preferences.c

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/* 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) 2022-2025 by CNRS and University of Strasbourg */
 
/*
* This file: 'configuration.c'
*
* Contains:
*
 
 - The GUI for the general configuration window
 - The associated controllers
 
*
* List of functions:
 
  int xml_save_color_to_file (xmlTextWriterPtr writer, int did, gchar * legend, gchar * key, ColRGBA col);
  int xml_save_xyz_to_file (xmlTextWriterPtr writer, int did, gchar * legend, gchar * key, vec3_t data);
  int xml_save_parameter_to_file (xmlTextWriterPtr writer, gchar * xml_leg, gchar * xml_key, gboolean doid, int xml_id, gchar * value);
  int save_preferences_to_xml_file ();
 
  ColRGBA get_spec_color (int z, , element_color * clist);
 
  gboolean are_identical_colors (ColRGBA col_a, ColRGBA col_b);
  gboolean not_in_cutoffs (int z_a, int z_b);
 
  float get_radius (int object, int col, int z, element_radius * rad_list);
 
  double xml_string_to_double (gchar * content);
 
  G_MODULE_EXPORT gboolean pref_color_button_event (GtkWidget * widget, GdkEventButton * event, gpointer data);
 
  bond_cutoff * duplicate_cutoffs (bond_cutoff * old_cutoff);
  element_radius * duplicate_element_radius (element_radius * old_list);
  element_color * duplicate_element_color (element_color * old_list);
 
  void set_parameter (gchar * content, gchar * key, int vid, dint * bond, vec3_t * vect, float start, float end, ColRGBA * col);
  void read_parameter (xmlNodePtr parameter_node);
  void read_light (xmlNodePtr light_node);
  void read_preferences (xmlNodePtr preference_node);
  void read_style_from_xml_file (xmlNodePtr style_node, int style);
  void read_preferences_from_xml_file ();
  void set_atomes_defaults ();
  void set_atomes_preferences ();
  void color_set_color (GtkTreeViewColumn * col, GtkCellRenderer * renderer, GtkTreeModel * mod, GtkTreeIter * iter, gpointer data);
  void radius_set_color_and_markup (GtkTreeViewColumn * col, GtkCellRenderer * renderer, GtkTreeModel * mod, GtkTreeIter * iter, gpointer data);
  void color_button_event (GtkWidget * widget, double event_x, double event_y, guint event_button, gpointer data);
  void add_cut_box ();
  void clean_all_tmp ();
  void duplicate_rep_data (rep_data * new_rep, rep_data * old_rep);
  void duplicate_background_data (background * new_back, background * old_back);
  void duplicate_box_data (box * new_box, box * old_box);
  void duplicate_axis_data (axis * new_axis, axis * old_axis);
  void prepare_tmp_default ();
  void save_preferences ();
  void adjust_preferences_window ();
  void create_configuration_dialog ();
  void add_global_option (GtkWidget * vbox, tint * oid);
 
  G_MODULE_EXPORT void set_measures (GtkComboBox * box, gpointer data);
  G_MODULE_EXPORT void set_selection_color (GtkColorChooser * colob, gpointer data);
  G_MODULE_EXPORT void toggled_default_stuff (GtkCheckButton * but, gpointer data);
  G_MODULE_EXPORT void toggled_default_stuff (GtkToggleButton * but, gpointer data);
  G_MODULE_EXPORT void set_default_stuff (GtkEntry * res, gpointer data);
  G_MODULE_EXPORT void edit_pref (GtkCellRendererText * cell, gchar * path_string, gchar * new_text, gpointer user_data);
  G_MODULE_EXPORT void edit_chem_preferences (GtkDialog * edit_chem, gint response_id, gpointer data);
  G_MODULE_EXPORT void run_ac_color (GtkDialog * win, gint response_id, gpointer data);
  G_MODULE_EXPORT void pref_color_button_pressed (GtkGesture * gesture, int n_press, double x, double y, gpointer data);
  G_MODULE_EXPORT void set_stuff_color (GtkColorChooser * colob, gpointer data);
  G_MODULE_EXPORT void edit_species_parameters (GtkButton * but, gpointer data);
  G_MODULE_EXPORT void set_default_style (GtkComboBox * box, gpointer data);
  G_MODULE_EXPORT void set_default_map (GtkComboBox * box, gpointer data);
  G_MODULE_EXPORT void set_default_num_delta (GtkEntry * res, gpointer data);
  G_MODULE_EXPORT void tunit_changed (GtkComboBox * box, gpointer data);
  G_MODULE_EXPORT void edit_pc_value (GtkEntry * res, gpointer data);
  G_MODULE_EXPORT void toggle_use_cutoff (GtkCheckButton * but, gpointer data);
  G_MODULE_EXPORT void toggle_use_cutoff (GtkToggleButton * but, gpointer data);
  G_MODULE_EXPORT void totcut_changed (GtkComboBox * box, gpointer data);
  G_MODULE_EXPORT void cut_spec_changed (GtkComboBox * box, gpointer data);
  G_MODULE_EXPORT void set_cutoffs_default (GtkButton * but, gpointer data);
  G_MODULE_EXPORT void update_projects (GtkDialog * proj_sel, gint response_id, gpointer data);
  G_MODULE_EXPORT void toggle_select_project (GtkCheckButton * but, gpointer data);
  G_MODULE_EXPORT void toggle_select_project (GtkToggleButton * but, gpointer data);
  G_MODULE_EXPORT void restore_all_defaults (GtkButton * but, gpointer data);
  G_MODULE_EXPORT void edit_preferences (GtkDialog * edit_prefs, gint response_id, gpointer data);
  G_MODULE_EXPORT void set_default_options (GtkButton * but, gpointer data);
 
  GtkWidget * pref_list (gchar * mess[2], int nelem, gchar * mlist[nelem][2], gchar * end);
  GtkWidget * view_preferences ();
  GtkWidget * over_param (int object, int style);
  GtkWidget * style_tab (int style);
  GtkWidget * model_preferences ();
  GtkWidget * combo_map (int obj);
  GtkWidget * opengl_preferences ();
  GtkWidget * calc_preferences ();
 
  GtkTreeModel * style_combo_tree ();
 
*/
 
#include "global.h"
#include "callbacks.h"
#include "interface.h"
#include "project.h"
#include "workspace.h"
#include "glview.h"
#include "glwin.h"
#include "bind.h"
#include "preferences.h"
#include <libxml/encoding.h>
#include <libxml/xmlwriter.h>
#include <libxml/xmlreader.h>
#include <libxml/parser.h>
#include <unistd.h>
#include <sys/types.h>
 
#ifndef G_OS_WIN32
#include <pwd.h>
#else
#include <errno.h>
#endif
 
extern void apply_default_parameters_to_project (project * this_proj);
extern xmlNodePtr findnode (xmlNodePtr startnode, char * nname);
extern int search_type;
extern void edit_bonds (GtkWidget * vbox);
extern void calc_rings (GtkWidget * vbox);
extern gchar * substitute_string (gchar * init, gchar * o_motif, gchar * n_motif);
extern G_MODULE_EXPORT gboolean scroll_scale_quality (GtkRange * range, GtkScrollType scroll, gdouble value, gpointer data);
extern GtkWidget * materials_tab (glwin * view, opengl_edition * ogl_edit, Material * the_mat);
extern GtkWidget * lights_tab (glwin * view, opengl_edition * ogl_edit, Lightning * the_light);
extern GtkWidget * fog_tab (glwin * view, opengl_edition * ogl_edit, Fog * the_fog);
extern GtkWidget * labels_tab (glwin * view, int lid);
extern void update_light_data (int li, opengl_edition * ogl_win);
extern void setup_fog_dialogs (opengl_edition * ogl_edit, int fid);
extern G_MODULE_EXPORT void box_advanced (GtkWidget * widg, gpointer data);
extern G_MODULE_EXPORT void axis_advanced (GtkWidget * widg, gpointer data);
extern G_MODULE_EXPORT void representation_advanced (GtkWidget * widg, gpointer data);
extern void update_gradient_widgets (gradient_edition * gradient_win, background * back);
extern G_MODULE_EXPORT void gradient_advanced (GtkWidget * widg, gpointer data);
extern G_MODULE_EXPORT void scale_quality (GtkRange * range, gpointer data);
extern void duplicate_fog (Fog * new_fog, Fog * old_fog);
extern void duplicate_material (Material * new_mat, Material * old_mat);
extern void duplicate_screen_label (screen_label * new_lab, screen_label * old_lab);
extern Light init_light_source (int type, float val, float vbl);
extern Light * copy_light_sources (int dima, int dimb, Light * old_sp);
extern GtkWidget * lightning_fix (glwin * view, Material * this_material);
extern GtkWidget * adv_box (GtkWidget * box, char * lab, int vspace, int size, float xalign);
extern float mat_min_max[5][2];
extern gchar * ogl_settings[3][10];
 
GtkWidget * atom_entry_over[8];
GtkWidget * bond_entry_over[6];
GtkWidget * meas_combo;
GtkWidget * meas_box[2];
GtkWidget * sel_combo;
GtkWidget * sel_box[2];
GtkWidget * preference_notebook = NULL;
 
double default_totcut;
double tmp_totcut;
bond_cutoff * default_bond_cutoff;
bond_cutoff * tmp_bond_cutoff;
int * default_num_delta = NULL;   
int * tmp_num_delta = NULL;
double * default_delta_t = NULL;  
double * tmp_delta_t = NULL;
 
int * default_rsparam = NULL;     
int * tmp_rsparam = NULL;
int * default_csparam = NULL;     
int * tmp_csparam = NULL;
 
// 5+3 styles + 5+3 cloned styles
element_radius * default_atomic_rad[16];
element_radius * tmp_atomic_rad[16];
// 3 styles + 3 cloned styles
element_radius * default_bond_rad[6];
element_radius * tmp_bond_rad[6];
// atoms + clones
element_color * default_atom_color[2];
element_color * tmp_atom_color[2];
element_color * default_label_color[2];
element_color * tmp_label_color[2];
 
int radius_id;
 
int * default_opengl = NULL;
int * tmp_opengl = NULL;
Material default_material;
Material tmp_material;
Lightning default_lightning;
Lightning tmp_lightning;
Fog default_fog;
Fog tmp_fog;
 
// Model
gboolean default_clones;
gboolean tmp_clones;
gboolean default_cell;
gboolean tmp_cell;
gboolean * default_o_at_rs;
gboolean * tmp_o_at_rs;
double * default_at_rs;
double * tmp_at_rs;
gboolean * default_o_bd_rw;
gboolean * tmp_o_bd_rw;
double * default_bd_rw;
double * tmp_bd_rw;
 
screen_label default_label[5];
screen_label * tmp_label[5];
int default_acl_format[2];
int tmp_acl_format[2];
gboolean default_mtilt[2];
gboolean tmp_mtilt[2];
int default_mpattern[2];
int tmp_mpattern[2];
int default_mfactor[2];
int tmp_mfactor[2];
double default_mwidth[2];
double tmp_mwidth[2];
 
rep_data default_rep;
rep_data * tmp_rep = NULL;
rep_edition * pref_rep_win = NULL;
background default_background;
background * tmp_background = NULL;
gradient_edition * pref_gradient_win = NULL;
box default_box;
box * tmp_box = NULL;
box_edition * pref_box_win = NULL;
axis default_axis;
axis * tmp_axis = NULL;
axis_edition * pref_axis_win = NULL;
ColRGBA default_sel_color[2];
ColRGBA tmp_sel_color[2];
 
gboolean preferences = FALSE;
opengl_edition * pref_ogl_edit = NULL;
gchar * pref_error = NULL;
 
tint * pref_pointer = NULL;
 
gchar * xml_style_leg[6] = {"ball_and_stick", "wireframes", "spacefilled", "spheres", "cylinders", "dots"};
gchar * xml_filled_leg[4] = {"covalent", "ionic", "van-der-waals", "crystal"};
gchar * xml_atom_leg[3] = {"atoms_radius", "dot_size", "sphere_radius"};
gchar * xml_bond_leg[3] = {"bond_radius", "wireframe_width", "cylinder_radius"};
 
int xml_save_color_to_file (xmlTextWriterPtr writer, int did, gchar * legend, gchar * key, ColRGBA col)
{
  int rc;
  gchar * str;
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"parameter");
  if (rc < 0) return 0;
  rc = xmlTextWriterWriteAttribute(writer, BAD_CAST (const xmlChar *)"info", BAD_CAST legend);
  if (rc < 0) return 0;
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"key", BAD_CAST key);
  if (rc < 0) return 0;
  if (did > -1)
  {
    str = g_strdup_printf ("%d", did);
    rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"id", BAD_CAST str);
    g_free (str);
    if (rc < 0) return 0;
  }
  str = g_strdup_printf ("%f", col.red);
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"red", BAD_CAST str);
  g_free (str);
  if (rc < 0) return 0;
  str = g_strdup_printf ("%f", col.green);
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"green", BAD_CAST str);
  g_free (str);
  if (rc < 0) return 0;
  str = g_strdup_printf ("%f", col.blue);
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"blue", BAD_CAST str);
  g_free (str);
  if (rc < 0) return 0;
  str = g_strdup_printf ("%f", col.alpha);
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"alpha", BAD_CAST str);
  g_free (str);
  if (rc < 0) return 0;
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
  return 1;
}
 
int xml_save_xyz_to_file (xmlTextWriterPtr writer, int did, gchar * legend, gchar * key, vec3_t data)
{
  int rc;
  gchar * str;
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"parameter");
  if (rc < 0) return 0;
  rc = xmlTextWriterWriteAttribute(writer, BAD_CAST (const xmlChar *)"info", BAD_CAST legend);
  if (rc < 0) return 0;
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"key", BAD_CAST key);
  if (rc < 0) return 0;
  if (did > -1)
  {
    str = g_strdup_printf ("%d", did);
    rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"id", BAD_CAST str);
    g_free (str);
    if (rc < 0) return 0;
  }
  str = g_strdup_printf ("%f", data.x);
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"x", BAD_CAST str);
  g_free (str);
  if (rc < 0) return 0;
  str = g_strdup_printf ("%f", data.y);
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"y", BAD_CAST str);
  g_free (str);
  if (rc < 0) return 0;
  str = g_strdup_printf ("%f", data.z);
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"z", BAD_CAST str);
  g_free (str);
  if (rc < 0) return 0;
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
  return 1;
}
 
int xml_save_parameter_to_file (xmlTextWriterPtr writer, gchar * xml_leg, gchar * xml_key, gboolean doid, int xml_id, gchar * value)
{
  int rc;
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"parameter");
  if (rc < 0) return 0;
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"info", BAD_CAST xml_leg);
  if (rc < 0) return 0;
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"key", BAD_CAST xml_key);
  if (rc < 0) return 0;
  if (doid)
  {
    gchar * str;
    str = g_strdup_printf ("%d", xml_id);
    rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"id", BAD_CAST (const xmlChar *)str);
    g_free (str);
    if (rc < 0) return 0;
  }
  rc = xmlTextWriterWriteFormatString (writer, "%s", value);
  if (rc < 0) return 0;
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
  return 1;
}
 
int save_preferences_to_xml_file ()
{
  int rc;
  pref_error = NULL;
  if (ATOMES_CONFIG_DIR)
  {
#ifdef G_OS_WIN32
    if (! CreateDirectory(ATOMES_CONFIG_DIR, NULL) && GetLastError() != ERROR_ALREADY_EXISTS)
    {
      pref_error = g_strdup_printf ("Error: impossible to create %s (code: %lu)\n", ATOMES_CONFIG_DIR, GetLastError());
      return 0;
    }
#else
    if (mkdir(ATOMES_CONFIG_DIR, S_IRWXU | S_IRWXG | S_IRWXO) && errno != EEXIST)
    {
      pref_error = g_strdup_printf ("Error: impossible to create %s (code: %s)\n", ATOMES_CONFIG_DIR, strerror(errno));
      return 0;
    }
#endif
  }
  xmlTextWriterPtr writer;
 
  gchar * xml_delta_num_leg[8] = {"g(r): number of δr", "s(q): number of δq", "s(k): number of δk", "g(r) FFT: number of δr",
                                  "Dij: number of δr [min(Dij)-max(Dij)]", "Angles distribution: number of δθ [0-180°]",
                                  "Spherical harmonics: l(max) in [2-40]", "MSD: steps between configurations"};
  gchar * xml_delta_t_leg[2] = {"MSD: time steps δt", "MSD: time unit"};
  gchar * xml_rings_leg[7] = {"Default search",
                              "Atom(s) to initiate the search from",
                              "Maximum size for a ring",
                              "Maximum number of rings of size n per MD step",
                              "Only search for ABAB rings",
                              "No homopolar bonds in the rings (A-A, B-B ...)",
                              "No homopolar bonds in the connectivity matrix"};
  gchar * xml_chain_leg[7] = {"Atom(s) to initiate the search from",
                              "Maximum size for a ring",
                              "Maximum number of rings of size n per MD step",
                              "Only search for AAAA chains",
                              "Only search for ABAB chains",
                              "No homopolar bonds in the chains (A-A, B-B ...)",
                              "Only search for 1-(2)n-1 chains"};
  gchar * xml_opengl_leg[4] = {"Default style",
                               "Atom(s) color map",
                               "Polyhedra color map",
                               "Quality"};
  gchar * xml_material_leg[8] = {"Predefine material",
                                 "Lightning model",
                                 "Metallic",
                                 "Roughness",
                                 "Back lightning",
                                 "Gamma",
                                 "Opacity",
                                 "Albedo"};
  gchar * xml_lightning_leg[7] = {"Type",
                                  "Fix",
                                  "Position",
                                  "Direction",
                                  "Intensity",
                                  "Attenuation",
                                  "Spot specifics"};
  gchar * xml_fog_leg[5] = {"Mode",
                            "Type",
                            "Density",
                            "Depth",
                            "Color"};
  gchar * xml_model_leg[2] = {"Show clones",
                              "Show box"};
  gchar * xml_label_leg[6] = {"Position",
                              "Rendering" ,
                              "Scaling",
                              "Font",
                              "Shift",
                              "Colors"};
  gchar * xml_axis_leg[3] = {"Legend on x",
                             "Legend on y",
                             "Legend on z"};
 
  /* Create a new XmlWriter for ATOMES_CONFIG, with no compression. */
  writer = xmlNewTextWriterFilename (ATOMES_CONFIG, 0);
  if (writer == NULL) return 0;
  rc = xmlTextWriterSetIndent(writer, 1);
  if (rc < 0) return 0;
  /* Start the document with the xml default for the version,
   * encoding MY_ENCODING and the default for the standalone
   * declaration. */
  rc = xmlTextWriterStartDocument (writer, NULL, MY_ENCODING, NULL);
  if (rc < 0) return 0;
 
  rc = xmlTextWriterWriteComment (writer, (const xmlChar *)"atomes preferences XML file");
  if (rc < 0) return 0;
 
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"atomes_preferences-xml");
  if (rc < 0) return 0;
 
