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_nwchem_system(gpointer scan, struct model_pak *model)
{
gint *symbols, num_symbols, num_tokens;
gchar **buff;
// rewind
scan_put_line(scan);
while (!scan_complete(scan))
{
symbols = scan_get_symbols(scan, &num_symbols);
if (num_symbols)
{
/* process first recognized symbol */
switch (symbols[0])
{
case NWCHEM_SYSTEM:
if (num_symbols > 1)
{
switch (symbols[1])
{
case NWCHEM_CRYSTAL:
model->periodic = 3;
model->fractional = TRUE;
/* lengths */
buff = scan_get_tokens(scan, &num_tokens);
if (num_tokens > 5)
{
model->pbc[0] = str_to_float(buff[1]);
model->pbc[1] = str_to_float(buff[3]);
model->pbc[2] = str_to_float(buff[5]);
}
g_strfreev(buff);
/* angles */
buff = scan_get_tokens(scan, &num_tokens);
if (num_tokens > 5)
{
model->pbc[3] = D2R*str_to_float(buff[1]);
model->pbc[4] = D2R*str_to_float(buff[3]);
model->pbc[5] = D2R*str_to_float(buff[5]);
}
g_strfreev(buff);
break;
case NWCHEM_SURFACE:
model->periodic = 2;
model->fractional = TRUE;
/* lengths */
buff = scan_get_tokens(scan, &num_tokens);
if (num_tokens > 3)
{
model->pbc[0] = str_to_float(buff[1]);
model->pbc[1] = str_to_float(buff[3]);
}
g_strfreev(buff);
/* angles */
buff = scan_get_tokens(scan, &num_tokens);
if (num_tokens > 1)
model->pbc[5] = D2R*str_to_float(buff[1]);
g_strfreev(buff);
break;
case NWCHEM_POLYMER:
model->periodic = 1;
model->fractional = TRUE;
/* length */
buff = scan_get_tokens(scan, &num_tokens);
if (num_tokens > 1)
model->pbc[0] = str_to_float(buff[1]);
g_strfreev(buff);
break;
default:
model->periodic = 0;
model->fractional = FALSE;
}
}
break;
case NWCHEM_END:
g_free(symbols);
return(0);
}
g_free(symbols);
}
}
return(0);
}
gint read_nwchem_geometry(gpointer scan, struct model_pak *model)
{
gint n, zmode=0, end_count=0;
gchar **buff;
struct core_pak *core;
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("read_nwchem_geometry(): start\n");
#endif
// TODO - rewrite this using symbol scanning functionality
while (!scan_complete(scan))
{
buff = scan_get_tokens(scan, &n);
// zmatrix?
if (g_ascii_strncasecmp(*buff, "zmatrix", 7) == 0)
{
zmode = 1;
g_strfreev(buff);
continue;
}
if (g_ascii_strncasecmp(*buff, "variables", 9) == 0)
{
zmode = 2;
g_strfreev(buff);
continue;
}
if (g_ascii_strncasecmp(*buff, "constants", 9) == 0)
{
zmode = 3;
g_strfreev(buff);
continue;
}
// end?
if (n)
{
if (g_ascii_strncasecmp(*buff, "end", 3) == 0)
{
g_strfreev(buff);
/* if we processed zmatrix entries - expect 2 x end */
if (zmode && !end_count)
{
/* keep going until we hit a second end ... */
end_count++;
continue;
}
/* exit */
break;
}
}
/* main parse */
switch (zmode)
{
// cartesian coords
case 0:
// can cart coord line have >4 tokens?
if (n == 4)
{
if (elem_test(*buff))
{
core = core_new(*buff, NULL, model);
model->cores = g_slist_prepend(model->cores, core);
core->x[0] = str_to_float(*(buff+1));
core->x[1] = str_to_float(*(buff+2));
core->x[2] = str_to_float(*(buff+3));
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("Added [%s] ", *buff);
P3VEC(": ", core->x);
#endif
}
}
break;
// zmatrix coords
case 1:
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("zcoord: %s", scan_cur_line(scan));
#endif
zmat_nwchem_core_add(scan_cur_line(scan), model->zmatrix);
break;
// zmatrix vars
case 2:
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("zvar: %s", scan_cur_line(scan));
#endif
zmat_var_add(scan_cur_line(scan), model->zmatrix);
break;
// zmatrix consts
case 3:
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("zconst: %s", scan_cur_line(scan));
#endif
zmat_const_add(scan_cur_line(scan), model->zmatrix);
break;
}
g_strfreev(buff);
}
if (zmode)
{
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("Creating zmatrix cores...\n");
#endif
zmat_angle_units_set(model->zmatrix, DEGREES);
zmat_process(model->zmatrix, model);
}
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("read_nwchem_geometry(): stop\n");
#endif
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);
}
