cpmd_nose.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: 'cpmd_nose.c'
*
* Contains:
*
 
 - The functions to prepare the thermostat(s) configuration widgets for QM / QM-MM input files
 
*
* List of functions:
 
  int get_num_thermo ();
  int is_not_thermostated (int at, int therm);
  int is_fixed_atom (int at);
  int in_dummy (int at, int id);
 
  gboolean are_all_atoms_thermostated ();
  gboolean was_it_selected (int id, int at);
 
  void set_going_forward ();
  void clean_nose_widgets ();
  void thermo_set_color (GtkTreeViewColumn * col, GtkCellRenderer * renderer, GtkTreeModel * mod, GtkTreeIter * iter, gpointer data);
  void thermo_set_visible (GtkTreeViewColumn * col, GtkCellRenderer * renderer, GtkTreeModel * mod, GtkTreeIter * iter, gpointer data);
  void remove_nose_thermostat (int num_to_remove);
  void init_thermostats (int type, int elec);
  void clean_thermostat (int new_type);
  void nose_parameters (GtkWidget * vbox, int id, int jd, gchar ** la, gchar ** lb);
  void atom_set_color (GtkTreeViewColumn * col, GtkCellRenderer * renderer, GtkTreeModel * mod, GtkTreeIter * iter, gpointer data);
  void atom_set_visible (GtkTreeViewColumn * col, GtkCellRenderer * renderer, GtkTreeModel * mod, GtkTreeIter * iter, gpointer data);
  void fill_thermo_atom_model (int therm);
  void select_atom_from_model (int therm);
  void create_selection_button (GtkWidget * box, int num, int id, gpointer data);
  void create_nose_thermo_param_box (int therm_id);
  void create_selection_combo (int id, int num, int type, GCallback handler);
  void add_thermostat (int extra);
  void prepare_therm_ions ();
  void prepare_therm_elec ();
  void thermo_type_box (GtkWidget * vbox, gchar * str, int id);
 
  G_MODULE_EXPORT void select_thermo (GtkCellRendererToggle * cell_renderer, gchar * string_path, gpointer data);
  G_MODULE_EXPORT void run_remove_nose_thermostat (GtkDialog * dialog, gint response_id, gpointer data);
  G_MODULE_EXPORT void cpmd_select_atom_id (GtkCellRendererToggle * cell_renderer, gchar * string_path, gpointer data);
  G_MODULE_EXPORT void cp2k_select_coord_id (GtkCellRendererToggle * cell_renderer, gchar * string_path, gpointer data);
  G_MODULE_EXPORT void select_atoms_not_thermostated (GtkCheckButton * but, gpointer data);
  G_MODULE_EXPORT void select_atoms_not_thermostated (GtkToggleButton * but, gpointer data);
  G_MODULE_EXPORT void run_select_atom_from_model (GtkDialog * dialog, gint response_id, gpointer data);
  G_MODULE_EXPORT void atom_selection_button (GtkButton * but, gpointer data);
  G_MODULE_EXPORT void changed_nose_thermo_id_box (GtkComboBox * box, gpointer data);
  G_MODULE_EXPORT void add_or_remove_thermostat (GtkSpinButton * res, gpointer data);
  G_MODULE_EXPORT void update_thermo_parameter (GtkEntry * res, gpointer data);
  G_MODULE_EXPORT void changed_thermo_box_nose (GtkComboBox * box, gpointer data);
  G_MODULE_EXPORT void changed_thermo_box (GtkComboBox * box, gpointer data);
 
  GtkWidget * create_nose_box (int n);
  GtkWidget * thermo_box ();
 
  thermostat * get_thermo ();
  thermostat * get_active_thermostat (int id);
  thermostat * init_thermo (int id, int type, int sys);
 
*/
 
#include "global.h"
#include "interface.h"
#include "glview.h"
#include "calc.h"
#include "cpmd.h"
#include "cp2k.h"
 
extern void print_the_section (int s, int p, GtkTextBuffer * buffer);
extern ColRGBA init_color (int id, int numid);
extern void proj_unselect_all_atoms ();
extern GtkWidget * cpmd_box (GtkWidget * box, gchar * lab, int v_space, int h_space, int dim);
extern dummy_atom * get_active_dummy (int id);
extern void create_dummy_param_box (int dummy_id);
 