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"analysis");
  if (rc < 0) return 0;
  int i, j, k, l, m, n, o;
  gchar * str;
 
  if (default_totcut > 0.0 || default_bond_cutoff)
  {
    rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"cutoffs");
    if (rc < 0) return 0;
    if (default_totcut > 0.0)
    {
       str = g_strdup_printf ("%lf",  default_totcut);
       rc = xml_save_parameter_to_file (writer, "Total cutoff", "default_totcut", TRUE, 0, str);
       g_free (str);
       if (! rc) return 0;
    }
    if (default_bond_cutoff)
    {
      rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"partials");
      if (rc < 0) return 0;
      bond_cutoff * tmp_cut = default_bond_cutoff;
      while (tmp_cut)
      {
        rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"parameter");
        if (rc < 0) return 0;
        str = g_strdup_printf ("cutoff %s-%s", periodic_table_info[tmp_cut -> Z[0]].lab, periodic_table_info[tmp_cut -> Z[1]].lab);
        rc = xmlTextWriterWriteAttribute(writer, BAD_CAST (const xmlChar *)"info", BAD_CAST str);
        g_free (str);
        if (rc < 0) return 0;
        str =  g_strdup_printf ("%d", tmp_cut -> Z[0]);
        rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"α", BAD_CAST str);
        g_free (str);
        if (rc < 0) return 0;
        str =  g_strdup_printf ("%d", tmp_cut -> Z[1]);
        rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"β", BAD_CAST str);
        g_free (str);
        if (rc < 0) return 0;
        str = g_strdup_printf ("%lf",  tmp_cut -> cutoff);
        rc = xmlTextWriterWriteFormatString (writer, "%s", str);
        g_free (str);
        if (rc < 0) return 0;
        rc = xmlTextWriterEndElement (writer);
        if (rc < 0) return 0;
        tmp_cut = tmp_cut -> next;
      }
      rc = xmlTextWriterEndElement (writer);
      if (rc < 0) return 0;
    }
    rc = xmlTextWriterEndElement (writer);
    if (rc < 0) return 0;
  }
 
  for (i=0; i<8; i++)
  {
    str = g_strdup_printf ("%d",  default_num_delta[i]);
    rc = xml_save_parameter_to_file (writer, xml_delta_num_leg[i], "default_num_delta", TRUE, i, str);
    g_free (str);
    if (! rc) return 0;
  }
  // Delta t
  for (i=0; i<2; i++)
  {
    str = g_strdup_printf ("%f", default_delta_t[i]);
    rc = xml_save_parameter_to_file (writer, xml_delta_t_leg[i], "default_delta_t", TRUE, i, str);
    g_free (str);
    if (! rc) return 0;
  }
  // Rings
  for (i=0; i<7; i++)
  {
    str = g_strdup_printf ("%d", default_rsparam[i]);
    rc = xml_save_parameter_to_file (writer,  xml_rings_leg[i], "default_rsparam", TRUE, i, str);
    g_free (str);
    if (! rc) return 0;
  }
  // Chains
  for (i=0; i<7; i++)
  {
    str = g_strdup_printf ("%d", default_csparam[i]);
    rc = xml_save_parameter_to_file (writer,  xml_chain_leg[i], "default_csparam", TRUE, i, str);
    g_free (str);
    if (! rc) return 0;
  }
 
  // End analysis
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"opengl");
  if (rc < 0) return 0;
  for (i=0; i<4; i++)
  {
 
    str = g_strdup_printf ("%d", default_opengl[i]);
    rc = xml_save_parameter_to_file (writer,  xml_opengl_leg[i], "default_opengl", TRUE, i, str);
    g_free (str);
    if (! rc) return 0;
  }
 
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"material");
  if (rc < 0) return 0;
 
  str = g_strdup_printf ("%d", default_material.predefine);
  rc = xml_save_parameter_to_file (writer,  xml_material_leg[0], "default_material", TRUE, -1, str);
  g_free (str);
  if (! rc) return 0;
 
  for (i=0; i<6; i++)
  {
    str = g_strdup_printf ("%f", default_material.param[i]);
    rc = xml_save_parameter_to_file (writer, xml_material_leg[i+1], "default_material", TRUE, i, str);
    g_free (str);
    if (! rc) return 0;
  }
 
  rc = xml_save_xyz_to_file (writer, 6, xml_material_leg[7], "default_material", default_material.albedo);
  if (! rc) return rc;
 
  // End material
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"lightning");
  if (rc < 0) return 0;
 
  str = g_strdup_printf ("%d", default_lightning.lights);
  rc = xml_save_parameter_to_file (writer, "Number of lights", "default_lightning", TRUE, 0, str);
  g_free (str);
  if (! rc) return 0;
 
  for (i=0; i<default_lightning.lights; i++)
  {
    rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"light");
    if (rc < 0) return 0;
    str = g_strdup_printf ("%d", i);
    rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"id", BAD_CAST (const xmlChar *)str);
    g_free (str);
    if (rc < 0) return 0;
 
    str = g_strdup_printf ("%d", default_lightning.spot[i].type);
    rc = xml_save_parameter_to_file (writer, xml_lightning_leg[0], "light.type", FALSE, 0, str);
    g_free (str);
    if (! rc) return 0;
    str = g_strdup_printf ("%d", default_lightning.spot[i].fix);
    rc = xml_save_parameter_to_file (writer, xml_lightning_leg[1], "light.fix", FALSE, 0, str);
    g_free (str);
    if (! rc) return 0;
 
    if (default_lightning.spot[i].type)
    {
      rc = xml_save_xyz_to_file (writer, -1, xml_lightning_leg[2], "light.position", default_lightning.spot[i].position);
      if (! rc) return rc;
    }
    if (default_lightning.spot[i].type != 1)
    {
      rc = xml_save_xyz_to_file (writer, -1, xml_lightning_leg[3], "light.direction", default_lightning.spot[i].direction);
      if (! rc) return rc;
    }
    rc = xml_save_xyz_to_file (writer, -1, xml_lightning_leg[4], "light.intensity", default_lightning.spot[i].intensity);
    if (! rc) return rc;
    if (default_lightning.spot[i].type)
    {
      rc = xml_save_xyz_to_file (writer, -1, xml_lightning_leg[5], "light.attenuation", default_lightning.spot[i].attenuation);
      if (! rc) return rc;
      rc = xml_save_xyz_to_file (writer, -1, xml_lightning_leg[6], "light.spot", default_lightning.spot[i].spot_data);
      if (! rc) return rc;
    }
     rc = xmlTextWriterEndElement (writer);
    if (rc < 0) return 0;
  }
 
  // End lightning
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"fog");
  if (rc < 0) return 0;
  // Mode
  str = g_strdup_printf ("%d", default_fog.mode);
  rc = xml_save_parameter_to_file (writer, xml_fog_leg[0], "fog.mode", TRUE, 0, str);
  g_free (str);
  if (! rc) return 0;
  // Type
  str = g_strdup_printf ("%d", default_fog.based);
  rc = xml_save_parameter_to_file (writer, xml_fog_leg[1], "fog.type", TRUE, 1, str);
  g_free (str);
  if (! rc) return 0;
  // Density
  str = g_strdup_printf ("%f", default_fog.density);
  rc = xml_save_parameter_to_file (writer, xml_fog_leg[2], "fog.density", TRUE, 2, str);
  g_free (str);
  if (! rc) return 0;
  // Depth
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"parameter");
  if (rc < 0) return 0;
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"info", BAD_CAST xml_fog_leg[3]);
  if (rc < 0) return 0;
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"key", BAD_CAST "fog.depth");
  if (rc < 0) return 0;
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"id", BAD_CAST "3");
  if (rc < 0) return 0;
  str = g_strdup_printf ("%f", default_fog.depth[0]);
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"start", BAD_CAST str);
  g_free (str);
  if (rc < 0) return 0;
  str = g_strdup_printf ("%f", default_fog.depth[1]);
  rc = xmlTextWriterWriteAttribute (writer, BAD_CAST (const xmlChar *)"end", BAD_CAST str);
  g_free (str);
  if (rc < 0) return 0;
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
  // Color
  rc = xml_save_xyz_to_file (writer, 4, xml_fog_leg[4], "fog.color", default_fog.color);
  if (! rc) return rc;
  // End fog
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
  // End opengl
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
  // Model
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"model");
  if (rc < 0) return 0;
 
  if (default_clones)
  {
    str = g_strdup_printf ("%d", default_clones);
    rc = xml_save_parameter_to_file (writer, xml_model_leg[0], "default_clones", FALSE, 0, str);
    g_free (str);
    if (! rc) return 0;
  }
  if (! default_cell)
  {
    str = g_strdup_printf ("%d", default_cell);
    rc = xml_save_parameter_to_file (writer, xml_model_leg[1], "default_cell", FALSE, 0, str);
    g_free (str);
    if (! rc) return 0;
  }
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"atoms_and_bonds");
  if (rc < 0) return 0;
 
  element_radius * tmp_rad;
  gboolean do_atoms;
  gboolean do_bonds;
  gchar * str_a, * str_b;
  for (i=0; i<OGL_STYLES; i++)
  {
    do_atoms = do_bonds = FALSE;
    if (i != 4)
    {
      j = (i < 4) ? i : 4;
      if (default_o_at_rs[j] || default_o_at_rs[j+5]) do_atoms = TRUE;
      if (default_atomic_rad[j] || default_atomic_rad[j+5]) do_atoms = TRUE;
      if (! do_atoms)
      {
        if (j == 2)
        {
          for (k=0; k<3; k++)
          {
            if (default_atomic_rad[10+k] || default_atomic_rad[13+k]) do_atoms = TRUE;
          }
        }
      }
    }
    if (i != 2 && i != 3 && i != 5)
    {
      j = (i < 2) ? i : 2;
      if (default_o_bd_rw[j] || default_o_bd_rw[j+3]) do_bonds = TRUE;
      if (default_bond_rad[j] || default_bond_rad[j+3]) do_bonds = TRUE;
    }
    if (do_atoms || do_bonds)
    {
      rc = xmlTextWriterStartElement (writer, BAD_CAST xml_style_leg[i]);
      if (rc < 0) return 0;
      if (do_atoms)
      {
        j = (i < 4) ? i : 4;
        k = (j == 0 || j == 2) ? 0 : (j == 1 || j == 4) ? 1 : 2;
        for (l=0; l<2; l++)
        {
          if (default_o_at_rs[j+l*5])
          {
            str_a = (l) ? g_strdup_printf ("clone-%s", xml_atom_leg[k]) : g_strdup_printf ("%s", xml_atom_leg[k]);
            str_b = g_strdup_printf ("%f", default_at_rs[j+l*5]);
            rc = xml_save_parameter_to_file (writer, str_a, "default_at_rs", TRUE, j+l*5, str_b);
            g_free (str_a);
            g_free (str_b);
            if (! rc) return 0;
          }
        }
        l = (j == 2) ? 4 : 1;
        for (m=0; m < l;  m++)
        {
          n = (m) ? 7 : 0;
          for (o= 0; o<2; o++)
          {
            n = (o && m) ? 5 : n;
            if (default_atomic_rad[j+n+5*o+m])
            {
              str_a = (o) ? g_strdup_printf ("clone-%s", (j == 2) ? xml_filled_leg[m] : xml_atom_leg[k]) : g_strdup_printf ("%s", (j == 2) ? xml_filled_leg[m] : xml_atom_leg[k]);
              rc = xmlTextWriterStartElement (writer, BAD_CAST str_a);
              g_free (str_a);
              if (rc < 0) return 0;
              tmp_rad = default_atomic_rad[j+n+5*o+m];
              while (tmp_rad)
              {
                str = g_strdup_printf ("%f", tmp_rad -> rad);
                rc = xml_save_parameter_to_file (writer, periodic_table_info[tmp_rad -> Z].lab, "default_atomic_rad", TRUE, tmp_rad -> Z, str);
                g_free (str);
                if (! rc) return 0;
                tmp_rad = tmp_rad -> next;
              }
              rc = xmlTextWriterEndElement (writer);
              if (rc < 0) return 0;
            }
          }
        }
      }
      if (do_bonds)
      {
        j = (i < 2) ? i : 2;
        for (k=0; k<2; k++)
        {
          if (default_o_bd_rw[j+k*3])
          {
            str_a = (k) ? g_strdup_printf ("clone-%s", xml_bond_leg[j]) : g_strdup_printf ("%s", xml_bond_leg[j]);
            str_b = g_strdup_printf ("%f", default_bd_rw[j+k*3]);
            rc = xml_save_parameter_to_file (writer, str_a, "default_bd_rw", TRUE, j+k*3, str_b);
            g_free (str_a);
            g_free (str_b);
            if (! rc) return 0;
          }
          if (default_bond_rad[j+k*3])
          {
            str_a = (k) ? g_strdup_printf ("clone-%s", xml_bond_leg[j]) : g_strdup_printf ("%s", xml_bond_leg[j]);
            rc = xmlTextWriterStartElement (writer, BAD_CAST str_a);
            g_free (str_a);
            if (rc < 0) return 0;
            tmp_rad = default_bond_rad[j+k*3];
            while (tmp_rad)
            {
              str = g_strdup_printf ("%f", tmp_rad -> rad);
              rc = xml_save_parameter_to_file (writer, periodic_table_info[tmp_rad -> Z].lab, "default_bond_rad", TRUE, tmp_rad -> Z, str);
              g_free (str);
              if (! rc) return 0;
              tmp_rad = tmp_rad -> next;
            }
            rc = xmlTextWriterEndElement (writer);
            if (rc < 0) return 0;
          }
        }
      }
      rc = xmlTextWriterEndElement (writer);
      if (rc < 0) return 0;
    }
  }
 
  // End atoms_and_bonds
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
  element_color * tmp_col;
  // atoms and clones labels
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"labels");
  if (rc < 0) return 0;
  gchar * obj[2]={"atoms", "clones"};
  for (i=0; i<2; i++)
  {
    rc = xmlTextWriterStartElement (writer, BAD_CAST obj[i]);
    if (rc < 0) return 0;
 
    str = g_strdup_printf ("%d", default_label[i].position);
    rc = xml_save_parameter_to_file (writer, xml_label_leg[0], "default_label", TRUE, 0, str);
    g_free (str);
    if (! rc) return 0;
    str = g_strdup_printf ("%d", default_label[i].render);
    rc = xml_save_parameter_to_file (writer, xml_label_leg[1], "default_label", TRUE, 1, str);
    g_free (str);
    if (! rc) return 0;
    str = g_strdup_printf ("%d", default_label[i].scale);
    rc = xml_save_parameter_to_file (writer, xml_label_leg[2], "default_label", TRUE, 2, str);
    g_free (str);
    if (! rc) return 0;
    rc = xml_save_parameter_to_file (writer, xml_label_leg[3], "default_label", TRUE, 3, default_label[i].font);
    if (! rc) return 0;
    rc = xml_save_xyz_to_file (writer, 4, xml_label_leg[4], "default_label", vec3(default_label[i].shift[0], default_label[i].shift[1], default_label[i].shift[2]));
    if (! rc) return 0;
    str = g_strdup_printf ("%d", default_acl_format[i]);
    rc = xml_save_parameter_to_file (writer, "Format", "default_label", TRUE, 5, str);
    g_free (str);
    if (! rc) return 0;
    if (default_label[i].n_colors || default_label_color[i])
    {
      rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"colors");
      if (rc < 0) return 0;
      if (default_label[i].n_colors)
      {
        xml_save_color_to_file (writer, i, "Only label color", "only_label_color", default_label[i].color[0]);
      }
      else
      {
        tmp_col = default_label_color[i];
        while (tmp_col)
        {
          rc = xml_save_color_to_file (writer, tmp_col -> Z, periodic_table_info[tmp_col -> Z].lab, "default_label_color", tmp_col -> col);
          if (! rc) return 0;
          tmp_col = tmp_col -> next;
        }
      }
      rc = xmlTextWriterEndElement (writer);
      if (rc < 0) return 0;
    }
 
    rc = xmlTextWriterEndElement (writer);
    if (rc < 0) return 0;
  }
 
  // End atoms and clones colors
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
  do_atoms = (default_atom_color[0] || default_atom_color[1]) ? TRUE : FALSE;
  if (do_atoms)
  {
    // atoms and clones colors
    rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"colors");
    if (rc < 0) return 0;
    for (i=0; i<2; i++)
    {
      if (default_atom_color[i])
      {
        rc = xmlTextWriterStartElement (writer, BAD_CAST obj[i]);
        if (rc < 0) return 0;
        tmp_col = default_atom_color[i];
        while (tmp_col)
        {
          rc = xml_save_color_to_file (writer, tmp_col -> Z, periodic_table_info[tmp_col -> Z].lab, "default_atom_color", tmp_col -> col);
          if (! rc) return 0;
          tmp_col = tmp_col -> next;
        }
        rc = xmlTextWriterEndElement (writer);
        if (rc < 0) return 0;
      }
    }
  }
 
  if (default_box.box != NONE)
  {
    rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"box");
    if (rc < 0) return 0;
    str = g_strdup_printf ("%f", (default_box.box == WIREFRAME) ? default_box.line : default_box.rad);
    rc = xml_save_parameter_to_file (writer, (default_box.box == WIREFRAME) ? "Wireframe width" : "Cylinder radius", "default_box", TRUE, default_box.box, str);
    g_free (str);
    if (! rc) return 0;
    rc = xml_save_color_to_file (writer, -1, "Color", "default_box", default_box.color);
    if (! rc) return 0;
    // End box
    rc = xmlTextWriterEndElement (writer);
    if (rc < 0) return 0;
  }
 
  // End model
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
  // View
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"view");
  if (rc < 0) return 0;
 
  // Background
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"background");
  str = g_strdup_printf ("%d", default_background.gradient);
  rc = xml_save_parameter_to_file (writer, "Gradient", "default_background", TRUE, 0, str);
  g_free (str);
  if (! rc) return 0;
  if (default_background.gradient)
  {
    str = g_strdup_printf ("%d", default_background.direction);
    rc = xml_save_parameter_to_file (writer, "Direction", "default_background", TRUE, 1, str);
    g_free (str);
    if (! rc) return 0;
    str = g_strdup_printf ("%f", default_background.position);
    rc = xml_save_parameter_to_file (writer, "Mixed position", "default_background", TRUE, 2, str);
    g_free (str);
    if (! rc) return 0;
    for (i=0; i<2; i++)
    {
      rc = xml_save_color_to_file (writer, i+3, "Color", "default_background", default_background.gradient_color[i]);
      if (! rc) return 0;
    }
  }
  else
  {
    rc = xml_save_color_to_file (writer, -1, "Color", "default_background", default_background.color);
    if (! rc) return 0;
  }
 
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
 
  // Representation
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"representation");
  if (rc < 0) return 0;
  str = g_strdup_printf ("%d", default_rep.rep);
  rc = xml_save_parameter_to_file (writer, "Representation type", "default_rep", TRUE, 0, str);
  g_free (str);
  if (! rc) return 0;
  if (default_rep.rep)
  {
    str = g_strdup_printf ("%lf", default_rep.gnear);
    rc = xml_save_parameter_to_file (writer, "Camera depth", "default_rep", TRUE, 1, str);
    g_free (str);
    if (! rc) return 0;
  }
 
  str = g_strdup_printf ("%lf", 1.0 - 0.5*default_rep.zoom);
  rc = xml_save_parameter_to_file (writer, "Zoom", "default_rep", TRUE, 2, str);
  g_free (str) ;
  if (! rc) return 0;
  for (i=0; i<2; i++)
  {
    str = g_strdup_printf ("%lf", - default_rep.c_angle[i]);
    rc = xml_save_parameter_to_file (writer, (i) ? "Camera pitch" : "Camera heading", "default_rep", TRUE, 3+i, str);
    g_free (str) ;
    if (! rc) return 0;
  }
  for (i=0; i<2; i++)
  {
    str = g_strdup_printf ("%lf", default_rep.c_shift[i]);
    rc = xml_save_parameter_to_file (writer, (i) ? "Camera x" : "Camera y", "default_rep", TRUE, 5+i, str);
    g_free (str) ;
    if (! rc) return 0;
  }
  // End representation
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
 
  if (default_axis.axis != NONE)
  {
    rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"axis");
    if (rc < 0) return 0;
    if (default_axis.t_pos != NONE)
    {
      str = g_strdup_printf ("%d", default_axis.t_pos);
      rc = xml_save_parameter_to_file (writer, "Template position", "default_axis", TRUE, 0, str);
      g_free (str);
      if (! rc) return 0;
    }
    else
    {
      rc = xml_save_xyz_to_file (writer, 0, "Custom position", "default_axis", vec3(default_axis.c_pos[0], default_axis.c_pos[1], default_axis.c_pos[2]));
      if (! rc) return 0;
    }
    str = g_strdup_printf ("%f", (default_axis.axis == WIREFRAME) ? default_axis.line : default_axis.rad);
    rc = xml_save_parameter_to_file (writer, (default_axis.axis == WIREFRAME) ? "Wireframe width" : "Cylinder radius", "default_axis", TRUE, default_axis.axis, str);
    g_free (str);
    if (! rc) return 0;
    str = g_strdup_printf ("%f", default_axis.length);
    rc = xml_save_parameter_to_file (writer, "Length", "default_axis", TRUE, 2, str);
    g_free (str);
    if (! rc) return 0;
    if (default_axis.labels)
    {
      rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"labels");
      if (rc < 0) return 0;
      str = g_strdup_printf ("%d", default_label[2].render);
      rc = xml_save_parameter_to_file (writer, xml_label_leg[1], "default_label", TRUE, 1, str);
      g_free (str);
      if (! rc) return 0;
      str = g_strdup_printf ("%d", default_label[2].scale);
      rc = xml_save_parameter_to_file (writer, xml_label_leg[2], "default_label", TRUE, 2, str);
      g_free (str);
      if (! rc) return 0;
      rc = xml_save_parameter_to_file (writer, xml_label_leg[3], "default_label", TRUE, 3, default_label[2].font);
      if (! rc) return 0;
      for (i=0; i<3; i++)
      {
        rc = xml_save_parameter_to_file (writer, xml_axis_leg[i], "axis_legend", TRUE, i, default_axis.title[i]);
        if (! rc) return 0;
      }
      rc = xmlTextWriterEndElement (writer);
      if (rc < 0) return 0;
    }
    if (default_axis.color)
    {
      for (i=0; i<3; i++)
      {
        rc = xml_save_color_to_file (writer, i, "Color", "default_axis", default_axis.color[i]);
        if (! rc) return 0;
      }
    }
    // End axis
    rc = xmlTextWriterEndElement (writer);
    if (rc < 0) return 0;
  }
 
