bool set_glob_advance (int iw)
{
char danswer[TERMSIZE];
xterm_get_focus(iw); clear_stdin_buffer();
sprintf (danswer, "%d", n[iw].glob_advance);
sscanf(readline_gets("\nFilelist step advance",danswer),
"%d", &(n[iw].glob_advance));
xterm_release_focus(iw);
n[iw].glob_advance = ABS(n[iw].glob_advance);
return (FALSE);
} /* set_glob_advance() */
bool find_atom (int iw)
{
static int last_atom = 0;
int i;
char question[MAX_FILENAME_SIZE],danswer[MAX_FILENAME_SIZE],*answer;
xterm_get_focus(iw); clear_stdin_buffer();
sprintf (question, "\nFind atom [0-%d]", np-1);
sprintf (danswer, "%d", last_atom);
answer = readline_gets(question,danswer);
sscanf (answer, "%d", &i);
xterm_release_focus(iw);
if ((i < 0) || (i >= np)) printf("find_atom: illegal index\n");
else
{
n[iw].anchor = i;
print_atom(iw,i);
last_atom = i;
}
return (FALSE);
} /* end find_atom() */
bool xtal_origin_goto (int iw)
{
double old_s[3], s[3];
char danswer[MAX_FILENAME_SIZE],*answer;
if (!n[iw].xtal_mode)
{
printf ("Crystal translation is only available under Xtal mode.\n");
return(FALSE);
}
V3mM3 (AX_3D[iw].x, HI, old_s);
xterm_get_focus(iw); clear_stdin_buffer();
sprintf (danswer, "%g %g %g", old_s[0],old_s[1],old_s[2]);
answer = readline_gets("\nCrystal origin s0,s1,s2",danswer);
sscanf (answer, "%lf %lf %lf", s, s+1, s+2);
xterm_release_focus(iw);
V3TRIM (s,s);
if (V3EQ(old_s,s)) return(FALSE);
V3mM3 (s, H, n[iw].xtal_origin);
atom_xtal_origin (n[iw].xtal_origin);
if (n[iw].bond_mode) bond_xtal_origin_update (iw);
else n[iw].bond_xtal_origin_need_update = TRUE;
return (TRUE);
} /* end xtal_origin_goto() */
/* Save atoms selected in a monoclinic filter to a file */
void save_atoms_in_monoclinic_filter (int iw)
{
M3 HH;
double d0, zmargin, xytolerance, origin[3];
char danswer[MAX_FILENAME_SIZE], *answer, fname[MAX_FILENAME_SIZE];
char *taglist = NULL;
int selected[2];
V3SUB( B->BALL[n[iw].atom_stack[0]].x,
B->BALL[n[iw].atom_stack[1]].x, HH[0] );
V3SUB( B->BALL[n[iw].atom_stack[2]].x,
B->BALL[n[iw].atom_stack[1]].x, HH[1] );
V3CROSS (HH[0], HH[1], HH[2]);
if (V3ISSMALL(HH[2]))
{
printf("The selected parallelogram is ill-conditioned\n"
"for constructing a monoclinic filter.\n");
return;
}
V3NORMALIZE (HH[2], d0);
printf ("\"up\" is [%g %g %g]\n"
"check it agrees with your mirror normal...\n", V3E(HH[2]));
d0 = 2.5;
zmargin = 0.01;
xytolerance = 0.01;
xterm_get_focus(iw); clear_stdin_buffer();
REALLOC (save_atoms_in_monoclinic_filter, taglist, np, char);
while (1)
{
sprintf (danswer, "%g %g %g", d0, zmargin, xytolerance);
answer = readline_gets
("Interplanar spacing [A] z-margin [A] xy-tolerance", danswer);
sscanf(answer, "%lf %lf %lf", &d0, &zmargin, &xytolerance);
V3ADDMUL (B->BALL[n[iw].atom_stack[1]].x, d0/2,HH[2], origin);
if (tag_atoms_in_monoclinic_filter