char * c_thermo[2][CP2NTHERM][4] = {{{"Initial temperature: ", " ", " ", " "},
                                     {"Target temperature: ","Tolerance: ", " ", " "},
                                     {"Target temperature: ", "Target frequency: ", " ", " "},
                                     {" ", " ", " ", " "},
                                     {" ", " ", " ", " "}},
                                    {{" ", " ", " ", " "},
                                     {"Time constant (Langevin): ", "Time constant (Nosë-Hoover): ", "Mass: ", "Chi: "},
                                     {"Time constant: ", " ", " ", " "},
                                     {" ", " ", " ", " "},
                                     {"Length: ", "Multiple time steps: ", "Time constant: ", "Yoshida integrator: "}}};
 
char * u_thermo[2][CP2NTHERM][4] = {{{" K", " ", " ", " "},
                                     {" K", " K", " ", " "},
                                     {" K", " cm<sup>-1</sup>", " ", " "},
                                     {" ", " ", " ", " "},
                                     {" ", " ", " ", " "}},
                                    {{" ", " ", " ", " "},
                                     {" fs", " fs", " fs<sup>-1</sup>", " fs<sup>-1</sup>"},
                                     {" fs", " ", " ", " "},
                                     {" ", " ", " ", " "},
                                     {" ", " ", " fs", " "}}};
 
char * ue_thermo[CP2NTHERM][4] = {{" a.u.", " ", " ", " "},
                                  {" a.u.", " ", " ", " "},
                                  {" a.u.", " a.u.", " ", " "},
                                  {" a.u.", " cm<sup>-1</sup>", " ", " "}};
 
int v_thermo[2][CP2NTHERM] = {{1, 2, 2, 0, 0}, {0, 4, 1, 0, 4}};
 
double d_thermo[2][CP2NTHERM][4] = {{{ 300.0, 0.0, 0.0, 0.0},
                                     { 300.0, 20.0, 0.0, 0.0},
                                     { 300.0, 200.0, 0.0, 0.0},
                                     { 0.0, 0.0, 0.0, 0.0},
                                     { 0.0, 0.0, 0.0, 0.0}},
                                    {{ 0.0, 0.0, 0.0, 0.0},
                                     { 100.0, 100.0, 1.0, 1.0},
                                     { 100.0, 0.0, 0.0, 0.0},
                                     { 0.0, 0.0, 0.0, 0.0},
                                     { 3.0, 2.0, 1000.0, 3.0}}};
GtkWidget * sel_but[3];
GtkWidget * sel_img[3];
GtkWidget * electron_box;
GtkWidget * therm_ions;
GtkWidget * therm_elec;
GtkWidget * therm_param_ions;
GtkWidget * therm_param_elec;
GtkWidget * nose_box;
GtkWidget * combo_id[2];
GtkWidget * combo_id_box[2];
GtkWidget * nose_id_box[2];
GtkCellRenderer * thermo_renderer[6];
GtkTreeViewColumn * thermo_col[6];
int n_therm;
int at_col;
int * old_thermo;
int ** old_fixed;
int num_cpmd_objects;
int the_therm;
gboolean fixco;
GtkTreeStore * add_model;
 
thermostat * get_thermo ()
{
  if (is_cpmd)
  {
    return tmp_cpmd -> ions_thermostat;
  }
  else
  {
    return tmp_cp2k -> ions_thermostat;
  }
}
 
int get_num_thermo ()
{
  if (is_cpmd)
  {
    return tmp_cpmd -> thermostats;
  }
  else
  {
    return tmp_cp2k -> thermostats;
  }
}
 
gboolean are_all_atoms_thermostated ()
{
  int i, j;
  thermostat * thermo = get_thermo();
  j = 0;
  if (thermo -> sys < LOCAL) return TRUE;
  for (i=0; i<get_num_thermo(); i++)
  {
    j += thermo -> natoms;
    if (thermo -> next != NULL) thermo = thermo -> next;
  }
  if (j == qm_proj -> natomes)
  {
    return TRUE;
  }
  else
  {
    return FALSE;
  }
}
 
void set_going_forward ()
{
  GtkAssistant * assist = GTK_ASSISTANT(qm_assistant);
  GtkWidget * page = gtk_assistant_get_nth_page (assist, (is_cpmd) ? 3 : 5);
  gtk_assistant_set_page_complete (assist, page, are_all_atoms_thermostated ());
}
 
void clean_nose_widgets ()
{
  combo_id_box[0] = destroy_this_widget (combo_id_box[0]);
  combo_id[0] = destroy_this_widget (combo_id[0]);
  nose_id_box[1] = destroy_this_widget (nose_id_box[1]);
  nose_id_box[0] = destroy_this_widget (nose_id_box[0]);
  nose_box = destroy_this_widget (nose_box);
}
 
thermostat * get_active_thermostat (int id)
{
  if (id < 0)
  {
    return tmp_cpmd -> elec_thermostat;
  }
  else
  {
    thermostat * thermo = get_thermo ();
    while (thermo -> id != id)
    {
      if (thermo -> next != NULL) thermo = thermo -> next;
    }
    return thermo;
  }
}
 
