struct core_pak *new_core(gchar *elem, struct model_pak *model)
{
struct core_pak *core;
core = core_new(elem, NULL, model);
return(core);
}
void core_trace(char* path, char* binpath)
{
core_obj_t* core = NULL;
bin_handler_t* binh = NULL;
backtrace_t* backtrace = NULL;
backt_t* backt = NULL;
core = core_new(path);
if (core == NULL)
errexit("ftrace: core_new:, %s", ftrace_strerror(errno));
/*
** Init binaries.
*/
if (binpath)
binh = bin_create_handler(binpath);
else
binh = bin_create_handler(core_get_bin_path(core));
if (binh == NULL)
errexit("ftrace: bin_create_handler, %s", ftrace_strerror(errno));
if (binh->tracee)
bin_refresh_depends_list(core_get_depends_list(core, binh->tracee->obj), binh);
backtrace = core_backtrace(core);
if (backtrace == NULL)
errexit("ftrace: core_backtrace, %s", ftrace_strerror(errno));
/*
** Start backtrace.
*/
pverbose(1, "\nStarting backtrace of %s\n\n", path);
for (; backtrace; )
{
backt = (backt_t*) backtrace->value;
print_backt(binh, backt->addr);
backtrace = list_del(backtrace, backt);
free(backt);
}
pverbose(1, "\n");
}
void zmat_build(void)
{
gint i, j, k, n, type;
gdouble r, a, d, x[4][3], v[3];
gdouble zaxis[3] = {0.0, 0.0, 1.0};
gchar *line;
GSList *list, *species;
struct zmat_pak *zmat;
struct core_pak *core[4] = {NULL, NULL, NULL, NULL};
struct model_pak *model;
model = sysenv.active_model;
if (!model)
return;
/* CURRENT - using selection as our list of cores to generate a zmatrix from */
if (!model->selection)
{
gui_text_show(WARNING, "ZMATRIX: please select a molecule.\n");
return;
}
/* destroy old zmatrix */
/* TODO - prompt if non null */
zmat_free(model->zmatrix);
zmat = model->zmatrix = zmat_new();
zmat_angle_units_set(model->zmatrix, DEGREES);
/* setup SIESTA species type */
species = fdf_species_build(model);
/* sort the list so it follows molecular connectivity */
model->selection = zmat_connect_sort(model->selection);
n=0;
for (list=model->selection ; list ; list=g_slist_next(list))
{
/* current atom/zmatrix line init */
core[0] = list->data;
type = fdf_species_index(core[0]->atom_label, species);
line = NULL;
zmat->zcores = g_slist_append(zmat->zcores, core[0]);
/* build a ZMATRIX line for processing */
switch (n)
{
case 0:
if (core[0])
{
ARR3SET(x[0], core[0]->x);
vecmat(model->latmat, x[0]);
}
line = g_strdup_printf("%d 0 0 0 %f %f %f 0 0 0\n", type, x[0][0], x[0][1], x[0][2]);
break;
case 1:
if (core[0])
{
ARR3SET(x[0], core[0]->x);
vecmat(model->latmat, x[0]);
}
if (core[1])
{
ARR3SET(x[1], core[1]->x);
vecmat(model->latmat, x[1]);
}
r = measure_distance(x[0], x[1]);
/* angle with z axis */
ARR3SET(v, x[0]);
ARR3SUB(v, x[1]);
a = R2D * via(v, zaxis, 3);
/* angle between xy projection and x axis */
d = R2D * angle_x_compute(v[0], v[1]);
line = g_strdup_printf("%d 1 0 0 %f %f %f 0 0 0\n", type, r, a, d);
break;
case 2:
/* coords init */
for (i=3 ; i-- ; )
{
if (core[i])
{
ARR3SET(x[i], core[i]->x);
vecmat(model->latmat, x[i]);
}
else
g_assert_not_reached();
}
r = measure_distance(x[0], x[1]);
a = measure_angle(x[0], x[1], x[2]);
/* create a fake core -> 1 unit displaced in the z direction */
g_assert(core[3] == NULL);
core[3] = core_new("x", NULL, model);
ARR3SET(core[3]->rx, core[2]->rx);
ARR3ADD(core[3]->rx, zaxis);