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"measures");
  if (rc < 0) return 0;
  gchar * m_key[2]={"standard", "selection"};
  for (i=0; i<2; i++)
  {
    rc = xmlTextWriterStartElement (writer, BAD_CAST m_key[i]);
    if (rc < 0) return 0;
    rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"labels");
    if (rc < 0) return 0;
    str = g_strdup_printf ("%d", default_label[i+3].position);
    rc = xml_save_parameter_to_file (writer, xml_label_leg[0], "default_label", TRUE, 0, str);
    g_free (str);
    if (! rc) return 0;
    str = g_strdup_printf ("%d", default_label[i+3].render);
    rc = xml_save_parameter_to_file (writer, xml_label_leg[1], "default_label", TRUE, 1, str);
    g_free (str);
    if (! rc) return 0;
    str = g_strdup_printf ("%d", default_label[i+3].scale);
    rc = xml_save_parameter_to_file (writer, xml_label_leg[2], "default_label", TRUE, 2, str);
    g_free (str);
    if (! rc) return 0;
    rc = xml_save_parameter_to_file (writer, xml_label_leg[3], "default_label", TRUE, 3, default_label[i+3].font);
    if (! rc) return 0;
    xml_save_color_to_file (writer, i+3, "Font color", "default_font_color", default_label[i+3].color[0]);
    if (! rc) return 0;
 
    rc = xmlTextWriterEndElement (writer); // End label
    if (rc < 0) return 0;
    // mtilt
    str = g_strdup_printf ("%d", default_mtilt[i]);
    rc = xml_save_parameter_to_file (writer, "Tilt along", "default_mtilt", TRUE, i, str);
    g_free (str);
    if (! rc) return 0;
    // mtilt
    str = g_strdup_printf ("%d", default_mpattern[i]);
    rc = xml_save_parameter_to_file (writer, "Pattern", "default_mpattern", TRUE, i, str);
    g_free (str);
    if (! rc) return 0;
    // mfactor
    str = g_strdup_printf ("%d", default_mfactor[i]);
    rc = xml_save_parameter_to_file (writer, "Factor", "default_mfactor", TRUE, i, str);
    g_free (str);
    if (! rc) return 0;
    // mfactor
    str = g_strdup_printf ("%lf", default_mwidth[i]);
    rc = xml_save_parameter_to_file (writer, "Width", "default_mwidth", TRUE, i, str);
    g_free (str);
    if (! rc) return 0;
 
    rc = xmlTextWriterEndElement (writer); // End measures type
    if (rc < 0) return 0;
  }
 
  rc = xmlTextWriterEndElement (writer); // End measures
  if (rc < 0) return 0;
 
  rc = xmlTextWriterStartElement (writer, BAD_CAST (const xmlChar *)"atom-selections");
  if (rc < 0) return 0;
  for (i=0; i<2; i++)
  {
    xml_save_color_to_file (writer, i, "Selection color", "default_sel_color", default_sel_color[i]);
    if (! rc) return 0;
  }
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
  // End view
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
  rc = xmlTextWriterEndElement (writer);
  if (rc < 0) return 0;
 
  rc = xmlTextWriterEndDocument (writer);
  if (rc < 0) return 0;
 
  xmlFreeTextWriter (writer);
  return 1;
}
 
int label_id;
 
double xml_string_to_double (gchar * content)
{
  return (g_strcmp0(content, "") == 0) ? 0.0 : string_to_double ((gpointer)content);
}
 
void set_parameter (gchar * content, gchar * key, int vid, dint * bond, vec3_t * vect, float start, float end, ColRGBA * col)
{
  element_radius * tmp_rad;
  element_color * tmp_col;
  if (bond)
  {
    bond_cutoff * cut;
    if (default_bond_cutoff)
    {
      cut = default_bond_cutoff;
      while (cut -> next)
      {
        cut = cut -> next;
      }
      cut -> next = g_malloc0(sizeof*cut);
      cut = cut -> next;
    }
    else
    {
      default_bond_cutoff = g_malloc0(sizeof*default_bond_cutoff);
      cut = default_bond_cutoff;
    }
    cut -> Z[0] = bond -> a;
    cut -> Z[1] = bond -> b;
    cut -> use = TRUE;
    cut -> cutoff = xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_totcut") == 0)
  {
    default_totcut = xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_num_delta") == 0)
  {
    default_num_delta[vid] = (int)xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_delta_t") == 0)
  {
    default_delta_t[vid] = xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_rsparam") == 0)
  {
    default_rsparam[vid] = (int)xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_csparam") == 0)
  {
    default_csparam[vid] = (int)xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_opengl") == 0)
  {
    default_opengl[vid] = (int)xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_material") == 0)
  {
    if (vid < 0)
    {
      default_material.predefine = (int)xml_string_to_double(content);
    }
    else if (vid == 6 && vect)
    {
      default_material.albedo = * vect;
    }
    else
    {
      default_material.param[vid] = xml_string_to_double(content);
    }
  }
  else if (g_strcmp0(key, "default_lightning") == 0)
  {
    default_lightning.lights = (int)xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "light.type") == 0)
  {
    default_lightning.spot[vid].type = (int)xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "light.fix") == 0)
  {
    default_lightning.spot[vid].fix = (int)xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "light.direction") == 0 && vect)
  {
    default_lightning.spot[vid].direction = * vect;
  }
  else if (g_strcmp0(key, "light.position") == 0 && vect)
  {
    default_lightning.spot[vid].position = * vect;
  }
  else if (g_strcmp0(key, "light.intensity") == 0 && vect)
  {
    default_lightning.spot[vid].intensity = * vect;
  }
  else if (g_strcmp0(key, "light.attenuation") == 0 && vect)
  {
    default_lightning.spot[vid].attenuation = * vect;
  }
  else if (g_strcmp0(key, "light.spot") == 0 && vect)
  {
    default_lightning.spot[vid].spot_data = * vect;
  }
  else if (g_strcmp0(key, "fog.mode") == 0)
  {
    default_fog.mode = (int)xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "fog.type") == 0)
  {
    default_fog.based = (int)xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "fog.density") == 0)
  {
    default_fog.density = xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "fog.depth") == 0)
  {
    if (start != -1.0) default_fog.depth[0] = start;
    if (end != -1.0) default_fog.depth[1] = end;
  }
  else if (g_strcmp0(key, "fog.color") == 0 && vect)
  {
    default_fog.color = * vect;
  }
  else if (g_strcmp0(key, "default_cell") == 0)
  {
    default_cell = (int)xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_clones") == 0)
  {
    default_clones = (int)xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_at_rs") == 0)
  {
    default_o_at_rs[vid] = TRUE;
    default_at_rs[vid] = xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_bd_rw") == 0)
  {
    default_o_bd_rw[vid] = TRUE;
    default_bd_rw[vid] = xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_atomic_rad") == 0)
  {
    if (default_atomic_rad[radius_id])
    {
      tmp_rad = default_atomic_rad[radius_id];
      while (tmp_rad -> next)
      {
        tmp_rad = tmp_rad -> next;
      }
      tmp_rad -> next = g_malloc0(sizeof*tmp_rad);
      tmp_rad = tmp_rad -> next;
    }
    else
    {
      default_atomic_rad[radius_id] = g_malloc0(sizeof*default_atomic_rad[radius_id]);
      tmp_rad = default_atomic_rad[radius_id];
    }
    tmp_rad -> Z = vid;
    tmp_rad -> rad = xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_bond_rad") == 0)
  {
    if (default_bond_rad[radius_id])
    {
      tmp_rad = default_bond_rad[radius_id];
      while (tmp_rad -> next)
      {
        tmp_rad = tmp_rad -> next;
      }
      tmp_rad -> next = g_malloc0(sizeof*tmp_rad);
      tmp_rad = tmp_rad -> next;
    }
    else
    {
      default_bond_rad[radius_id] = g_malloc0(sizeof*default_bond_rad[radius_id]);
      tmp_rad = default_bond_rad[radius_id];
    }
    tmp_rad -> Z = vid;
    tmp_rad -> rad = xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_label") == 0)
  {
    switch (vid)
    {
      case 0:
        default_label[label_id].position = (int)xml_string_to_double(content);
        break;
      case 1:
        default_label[label_id].render = (int)xml_string_to_double(content);
        break;
      case 2:
        default_label[label_id].scale = (int)xml_string_to_double(content);
        break;
      case 3:
        default_label[label_id].font = g_strdup_printf ("%s", content);
        break;
      case 4:
        default_label[label_id].shift[0] = vect -> x;
        default_label[label_id].shift[1] = vect -> y;
        default_label[label_id].shift[2] = vect -> z;
        break;
      case 5:
        default_acl_format[label_id] = (int)xml_string_to_double(content);
        break;
    }
  }
  else if (g_strcmp0(key, "default_label_color") == 0)
  {
    if (! vid)
    {
      default_label[label_id].color = g_malloc0(sizeof*default_label[label_id].color);
      default_label[label_id].color[0] = * col;
    }
    else
    {
      if (default_label_color[label_id])
      {
        tmp_col = default_label_color[label_id];
        while (tmp_col -> next)
        {
          tmp_col = tmp_col -> next;
        }
        tmp_col -> next = g_malloc0(sizeof*tmp_col);
        tmp_col = tmp_col -> next;
      }
      else
      {
        default_label_color[label_id] = g_malloc0(sizeof*default_label_color[label_id]);
        tmp_col = default_label_color[label_id];
      }
      tmp_col -> Z = vid;
      tmp_col -> col = * col;
    }
  }
  else if (g_strcmp0(key, "default_font_color") == 0)
  {
    default_label[label_id].color = g_malloc0(sizeof*default_label[label_id].color);
    default_label[label_id].color[0] = * col;
  }
  else if (g_strcmp0(key, "default_atom_color") == 0)
  {
    if (default_atom_color[label_id])
    {
      tmp_col = default_atom_color[label_id];
      while (tmp_col -> next)
      {
        tmp_col = tmp_col -> next;
      }
      tmp_col -> next = g_malloc0(sizeof*tmp_col);
      tmp_col = tmp_col -> next;
    }
    else
    {
      default_atom_color[label_id] = g_malloc0(sizeof*default_atom_color[label_id]);
      tmp_col = default_atom_color[label_id];
    }
    tmp_col -> Z = vid;
    tmp_col -> col = * col;
  }
  else if (g_strcmp0(key, "only_label_color") == 0)
  {
    default_label[label_id].n_colors = 1;
    default_label[label_id].color = g_malloc0(sizeof*default_label[label_id].color);
    default_label[label_id].color[0] = * col;
  }
  else if (g_strcmp0(key, "default_box") == 0)
  {
    if (col)
    {
      default_box.color = * col;
    }
    else
    {
      default_box.box = vid;
      if (default_box.box == WIREFRAME)
      {
        default_box.line = xml_string_to_double(content);
      }
      else
      {
        default_box.rad = xml_string_to_double(content);
      }
    }
  }
  else if (g_strcmp0(key, "default_background") == 0)
  {
    switch (vid)
    {
      case -1:
        if (col) default_background.color = * col;
        break;
      case 0:
        default_background.gradient = (int) xml_string_to_double(content);
        break;
      case 1:
        default_background.direction = (int) xml_string_to_double(content);
        break;
      case 2:
        default_background.position = xml_string_to_double(content);
        break;
      default:
        if (col) default_background.gradient_color[vid-3] = * col;
        break;
    }
  }
  else if (g_strcmp0(key, "default_rep") == 0)
  {
    switch (vid)
    {
      case 0:
        default_rep.rep = (int) xml_string_to_double(content);
        break;
      case 1:
        default_rep.gnear = xml_string_to_double(content);
        break;
      case 2:
        default_rep.zoom = 2.0*(1.0 - xml_string_to_double(content));
        break;
      default:
        if (vid < 5)
        {
          default_rep.c_angle[vid-3] = - xml_string_to_double(content);
        }
        else
        {
          default_rep.c_shift[vid-5] = xml_string_to_double(content);
        }
        break;
    }
  }
  else if (g_strcmp0(key, "default_axis") == 0)
  {
    if (vect)
    {
      default_axis.c_pos[0] = vect -> x;
      default_axis.c_pos[1] = vect -> y;
      default_axis.c_pos[2] = vect -> z;
    }
    else if (col)
    {
      if (! default_axis.color) default_axis.color = g_malloc0(3*sizeof*default_axis.color);
      default_axis.color[vid] = * col;
    }
    else
    {
      if (vid == 1 || vid == 4)
      {
        default_axis.axis = vid;
        if (vid == 1) default_axis.line = xml_string_to_double(content);
        if (vid == 4) default_axis.rad = xml_string_to_double(content);
      }
      else if (vid == 2)
      {
        default_axis.length = xml_string_to_double(content);
      }
      else if (! vid)
      {
        default_axis.t_pos = (int) xml_string_to_double(content);
      }
    }
  }
  else if (g_strcmp0(key, "axis_legend") == 0)
  {
    default_axis.title[vid] = g_strdup_printf ("%s", content);
  }
  else if (g_strcmp0(key, "default_mtilt") == 0)
  {
    default_mtilt[vid] = (int) xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_mpattern") == 0)
  {
    default_mpattern[vid] = (int) xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_mfactor") == 0)
  {
    default_mfactor[vid] = (int) xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_mwidth") == 0)
  {
    default_mwidth[vid] = xml_string_to_double(content);
  }
  else if (g_strcmp0(key, "default_sel_color") == 0)
  {
    if (col)
    {
      default_sel_color[vid] = * col;
    }
  }
}
 
void read_parameter (xmlNodePtr parameter_node)
{
  xmlNodePtr p_node;
  xmlAttrPtr p_details;
  gboolean set_codevar, set_id;
  gboolean set_x, set_y, set_z;
  gboolean set_r, set_g, set_b, set_a;
  gboolean set_alpha, set_beta;
  ColRGBA col;
  gchar * key;
  gchar * content;
  int id;
  dint bond;
  float start, end;
  vec3_t vec;
  while (parameter_node)
  {
    content = g_strdup_printf ("%s", xmlNodeGetContent(parameter_node));
    p_details = parameter_node -> properties;
    set_codevar = set_id = FALSE;
    set_x = set_y = set_z = FALSE;
    set_r = set_g = set_b = set_a = FALSE;
    set_alpha = set_beta = FALSE;
    start = end = -1.0;
    id = -1;
    while (p_details)
    {
      p_node = p_details -> children;
      if (p_node)
      {
        if (g_strcmp0("key",(char *)p_details -> name) == 0)
        {
          key = g_strdup_printf ("%s", xmlNodeGetContent(p_node));
          set_codevar = TRUE;
        }
        else if (g_strcmp0("id",(char *)p_details -> name) == 0)
        {
          id = (int) string_to_double ((gpointer)xmlNodeGetContent(p_node));
          set_id = TRUE;
        }
        else if (g_strcmp0("α",(char *)p_details -> name) == 0)
        {
          bond.a = (int) string_to_double ((gpointer)xmlNodeGetContent(p_node));
          set_alpha = TRUE;
        }
        else if (g_strcmp0("β",(char *)p_details -> name) == 0)
        {
          bond.b = (int) string_to_double ((gpointer)xmlNodeGetContent(p_node));
          set_beta = TRUE;
        }
        else if (g_strcmp0("x",(char *)p_details -> name) == 0)
        {
          vec.x = string_to_double ((gpointer)xmlNodeGetContent(p_node));
          set_x = TRUE;
        }
        else if (g_strcmp0("y",(char *)p_details -> name) == 0)
        {
          vec.y = string_to_double ((gpointer)xmlNodeGetContent(p_node));
          set_y = TRUE;
        }
        else if (g_strcmp0("z",(char *)p_details -> name) == 0)
        {
          vec.z = string_to_double ((gpointer)xmlNodeGetContent(p_node));
          set_z = TRUE;
        }
        else if (g_strcmp0("start",(char *)p_details -> name) == 0)
        {
          start = string_to_double ((gpointer)xmlNodeGetContent(p_node));
        }
        else if (g_strcmp0("end",(char *)p_details -> name) == 0)
        {
          end = string_to_double ((gpointer)xmlNodeGetContent(p_node));
        }
        else if (g_strcmp0("red",(char *)p_details -> name) == 0)
        {
          col.red = string_to_double ((gpointer)xmlNodeGetContent(p_node));
          set_r = TRUE;
        }
        else if (g_strcmp0("green",(char *)p_details -> name) == 0)
        {
          col.green = string_to_double ((gpointer)xmlNodeGetContent(p_node));
          set_g = TRUE;
        }
        else if (g_strcmp0("blue",(char *)p_details -> name) == 0)
        {
          col.blue = string_to_double ((gpointer)xmlNodeGetContent(p_node));
          set_b = TRUE;
        }
        else if (g_strcmp0("alpha",(char *)p_details -> name) == 0)
        {
          col.alpha = string_to_double ((gpointer)xmlNodeGetContent(p_node));
          set_a = TRUE;
        }
      }
      p_details = p_details -> next;
    }
 
    if ((set_codevar && (set_id || (set_r && set_g && set_b && set_a))) || (set_alpha && set_beta))
    {
      // g_print ("key= %s, id= %d, content= %s\n", key, id, content);
      set_parameter (content, key, id, (set_alpha && set_beta) ? & bond : NULL, (set_x && set_y && set_z) ? & vec : NULL, start, end, (set_r && set_g && set_b && set_a) ? & col : NULL);
    }
    g_free (content);
    parameter_node = parameter_node -> next;
    parameter_node = findnode (parameter_node, "parameter");
  }
}
 
void read_light (xmlNodePtr light_node)
{
  xmlNodePtr l_node, p_node;
  xmlNodePtr parameter_node;
  xmlAttrPtr l_details, p_details;
  gchar * key;
  int lid;
  gboolean set_codevar;
  gboolean set_lid = FALSE;
  gboolean set_x, set_y, set_z;
  gchar * content;
  vec3_t vec;
  l_details = light_node -> properties;
  while (l_details)
  {
    l_node = l_details -> children;
    if (l_node)
    {
      if (g_strcmp0("id",(char *)l_details -> name) == 0)
      {
        lid = (int) string_to_double ((gpointer)xmlNodeGetContent(l_node));
        set_lid = TRUE;
      }
    }
    l_details = l_details -> next;
  }
  if (set_lid)
  {
    parameter_node = findnode (light_node -> children, "parameter");
    set_codevar = FALSE;
    set_x = set_y = set_z = FALSE;
    while (parameter_node)
    {
      content = g_strdup_printf ("%s", xmlNodeGetContent(parameter_node));
      p_details = parameter_node -> properties;
      while (p_details)
      {
        p_node = p_details -> children;
        if (p_node)
        {
          if (g_strcmp0("key",(char *)p_details -> name) == 0)
          {
            key = g_strdup_printf ("%s", xmlNodeGetContent(p_node));
            set_codevar = TRUE;
          }
          else if (g_strcmp0("x",(char *)p_details -> name) == 0)
          {
            vec.x = string_to_double ((gpointer)xmlNodeGetContent(p_node));
            set_x = TRUE;
          }
          else if (g_strcmp0("y",(char *)p_details -> name) == 0)
          {
            vec.y = string_to_double ((gpointer)xmlNodeGetContent(p_node));
            set_y = TRUE;
          }
          else if (g_strcmp0("z",(char *)p_details -> name) == 0)
          {
            vec.z = string_to_double ((gpointer)xmlNodeGetContent(p_node));
            set_z = TRUE;
          }
        }
        p_details = p_details -> next;
      }
      if (set_codevar)
      {
        set_parameter (content, key, lid, NULL, (set_x && set_y && set_z) ? & vec : NULL, -1.0, -1.0, NULL);
      }
      g_free (content);
      parameter_node = parameter_node -> next;
      parameter_node = findnode (parameter_node, "parameter");
    }
  }
}
 
void read_preferences (xmlNodePtr preference_node)
{
  xmlNodePtr node;
  node = findnode (preference_node  -> children, "parameter");
  read_parameter (node);
}
 