G_MODULE_EXPORT void select_thermo (GtkCellRendererToggle * cell_renderer, gchar * string_path, gpointer data)
{
  GtkTreeStore ** model = (GtkTreeStore **)data;
  GtkTreeIter iter;
  GtkTreePath * path = gtk_tree_path_new_from_string (string_path);
  gtk_tree_model_get_iter (GTK_TREE_MODEL(* model), & iter, path);
  if (gtk_cell_renderer_toggle_get_active(cell_renderer))
  {
    get_active_thermostat (old_thermo[n_therm-1]) -> show = FALSE;
    old_thermo[n_therm-1] = -1;
    n_therm --;
    gtk_tree_store_set (* model, & iter, 5, 0, -1);
    //toviz.c = 0;
  }
  else
  {
    n_therm ++;
    gtk_tree_store_set (* model, & iter, 5, 1, -1);
    gtk_tree_model_get (GTK_TREE_MODEL(* model), & iter, 0, & old_thermo[n_therm-1], -1);
    old_thermo[n_therm-1] --;
    get_active_thermostat (old_thermo[n_therm-1]) -> show = TRUE;
    //toviz.c = 1;
  }
  // Viz
}
 
void thermo_set_color (GtkTreeViewColumn * col, GtkCellRenderer * renderer, GtkTreeModel * mod, GtkTreeIter * iter, gpointer data)
{
  int i, j;
  gtk_tree_model_get (mod, iter, 0, & i, -1);
  i = abs(i);
  gtk_tree_model_get (mod, iter, 5, & j, -1);
  set_renderer_color (j, renderer, init_color (i-1, num_cpmd_objects));
}
 
void thermo_set_visible (GtkTreeViewColumn * col, GtkCellRenderer * renderer, GtkTreeModel * mod, GtkTreeIter * iter, gpointer data)
{
  int i, j;
  i = GPOINTER_TO_INT(data);
  gtk_tree_model_get (mod, iter, 0, & j, -1);
  if (j > 0 && i != 4)
  {
    gtk_cell_renderer_set_visible (renderer, TRUE);
    if (i < 5) thermo_set_color (col, renderer, mod, iter, data);
  }
  else if (j > 0)
  {
    gtk_cell_renderer_set_visible (renderer, FALSE);
  }
  else if (i == 4)
  {
    gtk_cell_renderer_set_visible (renderer, TRUE);
    thermo_set_color (col, renderer, mod, iter, data);
  }
  else
  {
    gtk_cell_renderer_set_visible (renderer, FALSE);
  }
}
 
GtkWidget * create_nose_box (int n);
 
G_MODULE_EXPORT void run_remove_nose_thermostat (GtkDialog * dialog, gint response_id, gpointer data)
{
  int i, j;
  int num_to_remove = GPOINTER_TO_INT(data);
  gboolean done = FALSE;
  gchar * str;
  thermostat * thermo;
  switch (response_id)
  {
    case GTK_RESPONSE_APPLY:
      if (n_therm == num_to_remove)
      {
        done = TRUE;
        // Now we remove all selected thermostats:
        for (i=0; i<n_therm; i++)
        {
          thermo = get_thermo();
          for (j=0; j<get_num_thermo(); j++)
          {
            if (thermo -> id == old_thermo[i])
            {
              if (thermo -> next != NULL)
              {
                if (thermo -> prev != NULL)
                {
                  thermo -> next -> prev = thermo -> prev;
                  thermo -> prev -> next = thermo -> next;
                }
                else
                {
                  tmp_cpmd -> ions_thermostat = thermo -> next;
                  tmp_cpmd -> ions_thermostat -> prev = NULL;
                }
              }
              else
              {
                thermo -> prev -> next = NULL;
              }
              g_free (thermo);
              break;
            }
            if (thermo -> next != NULL) thermo = thermo -> next;
          }
        }
        if (is_cpmd)
        {
          tmp_cpmd -> thermostats -= num_to_remove;
        }
        else
        {
          tmp_cp2k -> thermostats -= num_to_remove;
        }
        thermo = get_thermo();
        for (j=0; j<get_num_thermo(); j++)
        {
          thermo -> id = j;
          if (thermo -> next != NULL) thermo = thermo -> next;
        }
        clean_nose_widgets ();
        nose_box = create_nose_box (get_thermo() ->  type);
        add_box_child_start (GTK_ORIENTATION_VERTICAL, therm_param_ions, nose_box, FALSE, FALSE, 0);
        //int j;
        //for (j=1; j<4; j++) print_the_section (j, 0, qmbuffer[j]););
        show_the_widgets (therm_param_ions);
      }
      else
      {
        str = g_strdup_printf ("You must select %d thermostat(s) to be deleted !", num_to_remove);
        show_warning (str, qm_assistant);
        g_free (str);
      }
      break;
    default:
      done = TRUE;
      break;
  }
  if (done) destroy_this_dialog (dialog);
}
 