(origin,HH, d0+2*zmargin,xytolerance, selected,taglist)>0) break;
strcpy (danswer, answer);
}
printf("down=%d and up=%d atoms selected in filter.\n",
selected[0], selected[1]);
while (1)
{
sprintf (danswer, "%s.idx", fbasename);
answer = readline_gets("Save the selected atoms to", danswer);
sscanf(answer, "%s", fname);
if ( tested_to_be_writable(fname) )
{
save_dipole_indices (selected, taglist, fname);
printf ("selected atom indices [0-%d] saved to %s.\n", np-1,fname);
Free (taglist);
break;
}
else
{
printf ("\n** %s: **\n", fname);
printf ("** This file is unwritable! **\n");
}
strcpy(danswer, answer);
}
xterm_release_focus(iw);
return;
} /* end save_atoms_in_monoclinic_filter() */
/* Load color/radii file for atoms */
bool load_atom_color_from_file (int iw)
{
char fname[MAX_FILENAME_SIZE], buf[COLOR_LINESIZE];
FILE *fp;
int m, j, k, items;
double c[4];
xterm_get_focus(iw); clear_stdin_buffer();
sprintf (buf, "%s.clr", fbasename);
strcpy(fname,readline_gets("\nLoad color properties from",buf));
xterm_release_focus(iw);
if (Freadable(fname))
{
fp = ROpen(fname);
for (m=0; ; m++)
if (fgets(buf,COLOR_LINESIZE,fp))
{
if (m >= np)
{
printf ("\n** %s has more rows than atoms **\n", fname);
return (FALSE);
}
items = sscanf (buf, "%lf %lf %lf %lf", c, c+1, c+2, c+3);
if (items == 1)
{
c[3] = c[0];
c[0] = B->BALL[m].r;
c[1] = B->BALL[m].g;
c[2] = B->BALL[m].b;
}
else if (items == 3)
c[3] = B->BALL[m].radius / n[iw].atom_r_ratio;
if (c[0]>1) c[0]/=255;
if (c[1]>1) c[1]/=255;
if (c[2]>1) c[2]/=255;
AX_3D_AssignRGB(B->BALL[m], c[0], c[1], c[2]);
B->BALL[m].radius = c[3] * n[iw].atom_r_ratio;
}
else if (m < np)
{
if (m == 0)
{
printf ("\n** %s has no data **\n", fname);
return (FALSE);
}
else if ( ISFACTOR (m, np) )
{ /* make a bold guess */
for (j=m; j<np; j++)
{
k = j % m;
AX_3D_AssignRGB (B->BALL[j], B->BALL[k].r,
B->BALL[k].g, B->BALL[k].b);
B->BALL[j].radius = B->BALL[k].radius;
}
}
else printf ("\n** premature ending of %s **\n", fname);
bond_atom_color_update (iw);
return (TRUE);
}
else break;
}
else
{
printf ("\n** %s: **\n", fname);
printf ("** This file is unreadable! **\n");
return (FALSE);
}
bond_atom_color_update (iw);
return (TRUE);
} /* end load_atom_color_from_file() */
/* Use script to produce jpeg frames */
void script_animate (int iw)
{
char buf[SCRIPT_LINE_SIZE],output[SCRIPT_LINE_SIZE],*ptr;
int i,hascontent,quality,frames;
FILE *fp;
glob_t globbuf;
strcpy(buf, "scr_anim");
if (!(fp=ropen(buf)))
{
printf ("\nAnimation script \"%s\" does not exist,\n", buf);
xterm_get_focus(iw); clear_stdin_buffer();
if (!strcasecmp("y", readline_gets
("Do you want a default one created (y/n)?","y")))
{
numerically_sorted_glob (config_fname, &globbuf);
fp=wopen(buf);
fprintf (fp, "%d\n", AX_JPG_DEF_QUALITY);
for (i=0; i<globbuf.gl_pathc; i++)
