atom_coord.c

Go to the documentation of this file.

/* This file is part of the 'atomes' software
 
'atomes' is free software: you can redistribute it and/or modify it under the terms
of the GNU Affero General Public License as published by the Free Software Foundation,
either version 3 of the License, or (at your option) any later version.
 
'atomes' is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
 
You should have received a copy of the GNU Affero General Public License along with 'atomes'.
If not, see <https://www.gnu.org/licenses/>
 
Copyright (C) 2022-2024 by CNRS and University of Strasbourg */
 
/*
* This file: 'atom_coord.c'
*
* Contains:
*
 
 - The functions to correct the coordination menus and the corresponding data pointers after edition
 
*
* List of functions:
 
  int test_this_coord (project * this_proj, int spec, int gid, int cid, int minc, int maxc);
 
  void print_coord_info (project * this_proj, coord_info * coord);
  void clean_coords_and_geoms (project * this_proj, atom_edition * edit,
                               int new_spec, int rem, int adds, int * spid, int *** tmpgeo,
                               gboolean * showcoord[2], gboolean * showpoly[2]);
  void new_coord_menus (project * this_proj, coord_info * coord, int new_spec, int nmols,
                        gboolean * showcoord[2], gboolean * showpoly[2], gboolean * showfrag,
                        gboolean update_it, gboolean update_mol);
  void recover_opengl_data (project * this_proj, int nmols, int add, int rem, int * num, int * rec, int *** tmpgeo, gboolean * showfrag);
 
  coord_info * duplicate_coord_info (coord_info * old_coord);
 
*/
 
#include "atom_edit.h"
 
int test_this_coord (project * this_proj, int spec, int gid, int cid, int minc, int maxc)
{
  int i, j, k, l;
  l = 0;
  for (i=0; i<this_proj -> natomes; i++)
  {
    j = this_proj -> atoms[0][i].sp;
    k = this_proj -> atoms[0][i].coord[gid];
    if (j == spec && (k > maxc && k < minc)) return -1;
    if (j == spec && k == cid)
    {
      l ++;
    }
  }
  return l;
}
 
void print_coord_info (project * this_proj, coord_info * coord)
{
  int * min_bs, * max_bs;
  int i, j, k, l, m;
  gchar * str;
  int test;
  if (coord -> species)
  {
    min_bs = allocint(coord -> species);
    max_bs = allocint(coord -> species);
    g_debug (" ");
    g_debug ("coord -> species = %d", coord -> species);
    g_debug (" ");
    for (i=0; i<4; i++)
    {
      g_debug (" --- start geo[%d] ---", i);
      g_debug ("geo i = %d, totcoord[%d] = %d", i, i, coord -> totcoord[i]);
      if ((i < 2 || i > 3) && coord -> totcoord[i])
      {
        j = (i < 2) ? coord -> species : 1;
        g_debug ("  spec i = %d, jmax= %d", i, j);
        g_debug (" ");
        for (k=0; k<j; k++)
        {
          min_bs[k] = max_bs[k] = coord -> partial_geo[k][0][0];
          for (m=0; m<coord -> species; m++)
          {
            min_bs[k] = min (min_bs[k], coord -> partial_geo[k][0][m]);
            max_bs[k] = max (max_bs[k], coord -> partial_geo[k][0][m]);
          }
          for (l=1; l<coord -> ntg[i][k]; l++)
          {
            for (m=0; m<coord -> species; m++)
            {
              min_bs[k] = min (min_bs[k], coord -> partial_geo[k][l][m]);
              max_bs[k] = max (max_bs[k], coord -> partial_geo[k][l][m]);
            }
          }
        }
        for (k=0; k<j; k++)
        {
          g_debug ("    coord i = %d, k = %d, coord -> ntg[%d][%d] = %d", i, k, i, k, coord -> ntg[i][k]);
          test = (this_proj) ? test_this_coord (this_proj, k, i, 0, min_bs[k], max_bs[k]) : 0;
          str = g_strdup_printf ("          l = %d, coord -> geolist[%d][%d][%d]= %d, num[at,%d]= %d", 0, i, k, 0, coord -> geolist[i][k][0], 0, test);
          if (coord -> ntg[i][k] > 1)
          {
            for (l=1; l<coord -> ntg[i][k]; l++)
            {
              test = (this_proj) ? test_this_coord (this_proj, k, i, l, min_bs[k], max_bs[k]) : 0;
              str = g_strdup_printf ("%s\n                                                  l = %d, coord -> geolist[%d][%d][%d]= %d, num[at,%d]= %d", str, l, i, k, l, coord -> geolist[i][k][l], l, test);
            }
          }
          g_debug ("%s", str);
          g_free (str);
        }
        if (i == 1)
        {
          g_debug (" ");
          for (k=0; k<j; k++)
          {
             str = g_strdup_printf ("    Partials geo\n                                                 k = %d, coord -> partial_geo[%d][%d][%d]= %d", k, k, 0, 0, coord -> partial_geo[k][0][0]);
             for (l=1; l<j; l++)
             {
                str = g_strdup_printf ("%s\n                                                 k = %d, coord -> partial_geo[%d][%d][%d]= %d", str, k, k, 0, l, coord -> partial_geo[k][0][l]);
             }
             if (coord -> ntg[i][k] > 1)
             {
               for (l=1; l<coord -> ntg[i][k]; l++)
               {
                 str = g_strdup_printf ("%s\n\n                                                 k = %d, coord -> partial_geo[%d][%d][%d]= %d", str, k, k, l, 0, coord -> partial_geo[k][l][0]);
                 for (m=1; m<j; m++)
                 {
                    str = g_strdup_printf ("%s\n                                                 k = %d, coord -> partial_geo[%d][%d][%d]= %d", str, k, k, l, m, coord -> partial_geo[k][l][m]);
                 }
               }
             }
             g_debug ("%s", str);
             g_free (str);
          }
        }
        g_debug (" ");
      }
      g_debug (" --- end geo[%d] ---", i);
      g_debug (" ");
    }
    g_free (min_bs);
    g_free (max_bs);
  }
  else
  {
    g_debug (" ");
    g_debug ("Coord is empty no species !");
    g_debug (" ");
  }
}
 
