void bond_xtal_origin_update (int iw)
{
register int i,j;
int k;
double *new_s, ds[3], tmp[3];
if (temporary_disable_bond) return;
MALLOC( bond_xtal_origin_update, new_s, DIMENSION*np, double );
V3mM3 (n[iw].xtal_origin, HI, ds);
V3TRIM (ds, ds);
for (i=0; i<np; i++)
{
V3SUB ( &(s[DIMENSION*i]), ds, &(new_s[DIMENSION*i]) );
V3TriM ( &(new_s[DIMENSION*i]) );
}
if (n[iw].bond_mode == BOND_MODE_USER)
for (k=0; k<C->n_cylinders; k++)
{
i = CylinderAtoms[2*k];
j = CylinderAtoms[2*k+1];
V3SUB (&(new_s[DIMENSION*j]), &(new_s[DIMENSION*i]), tmp);
if ( V3NEED_IMAGE(tmp) )
{ /* g<0 means geometric invisibility */
C->CYLINDER[k].g = -fabs(C->CYLINDER[k].g);
C->CYLINDER[k].radius = -fabs(C->CYLINDER[k].radius);
}
else
{
C->CYLINDER[k].g = fabs(C->CYLINDER[k].g);
C->CYLINDER[k].radius = fabs(C->CYLINDER[k].radius);
V3EQV (B->BALL[i].x, C->CYLINDER[k].x0);
}
}
else
for (i=0; i<np; i++)
for (j=N->idx[i]; j<N->idx[i+1]; j++)
{
V3SUB (&(new_s[DIMENSION*N->list[j]]),
&(new_s[DIMENSION*i]), tmp);
if ( V3NEED_IMAGE(tmp) )
{ /* g<0 means geometric invisibility */
C->CYLINDER[j].g = -fabs(C->CYLINDER[j].g);
C->CYLINDER[j].radius = -fabs(C->CYLINDER[j].radius);
}
else
{
C->CYLINDER[j].g = BOND_G(i, N->list[j]);
V3EQV (B->BALL[i].x, C->CYLINDER[j].x0);
if (C->CYLINDER[j].r >= 0)
C->CYLINDER[j].radius = n[iw].bond_radius;
}
}
free (new_s);
n[iw].bond_xtal_origin_need_update = FALSE;
return;
} /* end bond_xtal_origin_update() */
int Eyesight_Intersect_H_Box (int iw, int to_x, int to_y, double xx[3])
{
register int i,j;
int idx[6];
double k0, k1, s[6][3], x[6][3];
double z[6];
k0 = (to_x + 0.5 - AX_3D[iw].wx) / AX_3D[iw].k;
k1 = (to_y + 0.5 - AX_3D[iw].wy) / AX_3D[iw].k;
for (j=i=0; i<6; i++)
if ( ((z[i]=Eyesight_Intersect_H_Surface
(H, i, AX_3D[iw].x, AX_3D[iw].V, k0, k1, s[i], x[i])) > 0) &&
V3XIN(s[i],0,1) ) idx[j++] = i;
if (j > 0)
{
qsort_numerical_recipes (j, z, idx, USE_OLD_IDX);
V3EQV (x[idx[0]], xx);
return (idx[0]);
}
else return (-1);
} /* end Eyesight_Intersect_H_Box() */
/* Return z>0 if there is intersection, -1 otherwise. */
double Eyesight_Intersect_H_Surface
(double H[3][3], int surface_id,
double x0[3], double V[3][3], double k0, double k1,
double s[3], double x[3])
{
int i;
double b[3], M[3][3], MI[3][3], tmp;
i = surface_id / 2;
if (surface_id % 2) V3SUB(x0,H[i],b);
else V3EQV(x0,b);
M3EQV(H,M);
V3NEG(V[2],M[i]);
V3SUBmuL(M[i],k0,V[0]);
V3SUBmuL(M[i],k1,V[1]);
tmp = M3DETERMINANT(M);
if (ISTINY(tmp)) return(-1);
M3INV(M,MI,tmp);
V3mM3(b,MI,s);
tmp = s[i];
s[i] = surface_id % 2;
V3mM3 (s,H,x);
return (tmp);
} /* end Eyesight_Intersect_H_Surface() */
/* Allocate bonds */
void Config_to_3D_Bonds (double bond_radius)
{
register int i,j;
AX_Float ds[3], DS[3];