void remove_nose_thermostat (int num_to_remove)
{
  int i, j, k;
  gchar * str;
  // int cpmd_object = 0;
  str = g_strdup_printf ("Select the %d thermostat(s) to be removed", num_to_remove);
  GtkWidget * rthermo = dialogmodal (str, GTK_WINDOW(qm_assistant));
  g_free (str);
  gtk_dialog_add_button (GTK_DIALOG(rthermo), "Apply", GTK_RESPONSE_APPLY);
 
  gchar * mol_title[6] = {"Id", "Target T°", "Frequency", "Atom(s)", "      ", "Select"};
  gchar * ctype[6] = {"text", "text", "text", "text", "text", "active"};
  GType col_type[6] = {G_TYPE_INT, G_TYPE_DOUBLE, G_TYPE_DOUBLE, G_TYPE_INT, G_TYPE_STRING, G_TYPE_BOOLEAN};
 
  GtkTreeIter thermo_level, atom_level;
  n_therm = 0;
  old_thermo = allocint(get_num_thermo());
  GtkTreeStore * remove_model = gtk_tree_store_newv (6, col_type);
  GtkWidget * remove_tree = gtk_tree_view_new_with_model(GTK_TREE_MODEL(remove_model));
  for (i=0; i<6; i++)
  {
    if (i < 5)
    {
      thermo_renderer[i] = gtk_cell_renderer_text_new ();
    }
    else
    {
      thermo_renderer[i] = gtk_cell_renderer_toggle_new ();
      gtk_cell_renderer_toggle_set_radio (GTK_CELL_RENDERER_TOGGLE(thermo_renderer[i]), TRUE);
      g_signal_connect (G_OBJECT(thermo_renderer[i]), "toggled", G_CALLBACK(select_thermo), & remove_model);
    }
    thermo_col[i] = gtk_tree_view_column_new_with_attributes (mol_title[i], thermo_renderer[i], ctype[i], i, NULL);
    gtk_tree_view_column_set_alignment (thermo_col[i], 0.5);
    gtk_tree_view_append_column (GTK_TREE_VIEW(remove_tree), thermo_col[i]);
    gtk_tree_view_column_set_cell_data_func (thermo_col[i], thermo_renderer[i], thermo_set_visible, GINT_TO_POINTER(i), NULL);
  }
  // fill model
  thermostat * thermo = get_thermo();
  for (i=0; i<get_num_thermo(); i++)
  {
    gtk_tree_store_append (remove_model, & thermo_level, NULL);
    gtk_tree_store_set (remove_model, & thermo_level, 0, i+1,
                                                      1, thermo -> params[0],
                                                      2, thermo -> params[1],
                                                      3, thermo -> natoms,
                                                      4, " ",
                                                      5, 0, -1);
    for (j=0; j<thermo -> natoms; j++)
    {
      gtk_tree_store_append (remove_model, & atom_level, & thermo_level);
      k = qm_proj -> atoms[0][thermo -> list[j]].sp;
      str = g_strdup_printf ("%s<sub>%d</sub>", exact_name(qm_proj -> chemistry -> label[k]), thermo -> list[j]+1);
      gtk_tree_store_set (remove_model, & atom_level, 0, -(i+1), 1, 0.0, 2, 0.0, 3, 0, 4, str, 5, 0, -1);
      g_free (str);
    }
    if (thermo -> next != NULL) thermo = thermo -> next;
  }
  num_cpmd_objects = get_num_thermo();
  g_object_unref (remove_model);
  i = ((num_cpmd_objects+1)*40 < 500) ? (num_cpmd_objects+1)*40 : 500;
  GtkWidget * scrollsets = create_scroll (dialog_get_content_area (rthermo), 450, i, GTK_SHADOW_ETCHED_IN);
  add_container_child (CONTAINER_SCR, scrollsets, remove_tree);
  run_this_gtk_dialog (rthermo, G_CALLBACK(run_remove_nose_thermostat), GINT_TO_POINTER(num_to_remove));
}
 