coord_info * duplicate_coord_info (coord_info * old_coord)
{
  coord_info * new_coord = g_malloc0 (sizeof*new_coord);
  int i, j, k, l;
  if (! old_coord -> species) return new_coord;
  new_coord -> species = old_coord -> species;
  new_coord -> cmax = old_coord -> cmax;
  new_coord -> cmin = old_coord -> cmin;
  for (i=0; i<10; i++)
  {
    new_coord -> totcoord[i] = old_coord -> totcoord[i];
    if ((i < 2 || i > 3) && old_coord -> totcoord[i])
    {
      j = (i < 2) ? new_coord -> species : 1;
      new_coord -> ntg[i] = duplicate_int (j, old_coord -> ntg[i]);
      new_coord -> geolist[i] = g_malloc0 (j*sizeof*new_coord -> geolist[i]);
      if (i == 1) new_coord -> partial_geo = g_malloc0 (j*sizeof*new_coord -> partial_geo);
      for (k=0; k<j; k++)
      {
        new_coord -> geolist[i][k] = duplicate_int (new_coord -> ntg[i][k], old_coord -> geolist[i][k]);
        if (i == 1)
        {
          new_coord -> partial_geo[k] = g_malloc0 (new_coord -> ntg[i][k]*sizeof*new_coord -> partial_geo[k]);
          for (l=0; l<new_coord -> ntg[i][k]; l++)
          {
            new_coord -> partial_geo[k][l] = duplicate_int (new_coord -> species, old_coord -> partial_geo[k][l]);
          }
        }
      }
    }
  }
  return new_coord;
}
 