void read_style_from_xml_file (xmlNodePtr style_node, int style)
{
  xmlNodePtr node;
  gchar * str;
  int i, j, k, l;
  i = (style == 0 || style == 2) ? 0 : (style == 1 || style == 4) ? 1 : 2;
  for (j=0; j<2; j++)
  {
    k = (style == 2) ? 4 : 1;
    for (l=0; l<k; l++)
    {
      str = (j) ? g_strdup_printf ("clone-%s", (k == 4) ? xml_filled_leg[l] : xml_atom_leg[i]) : g_strdup_printf ("%s", (k == 4) ? xml_filled_leg[l] : xml_atom_leg[i]);
      node = findnode (style_node, str);
      if (node)
      {
        if (j)
        {
          radius_id = (l) ? 12 + l : style + 5;
        }
        else
        {
          radius_id = (l) ? 9 + l : style;
        }
        read_preferences (node);
      }
    }
  }
  i = (style < 2) ? style : 2;
  for (j=0; j<2; j++)
  {
    str = (j) ? g_strdup_printf ("clone-%s", xml_bond_leg[i]) : g_strdup_printf ("%s", xml_bond_leg[i]);
    node = findnode (style_node, str);
    radius_id = (j) ? style + 3 : style;
    if (node) read_preferences(node);
  }
}
 
void read_preferences_from_xml_file ()
{
  xmlDoc * doc;
  xmlTextReaderPtr reader;
  xmlNodePtr racine;
  xmlNodePtr node, p_node, l_node, c_node;
  const xmlChar aml[22]="atomes_preferences-xml";
  int i;
  reader = xmlReaderForFile (ATOMES_CONFIG, NULL, 0);
  if (reader)
  {
    doc = xmlParseFile (ATOMES_CONFIG);
    if (doc)
    {
      racine = xmlDocGetRootElement (doc);
      if (! g_strcmp0 ((char *)(racine -> name), (char *)aml))
      {
        node = findnode(racine -> children, "analysis");
        if (node)
        {
          p_node = findnode (node  -> children, "cutoffs");
          if (p_node)
          {
            read_preferences (p_node);
            l_node = findnode(p_node -> children, "partials");
            if (l_node)
            {
              read_preferences (l_node);
            }
          }
          read_preferences (node);
        }
        node = findnode(racine -> children, "opengl");
        if (node)
        {
          p_node = findnode (node  -> children, "material");
          if (p_node)
          {
            read_preferences (p_node);
          }
          p_node = findnode (node  -> children, "lightning");
          if (p_node)
          {
            read_preferences (p_node);
            l_node = findnode (p_node -> children, "light");
            while (l_node)
            {
              read_light (l_node);
              l_node = l_node -> next;
              l_node = findnode (l_node, "light");
            }
          }
          p_node = findnode (node  -> children, "fog");
          if (p_node)
          {
            read_preferences(p_node);
          }
          read_preferences (node);
        }
        node = findnode(racine -> children, "model");
        if (node)
        {
          read_preferences (node);
          p_node = findnode(node -> children, "atoms_and_bonds");
          if (p_node)
          {
            for (i=0; i<OGL_STYLES; i++)
            {
              l_node = findnode (p_node -> children, xml_style_leg[i]);
              if (l_node)
              {
                read_style_from_xml_file (l_node -> children, i);
              }
            }
          }
          p_node = findnode(node -> children, "labels");
          if (p_node)
          {
            for (i=0; i<2; i++)
            {
              l_node = findnode (p_node -> children, (i) ? "clones" : "atoms");
              if (l_node)
              {
                label_id = i;
                read_preferences (l_node);
                c_node = findnode(l_node -> children, "colors");
                if (c_node)
                {
                  read_preferences (c_node);
                }
              }
            }
          }
          c_node = findnode(node -> children, "colors");
          if (c_node)
          {
            for (i=0; i<2; i++)
            {
              l_node = findnode (c_node -> children, (i) ? "clones" : "atoms");
              if (l_node)
              {
                label_id = i;
                read_preferences (l_node);
              }
            }
          }
          p_node = findnode(node -> children, "box");
          if (p_node)
          {
            read_preferences (p_node);
          }
        }
        node = findnode(racine -> children, "view");
        if (node)
        {
          read_preferences (node);
          p_node = findnode(node -> children, "background");
          if (p_node)
          {
            read_preferences (p_node);
          }
          p_node = findnode(node -> children, "representation");
          if (p_node)
          {
            read_preferences (p_node);
          }
          p_node = findnode(node -> children, "axis");
          if (p_node)
          {
            read_preferences (p_node);
            l_node = findnode(p_node -> children, "labels");
            if (l_node)
            {
              label_id = 2;
              default_axis.labels = TRUE;
              read_preferences (l_node);
            }
            c_node = findnode(p_node -> children, "colors");
            if (c_node)
            {
              read_preferences (c_node);
            }
          }
          p_node = findnode(node -> children, "measures");
          if (p_node)
          {
            l_node = findnode(p_node -> children, "standard");
            if (l_node)
            {
              c_node = findnode(l_node -> children, "labels");
              if (c_node)
              {
                label_id = 3;
                read_preferences (c_node);
              }
              read_preferences (l_node);
            }
            l_node = findnode(p_node -> children, "selection");
            if (l_node)
            {
              c_node = findnode(l_node -> children, "labels");
              if (c_node)
              {
                label_id = 4;
                read_preferences (c_node);
              }
              read_preferences (l_node);
            }
          }
          p_node = findnode(node -> children, "atom-selections");
          if (p_node)
          {
            read_preferences (p_node);
          }
        }
      }
      xmlFreeDoc(doc);
    }
    xmlFreeTextReader(reader);
  }
  xmlCleanupParser();
}
 
void set_atomes_defaults ()
{
  int i, j;
  // Analysis preferences
 
  default_totcut = 0.0;
  if (default_bond_cutoff) g_free (default_bond_cutoff);
  default_bond_cutoff = NULL;
  default_num_delta[GR] = 1000;
  default_num_delta[SQ] = 1000;
  default_num_delta[SK] = 1000;
  default_num_delta[GK] = 1000;
  default_num_delta[BD] = 100;
  default_num_delta[AN] = 90;
  default_num_delta[CH-1] = 20;
  default_num_delta[MS-2] = 0;
  default_delta_t[0] = 0.0;
  default_delta_t[1] = -1.0;
 
  default_rsparam[0] = -1;
  default_rsparam[1] = 0;
  default_rsparam[2] = 10;
  default_rsparam[3] = 500;
  default_rsparam[4] = 0;
  default_rsparam[5] = 0;
  default_rsparam[6] = 0;
 
  default_csparam[0] = 0;
  default_csparam[1] = 10;
  default_csparam[2] = 500;
  default_csparam[3] = 0;
  default_csparam[4] = 0;
  default_csparam[5] = 0;
 
  for (i=0; i<3; i++) default_opengl[i] = 0;
  default_opengl[3] = QUALITY;
  // Material
  default_material.predefine = 4; // Plastic
  default_material.albedo = vec3(0.5, 0.5, 0.5);
  default_material.param[0] = DEFAULT_LIGHTNING;
  default_material.param[1] = DEFAULT_METALLIC;
  default_material.param[2] = DEFAULT_ROUGHNESS;
  default_material.param[3] = DEFAULT_AMBIANT_OCCLUSION;
  default_material.param[4] = DEFAULT_GAMMA_CORRECTION;
  default_material.param[5] = DEFAULT_OPACITY;
 
  // Lights
  default_lightning.lights = 3;
  if (default_lightning.spot) g_free (default_lightning.spot);
  default_lightning.spot = g_malloc0 (3*sizeof*default_lightning.spot);
  default_lightning.spot[0] = init_light_source (0, 1.0, 1.0);
  default_lightning.spot[1] = init_light_source (1, 1.0, 1.0);
  default_lightning.spot[2] = init_light_source (1, 1.0, 1.0);
 
  // Fog
  default_fog.mode = 1;
  default_fog.based = 0;
  default_fog.density = 0.5;
  default_fog.depth[0] = 15.0;
  default_fog.depth[1] = 40.0;
  default_fog.color = vec3 (0.01f, 0.01f, 0.01f);
 
  // Model
  default_clones = FALSE;
  default_cell = TRUE;
  for (i=0; i<5; i++)
  {
    default_o_at_rs[i] = default_o_at_rs[i+5] = FALSE;
    default_at_rs[i] = default_at_rs[i+5] = (i == 0 || i == 2) ? 0.5 : DEFAULT_SIZE;
  }
 
  for (i=0; i<16; i++)
  {
    if (default_atomic_rad[i])
    {
      g_free (default_atomic_rad[i]);
      default_atomic_rad[i] = NULL;
    }
  }
  for (i=0; i<3; i++)
  {
    default_o_bd_rw[i] = default_o_bd_rw[i+3] = (i == 2) ? TRUE : FALSE;
    default_bd_rw[i] = default_bd_rw[i+3] = (i == 0 || i == 2) ? 0.5 : DEFAULT_SIZE;
  }
  for (i=0; i<6; i++)
  {
    if (default_bond_rad[i])
    {
      g_free (default_bond_rad[i]);
      default_bond_rad[i] = NULL;
    }
  }
  for (i=0; i<2; i++)
  {
    if (default_atom_color[i])
    {
      g_free (default_atom_color[i]);
      default_atom_color[i] = NULL;
    }
    if (default_label_color[i])
    {
      g_free (default_label_color[i]);
      default_label_color[i] = NULL;
    }
  }
  for (i=0; i<5; i++)
  {
    default_label[i].position = 1;
    default_label[i].render = BETTER_TEXT;
    default_label[i].scale = 0;
    for (j=0; j<3; j++) default_label[i].shift[j] = 0.0;
    default_label[i].n_colors = (i > 2) ? 1 : 0;
    if (default_label[i].n_colors)
    {
      default_label[i].color = g_malloc (sizeof*default_label[i].color);
      default_label[i].color[0].red = 1.0;
      default_label[i].color[0].green = 1.0;
      default_label[i].color[0].blue = 1.0;
      default_label[i].color[0].alpha = 1.0;
    }
    default_label[i].font = (i > 2) ? g_strdup_printf ("FreeMono Bold 18") : g_strdup_printf ("Sans Bold 12");
    default_label[i].list = NULL;
  }
  for (i=0; i<2; i++)
  {
    default_acl_format[i] = SYMBOL_AND_NUM;
    default_mtilt[i] = TRUE;
    default_mpattern[i] = 0;
    default_mfactor[i] = 1;
    default_mwidth[i] = 1.0;
  }
 
  default_box.box = WIREFRAME;
  default_box.color.red = 0.0;
  default_box.color.green = 1.0;
  default_box.color.blue = 0.0;
  default_box.color.alpha = 1.0;
  default_box.line = DEFAULT_SIZE;
  default_box.rad = 0.05;
 
  // Representation
 
  // Background color
  default_background.color.red = 0.0;
  default_background.color.green = 0.0;
  default_background.color.blue = 0.0;
  default_background.color.alpha = 1.0;
  default_background.gradient = 2;
  default_background.direction = 8;
  default_background.position = 0.5;
  default_background.gradient_color[0].red = 0.0;
  default_background.gradient_color[0].green = 0.01;
  default_background.gradient_color[0].blue = 0.21;
  default_background.gradient_color[0].alpha = 1.0;
  default_background.gradient_color[1].red = 0.0;
  default_background.gradient_color[1].green = 0.0;
  default_background.gradient_color[1].blue = 0.0;
  default_background.gradient_color[1].alpha = 1.0;
 
  default_rep.rep = PERSPECTIVE;
  default_rep.proj = -1;
  default_rep.zoom = ZOOM;
  default_rep.c_angle[0] = - CAMERA_ANGLE_X;
  default_rep.c_angle[1] = - CAMERA_ANGLE_Y;
  for (i=0; i<2; i++) default_rep.c_shift[i] = 0.0;
  default_rep.gnear = 6.0;
 
  // Axis
  default_axis.axis = NONE;
  default_axis.line = DEFAULT_SIZE;
  default_axis.rad = 0.1;
  default_axis.t_pos = BOTTOM_RIGHT;
  default_axis.length = 2.0*DEFAULT_SIZE;
  default_axis.c_pos[0] = default_axis.c_pos[1] = 50.0;
  default_axis.c_pos[2] = 0.0;
  default_axis.title[0] = "x";
  default_axis.title[1] = "y";
  default_axis.title[2] = "z";
  if (default_axis.color) g_free (default_axis.color);
  default_axis.color = NULL;
 
  // Selection color
  default_sel_color[0].red = 0.0;
  default_sel_color[0].green = 1.0;
  default_sel_color[0].blue = 1.0;
  default_sel_color[0].alpha = DEFAULT_OPACITY*0.75;
  // Selection color - edition mode
  default_sel_color[1].red = 1.0;
  default_sel_color[1].green = 0.00;
  default_sel_color[1].blue = 0.84;
  default_sel_color[1].alpha = DEFAULT_OPACITY*0.75;
}
 
void set_atomes_preferences ()
{
  default_num_delta = allocint (8);
  default_delta_t = allocdouble (2);
  default_rsparam = allocint (7);
  default_csparam = allocint (7);
  default_opengl = allocint (4);
  default_at_rs = allocdouble (10);
  default_o_at_rs = allocbool (10);
  default_bd_rw = allocdouble (6);
  default_o_bd_rw = allocbool (6);
  preferences = TRUE;
  set_atomes_defaults();
  preferences = FALSE;
  if (ATOMES_CONFIG) read_preferences_from_xml_file ();
}
 
GtkWidget * pref_list (gchar * mess[2], int nelem, gchar * mlist[nelem][2], gchar * end)
{
  gchar * str;
  GtkWidget * vbox = create_vbox (BSEP);
  GtkWidget * vvbox = create_vbox (BSEP);
  GtkWidget * hbox;
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vvbox, markup_label(mess[0], -1, -1, 0.5, 0.5), FALSE, FALSE, 5);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vvbox, markup_label(mess[1], -1, -1, 0.5, 0.5), FALSE, FALSE, 0);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, vvbox, FALSE, FALSE, 20);
  int i;
  for (i=0; i<nelem; i++)
  {
    hbox = create_hbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(" ", 60, -1, 0.0, 0.5), FALSE, FALSE, 0);
    str = g_strdup_printf ("<b>%s</b>", mlist[i][0]);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(str, 120, -1, 0.0, 0.5), FALSE, FALSE, 5);
    g_free (str);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(":", -1, -1, 1.0, 0.5), FALSE, FALSE, 0);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(mlist[i][1], -1, -1, 0.0, 0.5), FALSE, FALSE, 10);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 0);
  }
  if (end)
  {
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label(end, -1, -1, 0.5, 0.5), FALSE, FALSE, 20);
  }
  return vbox;
}
 
G_MODULE_EXPORT void set_measures (GtkComboBox * box, gpointer data)
{
  int i, j;
  i = GPOINTER_TO_INT (data);
  j = combo_get_active ((GtkWidget *)box);
  if (i)
  {
    hide_the_widgets (sel_box[! j]);
    show_the_widgets (sel_box[j]);
  }
  else
  {
    hide_the_widgets (meas_box[! j]);
    show_the_widgets (meas_box[j]);
  }
}
 
G_MODULE_EXPORT void set_selection_color (GtkColorChooser * colob, gpointer data)
{
  int i = GPOINTER_TO_INT (data);
  tmp_sel_color[i] = get_button_color (colob);
}
 
GtkWidget * view_preferences ()
{
  GtkWidget * notebook = gtk_notebook_new ();
  gtk_notebook_set_scrollable (GTK_NOTEBOOK(notebook), TRUE);
  gtk_notebook_set_tab_pos (GTK_NOTEBOOK(notebook), GTK_POS_TOP);
  GtkWidget * vbox = create_vbox (BSEP);
  gchar * info[2] = {"The <b>View</b> tab regroups representation options",
                     "which effect apply to the general aspect of the model:"};
  gchar * m_list[3][2] = {{"Representation", "scene set-up and orientation"},
                          {"Axis", "axis options"},
                          {"Tools", "measures and selections option"}};
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label(" ", -1, 30, 0.0, 0.0), FALSE, FALSE, 0);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, pref_list (info, 3, m_list, NULL), FALSE, FALSE, 30);
 
  pref_gradient_win = g_malloc0(sizeof*pref_gradient_win);
  gradient_advanced (NULL, NULL);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, pref_gradient_win -> win, FALSE, FALSE, 5);
 
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), vbox, gtk_label_new ("General"));
 
  // Tab for representation
  pref_rep_win = g_malloc0(sizeof*pref_rep_win);
  representation_advanced (NULL, NULL);
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), pref_rep_win -> win, gtk_label_new ("Representation"));
 
  // Axis
  pref_axis_win = g_malloc0(sizeof*pref_axis_win);
  axis_advanced (NULL, NULL);
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), pref_axis_win -> win, gtk_label_new ("Axis"));
 
  // Measures
  vbox = create_vbox (BSEP);
  GtkWidget * hbox;
  hbox = adv_box (vbox, "<b>Select measure type</b>", 5, 120, 0.0);
  meas_combo = create_combo ();
  combo_text_append (meas_combo, "Standard");
  combo_text_append (meas_combo, "Edition mode");
  combo_set_active (meas_combo, 0);
  g_signal_connect (G_OBJECT(meas_combo), "changed", G_CALLBACK(set_measures), GINT_TO_POINTER(0));
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, meas_combo , FALSE, FALSE, 40);
  int i;
  for (i=0; i<2; i++)
  {
    meas_box[i] = create_vbox (BSEP);
    hbox = create_hbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, labels_tab(NULL, i+3), FALSE, FALSE, 60);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, meas_box[i], hbox, FALSE, FALSE, 5);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, meas_box[i], FALSE, FALSE, 0);
  }
 
  hbox = adv_box (vbox, "<b>Select selection type</b>", 15, 120, 0.0);
  sel_combo = create_combo ();
  combo_text_append (sel_combo, "Standard");
  combo_text_append (sel_combo, "Edition mode");
  combo_set_active (sel_combo, 0);
  g_signal_connect (G_OBJECT(sel_combo), "changed", G_CALLBACK(set_measures), GINT_TO_POINTER(1));
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, sel_combo , FALSE, FALSE, 40);
  GtkWidget * hhbox, * vvbox;
   for (i=0; i<2; i++)
  {
    sel_box[i] = create_vbox (BSEP);
    hbox = create_hbox (BSEP);
    vvbox = create_hbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, vvbox, FALSE, FALSE, 60);
    hhbox = abox (vvbox, "Color", 0);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hhbox, color_button(tmp_sel_color[i], TRUE, 100, -1, G_CALLBACK(set_selection_color), GINT_TO_POINTER(i)), FALSE, FALSE, 0);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, sel_box[i], hbox, FALSE, FALSE, 5);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, sel_box[i], FALSE, FALSE, 0);
  }
 
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), vbox, gtk_label_new ("Tools"));
 
  show_the_widgets (notebook);
 
  return notebook;
}
 
int the_object;
element_radius ** edit_list;
element_color * color_list;
GtkWidget * pref_tree;
gboolean user_defined;
GtkWidget * edit_scrol;
GtkWidget * edit_colob;
ColRGBA * tmp_color;
 
#ifdef GTK4
G_MODULE_EXPORT void toggled_default_stuff (GtkCheckButton * but, gpointer data)
#else
G_MODULE_EXPORT void toggled_default_stuff (GtkToggleButton * but, gpointer data)
#endif
{
  int status = button_get_status ((GtkWidget *)but);
  int object = GPOINTER_TO_INT(data);
  switch (object)
  {
    case 0:
      tmp_clones = status;
      break;
    case 1:
      tmp_cell = status;
      break;
    default:
      if (object < 0)
      {
        // Bonds
        tmp_o_bd_rw[-object-2] = status;
        widget_set_sensitive(bond_entry_over[-object-2], status);
      }
      else if (object < 100)
      {
        tmp_o_at_rs[object-2] = status;
        widget_set_sensitive(atom_entry_over[object-2], status);
      }
      else
      {
        widget_set_sensitive (edit_scrol, ! status);
        widget_set_sensitive (edit_colob,  status);
        ColRGBA col;
        col.red = col.green = col.blue = col.alpha = 1.0;
        if (status)
        {
          tmp_color = g_malloc0(sizeof*tmp_color);
          tmp_color -> red = tmp_color -> green = tmp_color -> blue = tmp_color -> alpha = 1.0;
        }
        else
        {
          if (tmp_color) g_free (tmp_color);
          tmp_color = NULL;
        }
        GdkRGBA rgb_col =  colrgba_togtkrgba(col);
        gtk_color_chooser_set_rgba (GTK_COLOR_CHOOSER(edit_colob), & rgb_col);
      }
      break;
  }
}
 