AX_3D_Cylinders_Realloc (C, N->idx[np]);
for (i=0; i<np; i++)
for (j=N->idx[i]; j<N->idx[i+1]; j++)
{
V3EQV ( B->BALL[i].x, C->CYLINDER[j].x0 );
V3SUB ( &s[DIMENSION*N->list[j]], &s[DIMENSION*i], ds );
V3IMAGE ( ds, DS );
V3mM3 ( DS, H, C->CYLINDER[j].axis );
AX_V3NORMALIZE ( C->CYLINDER[j].axis, C->CYLINDER[j].axis[3] );
BONDCOLOR (i, N->list[j], j);
if (V3NEED_IMAGE(ds))
{
C->CYLINDER[j].g = -1;
C->CYLINDER[j].radius = -1;
}
else C->CYLINDER[j].radius = bond_radius;
}
return;
} /* end Config_to_3D_Bonds() */
void p3dp_s(double *si, int i, int irank)
{
if (p3d_rank(p3dp_cell) == irank)
V3EQV(&s[DIMENSION*i], si);
p3d_bcast(p3dp_cell, si, 3, MPI_DOUBLE, irank);
}
bool print_status (int iw)
{
int i;
double x[3], V[3][3];
SimpleStatistics ss;
/* xterm_get_focus(iw); */
for (i=0; i<CONFIG_num_auxiliary; i++)
{
CalculateSimpleStatistics
(np, CHARP(CONFIG_auxiliary[i]), sizeof(double),
IOVAL_DOUBLE, &ss);
printf("\nauxiliary[%d]=%s [%s], threshold=[%g, %g]\n", i,
CONFIG_auxiliary_name[i], CONFIG_auxiliary_unit[i],
n[iw].auxiliary_threshold[i][0],
n[iw].auxiliary_threshold[i][1]);
printf("[%g(%d), %g(%d)], avg=%g, std.dev.=%g\n",
ss.min, ss.idx_min, ss.max, ss.idx_max,
ss.average, ss.standard_deviation);
}
printf("\n======================= Status of Viewport #%d "
"=======================\n",iw);
V3EQV (AX_3D[iw].x, x);
V3pr ("Viewpoint is at %M A,\n", x);
M3inv (H, V);
V3mM3 (AX_3D[iw].x, V, x);
V3pr("in reduced coordinates it is %M;\n", x);
M3EQV(AX_3D[iw].V, V); S3PR("viewport axes = %M;\n", V);
printf ("window width = %d, height = %d pixels,\n",
AX_size[iw].width, AX_size[iw].height);
printf ("and conversion factor is %g pixel/radian,\n", AX_3D[iw].k);
printf ("which converts to %g x %g degrees of field of view.\n",
RADIAN_TO_DEGREE(2*atan(AX_size[iw].width/2/AX_3D[iw].k)),
RADIAN_TO_DEGREE(2*atan(AX_size[iw].height/2/AX_3D[iw].k)));
printf ("The viewport is now anchored to %s",
(n[iw].anchor>=0)? "atom" : "hook" );
if (n[iw].anchor >= 0) print_atom(iw,n[iw].anchor);
else
{
M3inv (H, V);
V3mM3 (n[iw].hook, V, x);
printf("\nx = [%g %g %g] A, or s = [%g %g %g].\n", n[iw].hook[0],
n[iw].hook[1], n[iw].hook[2], x[0], x[1], x[2]);
}
printf("parallel projection mode is turned %s.\n",
n[iw].parallel_projection?"ON":"OFF");
printf("term printout suppression is turned %s.\n",
n[iw].suppress_printout?"ON":"OFF");
V3pr ("background color = %M.\n", n[iw].bgcolor);
printf ("atom r_ratio = %f, bond radius = %f A.\n",
n[iw].atom_r_ratio, n[iw].bond_radius);
printf("bond mode is turned %s.\n", n[iw].bond_mode?"ON":"OFF");
printf("system average IS%s subtracted off from atomistic strains.\n",
shear_strain_subtract_mean ? "" : "N'T");
printf("wireframe mode is %s.\n",
(n[iw].wireframe_mode==WIREFRAME_MODE_CONTRAST)?"CONTRAST":