void clean_coords_and_geoms (project * this_proj, atom_edition * edit,
                             int new_spec, int rem, int adds, int * spid, int *** tmpgeo,
                             gboolean * showcoord[2], gboolean * showpoly[2])
{
  int i, j, k, l, m, n, o, p, q, r, s;
  int * tntg;
  coord_info * old_coord = duplicate_coord_info (edit -> coord);
  g_free (edit -> coord);
  edit -> coord = g_malloc0 (sizeof*edit -> coord);
  coord_info * tmp_coord = edit -> coord;
  this_proj -> coord -> cmin = 20;
  this_proj -> coord -> cmax = 0;
  for (i=0; i<2; i++)
  {
    tmp_coord -> totcoord[i] = 0;
    tmp_coord -> geolist[i] = g_malloc (new_spec*sizeof*tmp_coord -> geolist[i]);
    tmp_coord -> ntg[i] = allocint (new_spec);
    if (i) tmp_coord -> partial_geo = g_malloc (new_spec*sizeof*tmp_coord -> partial_geo);
    showcoord[i] = allocbool(old_coord -> totcoord[i]);
    showpoly[i] = allocbool(old_coord -> totcoord[i]);
    // g_debug ("i= %d, allocating showcoord/poly of %d", i, old_coord -> totcoord[i]);
    tmp_coord -> totcoord[i] = 0;
    j = s = 0;
    // g_debug ("i= %d, new_spec= %d, rem= %d", i, new_spec, rem);
    for (k=0; k<new_spec+rem; k++)
    {
      if (spid[k])
      {
        l = 0;
        // g_debug ("k= %d, alloc tntg of: %d", k, old_coord -> ntg[i][k]);
        tntg = allocint (old_coord -> ntg[i][k]);
        // if (i == 0) g_debug ("         checking geom:: i= %d, SP= %d, ntg[%d][%d]= %d", i, k, i, k, old_coord -> ntg[i][k]);
        for (m=0; m<old_coord -> ntg[i][k]; m++)
        {
          // if (i == 0) g_debug ("                      :: m = %d, tmpgeo[%d][%d][%d]= %d", m, i, k, m, tmpgeo[i][k][m]);
          if (tmpgeo[i][k][m])
          {
            p = 1;
            if (i)
            {
              //g_debug ("checking partial, m= %d, l= %d", m, l);
              if (l)
              {
                p = 0;
                for (o=0; o<m; o++)
                {
                  for (q=0; q<new_spec+rem; q++)
                  {
                    if (spid[q] && old_coord -> partial_geo[k][m][q] != old_coord -> partial_geo[k][o][q])
                    {
                      p = 1;
                      break;
                    }
                  }
                  if (! p) break;
                }
              }
            }
            else
            {
              for (o=0; o<m; o++)
              {
                if (old_coord -> geolist[i][k][m] == old_coord -> geolist[i][k][o])
                {
                  // g_debug ("  WAS HERE:: k= %d, m= %d, o= %d, geolist = %d", k, m, o, old_coord -> geolist[i][k][m]);
                  p = 0;
                  break;
                }
              }
            }
            if (p)
            {
              // g_debug ("      i= %d, tntg[m]= 1, m= %d", i, m);
              tntg[m] = 1;
              o = l;
              l ++;
            }
            // if (i == 0) g_debug ("      geo= %d, old_sp= %d, new_sp= %d, old_geo= %d, new_geo= %d", i, k, s, m, o);
            for (p=0; p<this_proj -> natomes; p++)
            {
              if (this_proj -> atoms[0][p].sp == s)
              {
                if (this_proj -> atoms[0][p].coord[i] == m)
                {
                  this_proj -> atoms[0][p].coord[i] = o;
                }
              }
            }
          }
        }
        if (l)
        {
          tmp_coord -> geolist[i][j] = allocint(l);
          if (i)
          {
            // g_debug ("allocating partial[%d] of %d and %d", j, l, new_spec);
            tmp_coord -> partial_geo[j] = allocdint (l, new_spec);
          }
          // if (! i) g_debug ("   ntg[0][%d]= %d", j, l);
          tmp_coord -> ntg[i][j] = l;
          tmp_coord -> totcoord[i] += l;
 