G_MODULE_EXPORT void set_default_stuff (GtkEntry * res, gpointer data)
{
  int i = GPOINTER_TO_INT(data);
  const gchar * m = entry_get_text (res);
  double value = string_to_double ((gpointer)m);
  if (i < 0)
  {
    // Bonds
    tmp_bd_rw[-i-2] = value;
  }
  else
  {
    tmp_at_rs[i-2] = value;
  }
  update_entry_double (res, value);
}
 
element_radius * duplicate_element_radius (element_radius * old_list)
{
  if (! old_list) return NULL;
  element_radius * new_list = g_malloc0(sizeof*new_list);
  element_radius * tmp_rad, * tmp_rbd;
  tmp_rad = old_list;
  tmp_rbd = new_list;
  while (tmp_rad)
  {
    tmp_rbd -> Z = tmp_rad -> Z;
    tmp_rbd -> rad = tmp_rad -> rad;
    if (tmp_rad -> next)
    {
      tmp_rbd -> next = g_malloc0(sizeof*tmp_rbd -> next);
      tmp_rbd -> next -> prev = tmp_rbd;
      tmp_rbd = tmp_rbd -> next;
    }
    tmp_rad = tmp_rad -> next;
  }
  return new_list;
}
 
float get_radius (int object, int col, int z, element_radius * rad_list)
{
  element_radius * tmp_rad = rad_list;
  int ft;
  while (tmp_rad)
  {
    if (tmp_rad -> Z == z)
    {
      user_defined = TRUE;
      return tmp_rad -> rad;
    }
    tmp_rad = tmp_rad -> next;
  }
  if (object < 0)
  {
    object = - object - 2;
    // Bonds
    if (object == 0 || object == 3)
    {
      if (z < 119)
      {
        ft = 0;
        return set_radius_ (& z, & ft) / 4.0;
      }
    }
    else
    {
      return DEFAULT_SIZE;
    }
  }
  else
  {
    object -= 2;
    if (object == 2 || object == 7 || col)
    {
      ft = col;
      if (z < 119)
      {
        return set_radius_ (& z, & ft);
      }
    }
    else if (object == 1 || object == 4 || object == 6 || object == 9)
    {
      // Dots
      return DEFAULT_SIZE;
    }
    else if (object == 0 || object == 3 || object == 5 ||  object == 8)
    {
      ft = 0;
      return set_radius_ (& z, & ft) / 2.0;
    }
  }
  return 0.0;
}
 
element_color * duplicate_element_color (element_color * old_list)
{
  if (! old_list) return NULL;
  element_color * new_list = g_malloc0(sizeof*new_list);
  element_color * tmp_rad, * tmp_rbd;
  tmp_rad = old_list;
  tmp_rbd = new_list;
  while (tmp_rad)
  {
    tmp_rbd -> Z = tmp_rad -> Z;
    tmp_rbd -> col = tmp_rad -> col;
    if (tmp_rad -> next)
    {
      tmp_rbd -> next = g_malloc0(sizeof*tmp_rbd -> next);
      tmp_rbd -> next -> prev = tmp_rbd;
      tmp_rbd = tmp_rbd -> next;
    }
    tmp_rad = tmp_rad -> next;
  }
  return new_list;
}
 
ColRGBA get_spec_color (int z, element_color * clist)
{
  element_color * tmp_col = clist;
  while (tmp_col)
  {
    if (tmp_col -> Z == z)
    {
      user_defined = TRUE;
      return tmp_col -> col;
    }
    tmp_col = tmp_col -> next;
  }
  return set_default_color (z);
}
 
G_MODULE_EXPORT void edit_pref (GtkCellRendererText * cell, gchar * path_string, gchar * new_text, gpointer user_data)
{
  int col = GPOINTER_TO_INT(user_data);
  GtkTreeModel * pref_model = gtk_tree_view_get_model(GTK_TREE_VIEW(pref_tree));
  GtkTreeIter row;
  gtk_tree_model_get_iter_from_string (pref_model, & row, path_string);
  int z;
  float val = string_to_double ((gpointer)new_text);
  gtk_tree_model_get (pref_model, & row, 3, & z, -1);
  gtk_list_store_set (GTK_LIST_STORE(pref_model), & row, col+4, val, -1);
  gboolean add_elem = FALSE;
  gboolean remove_elem = FALSE;
  element_radius * tmp_list;
  int col_val[4] = {1, 3, 5, 10};
  float v = get_radius (the_object, col, z, NULL);
  if (edit_list[col])
  {
    tmp_list = edit_list[col];
    add_elem = TRUE;
    while (tmp_list)
    {
      if (tmp_list -> Z == z)
      {
        tmp_list -> rad = val;
        if (val == v)
        {
          remove_elem = TRUE;
          if (tmp_list -> next)
          {
            if (tmp_list -> prev)
            {
              tmp_list -> prev -> next = tmp_list -> next;
              tmp_list -> next -> prev = tmp_list -> prev;
            }
            else
            {
              edit_list[col] = tmp_list -> next;
              edit_list[col] -> prev = NULL;
            }
          }
          else if (tmp_list -> prev)
          {
            edit_list[col] -> rad = tmp_list -> rad;
            edit_list[col] -> Z = tmp_list -> Z;
            edit_list[col] -> prev = NULL;
          }
          else
          {
            g_free (edit_list[col]);
            edit_list[col] = NULL;
          }
          add_elem = FALSE;
        }
        else
        {
          add_elem = FALSE;
        }
      }
      tmp_list = tmp_list -> next;
    }
  }
  else if (val != v)
  {
    add_elem = TRUE;
  }
 
  if (add_elem)
  {
    if (edit_list[col])
    {
      tmp_list = edit_list[col];
      while (tmp_list)
      {
        if (! tmp_list -> next) break;
        tmp_list = tmp_list -> next;
      }
      tmp_list -> next = g_malloc0(sizeof*tmp_list -> next);
      tmp_list -> next -> prev = tmp_list;
      tmp_list = tmp_list -> next;
    }
    else
    {
      edit_list[col] = g_malloc0(sizeof*edit_list[col]);
      tmp_list = edit_list[col];
    }
    tmp_list -> Z = z;
    tmp_list -> rad = val;
    gtk_tree_model_get (pref_model, & row, 0, & z, -1);
    if (! z)
    {
      z = col_val[col];
    }
    else
    {
      int a, b, c, d;
      a = z / 10;
      b = (z - a * 10) / 5;
      c = (z - a * 10 - b * 5) / 3;
      d = z - a * 10 - b * 5 - c * 3;
      z = 0;
      if (a || col == 3) z += 10;
      if (b || col == 2) z += 5;
      if (c || col == 1) z += 3;
      if (d || col == 0) z += 1;
    }
    gtk_list_store_set (GTK_LIST_STORE(pref_model), & row, 0, z, -1);
  }
  else if (remove_elem)
  {
    gtk_tree_model_get (pref_model, & row, 0, & z, -1);
    z -= col_val[col];
    gtk_list_store_set (GTK_LIST_STORE(pref_model), & row, 0, z, -1);
  }
}
 
G_MODULE_EXPORT void edit_chem_preferences (GtkDialog * edit_chem, gint response_id, gpointer data)
{
  int i, j, k, l;
  int object = GPOINTER_TO_INT (data);
  gboolean do_style = (object < 100) ? TRUE : FALSE;
  gboolean do_label = (object == 1000 || object == 1001) ? TRUE : FALSE;
  switch (response_id)
  {
    case GTK_RESPONSE_APPLY:
      if (do_style)
      {
        if (object < 0)
        {
          object = - object - 2;
          if (tmp_bond_rad[object]) g_free (tmp_bond_rad[object]);
          tmp_bond_rad[object] = duplicate_element_radius (edit_list[0]);
        }
        else
        {
          j = (object == 4 || object == 9) ? 4 : 1;
          k = (object < 5) ? 7 : 5;
          object = object - 2;
          for (i=0; i<j; i++)
          {
            l = (i) ? 1 : 0;
            if (tmp_atomic_rad[object+l*k+i]) g_free (tmp_atomic_rad[object+l*k+i]);
            tmp_atomic_rad[object+l*k+i] = duplicate_element_radius (edit_list[i]);
          }
        }
      }
      else if (do_label)
      {
        object -= 1000;
        if (tmp_label_color[object]) g_free (tmp_label_color[object]);
        tmp_label_color[object] = duplicate_element_color (color_list);
        if (tmp_color)
        {
          if (! tmp_label[object] -> color) tmp_label[object] -> color = g_malloc0(sizeof*tmp_label[object] -> color);
          tmp_label[object] -> color[0] = * tmp_color;
          tmp_label[object] -> n_colors = 1;
        }
      }
      else
      {
        object -= 100;
        if (tmp_atom_color[object]) g_free (tmp_atom_color[object]);
        tmp_atom_color[object] = duplicate_element_color (color_list);
      }
      break;
    default:
      if (do_style)
      {
        j = (object < 0) ? 1 : (object == 4 || object == 9) ? 4 : 1;
        for (i=0; i<j; i++)
        {
          if (edit_list[i])
          {
            g_free (edit_list[i]);
            edit_list[i] = NULL;
          }
        }
        g_free (edit_list);
        edit_list = NULL;
      }
      else
      {
        g_free (color_list);
        color_list = NULL;
      }
      break;
  }
  if (tmp_color) g_free (tmp_color);
  tmp_color = NULL;
  destroy_this_dialog (edit_chem);
}
 
void color_set_color (GtkTreeViewColumn * col, GtkCellRenderer * renderer, GtkTreeModel * mod, GtkTreeIter * iter, gpointer data)
{
  int z;
  gtk_tree_model_get (mod, iter, 3, & z, -1);
  GdkRGBA colo = colrgba_togtkrgba (get_spec_color (z, color_list));
  if (tmp_color) colo.alpha = 0.5;
  g_object_set (renderer, "background-rgba", & colo, "background-set", TRUE, NULL);
}
 
void radius_set_color_and_markup (GtkTreeViewColumn * col, GtkCellRenderer * renderer, GtkTreeModel * mod, GtkTreeIter * iter, gpointer data)
{
  int cid = GPOINTER_TO_INT (data);
  int vid;
  gtk_tree_model_get (mod, iter, 0, & vid, -1);
  gboolean docol = FALSE;
  switch (vid)
  {
    case 1:
      docol = (cid == 0) ? TRUE : FALSE;
      break;
    case 3:
      docol = (cid == 1) ? TRUE : FALSE;
      break;
    case 5:
      docol = (cid == 2) ? TRUE : FALSE;
      break;
    case 10:
      docol = (cid == 3) ? TRUE : FALSE;
      break;
    case 4:
      docol = (cid == 0 || cid == 1) ? TRUE : FALSE;
      break;
    case 6:
      docol = (cid == 0 || cid == 2) ? TRUE : FALSE;
      break;
    case 8:
      docol = (cid == 1 || cid == 2) ? TRUE : FALSE;
      break;
    case 11:
      docol = (cid == 0 || cid == 3) ? TRUE : FALSE;
      break;
    case 13:
      docol = (cid == 1 || cid == 3) ? TRUE : FALSE;
      break;
    case 15:
      docol = (cid == 2 || cid == 3) ? TRUE : FALSE;
      break;
    case 9:
      docol = (cid != 3) ? TRUE : FALSE;
      break;
    case 14:
      docol = (cid != 2) ? TRUE : FALSE;
      break;
    case 16:
      docol = (cid != 1) ? TRUE : FALSE;
      break;
    case 18:
      docol = (cid != 0) ? TRUE : FALSE;
      break;
    case 19:
      docol = TRUE;
      break;
  }
  set_renderer_color (docol, renderer, init_color (cid, 4));
}
 
gboolean are_identical_colors (ColRGBA col_a, ColRGBA col_b)
{
  if (col_a.red != col_b.red) return FALSE;
  if (col_a.green != col_b.green) return FALSE;
  if (col_a.blue != col_b.blue) return FALSE;
  if (col_a.alpha != col_b.alpha) return FALSE;
  return TRUE;
}
 
G_MODULE_EXPORT void run_ac_color (GtkDialog * win, gint response_id, gpointer data)
{
  if (response_id == GTK_RESPONSE_OK)
  {
    ColRGBA colo = get_window_color (GTK_WIDGET(win));
    int i = GPOINTER_TO_INT (data);
    ColRGBA orig = set_default_color (i);
    gboolean add_elem;
    element_color * tmp_list;
    if (color_list)
    {
      tmp_list = color_list;
      add_elem = TRUE;
      while (tmp_list)
      {
        if (tmp_list -> Z == i)
        {
          tmp_list -> col = colo;
          if (are_identical_colors(colo, orig))
          {
            if (tmp_list -> next)
            {
              if (tmp_list -> prev)
              {
                tmp_list -> prev -> next = tmp_list -> next;
                tmp_list -> next -> prev = tmp_list -> prev;
              }
              else
              {
                color_list = tmp_list -> next;
                color_list -> prev = NULL;
              }
            }
            else if (tmp_list -> prev)
            {
              color_list -> col = tmp_list -> col;
              color_list -> Z = tmp_list -> Z;
              color_list -> prev = NULL;
            }
            else
            {
              g_free (color_list);
              color_list = NULL;
            }
            add_elem = FALSE;
          }
          else
          {
            add_elem = FALSE;
          }
        }
        tmp_list = tmp_list -> next;
      }
    }
    else if (! are_identical_colors(colo, orig))
    {
      add_elem = TRUE;
    }
    if (add_elem)
    {
      if (color_list)
      {
        tmp_list = color_list;
        while (tmp_list)
        {
          if (! tmp_list -> next) break;
          tmp_list = tmp_list -> next;
        }
        tmp_list -> next = g_malloc0(sizeof*tmp_list -> next);
        tmp_list -> next -> prev = tmp_list;
        tmp_list = tmp_list -> next;
      }
      else
      {
        color_list = g_malloc0(sizeof*color_list);
        tmp_list = color_list;
      }
      tmp_list -> Z = i;
      tmp_list -> col = colo;
    }
  }
  destroy_this_dialog (win);
}
 
void color_button_event (GtkWidget * widget, double event_x, double event_y, guint event_button, gpointer data)
{
  if (event_button == 1)
  {
    GtkTreeModel * model = gtk_tree_view_get_model(GTK_TREE_VIEW(widget));
    GtkTreePath * path;
    GtkTreeViewColumn * column;
    int i, j;
#ifdef GTK4
    int e_x, e_y;
    gtk_tree_view_convert_widget_to_bin_window_coords (GTK_TREE_VIEW(widget), event_x, event_y, & e_x, & e_y);
    if (gtk_tree_view_get_path_at_pos (GTK_TREE_VIEW(widget), e_x, e_y, & path, & column, & i, & j))
#else
    if (gtk_tree_view_get_path_at_pos (GTK_TREE_VIEW(widget), event_x, event_y, & path, & column, & i, & j))
#endif
    {
      if (g_strcmp0("Color", gtk_tree_view_column_get_title (column)) == 0)
      {
        GtkTreeIter row;
        if (gtk_tree_model_get_iter (model, & row, path))
        {
          i = GPOINTER_TO_INT(data);
          gchar * obj[2]={"atom", "clone"};
          int z;
          gtk_tree_model_get (model, & row, 3, & z, -1);
          gchar * str = g_strdup_printf ("%s %s color", periodic_table_info[z].lab, obj[i]);
          GdkRGBA col = colrgba_togtkrgba (get_spec_color (z, color_list));
          GtkWidget * win = gtk_color_chooser_dialog_new (str, GTK_WINDOW(MainWindow));
          gtk_window_set_modal (GTK_WINDOW(win), TRUE);
          gtk_color_chooser_set_use_alpha (GTK_COLOR_CHOOSER(win), TRUE);
          gtk_color_chooser_set_rgba (GTK_COLOR_CHOOSER(win), & col);
          g_free (str);
          run_this_gtk_dialog (win, G_CALLBACK(run_ac_color), GINT_TO_POINTER(z));
        }
      }
    }
  }
}
 
#ifdef GTK4
G_MODULE_EXPORT void pref_color_button_pressed (GtkGesture * gesture, int n_press, double x, double y, gpointer data)
{
  color_button_event (gtk_event_controller_get_widget ((GtkEventController*)gesture), x, y,
                      gtk_gesture_single_get_current_button ((GtkGestureSingle * )gesture), data);
}
#else
G_MODULE_EXPORT gboolean pref_color_button_event (GtkWidget * widget, GdkEvent * event, gpointer data)
{
  if (event -> type == GDK_BUTTON_PRESS)
  {
    GdkEventButton * bevent = (GdkEventButton*)event;
    color_button_event (widget, bevent -> x, bevent -> y, bevent -> button, data);
  }
  return FALSE;
}
#endif
 
G_MODULE_EXPORT void set_stuff_color (GtkColorChooser * colob, gpointer data)
{
  * tmp_color = get_button_color (colob);
}
 
G_MODULE_EXPORT void edit_species_parameters (GtkButton * but, gpointer data)
{
  gchar * ats[3]={"atom(s)", "dot(s)", "sphere(s)"};
  gchar * dim[3]={"radius", "size", "width"};
  gchar * bts[3]={"bond(s)", "wireframe(s)", "cylinder(s)"};
  the_object = GPOINTER_TO_INT(data);
  int i, j, k, l, n, m;
  int aid, bid;
  int num_col;
  gchar * str;
  gboolean do_style = (the_object < 100) ? TRUE : FALSE;
  gboolean do_label = FALSE;
  if (do_style)
  {
    if (the_object < 0)
    {
      // Going for bonds
      aid = - the_object - 2;
      aid = (aid) > 2 ? aid - 3 : aid;
      bid = (the_object == -3 || the_object == -6) ? 2 : 0;
      str = (the_object < -4) ? g_strdup_printf ("Edit cloned %s %s", bts[aid], dim[bid]) : g_strdup_printf ("Edit %s %s", bts[aid], dim[bid]);
      num_col = 5;
    }
    else
    {
      // Going for atoms
      aid = the_object - 2;
      aid = (aid == 0 || aid == 2 || aid == 5 || aid == 7) ? 0 : (aid == 1 || aid == 4 || aid == 6 || aid == 9) ? 1 : 2;
      bid = (the_object == 1 || the_object == 6) ? 1 : 0;
      str = (the_object - 2 > 4) ? g_strdup_printf ("Edit cloned %s %s", ats[aid], dim[bid]) : g_strdup_printf ("Edit %s %s", ats[aid], dim[bid]);
      num_col = (the_object == 4 || the_object == 9) ? 8 : 5;
    }
  }
  else
  {
    // Going for colors
    if (the_object < 1000)
    {
      aid = the_object - 100;
      str = g_strdup_printf ("Select %s color", (aid) ? "clone" : "atom");
    }
    else
    {
      aid = the_object - 1000;
      str = g_strdup_printf ("Select %s label color", (aid) ? "clone" : "atom");
      do_label = TRUE;
    }
    num_col = 5;
  }
  edit_list = NULL;
  color_list = NULL;
  tmp_color = NULL;
  GtkWidget * win = dialog_cancel_apply (str, MainWindow, TRUE);
  g_free (str);
  gtk_window_set_default_size (GTK_WINDOW(win), (num_col == 8) ? 600 : 300, 600);
  GtkWidget * vbox = dialog_get_content_area (win);
  GType s_type[8] = {G_TYPE_INT, G_TYPE_STRING, G_TYPE_STRING, G_TYPE_INT, G_TYPE_DOUBLE, G_TYPE_DOUBLE, G_TYPE_DOUBLE, G_TYPE_DOUBLE};
  GType c_type[5] = {G_TYPE_INT, G_TYPE_STRING, G_TYPE_STRING, G_TYPE_INT, G_TYPE_STRING};
  GtkTreeViewColumn * pref_col[num_col];
  GtkCellRenderer * pref_cel[num_col];
  GtkTreeSelection * pref_select;
  GtkListStore * pref_model;
  GtkTreeIter elem;
  if (do_style)
  {
    pref_model = gtk_list_store_newv (num_col, s_type);
    i = (the_object < 0) ? - the_object - 2 : the_object - 2;
    j = (num_col == 8) ? 4 : 1;
    k = ((the_object < 0 && i > 2) || (the_object > 0 && i > 4)) ? 1 : 0;
    edit_list = g_malloc0(j*sizeof*edit_list);
    for (l=0; l<j; l++)
    {
      if (the_object < 0)
      {
        edit_list[l] = duplicate_element_radius (tmp_bond_rad[i]);
      }
      else
      {
        m = (k) ? 5 : 7;
        n = (l) ? 1 : 0;
        edit_list[l] = duplicate_element_radius (tmp_atomic_rad[i+n*m+l]);
      }
    }
  }
  else
  {
    pref_model = gtk_list_store_newv (num_col, c_type);
    color_list = duplicate_element_color ((do_label) ? tmp_label_color[aid] : tmp_atom_color[aid]);
  }
 
