the */
/* user has put in something like H1 - compare this with the atom label */
if (code)
{
if (g_ascii_strcasecmp(label, elements[core->atom_code].symbol) != 0)
{
if (g_ascii_strcasecmp(core->atom_label, label) == 0)
return(1);
}
else
return(1);
}
else
return(1);
#if DEBUG_ATOM_MATCH
printf("rejected.\n");
#endif
return(0);
}
/* TEMP - parse diffax sfc data */
void parse_sfc(FILE *fp)
{
gint i, n;
gchar *line, *type, **buff;
gdouble *sfc;
GSList *list;
while ((line = file_read_line(fp)))
{
type = g_strstrip(g_strndup(line, 6));
if (elem_symbol_test(type))
{
/* tokenize everything after the atom type */
buff = tokenize(&line[6], &n);
printf("[%s] ", type);
list = NULL;
for (i=0 ; i<n ; i++)
{
sfc = g_malloc(sizeof(gdouble));
*sfc = str_to_float(*(buff+i));
printf("[%f] ", *sfc);
list = g_slist_prepend(list, sfc);
}
list = g_slist_reverse(list);
printf("\n");
g_hash_table_insert(sysenv.sfc_table, type, list);
g_strfreev(buff);
}
g_free(line);
}
}
gint read_aims(gchar *filename, struct model_pak *model)
{
gint i, num_tokens;
gchar **buff;
gpointer scan;
struct core_pak *core;
g_assert(model != NULL);
scan = scan_new(filename);
if (!scan) return(1);
while (!scan_complete(scan)) {
buff = scan_get_tokens(scan, &num_tokens);
/*
for debugging purposes
produces a compiler warning about an
implicit declaration of function 'g_printf'
though this is a valid glib function since 2.2
http://library.gnome.org/devel/glib/2.18/glib-String-Utility-Functions.html#g-printf
*/
/*
for (i=0; i<num_tokens; i++) {
g_printf(" %s ", buff[i]);
}
printf("\n");
*/
if (!buff) break;
/* read cell vectors */
if ( g_strrstr(*buff, "lattice_vector") != NULL ) {
for (i=0 ; i<3 ; i++) {
if (num_tokens >= 3) {
model->latmat[i] = str_to_float(*(buff+1));
model->latmat[i+3] = str_to_float(*(buff+2));
model->latmat[i+6] = str_to_float(*(buff+3));
}
else {
gui_text_show(ERROR, "error reading AIMS lattice vectors \n");
return(2);
}
g_strfreev(buff);
buff = scan_get_tokens(scan, &num_tokens);
}
model->periodic = 3;
model->construct_pbc = TRUE;
}
/* read coordinates */
if ( g_strrstr(*buff, "atom") != NULL ) {
if ( ( num_tokens >= 4 ) && ( elem_symbol_test(*(buff+4)) ) ) {
core = new_core(*(buff+4), model);
core->x[0] = str_to_float(*(buff+1));
core->x[1] = str_to_float(*(buff+2));
core->x[2] = str_to_float(*(buff+3));
model->cores = g_slist_prepend(model->cores, core);
}
else {
gui_text_show(ERROR, "error reading AIMS lattice vectors \n");
return(2);
}
}
g_strfreev(buff);
}
/* done reading */
scan_free(scan);
/* model setup */
g_free(model->filename);
model->filename = g_strdup(filename);
g_free(model->basename);
model->basename = g_path_get_basename(filename);
model->fractional = FALSE;
model_prep(model);
return(0);
}
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;
}
gint read_dmol_frame(FILE *fp, struct model_pak *model)
{
gint i, num_tokens;
gchar *line, **buff;
struct core_pak *core;
g_assert(fp != NULL);
line = file_read_line(fp);
while (line)
{
/* read cell vectors */
if (g_ascii_strncasecmp(line, "$cell", 5) == 0 && model)
{
for (i=0 ; i<3 ; i++)
{
g_free(line);
line = file_read_line(fp);
buff = tokenize(line, &num_tokens);