          p = (k < new_spec+rem-adds) ? k : new_spec+rem-adds;
          q = 0;
          for (r=0; r<p; r++) q += this_proj -> coord -> ntg[i][r];
          p = 0;
          for (r=0; r<j; r++) p += tmp_coord -> ntg[i][r];
          m = 0;
          for (n=0; n<old_coord -> ntg[i][k]; n++)
          {
            // g_debug ("n= %d, tntg[%d]= %d", n, n, tntg[n]);
            if (tntg[n])
            {
              tmp_coord -> geolist[i][j][m] = old_coord -> geolist[i][k][n];
              this_proj -> coord -> cmax = max (tmp_coord -> geolist[i][j][m], this_proj -> coord -> cmax);
              this_proj -> coord -> cmin = min (tmp_coord -> geolist[i][j][m], this_proj -> coord -> cmin);
              if (k < new_spec-adds+rem)
              {
                if (n < this_proj -> coord -> ntg[i][k])
                {
                  //g_debug ("p= %d, m= %d, p+m= %d, q= %d, n= %d, q+n= %d", p, m, p+m, q, n, q+n);
                  showcoord[i][p+m] = this_proj -> modelgl -> anim -> last -> img -> show_coord[i][q+n];
                  showpoly[i][p+m] = this_proj -> modelgl -> anim -> last -> img -> show_poly[i][q+n];
                }
                else
                {
                  showcoord[i][p+m] = TRUE;
                  showpoly[i][p+m] = FALSE;
                }
              }
              else
              {
                //g_debug ("p= %d, m= %d, p+m= %d", p, m, p+m);
                showcoord[i][p+m] = TRUE;
                showpoly[i][p+m] = FALSE;
              }
              if (i)
              {
                o = 0;
                for (r=0; r<new_spec+rem; r++)
                {
                  if (spid[r])
                  {
                    tmp_coord -> partial_geo[j][m][o] = old_coord -> partial_geo[k][n][r];
                    //g_debug ("j= %d, m= %d, o= %d, partial= %d, %d", j, m, o, tmp_coord -> partial_geo[j][m][o], old_coord -> partial_geo[k][n][r]);
                    o ++;
                  }
                }
              }
              m ++;
            }
          }
        }
        g_free (tntg);
        j ++;
      }
      s += (spid[k]) ? 1 : 0;
    }
  }
}
 
void new_coord_menus (project * this_proj, coord_info * coord, int new_spec, int nmols,
                      gboolean * showcoord[2], gboolean * showpoly[2], gboolean * showfrag,
                      gboolean update_it, gboolean update_mol)
{
  int i, j, k;
  for (i=0; i<4; i++)
  {
    g_free (this_proj -> modelgl -> gcid[i]);
    this_proj -> modelgl -> gcid[i] = NULL;
  }
 
  for (i=0; i<2; i++) init_opengl_coords (i, coord -> totcoord[i], 0);
  i = 0;
  for (j=0; j<new_spec; j++)
  {
    init_menu_coordinations_ (& i, & j, & coord -> ntg[0][j], coord -> geolist[0][j]);
  }
  i ++;
  for (j=0; j<new_spec; j++)
  {
    allocate_partial_geo_ (& j, & coord -> ntg[1][j]);
    for (k=0; k<coord -> ntg[1][j]; k++) partial_geo_out_ (& j, & k, & new_spec, coord -> partial_geo[j][k]);
    init_menu_coordinations_ (& i, & j, & coord -> ntg[1][j], coord -> geolist[1][j]);
  }
 
  i = 2;
  this_proj -> coord -> totcoord[i] += nmols;
  if (this_proj -> coord -> totcoord[i])
  {
    this_proj -> modelgl -> adv_bonding[i-2] = TRUE;
    init_opengl_coords (i, this_proj -> coord -> totcoord[i], 0);
    init_menu_fragmol_ (& i);
  }
  else
  {
    this_proj -> modelgl -> adv_bonding[i-2] = FALSE;
  }
  if (update_mol)
  {
    i = 3;
    if (this_proj -> coord -> totcoord[i])
    {
      this_proj -> modelgl -> adv_bonding[i-2] = TRUE;
      init_opengl_coords (i, this_proj -> coord -> totcoord[i], 0);
      init_menu_fragmol_ (& i);
    }
  }
  else
  {
    this_proj -> modelgl -> adv_bonding[1] = FALSE;
    this_proj -> coord -> totcoord[3] = 0;
  }
 