  for (i=1; i<119; i++)
  {
    user_defined = FALSE;
    gtk_list_store_append (pref_model, & elem);
    if (do_style)
    {
      gtk_list_store_set (pref_model, & elem, 0, user_defined,
                          1, periodic_table_info[i].name,
                          2, periodic_table_info[i].lab,
                          3, periodic_table_info[i].Z,
                          4, get_radius (the_object, 0, i, edit_list[0]), -1);
      if (num_col == 8)
      {
        j = user_defined;
        user_defined = FALSE;
        gtk_list_store_set (pref_model, & elem, 5,  get_radius (the_object, 1, i, edit_list[1]), -1);
        j += (user_defined) ? 3 : 0;
        user_defined = FALSE;
        gtk_list_store_set (pref_model, & elem, 6, get_radius (the_object, 2, i, edit_list[2]), -1);
        j += (user_defined) ? 5 : 0;
        user_defined = FALSE;
        gtk_list_store_set (pref_model, & elem, 7, get_radius (the_object, 3, i, edit_list[3]), -1);
        j += (user_defined) ? 10 : 0;
        user_defined = FALSE;
        gtk_list_store_set (pref_model, & elem, 0, j, -1);
      }
    }
    else
    {
      gtk_list_store_set (pref_model, & elem, 0, user_defined,
                          1, periodic_table_info[i].name,
                          2, periodic_table_info[i].lab,
                          3, periodic_table_info[i].Z,
                          4, NULL, -1);
    }
  }
 
  pref_tree = gtk_tree_view_new_with_model (GTK_TREE_MODEL(pref_model));
  gchar * name[3] = {"Element", "Symbol", "Z"};
  gchar * g_name[3] = {"Radius", "Size", "Width"};
  gchar * f_name[4] = {"Covalent [1]","Ionic [2]","van Der Waals [3]", "Crystal [4,5]"};
  for (i=0; i<num_col; i++)
  {
    pref_cel[i] = gtk_cell_renderer_text_new();
    if (i > 3)
    {
      if (do_style)
      {
        g_object_set (pref_cel[i], "editable", TRUE, NULL);
        gtk_cell_renderer_set_alignment (pref_cel[i], 0.5, 0.5);
        g_signal_connect (G_OBJECT(pref_cel[i]), "edited", G_CALLBACK(edit_pref), GINT_TO_POINTER(i-4));
        pref_col[i] = gtk_tree_view_column_new_with_attributes((num_col) == 8 ? f_name[i-4] : g_name[bid], pref_cel[i], "text", i, NULL);
        gtk_tree_view_column_set_cell_data_func (pref_col[i], pref_cel[i], radius_set_color_and_markup, GINT_TO_POINTER(i-4), NULL);
      }
      else
      {
        gtk_cell_renderer_set_alignment (pref_cel[i], 0.5, 0.5);
        pref_col[i] = gtk_tree_view_column_new_with_attributes("Color", pref_cel[i], "text", i, NULL);
        gtk_tree_view_column_set_cell_data_func (pref_col[i], pref_cel[i], color_set_color, NULL, NULL);
      }
    }
    else if (i)
    {
      pref_col[i] = gtk_tree_view_column_new_with_attributes(name[i-1], pref_cel[i], "text", i, NULL);
      gtk_tree_view_column_set_alignment (pref_col[i], 0.5);
      gtk_tree_view_column_set_resizable (pref_col[i], TRUE);
      gtk_tree_view_column_set_min_width (pref_col[i], 50);
    }
    else
    {
      pref_col[i] = gtk_tree_view_column_new_with_attributes("", pref_cel[i], "text", i, NULL);
      gtk_tree_view_column_set_visible (pref_col[i], FALSE);
    }
    gtk_tree_view_append_column(GTK_TREE_VIEW(pref_tree), pref_col[i]);
  }
  g_object_unref (pref_model);
  pref_select = gtk_tree_view_get_selection (GTK_TREE_VIEW(pref_tree));
  gtk_tree_selection_set_mode (pref_select, GTK_SELECTION_SINGLE);
  gtk_tree_view_expand_all (GTK_TREE_VIEW(pref_tree));
 
#ifdef GTK3
  g_signal_connect (G_OBJECT(pref_tree), "button_press_event", G_CALLBACK(pref_color_button_event), GINT_TO_POINTER(aid));
#else
  add_widget_gesture_and_key_action (pref_tree, "pref-context-click", G_CALLBACK(pref_color_button_pressed), GINT_TO_POINTER(aid),
                                                 NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL);
#endif
 
  edit_scrol = create_scroll (vbox, -1, 570, GTK_SHADOW_ETCHED_IN);
  add_container_child (CONTAINER_SCR, edit_scrol, pref_tree);
  if (! do_label)
  {
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label("<i>User defined values appear in colored bold font.</i>", -1, 40, 0.5, 0.5), FALSE, FALSE, 0);
    if (num_col == 8)
    {
      gchar * legend={"\n<sub>[1] B. Cordero and al. <i>Dalton Trans</i>, <b>213</b>:1112 (2008).</sub>\n"
                      "<sub>[2] Slater. <i>J. Chem. Phys.</i>, <b>41</b>:3199 (1964).</sub>\n"
                      "<sub>[3] Bondi A. <i>J. Phys. Chem.</i>, <b>68</b>:441 (1964).</sub>\n"
                      "<sub>[4] R.D. Shannon and C.T. Prewitt <i>Acta Cryst. B</i>, <b>25</b>:925-946 (1969).</sub>\n"
                      "<sub>[5] R.D. Shannon <i>Acta Cryst. A</i>, <b>23</b>:751-767 (1976).</sub>"};
       add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label(legend, -1, 25, 0.0, 0.5), FALSE, FALSE, 0);
   }
  }
  else if (do_label)
  {
    gtk_widget_set_sensitive (edit_scrol, ! tmp_label[aid] -> n_colors);
    GtkWidget * vvbox = create_vbox (BSEP);
    GtkWidget * hbox = create_hbox (BSEP);
    gchar * info[3] = {"By default label and species colors are similar,", "you can modify that using this dialog window.", "You can also use a single color for all labels:"};
    for (i=0; i<2; i++)
    {
      hbox = create_hbox (BSEP);
      add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(info[i], 300, -1, 0.5, 0.5), FALSE, FALSE, 5);
      add_box_child_start (GTK_ORIENTATION_VERTICAL, vvbox, hbox, FALSE, FALSE, 0);
    }
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, vvbox, FALSE, FALSE, 10);
    hbox = create_hbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(info[i], 300, -1, 0.5, 0.5), FALSE, FALSE, 5);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 0);
    hbox = create_hbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, check_button ("Use single color", -1, -1, tmp_label[aid] -> n_colors, G_CALLBACK(toggled_default_stuff), data), FALSE, FALSE, 30);
    ColRGBA active_col;
    if (tmp_label[aid] -> n_colors)
    {
      tmp_color = g_malloc0(sizeof*tmp_color);
      * tmp_color = tmp_label[aid] -> color[0];
      active_col = tmp_label[aid] -> color[0];
    }
    active_col.red = active_col.green = active_col.blue = active_col.alpha = 1.0;
    edit_colob = color_button (active_col, TRUE, 100, -1, G_CALLBACK(set_stuff_color), tmp_color);
    widget_set_sensitive (edit_colob, tmp_label[aid] -> n_colors);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, edit_colob, FALSE, FALSE, 0);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 10);
  }
  run_this_gtk_dialog (win, G_CALLBACK(edit_chem_preferences), data);
}
 
GtkWidget * over_param (int object, int style)
{
  GtkWidget * vbox = create_vbox (BSEP);
  GtkWidget * hbox = create_hbox (BSEP);
  int clone = ((object && style > 2) || (! object && style > 4)) ? 20 : 0;
  int mod = (object) ? -1 : 1;
  gboolean over = (! object) ? TRUE : (object && (style != 2 && style != 5)) ? TRUE : FALSE;
  gchar * leg;
  if (over)
  {
    hbox = create_hbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(" ", 60+clone, -1, 0.0, 0.0), FALSE, FALSE, 0);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, create_button ("Edit species related parameters", IMG_NONE, NULL, -1, -1, GTK_RELIEF_NORMAL, G_CALLBACK(edit_species_parameters), GINT_TO_POINTER(mod*(style+2))), FALSE, FALSE, 60);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 5);
    hbox = create_hbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(" ", 60+clone, -1, 0.0, 0.0), FALSE, FALSE, 0);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, check_button ("Override species based parameters", -1, -1, (object) ? tmp_o_bd_rw[style] : tmp_o_at_rs[style], G_CALLBACK(toggled_default_stuff), GINT_TO_POINTER(mod*(style+2))), FALSE, FALSE, 10);
  }
  else
  {
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(" ", 60+clone, -1, 0.0, 0.0), FALSE, FALSE, 0);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label("Set default value", -1, -1, 0.0, 0.5), FALSE, FALSE, 10);
  }
  if (object)
  {
    bond_entry_over[style] = create_entry(G_CALLBACK(set_default_stuff), 100, 10, FALSE, GINT_TO_POINTER(mod*(style+2)));
    update_entry_double (GTK_ENTRY(bond_entry_over[style]), tmp_bd_rw[style]);
    if (over) widget_set_sensitive (bond_entry_over[style], tmp_o_bd_rw[style]);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, bond_entry_over[style], FALSE, FALSE, 0);
    leg = g_strdup_printf ("%s", (style == 1 || style == 4) ? "pts" : "&#xC5;");
  }
  else
  {
    atom_entry_over[style] = create_entry(G_CALLBACK(set_default_stuff), 100, 10, FALSE, GINT_TO_POINTER(mod*(style+2)));
    update_entry_double (GTK_ENTRY(atom_entry_over[style]), tmp_at_rs[style]);
    if (over) widget_set_sensitive (atom_entry_over[style], tmp_o_at_rs[style]);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, atom_entry_over[style], FALSE, FALSE, 0);
    leg = g_strdup_printf ("%s", (style == 1 || style == 6 || style == 4 || style == 9) ? "pts" : "&#xC5;");
  }
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(leg, -1, -1, 0.0, 0.5), FALSE, FALSE, 5);
  g_free (leg);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 5);
  return vbox;
}
 
GtkWidget * style_tab (int style)
{
  GtkWidget * vbox = create_vbox (BSEP);
  gchar * object[3]={"<b>Atom(s)</b>", "<b>Bond(s)</b>", "\t<u>Clone(s)</u>"};
  gchar * ats[3]={"tom(s) ", "ot(s)", "phere(s)"};
  gchar * ha_init[3]={"A", "D", "S"};
  gchar * la_init[3]={"a", "d", "s"};
  gchar * dim[3]={"radius", "size", "width"};
  gchar * bts[3]={"ond(s)", "ireframe(s)", "ylinder(s)"};
  gchar * hb_init[3]={"B", "W", "C"};
  gchar * lb_init[3]={"b", "w", "c"};
  int i;
  int bsid;
  int lid;
  gchar * str;
  gboolean do_atoms = FALSE;
  gboolean do_bonds = FALSE;
  if (style == 0 || style == 1 || style == 2 || style == 3 || style == 5)
  {
    do_atoms = TRUE;
  }
  if (style == 0 || style == 1 || style == 4)
  {
    do_bonds = TRUE;
    bsid = (style == 4) ? 2 : style;
  }
  if (do_atoms)
  {
    lid = (style == 3) ? 2 : (style == 1 || style == 5) ? 1 : 0;
    for (i=0; i<2; i++)
    {
      adv_box (vbox, object[i*2], 10-5*i, 120, 0.0);
      if (! i)
      {
        str = g_strdup_printf ("\t%s%s %s", ha_init[lid], ats[lid], dim[(lid != 1) ? 0 : 1]);
      }
      else
      {
        str = g_strdup_printf ("\t\tClone %s%s %s", la_init[lid], ats[lid], dim[(lid != 1) ? 0 : 1]);
      }
      adv_box (vbox, str, 10, 120, 0.0);
      g_free (str);
      add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, over_param (0, (style < 5) ? style+5*i : 4 + 5*i), FALSE, FALSE, 0);
    }
  }
  if (do_bonds)
  {
    // Bond(s) parameters
    for (i=0; i<2; i++)
    {
      adv_box (vbox, object[i+1], 10-5*i, 120, 0.0);
      if (! i)
      {
        str = g_strdup_printf ("\t%s%s %s", hb_init[bsid], bts[bsid], dim[(bsid != 1) ? 0 : 2]);
      }
      else
      {
        str = g_strdup_printf ("\t\tClone %s%s %s", lb_init[bsid], bts[bsid], dim[(bsid != 1) ? 0 : 2]);
      }
      adv_box (vbox, str, 10, 120, 0.0);
      g_free (str);
      add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, over_param (1, bsid+3*i), FALSE, FALSE, 0);
    }
  }
 
  return vbox;
}
 
GtkWidget * model_preferences ()
{
  GtkWidget * notebook = gtk_notebook_new ();
  gtk_notebook_set_scrollable (GTK_NOTEBOOK(notebook), TRUE);
  gtk_notebook_set_tab_pos (GTK_NOTEBOOK(notebook), GTK_POS_TOP);
  GtkWidget * vbox = create_vbox (BSEP);
  //GtkWidget * hbox;
  //GtkWidget * combo;
  gchar * info[2] = {"The <b>Model</b> tab regroups atom(s), bond(s) and clone(s) options",
                     "which effect apply when the corresponding <b>OpenGL</b> style is used:"};
  gchar * m_list[4][2] = {{"Ball and stick", "atoms<sup>*</sup> and bonds radii"},
                          {"Wireframe", "dots<sup>**</sup> size and wireframes width"},
                          {"Spacefill", "tabulated parameters"},
                          {"Cylinders", "bonds radii"}};
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label(" ", -1, 30, 0.0, 0.0), FALSE, FALSE, 0);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, pref_list (info, 4, m_list, NULL), FALSE, FALSE, 0);
  gchar * other_info[2] = {"It also provides options to customize atomic label(s),", "and, the model box, if any:"};
  gchar * o_list[2][2] = {{"Labels", "atom labels"},
                          {"Box", "model box details"}};
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, pref_list (other_info, 2, o_list, NULL), FALSE, FALSE, 15);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label(" ", -1, 20, 0.0, 0.0), FALSE, FALSE, 0);
 
  GtkWidget * hbox;
  gchar * obj[2] = {"<b>Atoms</b>", "<b>Clones</b>"};
  int i;
  for (i=0; i<2; i++)
  {
    hbox = adv_box (vbox, obj[i], 5, 150, 1.0);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, create_button ("Edit species colors", IMG_NONE, NULL, -1, -1, GTK_RELIEF_NORMAL, G_CALLBACK(edit_species_parameters), GINT_TO_POINTER(100+i)), FALSE, FALSE, 30);
  }
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label(" ", -1, 5, 0.0, 0.0), FALSE, FALSE, 0);
  hbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, check_button ("Always show clone(s), if any.", 250, -1, tmp_clones, G_CALLBACK(toggled_default_stuff), GINT_TO_POINTER(0)), FALSE, FALSE, 30);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 5);
  hbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, check_button ("Always show box, if any.", 250, -1, tmp_clones, G_CALLBACK(toggled_default_stuff), GINT_TO_POINTER(1)), FALSE, FALSE, 30);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 5);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label(" ", -1, 5, 0.0, 0.0), FALSE, FALSE, 0);
 
  append_comments (vbox, "<sup>*</sup>", "the same parameters are also used for the <b>spheres</b> style");
  append_comments (vbox, "<sup>**</sup>", "the same parameters are also used for the <b>dots</b> style");
 
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), vbox, gtk_label_new ("General"));
 
  for (i=0; i<OGL_STYLES; i++)
  {
    if (i != 3 && i != 5) gtk_notebook_append_page (GTK_NOTEBOOK(notebook), style_tab (i), gtk_label_new (text_styles[i]));
  }
 
  vbox = create_vbox (BSEP);
  GtkWidget * hhbox;
  for (i=0; i<2; i++)
  {
    hbox = adv_box (vbox, obj[i], 5, 120, 0.0);
    hbox = create_hbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, labels_tab(NULL, i), FALSE, FALSE, 40);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 5);
    hbox = create_hbox (BSEP);
    hhbox = create_hbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hhbox, markup_label("<b>.</b>", 5, -1, 0.0, 0.25), FALSE, FALSE, 10);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hhbox, markup_label("Colors", 150, 30, 0.0, 0.5), FALSE, FALSE, 0);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hhbox, create_button ("Adjust color(s)", IMG_NONE, NULL, 220, -1, GTK_RELIEF_NORMAL, G_CALLBACK(edit_species_parameters), GINT_TO_POINTER(1000+i)), FALSE, FALSE, 15);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, hbox, hhbox, FALSE, FALSE, 40);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 0);
  }
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), vbox, gtk_label_new ("Labels"));
 
  pref_box_win = g_malloc0(sizeof*pref_box_win);
  box_advanced (NULL, NULL);
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), pref_box_win -> win, gtk_label_new ("Box"));
  show_the_widgets (notebook);
  return notebook;
}
 
G_MODULE_EXPORT void set_default_style (GtkComboBox * box, gpointer data)
{
  GtkTreeIter iter;
  if (gtk_combo_box_get_active_iter (box, & iter))
  {
    GtkTreeModel * model = gtk_combo_box_get_model (box);
    int i;
    gtk_tree_model_get (model, & iter, 1, & i, -1);
    tmp_opengl[0] = (! i) ? 0 : i;
  }
}
 
GtkTreeModel * style_combo_tree ()
{
  GtkTreeIter iter, iter2;
  GtkTreeStore * store;
  int i, j;
  store = gtk_tree_store_new (2, G_TYPE_STRING, G_TYPE_INT);
  gtk_tree_store_append (store, & iter, NULL);
  gtk_tree_store_set (store, & iter, 0, "f(atoms) <sup>*</sup>", 1, 0, -1);
  for (i=0; i<OGL_STYLES; i++)
  {
    gtk_tree_store_append (store, & iter, NULL);
    gtk_tree_store_set (store, & iter, 0, text_styles[i], 1, i+1, -1);
    if (i == SPACEFILL)
    {
      for (j=0; j<FILLED_STYLES; j++)
      {
        gtk_tree_store_append (store, & iter2, & iter);
        gtk_tree_store_set (store, & iter2, 0, text_filled[j], 1, -j-1, -1);
      }
    }
  }
  return  GTK_TREE_MODEL (store);
}
 
G_MODULE_EXPORT void set_default_map (GtkComboBox * box, gpointer data)
{
  int i, j;
  i = combo_get_active ((GtkWidget *)box);
  j = GPOINTER_TO_INT(data);
  tmp_opengl[j+1] = i;
}
 
GtkWidget * combo_map (int obj)
{
  GtkWidget * combo = create_combo ();
  combo_text_append (combo, "Atomic species");
  combo_text_append (combo, "Total coordination(s)");
  combo_text_append (combo, "Partial coordination(s)");
  combo_set_active (combo, tmp_opengl[1+obj]);
  g_signal_connect (G_OBJECT(combo), "changed", G_CALLBACK(set_default_map), GINT_TO_POINTER(obj));
  return combo;
}
 
GtkWidget * opengl_preferences ()
{
  GtkWidget * notebook = gtk_notebook_new ();
  gtk_notebook_set_scrollable (GTK_NOTEBOOK(notebook), TRUE);
  gtk_notebook_set_tab_pos (GTK_NOTEBOOK(notebook), GTK_POS_TOP);
  GtkWidget * vbox = create_vbox (BSEP);
  GtkWidget * hbox;
  GtkWidget * combo;
 