d = measure_torsion(core);
core_free(core[3]);
line = g_strdup_printf("%d 2 1 0 %f %f %f 0 0 0\n", type,r,a,d);
break;
default:
/* connectivity test */
if (!zmat_bond_check(core[0], core[1]))
{
#if DEBUG_ZMAT_BUILD
printf("[%d] non-connected atoms [%f]\n", n, measure_distance(x[0], x[1]));
#endif
/* need to build a new connectivity chain starting from core[0] */
core[1] = core[2] = core[3] = NULL;
if (!zmat_connect_find(n, core, zmat))
{
gui_text_show(WARNING, "ZMATRIX: bad connectivity (molecule will be incomplete)\n");
goto zmat_build_done;
}
}
/* coords init */
for (i=3 ; i-- ; )
{
if (core[i])
{
ARR3SET(x[i], core[i]->x);
vecmat(model->latmat, x[i]);
}
else
g_assert_not_reached();
}
r = measure_distance(x[0], x[1]);
a = measure_angle(x[0], x[1], x[2]);
d = measure_torsion(core);
/* NB: indexing starts from 0, siesta starts from 1 (naturally) */
i = 1+g_slist_index(zmat->zcores, core[1]);
j = 1+g_slist_index(zmat->zcores, core[2]);
k = 1+g_slist_index(zmat->zcores, core[3]);
line = g_strdup_printf("%d %d %d %d %f %f %f 0 0 0\n", type,i,j,k,r,a,d);
}
/* process a successfully constructed ZMATRIX line */
if (line)
{
zmat_core_add(line, model->zmatrix);
g_free(line);
}
/* shuffle */
core[3] = core[2];
core[2] = core[1];
core[1] = core[0];
n++;
}
zmat_build_done:
/* do the species typing */
zmat_type(model->zmatrix, species);
free_slist(species);
}
gint read_about(gchar *filename, struct model_pak *model)
{
gint i, flag, frame, num_tokens, tot_tokens;
gint natom=0, ntype=0;
GString *title;
gchar **buff, **curr_token, *ptr, *tmp, line[LINELEN];
struct core_pak *core;
GSList *clist;
FILE *fp;
fp = fopen(filename, "rt");
if (!fp)
return(1);
flag=frame=0;
while (!fgetline(fp, line))
{
/* space group info */
if (g_ascii_strncasecmp(" Symmetries :", line, 13) == 0)
{
ptr = g_strrstr(line, "(#");
model->sginfo.spacenum = (gint) str_to_float(ptr+2);
}
/* default cell dimensions */
/* NB: gdis wants transposed ABINIT matrix */
if (g_ascii_strncasecmp(" Real(R)+Recip(G)", line, 17) == 0)
{
for (i=0; i<3; i++)
{
if (fgetline(fp, line))
{
gui_text_show(ERROR, "unexpected end of file reading cell dimensions\n");
fclose(fp);
return(2);
}
buff = tokenize(line, &num_tokens);
model->latmat[0+i] = str_to_float(*(buff+1))*AU2ANG;
model->latmat[3+i] = str_to_float(*(buff+2))*AU2ANG;
model->latmat[6+i] = str_to_float(*(buff+3))*AU2ANG;
g_strfreev(buff);
}
model->construct_pbc = TRUE;
model->periodic = 3;
/* last part of data in output file before minimisation */
break;
}
/* optimisation type */
if (g_ascii_strncasecmp(" optcell", line, 10) == 0)
{
buff = tokenize(line, &num_tokens);
optcell = (gint) str_to_float(*(buff+1));
g_strfreev(buff);
}
/* coordinates */
if (g_ascii_strncasecmp(" natom", line, 10) == 0)
{
buff = tokenize(line, &num_tokens);
natom = (gint) str_to_float(*(buff+1));
g_strfreev(buff);
}
/* NEW - cope with format change and avoid false positives */
// if (g_ascii_strncasecmp(" ntype", line, 10) == 0)
if (g_strrstr(line, " ntyp"))
{
buff = tokenize(line, &num_tokens);
ntype = (gint) str_to_float(*(buff+1));
g_strfreev(buff);
}
/* NEW - cope with format change and avoid false positives */
// if (g_ascii_strncasecmp(" type", line, 10) == 0)
if (g_strrstr(line, " typ"))
{
tot_tokens = 0;