#ifdef GTK3
  prep_all_coord_menus (this_proj -> modelgl);
#endif
  if (update_it)
  {
    gboolean * viz[2];
    for (i=0; i<2; i++) viz[i] = allocbool (this_proj -> natomes);
    for (i=0; i<this_proj -> natomes; i++)
    {
      for (j=0; j<2; j++) viz[j][i] = this_proj -> atoms[0][i].show[j];
    }
#ifdef GTK3
    // GTK3 Menu Action To Check
    for (i=0; i<2; i++)
    {
      for (j=0; j<this_proj -> coord -> totcoord[i]; j++)
      {
        if (this_proj -> modelgl -> ogl_geom[0][i][j])
        {
          if (GTK_IS_WIDGET(this_proj -> modelgl -> ogl_geom[0][i][j]))
          {
            if (gtk_check_menu_item_get_active ((GtkCheckMenuItem *)this_proj -> modelgl -> ogl_geom[0][i][j]) != showcoord[i][j])
            {
              gtk_check_menu_item_set_active ((GtkCheckMenuItem *)this_proj -> modelgl -> ogl_geom[0][i][j], showcoord[i][j]);
            }
          }
        }
        if (this_proj -> modelgl -> ogl_poly[0][i][j])
        {
          if (GTK_IS_WIDGET(this_proj -> modelgl -> ogl_poly[0][i][j]))
          {
            if (gtk_check_menu_item_get_active ((GtkCheckMenuItem *)this_proj -> modelgl -> ogl_poly[0][i][j]) != showpoly[i][j])
            {
              gtk_check_menu_item_set_active ((GtkCheckMenuItem *)this_proj -> modelgl -> ogl_poly[0][i][j], showpoly[i][j]);
            }
          }
        }
      }
      g_free (showcoord[i]);
      g_free (showpoly[i]);
    }
    for (i=0; i<this_proj -> coord -> totcoord[2]; i++)
    {
      if (this_proj -> modelgl -> ogl_geom[0][2][i])
      {
        if (GTK_IS_WIDGET(this_proj -> modelgl -> ogl_geom[0][2][i]))
        {
          if (gtk_check_menu_item_get_active ((GtkCheckMenuItem *)this_proj -> modelgl -> ogl_geom[0][2][i]) != showfrag[i])
          {
            gtk_check_menu_item_set_active ((GtkCheckMenuItem *)this_proj -> modelgl -> ogl_geom[0][2][i], showfrag[i]);
          }
        }
      }
    }
#endif
    for (i=0; i<this_proj -> natomes; i++)
    {
      for (j=0; j<2; j++) this_proj -> atoms[0][i].show[j] = viz[j][i];
    }
    for (i=0; i<2; i++) g_free (viz[i]);
  }
}
 
void recover_opengl_data (project * this_proj, int nmols, int add, int rem, int * num, int * rec, int *** tmpgeo, gboolean * showfrag)
{
  // Now OpenGL data
  int old_spec = this_proj -> nspec;
  //g_debug ("recover opengl:: old_spec= %d, add= %d, rem= %d", old_spec, add, rem);
  int new_spec = old_spec + add - rem;
  gboolean * showcoord[2];
  gboolean * showpoly[2];
  gboolean update_it = FALSE;
 
  clean_coords_and_geoms (this_proj, this_proj -> modelgl -> atom_win, new_spec, rem, add, num, tmpgeo, showcoord, showpoly);
 
  if (add || rem)
  {
    if (old_spec) free_glwin_spec_data (this_proj, old_spec);
    glwin_init_spec_data (this_proj, new_spec);
  }
 
  this_proj -> nspec = new_spec;
  active_project_changed (this_proj -> id);
 