  // Creating an OpenGL edition data structure
  pref_ogl_edit = g_malloc0(sizeof*pref_ogl_edit);
  int i;
  for (i=0; i<6; i++)
  {
    pref_ogl_edit -> pointer[i].a = -1;
    pref_ogl_edit -> pointer[i].b = i;
  }
 
  gchar * info[2] = {"The <b>OpenGL</b> tab regroups rendering options",
                     "use it to configure the OpenGL 3D scene:"};
  gchar * m_list[3][2] = {{"Material", "aspect for atom(s) and bond(s)"},
                          {"Lights", "lightning of the scene"},
                          {"Fog", "atmosphere effects"}};
  gchar * end = {"It also offers to adjust the main visualization style and the color maps"};
 
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, pref_list (info, 3, m_list, end), FALSE, FALSE, 30);
 
  hbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label ("<b>Style</b>", 250, -1, 0.0, 0.5), FALSE, FALSE, 15);
  GtkTreeModel * model = style_combo_tree ();
  combo = gtk_combo_box_new_with_model (model);
  g_object_unref (model);
  GtkCellRenderer * renderer = gtk_cell_renderer_combo_new ();
  gtk_cell_layout_pack_start (GTK_CELL_LAYOUT (combo), renderer, TRUE);
  gtk_cell_layout_set_attributes (GTK_CELL_LAYOUT (combo), renderer, "text", 0, NULL);
  combo_set_active (combo, tmp_opengl[0]);
  combo_set_markup (combo);
  g_signal_connect (G_OBJECT(combo), "changed", G_CALLBACK(set_default_style), NULL);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, combo, FALSE, FALSE, 0);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 10);
  append_comments (vbox, "<sup>*</sup>", "if 10 000 atoms or more: <b>Wireframe</b>, otherwise: <b>Ball and stick</b>");
 
  hbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label ("<b>Color maps</b>", 250, -1, 0.0, 0.5), FALSE, FALSE, 15);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 15);
  hbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label ("\tatom(s) and bond(s)", 250, -1, 0.0, 0.5), FALSE, FALSE, 15);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, combo_map(0), FALSE, FALSE, 0);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 0);
 
  hbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label ("\tpolyhedra", 250, -1, 0.0, 0.5), FALSE, FALSE, 15);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, combo_map(1), FALSE, FALSE, 0);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 10);
 
  show_the_widgets (vbox);
 
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), vbox, gtk_label_new ("General"));
 
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), materials_tab (NULL, pref_ogl_edit, & tmp_material), gtk_label_new ("Material"));
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), lights_tab (NULL, pref_ogl_edit, & tmp_lightning), gtk_label_new ("Lights"));
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), fog_tab (NULL, pref_ogl_edit, & tmp_fog), gtk_label_new ("Fog"));
 
  gtk_notebook_set_current_page (GTK_NOTEBOOK(notebook), 0);
  return notebook;
}
 
G_MODULE_EXPORT void set_default_num_delta (GtkEntry * res, gpointer data)
{
  int i = GPOINTER_TO_INT(data);
  const gchar * m = entry_get_text (res);
  double value = string_to_double ((gpointer)m);
  if (i == -1)
  {
    if (value > 0.0)
    {
      tmp_totcut = value;
    }
    update_entry_double (res, tmp_totcut);
  }
  else if (i < 8)
  {
    if (value > 0) tmp_num_delta[i] = (int) value;
    update_entry_int (res, tmp_num_delta[i]);
  }
  else
  {
    if (value > 0.0) tmp_delta_t[0] = value;
    update_entry_double (res, tmp_delta_t[0]);
  }
}
 
G_MODULE_EXPORT void tunit_changed (GtkComboBox * box, gpointer data)
{
  tmp_delta_t[1] = (double) combo_get_active ((GtkWidget *)box);
}
 
GtkWidget * all_cut_box;
GtkWidget * cut_combo[2];
GtkWidget * pcut_box[2];
GtkWidget * tcut_entry;
GtkWidget * tcut_box;
GtkWidget * cut_comments;
bond_cutoff * cut_list;
 
G_MODULE_EXPORT void totcut_changed (GtkComboBox * box, gpointer data)
{
  if (combo_get_active((GtkWidget *)box))
  {
    tmp_totcut = 2.0;
    show_the_widgets (tcut_box);
  }
  else
  {
    tmp_totcut = 0.0;
    hide_the_widgets (tcut_box);
  }
  update_entry_double((GtkEntry *)tcut_entry, tmp_totcut);
}
 
G_MODULE_EXPORT void edit_pc_value (GtkEntry * res, gpointer data)
{
  bond_cutoff * cut = (bond_cutoff *)data;
  const gchar * m = entry_get_text (res);
  double value = string_to_double ((gpointer)m);
  if (value > 0.0)
  {
    cut -> cutoff = value;
  }
  update_entry_double (res, cut -> cutoff);
}
 
#ifdef GTK4
G_MODULE_EXPORT void toggled_use_cutoff (GtkCheckButton * but, gpointer data)
#else
G_MODULE_EXPORT void toggled_use_cutoff (GtkToggleButton * but, gpointer data)
#endif
{
  bond_cutoff * cut = (bond_cutoff *)data;
  cut -> use = button_get_status ((GtkWidget *)but);
}
 
void add_cut_box ()
{
  GtkWidget * hbox;
  GtkWidget * entry;
 
  int i;
  for (i=0; i<2; i++)
  {
    if (pcut_box[i])
    {
     pcut_box[i] = destroy_this_widget(pcut_box[i]);
    }
  }
  pcut_box[0] = create_vbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, all_cut_box, pcut_box[0], FALSE, FALSE, 10);
  if (cut_list)
  {
    hbox = create_hbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, pcut_box[0], hbox, FALSE, FALSE, 10);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label("Spec. &#x3B1;", 60, -1, 0.0, 0.5), FALSE, FALSE, 10);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label("Spec. &#x3B2;", 60, -1, 0.0, 0.5), FALSE, FALSE, 10);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label("R<sub>cut</sub> (&#x3B1;, &#x3B2;)", 100, -1, 0.5, 0.5), FALSE, FALSE, 10);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label("Use <sup>*</sup>", 20, -1, 0.5, 0.5), FALSE, FALSE, 10);
  }
  pcut_box[1] = create_vbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, all_cut_box, pcut_box[1], FALSE, FALSE, 10);
  bond_cutoff * tmp_cut = cut_list;
  while (tmp_cut)
  {
    hbox = create_hbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, pcut_box[1], hbox, FALSE, FALSE, 0);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(periodic_table_info[tmp_cut -> Z[0]].lab, 60, -1, 0.5, 0.5), FALSE, FALSE, 10);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(periodic_table_info[tmp_cut -> Z[1]].lab, 60, -1, 0.5, 0.5), FALSE, FALSE, 10);
    entry = create_entry (G_CALLBACK(edit_pc_value), 100, 10, FALSE, (gpointer)tmp_cut);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, entry, FALSE, FALSE, 10);
    update_entry_double ((GtkEntry *)entry, tmp_cut -> cutoff);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, check_button (NULL, 20, -1, tmp_cut -> use, G_CALLBACK(toggled_use_cutoff), (gpointer)tmp_cut), FALSE, FALSE, 10);
    tmp_cut = tmp_cut -> next;
  }
 
  cut_comments = destroy_this_widget (cut_comments);
  cut_comments = create_vbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, all_cut_box, cut_comments, FALSE, FALSE, 10);
  if (cut_list) append_comments (cut_comments, "<sup>*</sup>", "Unused values will not be saved !");
 
  for (i=0; i<2; i++) combo_set_active (cut_combo[i], -1);
  show_the_widgets (all_cut_box);
}
 
gboolean not_in_cutoffs (int z_a, int z_b)
{
  bond_cutoff * tmp_cut = cut_list;
  while (tmp_cut)
  {
    if (tmp_cut -> Z[0] == z_a && tmp_cut -> Z[1] == z_b) return FALSE;
    tmp_cut = tmp_cut -> next;
  }
  return TRUE;
}
 
G_MODULE_EXPORT void cut_spec_changed (GtkComboBox * box, gpointer data)
{
  int i, j, k, l;
  i = combo_get_active (cut_combo[0]);
  j = combo_get_active (cut_combo[1]);
  k = min (i+1, j+1);
  l = max (i+1, j+1);
  if (k && l)
  {
    if (not_in_cutoffs(k, l))
    {
      bond_cutoff * tmp_cut;
      if (! cut_list)
      {
        cut_list = g_malloc0(sizeof*cut_list);
        tmp_cut = cut_list;
      }
      else
      {
        tmp_cut = cut_list;
        while (tmp_cut -> next)
        {
          tmp_cut = tmp_cut -> next;
        }
        tmp_cut -> next = g_malloc0(sizeof*tmp_cut -> next);
        tmp_cut -> next -> prev = tmp_cut;
        tmp_cut = tmp_cut -> next;
      }
      tmp_cut -> Z[0] = min(k, l);
      tmp_cut -> Z[1] = max(k, l);
      tmp_cut -> use = FALSE;
      tmp_cut -> cutoff = 1.0;
      add_cut_box ();
    }
  }
}
 
bond_cutoff * duplicate_cutoffs (bond_cutoff * old_cutoff)
{
  bond_cutoff * new_cutoff = NULL;
  bond_cutoff * cut_a, * cut_b;
  cut_a = old_cutoff;
  while (cut_a)
  {
    if (cut_a -> use)
    {
      if (! new_cutoff)
      {
        new_cutoff = g_malloc0(sizeof*new_cutoff);
        cut_b = new_cutoff;
      }
      else
      {
        cut_b -> next = g_malloc0(sizeof*cut_b -> next);
        cut_b -> next -> prev = cut_b;
        cut_b = cut_b -> next;
      }
      cut_b -> Z[0] = cut_a -> Z[0];
      cut_b -> Z[1] = cut_a -> Z[1];
      cut_b -> use = cut_a -> use;
      cut_b -> cutoff = cut_a -> cutoff;
    }
    cut_a = cut_a -> next;
  }
  return new_cutoff;
}
 
G_MODULE_EXPORT void edit_cutoffs (GtkDialog * edit_cuts, gint response_id, gpointer data)
{
  switch (response_id)
  {
    case GTK_RESPONSE_APPLY:
      tmp_bond_cutoff = duplicate_cutoffs (cut_list);
      break;
  }
  if (cut_list)
  {
    g_free (cut_list);
    cut_list = NULL;
  }
  int i;
  for (i=0; i<2; i++)
  {
    cut_combo[i] = destroy_this_widget (cut_combo[i]);
    pcut_box[i] = destroy_this_widget (pcut_box[i]);
  }
  cut_comments = destroy_this_widget (cut_comments);
  all_cut_box = destroy_this_widget (all_cut_box);
  destroy_this_widget ((GtkWidget *)edit_cuts);
}
 
G_MODULE_EXPORT void set_cutoffs_default (GtkButton * but, gpointer data)
{
  GtkWidget * win = dialog_cancel_apply ("Select partial cutoffs(s)", MainWindow, TRUE);
  GtkWidget * vbox = dialog_get_content_area (win);
  GtkWidget * hbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 5);
  all_cut_box = create_vbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, all_cut_box, FALSE, FALSE, 50);
  cut_list = duplicate_cutoffs (tmp_bond_cutoff);
  hbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, all_cut_box, hbox, FALSE, FALSE, 5);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label("Spec. &#x3B1;", 60, -1, 0.0, 0.5), FALSE, FALSE, 0);
  int i, j;
  for (i=0; i<2; i++)
  {
    cut_combo[i] = NULL;
    cut_combo[i] = create_combo ();
    for (j=1; j<119; j++)
    {
       combo_text_append (cut_combo[i], periodic_table_info[j].lab);
    }
    g_signal_connect(G_OBJECT(cut_combo[i]), "changed", G_CALLBACK(cut_spec_changed), NULL);
    show_the_widgets (cut_combo[i]);
  }
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, cut_combo[0], FALSE, FALSE, 5);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(" ", 20, -1, 0.0, 0.5), FALSE, FALSE, 0);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label("Spec. &#x3B2;", 60, -1, 0.0, 0.5), FALSE, FALSE, 0);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, cut_combo[1], FALSE, FALSE, 5);
 
  add_cut_box ();
 
  run_this_gtk_dialog (win, G_CALLBACK(edit_cutoffs), NULL);
}
 
GtkWidget * calc_preferences ()
{
  GtkWidget * notebook = gtk_notebook_new ();
  GtkWidget * vbox;
  GtkWidget * hbox;
  gtk_notebook_set_scrollable (GTK_NOTEBOOK(notebook), TRUE);
  gtk_notebook_set_tab_pos (GTK_NOTEBOOK(notebook), GTK_POS_TOP);
  gchar * default_delta_num_leg[8] = {"<b>g(r)</b>: number of &#x3b4;r", "<b>s(q)</b>: number of &#x3b4;q", "<b>s(k)</b>: number of &#x3b4;k", "<b>g(r) FFT</b>: number of &#x3b4;r",
                                      "<b>D<sub>ij</sub></b>: number of &#x3b4;r [D<sub>ij</sub>min-D<sub>ij</sub>max]", "<b>Angles distribution</b>: number of &#x3b4;&#x3b8; [0-180°]",
                                      "<b>Spherical harmonics</b>: l<sub>max</sub> in [2-40]", "step(s) between configurations"};
  gchar * info[2] = {"The <b>Analysis</b> tab regroups calculation options",
                     "use it to setup your own default parameters:"};
  gchar * m_list[3][2] = {{"Calculations", "most analysis options"},
                          {"Rings", "ring statistics options"},
                          {"Chains", "chain statistics options"}};
 
  vbox = create_vbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, pref_list (info, 3, m_list, NULL), FALSE, FALSE, 20);
 
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label("To determine the existence, or the absence, of a chemical bond", -1, -1, 0.5, 0.5), FALSE, FALSE, 0);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label("between 2 atoms is a key feature in the <b>atomes</b> software", -1, -1, 0.5, 0.5), FALSE, FALSE, 0);
  GtkWidget * vvbox = create_vbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, vvbox, FALSE, FALSE, 10);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vvbox, markup_label("It is used for analysis purposes, and, to draw bonds in the OpenGL window.", -1, -1, 0.5, 0.5), FALSE, FALSE, 0);
  edit_bonds (vbox);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label("You can adapt below the distance cutoffs:", -1, -1, 0.5, 0.5), FALSE, FALSE, 5);
 
  hbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 5);
  GtkWidget * hhbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, hhbox, FALSE, FALSE, 40);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hhbox, markup_label("<b>Total cutoff</b>", 120, -1, 0.0, 0.5), FALSE, FALSE, 0);
  GtkWidget * combo = create_combo();
  combo_text_append (combo, "Evaluated by <b>atomes</b>");
  combo_text_append (combo, "User defined <sup>*</sup>");
  combo_set_markup (combo);
  gtk_widget_set_size_request (combo, 180, -1);
  combo_set_active (combo, (tmp_totcut == 0.0) ? 0 : 1);
  g_signal_connect(G_OBJECT(combo), "changed", G_CALLBACK(totcut_changed), NULL);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hhbox, combo, FALSE, FALSE, 10);
 
  tcut_box = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hhbox, tcut_box, FALSE, FALSE, 10);
  tcut_entry = create_entry (G_CALLBACK(set_default_num_delta), 100, 10, FALSE, GINT_TO_POINTER(-1));
  update_entry_double ((GtkEntry *)tcut_entry, tmp_totcut);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, tcut_box, tcut_entry, FALSE, FALSE, 0);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, tcut_box, markup_label ("&#xC5;", -1, -1, 0.0, 0.5), FALSE, FALSE, 5);
 
  hbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 0);
  hhbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, hhbox, FALSE, FALSE, 40);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hhbox, markup_label("<b>Partial cutoff(s)</b>", 120, -1, 0.0, 0.5), FALSE, FALSE, 0);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hhbox, create_button ("Set default cutoff(s)", IMG_NONE, NULL, 180, -1, GTK_RELIEF_NORMAL, G_CALLBACK(set_cutoffs_default), NULL), FALSE, FALSE, 10);
 
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label(" ", -1, 20, 0.0, 0.0), FALSE, FALSE, 0);
  append_comments (vbox, "<sup>*</sup>", "The highest this value is, the highest the number of neighbors around an atom.");
 
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), vbox, gtk_label_new ("General"));
 
  GtkWidget * entry;
  vbox = create_vbox (BSEP);
  int i;
  for (i=0; i<8; i++)
  {
    if (i == 7)
    {
      hbox = create_hbox (BSEP);
      add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label ("<b>Mean Squared Displacement</b>:", 310, -1, 0.0, 0.5), FALSE, FALSE, 15);
      add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 5);
    }
    hbox = create_hbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label (default_delta_num_leg[i], (i ==7) ? 285 : 310, -1, 0.0, 0.5), FALSE, FALSE, (i == 7) ? 30 : 15);
    entry = create_entry (G_CALLBACK(set_default_num_delta), 110, 10, FALSE, GINT_TO_POINTER(i));
    update_entry_int ((GtkEntry *)entry, tmp_num_delta[i]);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, entry, FALSE, FALSE, 0);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 5);
  }
  hbox = create_hbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label ("time step(s) &#x3b4;t", 285, -1, 0.0, 0.5), FALSE, FALSE, 30);
  entry = create_entry (G_CALLBACK(set_default_num_delta), 110, 10, FALSE, GINT_TO_POINTER(i));
  update_entry_double ((GtkEntry *)entry, tmp_delta_t[0]);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, entry, FALSE, FALSE, 0);
  GtkWidget * tcombo = create_combo ();
  for (i=0; i<5 ; i++) combo_text_append (tcombo, untime[i]);
 
  combo_set_active (tcombo, (int)tmp_delta_t[1]);
  g_signal_connect(G_OBJECT(tcombo), "changed", G_CALLBACK(tunit_changed), NULL);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, tcombo, FALSE, FALSE, 0);
 