fprintf (fp, "%s Jpg/%05d.jpg\n", globbuf.gl_pathv[i], i);
globfree (&globbuf);
fclose(fp);
fp = ropen(buf);
}
else
{
xterm_release_focus(iw);
return;
}
}
if (!(ptr=fgets(buf,SCRIPT_LINE_SIZE,fp)))
{
printf ("\nThere is nothing in animation script \"%s\".\n", buf);
fclose (fp);
return;
}
for (hascontent=i=0; (buf[i]!=EOS) &&
(ISDIGIT(buf[i]) || ISBLANK(buf[i]) || (buf[i]=='\n')); i++)
if (ISALNUM(buf[i])) hascontent=1;
if (!hascontent)
{
printf ("\nThere is no content in animation script \"%s\".\n", buf);
fclose (fp);
return;
}
if (buf[i] == EOS)
{
sscanf (buf, "%d", &quality);
if ((quality<0) || (quality>100))
{
printf ("\nquality = %d is out of valid range ([0,100]).\n",
quality);
return;
}
else printf ("\nquality = %d\n", quality);
ptr = fgets(buf,SCRIPT_LINE_SIZE,fp);
}
else quality = AX_JPG_DEF_QUALITY;
frames = 0;
/* If bonds are not on now, there is no need to refresh */
temporary_disable_bond = !n[iw].bond_mode;
/* cylinder data structure during the rendering. */
while (ptr)
{
buf[SCRIPT_LINE_CHAR] = EOS;
sscanf (buf, "%s %s", config_fname, output);
reload_config (iw, FALSE);
paint_scene(iw);
AX_dump(iw); AX_show(iw);
if (str_caseend_with(output,".png"))
AX_save_pixmap_as_png
(iw,AX_JPG_QUALITY_TO_PNG_LEVEL(quality),output);
else if (str_caseend_with(output,".eps"))
AX_save_pixmap_as_eps(iw,quality,output);
else AX_save_pixmap_as_jpg(iw,quality,output);
frames++;
ptr = fgets(buf,SCRIPT_LINE_SIZE,fp);
}
fclose(fp);
printf ("%d frames saved.\n\n", frames);
if (temporary_disable_bond)
{
Config_to_3D_Bonds (n[iw].bond_radius);
if (n[iw].bond_mode)
{
bond_xtal_origin_update (iw);
bond_atom_color_update(iw);
}
else
{
n[iw].bond_xtal_origin_need_update = TRUE;
n[iw].bond_atom_color_need_update = TRUE;
}
temporary_disable_bond = 0;
}
return;
} /* end script_animate() */
/* Reload the configuration but keeping the rendering state */
void reload_config (int iw, bool term_input_filename)
{
register int i;
int j, k, old_np;
char fname[MAX_FILENAME_SIZE], oldfname[MAX_FILENAME_SIZE];
V3 hook_s, tmp, dx;
char *old_symbol=NULL;
bool incompatible_config;
strcpy(oldfname, config_fname);
if (n[iw].anchor >= 0)
{ /* the new configuration may not even have the atom */
V3EQV (B->BALL[n[iw].anchor].x, n[iw].hook);
n[iw].anchor = -1;
}
/* hook_s[] is what is kept invariant */
V3mM3 (n[iw].hook, HI, hook_s);
if (term_input_filename)
{
xterm_get_focus(iw); clear_stdin_buffer();
strcpy(fname,readline_gets("\nLoad configuration",config_fname));
strcpy(config_fname,fname);
xterm_release_focus(iw);
}
if (!Fexists(config_fname))
{
printf ("\n** %s: **\n", config_fname);
printf ("** There is no such file! **\n");
strcpy(config_fname, oldfname);
return;
}
if (!Freadable(config_fname))
{
printf ("\n** %s: **\n", config_fname);
printf ("** This file is unreadable! **\n");