  if ((add && old_spec) || rem)
  {
    int h, i, j, k, l, m, n, o, p, q;
    image * new_img = g_malloc0 (sizeof*new_img);
    image_init_spec_data (new_img, this_proj, new_spec);
    image * old_img = this_proj -> modelgl -> anim -> last -> img;
    // copy info in new data, then clean old data and copy it back
    for (i=0; i<2; i++)
    {
      for (j=0; j<old_spec; j++)
      {
        if (num[j])
        {
          k = rec[j];
          new_img -> show_atom[i][j-k] = old_img -> show_atom[i][j];
          new_img -> show_label[i][j-k] = old_img -> show_label[i][j];
        }
      }
    }
    for (h=0; h<2*old_spec; h++)
    {
      i = (h < old_spec) ? h : h - old_spec;
      if (num[i])
      {
        j = rec[i];
        k = (h < old_spec) ? 0 : 1;
        l = h - k*old_spec - j + k*new_spec;
        new_img -> sphererad[l] = old_img -> sphererad[h];
        new_img -> atomicrad[l] = old_img -> atomicrad[h];
        new_img -> pointrad[l] = old_img -> pointrad[h];
        new_img -> at_color[l].red = old_img -> at_color[h].red;
        new_img -> at_color[l].green = old_img -> at_color[h].green;
        new_img -> at_color[l].blue = old_img -> at_color[h].blue;
        new_img -> at_color[l].alpha = old_img -> at_color[h].alpha;
        for (m=0; m<2*old_spec; m++)
        {
          n = (m < old_spec) ? m : m - old_spec;
          if (num[n])
          {
            o = rec[n];
            p = (m < old_spec) ? 0 : 1;
            q = m - p*old_spec - o + p*new_spec;
            new_img -> linerad[l][q] = old_img  -> linerad[h][m];
            new_img -> bondrad[l][q] = old_img  -> bondrad[h][m];
          }
        }
      }
    }
    for (i=0; i<2; i++)
    {
      if (old_img -> show_atom[i] != NULL)
      {
        g_free (old_img -> show_atom[i]);
        old_img -> show_atom[i] = NULL;
      }
      if (old_img -> show_label[i] != NULL)
      {
        g_free (old_img -> show_label[i]);
        old_img -> show_label[i] = NULL;
      }
    }
    for (i=0; i<9; i++)
    {
      g_free (old_img -> spcolor[i]);
      old_img -> spcolor[i] = NULL;
    }
    g_free (old_img -> sphererad);
    g_free (old_img -> atomicrad);
    g_free (old_img -> pointrad);
    g_free (old_img -> at_color);
    g_free (old_img -> linerad);
    g_free (old_img -> bondrad);
    for (i=0; i<2; i++)
    {
      old_img -> show_atom[i] = duplicate_bool (new_spec, new_img -> show_atom[i]);
      old_img -> show_label[i] = duplicate_bool (new_spec, new_img -> show_label[i]);
    }
    old_img -> sphererad = duplicate_double (2*new_spec, new_img -> sphererad);
    old_img -> atomicrad = duplicate_double (2*new_spec, new_img -> atomicrad);
    old_img -> pointrad = duplicate_double (2*new_spec, new_img -> pointrad);
    old_img -> at_color = duplicate_color (2*new_spec, new_img -> at_color);
    old_img -> linerad = g_malloc (2*new_spec*sizeof*old_img -> linerad);
    old_img -> bondrad = g_malloc (2*new_spec*sizeof*old_img -> bondrad);
    for (i=0; i<2*new_spec; i++)
    {
      old_img -> linerad[i] = duplicate_double (2*new_spec, new_img -> linerad[i]);
      old_img -> bondrad[i] = duplicate_double (2*new_spec, new_img -> bondrad[i]);
    }
    for (i=0; i<9; i++)
    {
      old_img -> spcolor[i] = NULL;
      if (i < 2)
      {
        old_img -> spcolor[i] = g_malloc (new_spec*sizeof*old_img -> spcolor[i]);
      }
      else
      {
        old_img -> spcolor[i] = g_malloc (1*sizeof*old_img -> spcolor[i]);
        old_img -> spcolor[i][0] = NULL;
      }
    }
    g_free (new_img);
    update_it = TRUE;
  }
  else if (add)
  {
    image_init_spec_data (this_proj -> modelgl -> anim -> last -> img, this_proj, new_spec);
  }
 
  if (add || rem)
  {
#ifdef GTK3
    // GTK3 Menu Action To Check
    int i;
    for (i=1; i<OGL_COORDS; i++) this_proj -> modelgl -> ogl_coord[i] = NULL;
    for (i=0; i<OGL_RINGS; i++) this_proj -> modelgl -> ogl_rings[i] = NULL;
    this_proj -> modelgl -> ogl_chains[0] = NULL;
    prepare_opengl_menu_bar (this_proj -> modelgl);
    // GTK3 Menu Action To Check
    set_advanced_bonding_menus (this_proj -> modelgl);
#endif
  }
  new_coord_menus (this_proj, this_proj -> modelgl -> atom_win -> coord, new_spec, nmols, showcoord, showpoly, showfrag, update_it, (add || rem) ? FALSE : (! nmols) ? TRUE : FALSE);
}