thermostat * init_thermo (int id, int type, int sys)
{
  thermostat * thermo = g_malloc0 (sizeof*thermo);
  thermo -> id = id;
  thermo -> type = type;
  thermo -> sys = sys;
  thermo -> show = FALSE;
  if (id < 0)
  {
    thermo -> params[0] = 0.5;
    thermo -> params[1] = (type == 0) ? 0.2: 200.0;
  }
  else
  {
    int i;
    for (i=0; i<v_thermo[!is_cpmd][type]; i++)
    {
      thermo -> params[i] = d_thermo[!is_cpmd][type][i];
    }
  }
  return thermo;
}
 
void init_thermostats (int type, int elec)
{
  //int i = (type == ULTRA) ? qm_proj -> nspec: 1;
  if (is_cpmd)
  {
    tmp_cpmd -> thermostats = 1;
    tmp_cpmd -> ions_thermostat = init_thermo (0, type, 0);
  }
  else
  {
    tmp_cp2k -> thermostats = 1;
    tmp_cp2k -> ions_thermostat = init_thermo (0, type, 0);
  }
  if (is_cpmd && elec) tmp_cpmd -> elec_thermostat = init_thermo (-1, type, 0);
}
 
void clean_thermostat (int new_type)
{
  int i;
  thermostat * thermo = get_thermo ();
  if (thermo -> sys > 0)
  {
    for (i=0; i<get_num_thermo(); i++)
    {
      if (thermo -> next != NULL) thermo = thermo -> next;
    }
    for (i=0; i<get_num_thermo(); i++)
    {
      if (thermo -> prev != NULL)
      {
        thermo = thermo -> prev;
        g_free (thermo -> next);
      }
    }
  }
  g_free (thermo);
  init_thermostats (new_type, 0);
}
 
G_MODULE_EXPORT void update_thermo_parameter (GtkEntry * res, gpointer data);
 
void nose_parameters (GtkWidget * vbox, int id, int jd, gchar ** la, gchar ** lb)
{
  thermostat * thermo = get_active_thermostat (id);
  //gchar * itemp[2]={"Initial temperature:", "Target temperature:"};
  GtkWidget * hbox;
  GtkWidget * widg;
  int i, j;
  i = (id < 0) ? id : 0;
  for (j=0; j<jd; j++)
  {
    hbox = cpmd_box (vbox, la[j], 5, (is_cpmd) ? 20 : 50, 220);
    widg = create_entry (G_CALLBACK(update_thermo_parameter), 100, 15, FALSE, GINT_TO_POINTER(i+j));
    update_entry_double (GTK_ENTRY(widg), thermo -> params[j]);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, widg, FALSE, FALSE, 0);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(lb[j], -1, -1, 0.0, 0.5), FALSE, FALSE, 0);
  }
}
 
G_MODULE_EXPORT void cpmd_select_atom_id (GtkCellRendererToggle * cell_renderer, gchar * string_path, gpointer data)
{
  GtkTreeStore ** model = (GtkTreeStore **)data;
  GtkTreeIter iter;
  int i, j;
  GtkTreePath * path = gtk_tree_path_new_from_string (string_path);
  gtk_tree_model_get_iter (GTK_TREE_MODEL(* model), & iter, path);
 
  gtk_tree_model_get (GTK_TREE_MODEL(* model), & iter, at_col, & i, -1);
  if (gtk_cell_renderer_toggle_get_active(cell_renderer))
  {
    j = 0;
    n_therm --;
    old_thermo[i-1] = 0;
    qm_view -> picked --;
  }
  else
  {
    j = 1;
    n_therm ++;
    old_thermo[i-1] = 1;
    qm_view -> picked ++;
  }
  qm_proj -> atoms[0][i-1].pick[0] = j;
  qm_proj -> atoms[0][i-1].label[0] = j;
  init_default_shaders (qm_view);
  gtk_tree_store_set (* model, & iter, 3, j, -1);
}
 