strcpy(config_fname, oldfname);
return;
}
cr();
old_np = np;
CLONE(symbol, SYMBOL_SIZE*np, char, old_symbol);
i = CONFIG_LOAD (config_fname, Config_Aapp_to_Alib);
for (k=0; k<CONFIG_num_auxiliary; k++)
if (*blank_advance(CONFIG_auxiliary_name[k])==EOS)
sprintf(CONFIG_auxiliary_name[k], "auxiliary%d", k);
rebind_CT (Config_Aapp_to_Alib, "", ct, &tp); cr();
Neighborlist_Recreate_Form (Config_Aapp_to_Alib, ct, N);
if (i == CONFIG_CFG_LOADED)
N->s_overflow_err_handler =
NEIGHBORLIST_S_OVERFLOW_ERR_HANDLER_FOLD_INTO_PBC;
else
N->s_overflow_err_handler =
NEIGHBORLIST_S_OVERFLOW_ERR_HANDLER_BOUNDING_BOX;
N->small_cell_err_handler = NEIGHBORLIST_SMALL_CELL_ERR_HANDLER_MULTIPLY;
for (i=0; i<ct->t; i++)
for (j=i; j<ct->t; j++)
for (k=0; k<rcut_patch_top; k++)
if ( ( ( (rcut_patch[k].Zi == ct->Z[i]) &&
(rcut_patch[k].Zj == ct->Z[j]) ) ||
( (rcut_patch[k].Zi == ct->Z[j]) &&
(rcut_patch[k].Zj == ct->Z[i]) ) ) )
NEIGHBOR_TABLE(N->rcut,ct,i,j) =
NEIGHBOR_TABLE(N->rcut,ct,j,i) = rcut_patch[k].rcut;
Neighborlist_Recreate (Config_Aapp_to_Alib, stdout, ct, &tp, N);
V3mM3 (hook_s, H, tmp);
V3SUB (tmp, n[iw].hook, dx);
V3EQV (tmp, n[iw].hook);
V3AdD (dx, AX_3D[iw].x);
M3InV (H, HI, volume);
lengthscale = cbrt(volume);
V3ASSIGN (0.5,0.5,0.5,tmp);
V3mM3 (tmp, H, cm);
geo_clear_has_evaluated_flags();
evaluate_geo_measures(); Free(s1); Free(mass);
if ( ComputeLeastSquareStrain )
{
if (ConfigChecksum(Config_Aapp_to_Alib) != ref->checksum)
printf ("This configuration is not isoatomic with the imprinted "
"reference\n%s. Least-square strain NOT calculated.\n",
ref_fbasename);
else LeastSquareStrain_Append();
}
incompatible_config = (np != old_np) ||
memcmp(symbol, old_symbol, SYMBOL_SIZE*MIN(np,old_np));
Free(old_symbol);
if (incompatible_config)
Config_to_3D_Balls (n[iw].atom_r_ratio);
else for (i=0; i<np; i++) V3mM3 ( &(s[DIMENSION*i]), H, B->BALL[i].x );
atom_xtal_origin (n[iw].xtal_origin);
if (!n[iw].auxiliary_thresholds_rigid)
{
for (i=0; i<CONFIG_num_auxiliary; i++)
reset_auxiliary_threshold(iw,i);
for (i=0; i<MAX_GEO_MEASURES; i++)
if (geolist[i].has_evaluated)
reset_auxiliary_threshold(iw,CONFIG_MAX_AUXILIARY+i);
}
if (!temporary_disable_bond) Config_to_3D_Bonds (n[iw].bond_radius);
select_fbasename (config_fname);
if ((n[iw].xtal_mode) && (n[iw].color_mode == COLOR_MODE_COORD))
assign_coordination_color(iw);
else if (n[iw].color_mode == COLOR_MODE_AUXILIARY)
color_encode_auxiliary(iw);
else if (n[iw].color_mode == COLOR_MODE_SCRATCH)
scratch_color (iw);
else
{
strcpy (AX_title[iw],fbasename);
AXSetName (iw);
XStoreName(AX_display[iw],xterm_win,AX_title[iw]);
XSetIconName(AX_display[iw],xterm_win,AX_title[iw]);
if (!temporary_disable_bond)
{
bond_xtal_origin_update (iw);
bond_atom_color_update (iw);
}
}
return;
} /* end reload_config() */