buff = tokenize(line, &num_tokens);
curr_token = buff + 1;
while (tot_tokens < natom)
{
if (*curr_token == NULL)
{
g_strfreev(buff);
buff = get_tokenized_line(fp, &num_tokens);
curr_token = buff;
}
/* NB: number here is the internal reference to pseudopotential number */
core = core_new(*curr_token, NULL, model);
model->cores = g_slist_prepend(model->cores, core);
tot_tokens++;
curr_token++;
}
model->cores = g_slist_reverse(model->cores);
g_strfreev(buff);
flag++;
}
if (g_ascii_strncasecmp(" xangst", line, 10) == 0)
{
clist = model->cores;
if (clist == NULL)
{
gui_text_show(ERROR, "no atoms found\n");
fclose(fp);
return(2);
}
buff = tokenize(line+10, &num_tokens);
for (i=0; i<natom; i++)
{
core = clist->data;
core->x[0] = str_to_float(*(buff+0));
core->x[1] = str_to_float(*(buff+1));
core->x[2] = str_to_float(*(buff+2));
g_strfreev(buff);
buff = get_tokenized_line(fp, &num_tokens);
clist = g_slist_next(clist);
}
}
/* process the list of atom nuc charges to get atomic numbers */
if (g_ascii_strncasecmp(" znucl", line, 10) == 0)
{
buff = tokenize(line, &num_tokens);
for (clist=model->cores ; clist ; clist=g_slist_next(clist))
{
core = clist->data;
if (core->atom_code > 0 && core->atom_code < num_tokens)
{
/* assign the atomic number */
core->atom_code = str_to_float(*(buff+core->atom_code));
/* wipe the label clean so the element symbol is used */
g_free(core->atom_label);
core->atom_label = NULL;
/* refresh atom's element data */
elem_init(core, model);
}
}
}
}
/* Additional info */
while (!fgetline(fp, line))
{
/* energy */
/* NEW - cope with format change */
if (g_strrstr(line, "Etotal="))
{
buff = g_strsplit(line, "=", 2);
if (buff)
{
model->abinit.energy = str_to_float(*(buff+1));
/* display energy in properties panel */
tmp = g_strdup_printf("%f Hartrees", model->abinit.energy);
property_add_ranked(1, "Total energy", tmp, model);
g_free(tmp);
}
g_strfreev(buff);
}
/* gradient */
else if ((g_ascii_strncasecmp(line, " frms,max,avg=", 14) == 0) && g_strrstr(line, "h/b"))
{
// printf("reading gradient\n");
buff = tokenize(line, &num_tokens);
if (num_tokens > 2)
{
model->abinit.max_grad = str_to_float(*(buff+2));
model->abinit.rms_grad = str_to_float(*(buff+1));
property_add_ranked(1, "Gradient", *(buff+2), model);
}
g_strfreev(buff);
// printf("gradient is %lf\n", model->abinit.max_grad);
}
/* coordinates */
else if ((g_ascii_strncasecmp(line, " Cartesian coordinates (bohr)", 29) == 0 && optcell == 0)
|| (g_ascii_strncasecmp(line, " Unit cell characteristics :", 28) == 0 && optcell > 0))
{
/* go through all frames to count them */
read_about_block(fp, model);
animate_frame_store(model);
frame++;
}
}
fclose(fp);
/* done */
if (flag)
{
g_free(model->filename);
model->filename = g_strdup(filename);
g_free(model->basename);
model->basename = parse_strip(filename);
model->num_frames = model->cur_frame = frame;
model->cur_frame--;
title = g_string_new("");
g_string_append_printf(title, "E");
g_string_append_printf(title, " = %.4f Ha, ", model->abinit.energy);
g_string_append_printf(title, "max grad = %.5f", model->abinit.max_grad);
model->title = g_strdup(title->str);
g_string_free(title, TRUE);
model_prep(model);
}
else
return(2);
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);
}
