// no coords - just control data for the run
// coords - .pdb file
// topology - .frx file
gint reaxmd_input_import(gpointer import)
{
gint *symbols, num_symbols, unknown;
gchar *line, *fullname_model;
gchar *filename, *filepath;
gpointer scan, config;
GString *unparsed;
struct reaxmd_pak *reaxmd;
struct model_pak *model;
FILE *fp;
scan = scan_new(import_fullpath(import));
if (!scan)
return(1);
/* populate symbol table */
reaxmd_symbols_init(scan);
config = config_new(REAXMD, NULL);
reaxmd = config_data(config);
unparsed = g_string_new(NULL);
while (!scan_complete(scan))
{
symbols = scan_get_symbols(scan, &num_symbols);
if (num_symbols)
{
unknown = FALSE;
/* process first recognized symbol */
switch (symbols[0])
{
case REAXMD_NSTEPS:
reaxmd->total_steps = parse_nth_token_dup(1, scan_cur_line(scan));
break;
case REAXMD_TIMESTEP:
case REAXMD_TEMPERATURE:
case REAXMD_THERMOSTAT:
case REAXMD_BAROSTAT:
case REAXMD_CUTOFF:
case REAXMD_UPDATE:
case REAXMD_NWRITE:
case REAXMD_GRID:
break;
case REAXMD_PLUMED_FILE:
filename = parse_nth_token_dup(1, scan_cur_line(scan));
filepath = g_build_filename(import_path(import), filename, NULL);
//printf("Looking for: %s\n", filepath);
if (g_file_test(filepath, G_FILE_TEST_EXISTS))
project_job_file_append(NULL, filepath, sysenv.workspace);
else
gui_text_show(ERROR, "REAXMD plumed file was not found!\n");
g_free(filename);
g_free(filepath);
break;
default:
unknown = TRUE;
}
g_free(symbols);
}
else
unknown=TRUE;
if (unknown)
{
line = scan_cur_line(scan);
if (line)
g_string_append(unparsed, line);
}
}
config_unparsed_set(g_string_free(unparsed, FALSE), config);
/* CURRENT - free this, until we add a GUI */
//import_object_add(IMPORT_CONFIG, config, import);
config_free(config);
/* done irx parse */
scan_free(scan);
/* NEW - attempt to load reference coordinates */
fullname_model = parse_extension_set(import_fullpath(import), "pdb");
fp = fopen(fullname_model, "rt");
if (fp)
{
model = model_new();
read_pdb_block(fp, model);
fclose(fp);
import_object_add(IMPORT_MODEL, model, import);
}
else
{
gui_text_show(WARNING, "Failed to open reference PDB model for ReaxMD.\n");
}
g_free(fullname_model);
/* init */
import_init(import);
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 nwchem_input_import(gpointer import)
{
gint *symbols, num_symbols, num_tokens, value;
gchar *line, **buff;
gpointer scan, config;
GString *unparsed;
struct model_pak *model=NULL; // CURRENT - will break if more than one in a file
struct nwchem_pak *nwchem;
scan = scan_new(import_fullpath(import));
if (!scan)
return(1);
/* populate symbol table */
nwchem_scan_symbols_init(scan);
config = config_new(NWCHEM, NULL);
nwchem = config_data(config);
unparsed = g_string_new(NULL);
while (!scan_complete(scan))
{
symbols = scan_get_symbols(scan, &num_symbols);
if (num_symbols)
{
/* process first recognized symbol */
value = symbols[0];
switch (value)
{
case NWCHEM_START:
/* TODO - could this serve as title? */
nwchem->start = parse_strip(scan_cur_line(scan));
break;
case NWCHEM_BASIS:
// TODO - don't want to use this for predefined basis sets
read_nwchem_basis_library(scan, config);
break;
case NWCHEM_CHARGE:
line = scan_cur_line(scan);
buff = tokenize(line, &num_tokens);
if (num_tokens > 1)
nwchem->charge = g_strdup(buff[1]);
g_strfreev(buff);
break;
case NWCHEM_GEOMETRY:
if (!model)
{
model = model_new();
import_object_add(IMPORT_MODEL, model, import);
}
read_nwchem_geometry(scan, model);
break;
case NWCHEM_SYSTEM:
if (!model)
{
model = model_new();
import_object_add(IMPORT_MODEL, model, import);
}
read_nwchem_system(scan, model);
break;
case NWCHEM_TASK:
read_nwchem_task(scan, config, symbols, num_symbols);
break;
default:
/* add lines that have recognized symbols (but no special trigger) to unparsed */
/* this'll happen for symbols that occur in multiple locations (eg dft) */
line = scan_cur_line(scan);
if (line)
g_string_append(unparsed, line);
}
g_free(symbols);
}
else
{
/* add non-NULL lines to unparsed list */
line = scan_cur_line(scan);
if (line)
g_string_append(unparsed, line);
}
}
config_unparsed_set(g_string_free(unparsed, FALSE), config);
import_object_add(IMPORT_CONFIG, config, import);
scan_free(scan);
import_init(import);
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);
}