(n[iw].wireframe_mode==WIREFRAME_MODE_NONE)?"NONE":
(n[iw].wireframe_mode==WIREFRAME_MODE_RGBO)?"RGBO":
(n[iw].wireframe_mode==WIREFRAME_MODE_RGBK)?"RGBK":
(n[iw].wireframe_mode==WIREFRAME_MODE_RGB)?"RGB":
"UNKNOWN");
if (n[iw].xtal_mode)
{
printf ("Xtal mode is turned ON:\n");
V3mM3 (n[iw].xtal_origin, HI, x);
V3TRIM (x, x);
V3pr ("xtal_origin = %M.\n", x);
}
else printf ("Xtal mode is turned OFF.\n");
printf ("color mode = %s.\n",
(n[iw].color_mode==COLOR_MODE_NORMAL)? "NORMAL" :
(n[iw].color_mode==COLOR_MODE_COORD)? "COORDINATION" :
(n[iw].color_mode==COLOR_MODE_AUXILIARY)? "Auxiliary Properties" :
(n[iw].color_mode==COLOR_MODE_SCRATCH)? "SCRATCH" : "UNKNOWN");
if (n[iw].shell_viewer_mode)
printf("Shell viewer auto-invoke is turned ON.\n");
else printf("Shell viewer auto-invoke is turned OFF.\n");
printf("s[%d]=%d surface is now seen or selected.\n",
n[iw].last_surface_id/2, n[iw].last_surface_id%2);
if (rcut_patching)
printf ("Neighbor distance cutoff between %s = %g.\n",
rcut_patch_pairname, rcut_patch[rcut_patch_item].rcut);
printf ("rate of change = %g.\n", n[iw].delta);
if (n[iw].color_mode==COLOR_MODE_AUXILIARY)
{
i = n[iw].auxiliary_idx;
if (i < CONFIG_num_auxiliary)
printf("auxiliary[%d] = %s [%s], threshold = [%g, %g],\n", i,
CONFIG_auxiliary_name[i], CONFIG_auxiliary_unit[i],
n[iw].auxiliary_threshold[i][0],
n[iw].auxiliary_threshold[i][1]);
else printf("auxiliary = %s, threshold = [%g, %g],\n",
geolist[i-CONFIG_MAX_AUXILIARY].token,
n[iw].auxiliary_threshold[i][0],
n[iw].auxiliary_threshold[i][1]);
CalculateSimpleStatistics
(np, CHARP(INW(n[iw].auxiliary_idx,CONFIG_num_auxiliary) ?
CONFIG_auxiliary[i] : geo[i-CONFIG_MAX_AUXILIARY]),
sizeof(double), IOVAL_DOUBLE, &ss);
printf("[%g(%d),%g(%d)], avg=%g, std.dev.=%g,\n",
ss.min, ss.idx_min, ss.max, ss.idx_max,
ss.average, ss.standard_deviation);
printf("auxiliaries' colormap = %s \"%s\".\n",
AX_cmap_funs[n[iw].auxiliary_cmap].name,
AX_cmap_funs[n[iw].auxiliary_cmap].description);
printf("invisible outside auxiliary thresholds flag = %s.\n",
n[iw].auxiliary_thresholds_saturation?"OFF":"ON");
printf("floating auxiliary thresholds flag = %s.\n",
n[iw].auxiliary_thresholds_rigid?"OFF":"ON");
}
printf ("clicked atoms = [ ");
for (i=0; i<ATOM_STACK_SIZE; i++) printf ("%d ", n[iw].atom_stack[i]);
printf ("];\n");
for (i=0; i<AX_3D_MAX_FILTER_PLANE; i++)
if (AX_V3NEZERO(AX_3D[iw].fp[i].dx))
printf("%s fp %d: dx = [%g %g %g], s = [%g %g %g]\n",
(n[iw].just_activated_fp==i) ? "*" : " ",
i, V3E(AX_3D[iw].fp[i].dx), V3E(n[iw].fp[i].s0));
printf("=============================================="
"=======================\n");
return(FALSE);
} /* end print_status() */
/* Allocate arrows */