if (num_tokens > 2)
{
model->latmat[i] = AU2ANG*str_to_float(*(buff));
model->latmat[i+3] = AU2ANG*str_to_float(*(buff+1));
model->latmat[i+6] = AU2ANG*str_to_float(*(buff+2));
}
g_strfreev(buff);
}
model->periodic = 3;
model->construct_pbc = TRUE;
}
/* read coordinates */
if (g_ascii_strncasecmp(line, "$coord", 5) == 0 && model)
{
g_free(line);
line = file_read_line(fp);
buff = tokenize(line, &num_tokens);
while (num_tokens > 3)
{
if (elem_symbol_test(*buff))
{
core = new_core(*buff, model);
model->cores = g_slist_prepend(model->cores, core);
core->x[0] = AU2ANG*str_to_float(*(buff+1));
core->x[1] = AU2ANG*str_to_float(*(buff+2));
core->x[2] = AU2ANG*str_to_float(*(buff+3));
}
g_free(line);
line = file_read_line(fp);
g_strfreev(buff);
buff = tokenize(line, &num_tokens);
}
g_strfreev(buff);
model->fractional = FALSE;
}
/* terminate frame read */
if (g_ascii_strncasecmp(line, "$end", 4) == 0)
return(0);
g_free(line);
line = file_read_line(fp);
}
return(1);
}
gint read_diffax(gchar *filename, struct model_pak *model)
{
gint num_tokens, num_layer, tot_layer;
gdouble offset;
gchar **buff;
GSList *list1, *list2;
struct core_pak *core;
struct layer_pak *layer;
FILE *fp;
/* 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);
/* setup */
model->id = DIFFAX_INP;
model->fractional = TRUE;
model->periodic = 3;
model->colour_scheme = REGION;
strcpy(model->filename, filename);
g_free(model->basename);
model->basename = parse_strip(filename);
/* scan the file */
while ((buff = get_tokenized_line(fp, &num_tokens)))
{
diffax_keyword_search:;
/* restricted unit cell */
if (g_ascii_strncasecmp("structural", *buff, 10) == 0)
{
g_strfreev(buff);
buff = get_tokenized_line(fp, &num_tokens);
if (num_tokens > 3)
{
model->pbc[0] = str_to_float(*(buff+0));
model->pbc[1] = str_to_float(*(buff+1));
model->pbc[2] = str_to_float(*(buff+2));
model->pbc[3] = PI/2.0;
model->pbc[4] = PI/2.0;
model->pbc[5] = D2R*str_to_float(*(buff+3));
}
}
/* layer testing */
if (g_ascii_strncasecmp("layer", *buff, 5) == 0)
{
layer = g_malloc(sizeof(struct model_pak));
layer->width = 1.0;
VEC3SET(layer->centroid, 0.5, 0.5, 0.5);
layer->cores = NULL;
model->layer_list = g_slist_prepend(model->layer_list, layer);
g_strfreev(buff);
buff = get_tokenized_line(fp, &num_tokens);
if (buff)
{
/* TODO - if centrosymmetric : add a -1 operation */
}
/* get layer data */
g_strfreev(buff);
buff = get_tokenized_line(fp, &num_tokens);
while (buff)
{
if (elem_symbol_test(*buff))
{
if (num_tokens > 6)
{
/*
printf("[%s] [%s %s %s]\n", *buff, *(buff+2), *(buff+3), *(buff+4));
*/
core = new_core(*buff, model);
model->cores = g_slist_prepend(model->cores, core);
layer->cores = g_slist_prepend(layer->cores, core);
core->x[0] = str_to_float(*(buff+2));
core->x[1] = str_to_float(*(buff+3));
core->x[2] = str_to_float(*(buff+4));
core->sof = str_to_float(*(buff+5));
}
}
else
goto diffax_keyword_search;
/* get next line of tokens */
g_strfreev(buff);
buff = get_tokenized_line(fp, &num_tokens);
}
}
g_strfreev(buff);
}
/* TODO - enumerate layers and scale, so they are stacked 1..n in a single cell */
/* also label the layers as different region types */
model->layer_list = g_slist_reverse(model->layer_list);