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 5);
 
  gtk_notebook_append_page (GTK_NOTEBOOK(notebook), vbox, gtk_label_new ("Calculations"));
 
  for (i=0; i<2; i++)
  {
    vbox = create_vbox (BSEP);
    search_type = i;
    calc_rings (vbox);
    gtk_notebook_append_page (GTK_NOTEBOOK(notebook), vbox, gtk_label_new ((i) ? "Chains" : "Rings"));
  }
  show_the_widgets (notebook);
  return notebook;
}
 
void clean_all_tmp ()
{
  if (tmp_num_delta)
  {
    g_free (tmp_num_delta);
    tmp_num_delta = NULL;
  }
  if (tmp_delta_t)
  {
    g_free (tmp_delta_t);
    tmp_delta_t = NULL;
  }
  if (tmp_rsparam)
  {
    g_free (tmp_rsparam);
    tmp_rsparam = NULL;
  }
  if (tmp_csparam)
  {
    g_free (tmp_csparam);
    tmp_csparam = NULL;
  }
  if (tmp_opengl)
  {
    g_free (tmp_opengl);
    tmp_opengl = NULL;
  }
  if (tmp_lightning.spot)
  {
    g_free (tmp_lightning.spot);
    tmp_lightning.spot = NULL;
  }
  if (tmp_o_at_rs)
  {
    g_free (tmp_o_at_rs);
    tmp_o_at_rs = NULL;
  }
  if (tmp_at_rs)
  {
    g_free (tmp_at_rs);
    tmp_at_rs = NULL;
  }
  if (tmp_o_bd_rw)
  {
    g_free (tmp_o_bd_rw);
    tmp_o_bd_rw = NULL;
  }
  if (tmp_bd_rw)
  {
    g_free (tmp_bd_rw);
    tmp_bd_rw = NULL;
  }
  int i;
  for (i=0; i<16; i++)
  {
    if (tmp_atomic_rad[i])
    {
      g_free (tmp_atomic_rad[i]);
      tmp_atomic_rad[i] = NULL;
    }
  }
  for (i=0; i<6; i++)
  {
    if (tmp_bond_rad[i])
    {
      g_free (tmp_bond_rad[i]);
      tmp_bond_rad[i] = NULL;
    }
  }
  for (i=0; i<2; i++)
  {
    if (tmp_atom_color[i])
    {
      g_free (tmp_atom_color[i]);
      tmp_atom_color[i] = NULL;
    }
    if (tmp_label_color[i])
    {
      g_free (tmp_label_color[i]);
      tmp_label_color[i] = NULL;
    }
  }
  for (i=0; i<5; i++)
  {
    if (tmp_label[i])
    {
      g_free (tmp_label[i]);
      tmp_label[i] = NULL;
    }
  }
  if (tmp_box)
  {
    g_free (tmp_box);
    tmp_box = NULL;
  }
  if (tmp_axis)
  {
    g_free (tmp_axis);
    tmp_axis = NULL;
  }
  if (tmp_rep)
  {
    g_free (tmp_rep);
    tmp_rep = NULL;
  }
}
 
void duplicate_rep_data (rep_data * new_rep, rep_data * old_rep)
{
  new_rep -> rep = old_rep -> rep;
  new_rep -> proj = old_rep -> proj;
  new_rep -> zoom = old_rep -> zoom;
  new_rep -> gnear = old_rep -> gnear;
  int i;
  for (i=0; i<2; i++)
  {
    new_rep -> c_angle[i] = old_rep -> c_angle[i];
    new_rep -> c_shift[i] = old_rep -> c_shift[i];
  }
}
 
void duplicate_background_data (background * new_back, background * old_back)
{
  new_back -> gradient = old_back -> gradient;
  new_back -> direction = old_back -> direction;
  new_back -> position = old_back -> position;
  new_back -> color = old_back -> color;
  int i;
  for (i=0; i<2; i++)
  {
    new_back -> gradient_color[i] = old_back -> gradient_color[i];
  }
}
 
void duplicate_box_data (box * new_box, box * old_box)
{
  new_box -> box = old_box -> box;
  new_box -> color = old_box -> color;
  new_box -> line = old_box -> line;
  new_box -> rad = old_box -> rad;
}
 
void duplicate_axis_data (axis * new_axis, axis * old_axis)
{
  new_axis -> axis = old_axis -> axis;
  new_axis -> length = old_axis -> length;
  new_axis -> color = old_axis -> color;
  new_axis -> line = old_axis -> line;
  new_axis -> rad = old_axis -> rad;
  new_axis -> t_pos = old_axis -> t_pos;
  new_axis -> labels = old_axis -> labels;
  int i;
  for (i=0; i<3; i++)
  {
    new_axis -> c_pos[i] = old_axis -> c_pos[i];
    if (old_axis -> title[i]) new_axis -> title[i] = g_strdup_printf ("%s", old_axis -> title[i]);
  }
  if (old_axis -> color)
  {
    new_axis -> color = duplicate_color (3, old_axis -> color);
  }
}
 
void prepare_tmp_default ()
{
  clean_all_tmp ();
  tmp_totcut = default_totcut;
  tmp_bond_cutoff = duplicate_cutoffs (default_bond_cutoff);
  tmp_num_delta = duplicate_int (8, default_num_delta);
  tmp_delta_t = duplicate_double (2, default_delta_t);
  tmp_rsparam = duplicate_int (7, default_rsparam);
  tmp_csparam = duplicate_int (7, default_csparam);
  tmp_opengl = duplicate_int (4, default_opengl);
  duplicate_material (& tmp_material, & default_material);
  tmp_lightning.lights = default_lightning.lights;
  tmp_lightning.spot = copy_light_sources (tmp_lightning.lights, tmp_lightning.lights, default_lightning.spot);
  duplicate_fog (& tmp_fog, & default_fog);
  tmp_clones = default_clones;
  tmp_cell = default_cell;
  tmp_o_at_rs = duplicate_bool (10, default_o_at_rs);
  tmp_at_rs = duplicate_double (10, default_at_rs);
  tmp_o_bd_rw = duplicate_bool (6, default_o_bd_rw);
  tmp_bd_rw = duplicate_double (6, default_bd_rw);
  int i;
  for (i=0; i<16; i++)tmp_atomic_rad[i] = duplicate_element_radius (default_atomic_rad[i]);
  for (i=0; i<6; i++) tmp_bond_rad[i] = duplicate_element_radius (default_bond_rad[i]);
  for (i=0; i<2; i++)
  {
    tmp_atom_color[i] = duplicate_element_color (default_atom_color[i]);
    tmp_label_color[i] = duplicate_element_color (default_label_color[i]);
  }
  for (i=0; i<5; i++)
  {
    tmp_label[i] = g_malloc(sizeof*tmp_label[i]);
    duplicate_screen_label (tmp_label[i], & default_label[i]);
  }
  for (i=0; i<2; i++)
  {
    tmp_acl_format[i] = default_acl_format[i];
    tmp_mtilt[i] = default_mtilt[i];
    tmp_mpattern[i] = default_mpattern[i];
    tmp_mfactor[i] = default_mfactor[i];
    tmp_mwidth[i] = default_mwidth[i];
  }
 
  tmp_box = g_malloc0(sizeof*tmp_box);
  duplicate_box_data (tmp_box, & default_box);
 
  tmp_background = g_malloc0(sizeof*tmp_background);
  duplicate_background_data (tmp_background, & default_background);
 
  tmp_rep = g_malloc0(sizeof*tmp_rep);
  duplicate_rep_data (tmp_rep, & default_rep);
 
  tmp_axis = g_malloc0(sizeof*tmp_axis);
  duplicate_axis_data (tmp_axis, & default_axis);
 
  for (i=0; i<2; i++) tmp_sel_color[i] = default_sel_color[i];
}
 
gboolean * up_project;
 
G_MODULE_EXPORT void update_projects (GtkDialog * proj_sel, gint response_id, gpointer data)
{
  int i;
  switch (response_id)
  {
    case GTK_RESPONSE_OK:
      // To write apply to opened projects
      for (i=0; i<nprojects; i++)
      {
        if (up_project[i]) apply_default_parameters_to_project (get_project_by_id(i));
      }
      break;
    default:
      break;
  }
  g_free (up_project);
  up_project = NULL;
  destroy_this_dialog (proj_sel);
}
 
#ifdef GTK4
G_MODULE_EXPORT void toggled_select_project (GtkCheckButton * but, gpointer data)
#else
G_MODULE_EXPORT void toggled_select_project (GtkToggleButton * but, gpointer data)
#endif
{
  up_project[GPOINTER_TO_INT(data)] = button_get_status ((GtkWidget *)but);
}
 
void save_preferences ()
{
  default_totcut = tmp_totcut;
  if (default_bond_cutoff)
  {
    g_free (default_bond_cutoff);
    default_bond_cutoff = NULL;
  }
  default_bond_cutoff = duplicate_cutoffs (tmp_bond_cutoff);
  if (default_num_delta)
  {
    g_free (default_num_delta);
    default_num_delta = NULL;
  }
  default_num_delta = duplicate_int (8, tmp_num_delta);
  default_delta_t = duplicate_double (2, tmp_delta_t);
  if (default_rsparam)
  {
    g_free (default_rsparam);
    default_rsparam = NULL;
  }
  default_rsparam = duplicate_int (7, tmp_rsparam);
  if (default_csparam)
  {
    g_free (default_csparam);
    default_csparam = NULL;
  }
  default_csparam = duplicate_int (7, tmp_csparam);
  if (default_opengl)
  {
    g_free (default_opengl);
    default_opengl = NULL;
  }
  default_opengl = duplicate_int (4, tmp_opengl);
  duplicate_material (& default_material, & tmp_material);
  default_lightning.lights = tmp_lightning.lights;
  default_lightning.spot = copy_light_sources (tmp_lightning.lights, tmp_lightning.lights, tmp_lightning.spot);
  duplicate_fog (& default_fog, & tmp_fog);
 
  // Model
  default_clones = tmp_clones;
  default_cell = tmp_cell;
  if (default_o_at_rs)
  {
    g_free (default_o_at_rs);
    default_o_at_rs = NULL;
  }
  default_o_at_rs = duplicate_bool (10, tmp_o_at_rs);
  if (default_at_rs)
  {
    g_free (default_at_rs);
    default_at_rs = NULL;
  }
  default_at_rs = duplicate_double (10, tmp_at_rs);
  if (default_o_bd_rw)
  {
    g_free (default_o_bd_rw);
    default_o_bd_rw = NULL;
  }
  default_o_bd_rw = duplicate_bool (6, tmp_o_bd_rw);
  if (default_bd_rw)
  {
    g_free (default_bd_rw);
    default_bd_rw = NULL;
  }
  default_bd_rw = duplicate_double (6, tmp_bd_rw);
  int i;
  for (i=0; i<16; i++)
  {
    if (default_atomic_rad[i]) g_free (default_atomic_rad[i]);
    default_atomic_rad[i] = duplicate_element_radius (tmp_atomic_rad[i]);
  }
  for (i=0; i<6; i++)
  {
    if (default_bond_rad[i]) g_free (default_bond_rad[i]);
    default_bond_rad[i] = duplicate_element_radius (tmp_bond_rad[i]);
  }
  for (i=0; i<2; i++)
  {
    if (default_atom_color[i]) g_free (default_atom_color[i]);
    default_atom_color[i] = duplicate_element_color (tmp_atom_color[i]);
    if (default_label_color[i]) g_free (default_label_color[i]);
    default_label_color[i] = duplicate_element_color (tmp_label_color[i]);
  }
  for (i=0; i<5; i++)
  {
    duplicate_screen_label (& default_label[i], tmp_label[i]);
  }
  for (i=0; i<2; i++)
  {
    default_acl_format[i] = tmp_acl_format[i];
    default_mtilt[i] = tmp_mtilt[i];
    default_mpattern[i] = tmp_mpattern[i];
    default_mfactor[i] = tmp_mfactor[i];
    default_mwidth[i] = tmp_mwidth[i];
  }
  duplicate_rep_data (& default_rep, tmp_rep);
  duplicate_background_data (& default_background, tmp_background);
  duplicate_box_data (& default_box, tmp_box);
  duplicate_axis_data (& default_axis, tmp_axis);
 
  for (i=0; i<2; i++) default_sel_color[i] = tmp_sel_color[i];
 
  if (nprojects)
  {
    if (ask_yes_no("Apply to projet(s) in workspace ?", "Preferences were saved for the active session !\n Do you want to apply preferences to the project(s) opened in the workspace ?", GTK_MESSAGE_QUESTION, pref_ogl_edit -> win))
    {
     // Select project here
     GtkWidget * proj_sel = message_dialogmodal ("Project selection", "Select to apply preferences", GTK_MESSAGE_QUESTION, GTK_BUTTONS_OK, MainWindow);
     GtkWidget * vbox = dialog_get_content_area (proj_sel);
     GtkWidget * hbox;
     up_project = allocbool (nprojects);
     for (i=0; i<nprojects; i++)
     {
       hbox = create_hbox (BSEP);
       add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 0);
       add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, check_button (get_project_by_id(i) -> name, 200, -1, FALSE, G_CALLBACK(toggled_select_project), GINT_TO_POINTER(i)), FALSE, FALSE, 40);
     }
     run_this_gtk_dialog (proj_sel, G_CALLBACK(update_projects), NULL);
    }
  }
}
 
void adjust_preferences_window ()
{
  int i;
  if (tmp_totcut == 0.0)
  {
    hide_the_widgets (tcut_box);
  }
  else
  {
    show_the_widgets (tcut_box);
  }
  update_entry_double ((GtkEntry *)tcut_entry, tmp_totcut);
  update_light_data (0, pref_ogl_edit);
  setup_fog_dialogs (pref_ogl_edit, tmp_fog.mode);
  if (tmp_box -> box > NONE)
  {
    hide_the_widgets ((tmp_box -> box == WIREFRAME) ? pref_box_win -> radius_box : pref_box_win -> width_box);
  }
  hide_the_widgets ((tmp_axis -> axis == WIREFRAME) ? pref_axis_win -> radius_box : pref_axis_win -> width_box);
  for (i=0; i<2; i++) widget_set_sensitive (pref_axis_win -> axis_label_box[i], tmp_axis -> labels);
  update_gradient_widgets (pref_gradient_win, tmp_background);
  i = combo_get_active (meas_combo);
  i = (i < 0) ? 0 : i;
  hide_the_widgets (meas_box[! i]);
  show_the_widgets (meas_box[i]);
  i = combo_get_active (sel_combo);
  i = (i < 0) ? 0 : i;
  hide_the_widgets (sel_box[! i]);
  show_the_widgets (sel_box[i]);
}
 
G_MODULE_EXPORT void restore_defaults_parameters (GtkButton * but, gpointer data)
{
 
  if (ask_yes_no("Restore default parameters", "Are you sure ?", GTK_MESSAGE_QUESTION, MainWindow))
  {
    set_atomes_defaults ();
    prepare_tmp_default ();
    int i;
    for (i=4; i>0; i--)
    {
      destroy_this_widget (gtk_notebook_get_nth_page (GTK_NOTEBOOK (preference_notebook), i));
    }
    gtk_notebook_append_page (GTK_NOTEBOOK(preference_notebook), calc_preferences(), gtk_label_new ("Analysis"));
    gtk_notebook_append_page (GTK_NOTEBOOK(preference_notebook), opengl_preferences(), gtk_label_new ("OpenGL"));
    gtk_notebook_append_page (GTK_NOTEBOOK(preference_notebook), model_preferences(), gtk_label_new ("Model"));
    gtk_notebook_append_page (GTK_NOTEBOOK(preference_notebook), view_preferences(), gtk_label_new ("View"));
    gtk_notebook_set_current_page (GTK_NOTEBOOK(preference_notebook), 0);
    show_the_widgets (preference_notebook);
    adjust_preferences_window ();
  }
}
 
G_MODULE_EXPORT void edit_preferences (GtkDialog * edit_prefs, gint response_id, gpointer data)
{
  switch (response_id)
  {
    case GTK_RESPONSE_APPLY:
      if (ask_yes_no("Save parameters", "Are you sure ?", GTK_MESSAGE_QUESTION, MainWindow))
      {
        save_preferences ();
        gchar * str = g_strdup_printf ("Do you want to save <b>atomes</b> preferences in:\n\n\t%s\n\nIf found this file is processed at every <b>atomes</b> startup.\n\n\t\t\t\t\t\tSave file ?", ATOMES_CONFIG);
        if (ask_yes_no("Save atomes preferences to file ?", str, GTK_MESSAGE_QUESTION, (GtkWidget *)edit_prefs))
        {
          if (! save_preferences_to_xml_file ())
          {
            show_error ((pref_error) ? pref_error : "Error while trying to save preferences to file", 0, MainWindow);
            g_free (pref_error);
            pref_error = NULL;
          }
        }
        g_free (str);
      }
      break;
    default:
      destroy_this_dialog (edit_prefs);
      preferences = FALSE;
      clean_all_tmp ();
      g_free (pref_pointer);
      pref_pointer = NULL;
      if (pref_box_win) g_free (pref_box_win);
      pref_box_win = NULL;
      if (pref_rep_win) g_free (pref_rep_win);
      pref_rep_win = NULL;
      if (pref_axis_win) g_free (pref_axis_win);
      pref_axis_win = NULL;
      if (pref_gradient_win) g_free (pref_gradient_win);
      pref_gradient_win = NULL;
      preference_notebook = NULL;
      break;
  }
}
 
void create_user_preferences_dialog ()
{
  GtkWidget * win = dialog_cancel_apply ("User preferences", MainWindow, TRUE);
  preferences = TRUE;
  prepare_tmp_default ();
  GtkWidget * vbox = dialog_get_content_area (win);
  gtk_widget_set_size_request (win, 625, 645);
  gtk_window_set_resizable (GTK_WINDOW (win), FALSE);
  preference_notebook = gtk_notebook_new ();
  gtk_notebook_set_scrollable (GTK_NOTEBOOK(preference_notebook), TRUE);
  gtk_notebook_set_tab_pos (GTK_NOTEBOOK(preference_notebook), GTK_POS_LEFT);
  gtk_widget_set_size_request (preference_notebook, 600, 635);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, preference_notebook, FALSE, FALSE, 0);
 
  GtkWidget * gbox = create_vbox (BSEP);
  gchar * mess[2] = {"Browse the following to modify the default configuration of <b>atomes</b>",
                     "by replacing internal parameters by user defined preferences."};
  gchar * mlist[4][2]= {{"Analysis", "calculation preferences"},
                        {"OpenGL", "rendering preferences"},
                        {"Model", "atom(s), bond(s) and box preferences"},
                        {"View", "representation and projection preferences"}};
  gchar * end = "Default parameters are used for any new project added to the workspace\n";
 
  pref_pointer = g_malloc0(NUM_COLORS*sizeof*pref_pointer);
  int i;
  for (i=0; i<NUM_COLORS; i++)
  {
    pref_pointer[i].a = -1;
    pref_pointer[i].b = i;
    pref_pointer[i].c = -1;
  }
 
  add_box_child_start (GTK_ORIENTATION_VERTICAL, gbox, pref_list(mess, 4, mlist, end), FALSE, FALSE, 20);
 
  GtkWidget * hbox = create_hbox (BSEP);
  GtkWidget * but = create_button (NULL, IMG_NONE, NULL, -1, -1, GTK_RELIEF_NORMAL, G_CALLBACK(restore_defaults_parameters), NULL);
  GtkWidget * but_lab = markup_label ("Restore <b>atomes</b> default parameters", -1, -1, 0.5, 0.5);
  add_container_child (CONTAINER_BUT, but, but_lab);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, but, FALSE, FALSE, 150);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, gbox, hbox, FALSE, FALSE, 0);
  gtk_notebook_append_page (GTK_NOTEBOOK(preference_notebook), gbox, gtk_label_new ("General"));
 
  gtk_notebook_append_page (GTK_NOTEBOOK(preference_notebook), calc_preferences(), gtk_label_new ("Analysis"));
  gtk_notebook_append_page (GTK_NOTEBOOK(preference_notebook), opengl_preferences(), gtk_label_new ("OpenGL"));
  gtk_notebook_append_page (GTK_NOTEBOOK(preference_notebook), model_preferences(), gtk_label_new ("Model"));
  gtk_notebook_append_page (GTK_NOTEBOOK(preference_notebook), view_preferences(), gtk_label_new ("View"));
  show_the_widgets (preference_notebook);
  gtk_notebook_set_current_page (GTK_NOTEBOOK(preference_notebook), 0);
  run_this_gtk_dialog (win, G_CALLBACK(edit_preferences), NULL);
}
 
G_MODULE_EXPORT void set_default_options (GtkButton * but, gpointer data)
{
  tint * oid = (tint *)data;
  gchar * pstring[5]={"rendering", "box", "axis", "backgorund", "representation"};
  gchar * str = g_strdup_printf ("Set %s preferences as default preferences ?", pstring[oid -> b]);
  project * this_proj = get_project_by_id(oid -> a);
  if (ask_yes_no("Set model preferences as default ?", str, GTK_MESSAGE_QUESTION, this_proj -> modelgl -> win))
  {
    g_free (str);
    image * img = this_proj -> modelgl -> anim -> last -> img;
    switch (oid -> b)
    {
      case 0:
        // OpenGL preferences, style and color mpas not included : rendering only
        default_opengl[3] = img -> quality;
        duplicate_material (& default_material, & img -> m_terial);
        default_lightning.lights = img -> l_ghtning.lights;
        default_lightning.spot = copy_light_sources (img -> l_ghtning.lights, img -> l_ghtning.lights, img ->  l_ghtning.spot);
        duplicate_fog (& default_fog, & img -> f_g);
        break;
      case 1:
        // Box
        duplicate_box_data (& default_box, img -> abc);
        break;
      case 2:
        // Axis
        duplicate_axis_data (& default_axis, img -> xyz);
        break;
      case 3:
        // Background
        duplicate_background_data (& default_background, img -> back);
        break;
      case 4:
        // Representation
        default_rep.rep = img -> rep;
        default_rep.zoom =  img -> zoom;
        default_rep.gnear = img -> gnear;
        int i;
        for (i=0; i<2; i++)
        {
          default_rep.c_angle[i] = img -> c_angle[i];
          default_rep.c_shift[i] = img -> c_shift[i];
        }
        break;
    }
    str = g_strdup_printf ("Do you want to save <b>atomes</b> preferences in:\n\n\t%s\n\nIf found this file is processed at every <b>atomes</b> startup.\n\n\t\t\t\t\t\tSave file ?", ATOMES_CONFIG);
    if (ask_yes_no("Save atomes preferences to file ?", str, GTK_MESSAGE_QUESTION, this_proj -> modelgl -> win))
    {
      if (! save_preferences_to_xml_file ())
      {
        show_error ((pref_error) ? pref_error : "Error while trying to save preferences to file", 0, MainWindow);
        g_free (pref_error);
        pref_error = NULL;
      }
    }
    g_free (str);
  }
  else
  {
    g_free (str);
  }
}
 
void add_global_option (GtkWidget * vbox, tint * oid)
{
  GtkWidget * hbox = create_hbox (5);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, TRUE, FALSE, 0);
  GtkWidget * but = create_button ("Set default", IMG_NONE, NULL, -1, -1, GTK_RELIEF_NORMAL, G_CALLBACK(set_default_options), oid);
  add_box_child_end (hbox, but, FALSE, FALSE, 0);
}