void Config_to_3D_Arrows(int arrow_idx, double scale_factor, double head_height, double head_width, double up[3], int overlay, double color[3])
{
register int i, j, offset;
double dx[3], head[3], head1[3], perp[3], perp2[3], sum;
AX_3D_Lines tmp_arrows[1] = {{0}};
tmp_arrows[0].LINE = NULL;
if (overlay) {
offset = arrows->n_lines;
if (offset != 0) {
AX_3D_Lines_Realloc(tmp_arrows, arrows->n_lines);
for (i=0; i<arrows->n_lines; i++) {
V3EQV(arrows->LINE[i].x0, tmp_arrows->LINE[i].x0);
V3EQV(arrows->LINE[i].x1, tmp_arrows->LINE[i].x1);
AX_3D_AssignRGB (tmp_arrows->LINE[i], arrows->LINE[i].r, arrows->LINE[i].g, arrows->LINE[i].b);
}
}
AX_3D_Lines_Realloc(arrows, arrows->n_lines + 3*np);
if (offset != 0) {
for (i=0; i<tmp_arrows->n_lines; i++) {
V3EQV(tmp_arrows->LINE[i].x0, arrows->LINE[i].x0);
V3EQV(tmp_arrows->LINE[i].x1, arrows->LINE[i].x1);
AX_3D_AssignRGB (arrows->LINE[i], tmp_arrows->LINE[i].r, tmp_arrows->LINE[i].g, tmp_arrows->LINE[i].b);
}
AX_3D_Lines_Free(tmp_arrows);
}
} else {
AX_3D_Lines_Realloc(arrows, 3*np);
offset = 0;
}
/* auto scale */
if (scale_factor == 0.0) {
sum = 0.0;
for (i=0; i<np; i++) {
dx[0] = *(CONFIG_auxiliary[arrow_idx+0]+i);
dx[1] = *(CONFIG_auxiliary[arrow_idx+1]+i);
dx[2] = *(CONFIG_auxiliary[arrow_idx+2]+i);
sum += V3LENGTH(dx);
}
scale_factor = 1.0/(sum/np);
printf("Config_to_3D_Arrows: average magnitude = %f, scale_factor set to %f\n", 1.0/scale_factor, scale_factor);
}
printf("Config_to_3D_Arrows: color = <%.3f,%.3f,%.3f>\n", color[0], color[1], color[2]);
for (i=0; i<np; i++)
{
AX_3D_AssignRGB (arrows->LINE[offset+3*i], color[0], color[1], color[2]);
AX_3D_AssignRGB (arrows->LINE[offset+3*i+1], color[0], color[1], color[2]);
AX_3D_AssignRGB (arrows->LINE[offset+3*i+2], color[0], color[1], color[2]);
dx[0] = *(CONFIG_auxiliary[arrow_idx+0]+i)*scale_factor;
dx[1] = *(CONFIG_auxiliary[arrow_idx+1]+i)*scale_factor;
dx[2] = *(CONFIG_auxiliary[arrow_idx+2]+i)*scale_factor;
if (V3EQZERO(dx)) {
for (j=0; j<3; j++) {
V3EQV(B->BALL[i].x, arrows->LINE[offset+3*i+j].x0);
V3EQV(B->BALL[i].x, arrows->LINE[offset+3*i+j].x1);
}
} else {
V3ADD(B->BALL[i].x, dx, head);
V3EQV(B->BALL[i].x, arrows->LINE[offset+3*i+0].x0);
V3EQV(head, arrows->LINE[offset+3*i+0].x1);
V3EQV(head, arrows->LINE[offset+3*i+1].x0);
V3EQV(head, arrows->LINE[offset+3*i+2].x0);
V3CROSS(dx, up, perp2);
if (V3EQZERO(perp2)) {
V3ASSIGN(1.0, 0.0, 0.0,perp);
} else {
V3CROSS(dx, perp2, perp);
V3normalize(perp);
}
V3mul(head_width*V3LENGTH(dx),perp,perp);
V3EQV(dx, head1);
V3mul(head_height,head1,head1);
V3SUB(head,head1,head1);
V3ADD(head1,perp,arrows->LINE[offset+3*i+1].x1);
V3SUB(head1,perp,arrows->LINE[offset+3*i+2].x1);
}
}
}
/* 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() */