num_layer = 0;
tot_layer = g_slist_length(model->layer_list);
model->pbc[2] *= tot_layer;
#if DEBUG_READ_DIFFAX
printf("Read in %d layers.\n", tot_layer);
#endif
for (list1=model->layer_list ; list1 ; list1=g_slist_next(list1))
{
layer = (struct layer_pak *) list1->data;
layer->width = 1.0 / (gdouble) tot_layer;
offset = (gdouble) num_layer * layer->width;
VEC3SET(layer->centroid, 0.0, 0.0, offset);
for (list2=layer->cores ; list2 ; list2=g_slist_next(list2))
{
core = (struct core_pak *) list2->data;
/* scale to within the big cell (encloses all DIFFAX layers) */
core->x[2] *= layer->width;
/* offset each particular layer */
core->x[2] += offset;
core->region = num_layer;
}
num_layer++;
}
/* end of read */
fclose(fp);
/* post read setup */
model->cores = g_slist_reverse(model->cores);
model_prep(model);
return(0);
}
gint read_rietica(gchar *filename, struct model_pak *model)
{
gint i, phases=0, skip, num_tokens;
gchar **buff, *line;
float x, y, z;
gpointer scan;
GSList *list;
struct core_pak *core;
/* checks */
g_assert(model != NULL);
scan = scan_new(filename);
if (!scan)
return(1);
/* FIXME - stop the previous file routines setting this */
model->id = -1;
while (!scan_complete(scan))
{
buff = scan_get_tokens(scan, &num_tokens);
/* search for structure start */
if (num_tokens)
{
if (g_ascii_strncasecmp(*buff, "***", 3) == 0)
{
if (phases)
model = model_new();
phases++;
/* structure name - omit the 1st and last tokens (ie "***") */
if (num_tokens > 1)
{
g_free(*(buff+num_tokens-1));
*(buff+num_tokens-1) = NULL;
g_free(model->basename);
model->basename = g_strjoinv(" ", buff+1);
}
/* parse spacegroup */
line = scan_get_line(scan);
line = scan_get_line(scan);
model->sginfo.spacename = g_strstrip(g_strdup(line));
model->sginfo.spacenum = -1;
/* parse a structure */
skip = 0;
while (!scan_complete(scan))
{
g_strfreev(buff);
buff = scan_get_tokens(scan, &num_tokens);
if (num_tokens)
{
if (elem_symbol_test(*buff))
{
/* new core */
/*
if (num_tokens > 6)
*/
{
core = new_core(*buff, model);
model->cores = g_slist_prepend(model->cores, core);
/* formatted output can result in -ve signs "joining" tokens */
line = scan_cur_line(scan);
/* no doubt some fortran programmer thought this was a clever format */
sscanf(line, "%*16c%8f%8f%8f", &x, &y, &z);
VEC3SET(core->x, x, y, z);
/*
printf("> %s", line);
P3VEC(" - ", core->x);
core->x[0] = str_to_float(*(buff+2));
core->x[1] = str_to_float(*(buff+3));
core->x[2] = str_to_float(*(buff+4));
core->sof = str_to_float(*(buff+6));
*/
skip = 0;
}
}
else
skip++;
}
/* 4 lines after the last core - parse cell info and terminate structure */
if (skip == 4)
{
if (num_tokens > 5)
{
for (i=6 ; i-- ; )
model->pbc[i] = str_to_float(*(buff+i));
model->pbc[3] *= D2R;
model->pbc[4] *= D2R;
model->pbc[5] *= D2R;
}
break;
}
}
}
}
g_strfreev(buff);
}
/* setup all new structures */
for (list=sysenv.mal ; list ; list=g_slist_next(list))
{
model = list->data;
if (model->id == -1)
{
model->id = RIETICA;
model->periodic = 3;
model->fractional = TRUE;
strcpy(model->filename, filename);
model->cores = g_slist_reverse(model->cores);
model_prep(model);
}
}
scan_free(scan);
return(0);
}