G_MODULE_EXPORT void cp2k_select_coord_id (GtkCellRendererToggle * cell_renderer, gchar * string_path, gpointer data)
{
  int i, j;
  j = GPOINTER_TO_INT(data);
  GtkTreeIter iter;
  GtkTreePath * path = gtk_tree_path_new_from_string (string_path);
  gtk_tree_model_get_iter (GTK_TREE_MODEL(add_model), & iter, path);
  gtk_tree_model_get (GTK_TREE_MODEL(add_model), & iter, at_col, & i, -1);
  if (gtk_cell_renderer_toggle_get_active(cell_renderer))
  {
    old_fixed[i-1][j-4] = 0;
  }
  else
  {
    old_fixed[i-1][j-4] = 1;
  }
  gtk_tree_store_set (add_model, & iter, (fixco) ? j : j-2, old_fixed[i-1][j-4], -1);
}
 
void atom_set_color (GtkTreeViewColumn * col, GtkCellRenderer * renderer, GtkTreeModel * mod, GtkTreeIter * iter, gpointer data)
{
  int i, j, k;
  gtk_tree_model_get (mod, iter, 1, & i, -1);
  gtk_tree_model_get (mod, iter, 3, & j, -1);
  set_renderer_color (j, renderer, init_color (i-1, num_cpmd_objects));
  k = GPOINTER_TO_INT(data);
  if (k == 2)
  {
    gchar * str;
    gtk_tree_model_get (mod, iter, 2, & str, -1);
    g_object_set (renderer, "markup", str, NULL, NULL);
    g_free (str);
  }
}
 
void atom_set_visible (GtkTreeViewColumn * col, GtkCellRenderer * renderer, GtkTreeModel * mod, GtkTreeIter * iter, gpointer data)
{
  int i, j, k;
  i = GPOINTER_TO_INT(data);
  gtk_tree_model_get (mod, iter, at_col, & j, -1);
  if (j == 0 && i != 0)
  {
    gtk_cell_renderer_set_visible (renderer, FALSE);
  }
  else if (j == 0)
  {
    gtk_cell_renderer_set_visible (renderer, TRUE);
  }
  else if (j > 0 && i == 0)
  {
    gtk_cell_renderer_set_visible (renderer, FALSE);
  }
  else if (j > 0)
  {
    if (i < 4)
    {
      gtk_cell_renderer_set_visible (renderer, TRUE);
    }
    else
    {
      gtk_tree_model_get (mod, iter, 3, & k, -1);
      gtk_cell_renderer_set_visible (renderer, k);
    }
    if (i < 3) atom_set_color (col, renderer, mod, iter, data);
  }
}
 
int is_not_thermostated (int at, int therm)
{
  int i, j;
  thermostat * thermo = get_thermo ();
  for (i=0; i<get_num_thermo(); i++)
  {
    for (j=0; j<thermo -> natoms; j++)
    {
      if (thermo -> list[j] == at)
      {
        if (i == therm)
        {
          return 2;
        }
        else
        {
          return 0;
        }
      }
    }
    if (thermo -> next != NULL) thermo = thermo -> next;
  }
  return 1;
}
 
int is_fixed_atom (int at)
{
  int i;
  if (is_cpmd)
  {
    for (i=0; i<tmp_cpmd -> fixat; i++)
    {
      if (tmp_cpmd -> fixlist[i] == at)
      {
        return i+2;
      }
    }
  }
  else
  {
    for (i=0; i<tmp_cp2k -> fixat[0]; i++)
    {
      if (tmp_cp2k -> fixlist[0][i] == at)
      {
        return i+2;
      }
    }
  }
  return 1;
}
 
int in_dummy (int at, int id)
{
  dummy_atom * dummy = get_active_dummy (-(id+2));
  int i;
  if (dummy -> natoms == qm_proj -> natomes) return 2;
  for (i=0; i<dummy -> natoms; i++)
  {
    if (dummy -> list[i] == at) return 2;
  }
  return 1;
}
 
gboolean was_it_selected (int id, int at)
{
  if (id < -1)
  {
    return in_dummy (at, id);
  }
  else if (id == -1)
  {
    return is_fixed_atom (at);
  }
  else
  {
    return is_not_thermostated (at, id);
  }
}
 
void fill_thermo_atom_model (int therm)
{
  int i, j, k, l, m;
  gchar * str;
  GtkTreeIter spec_level;
  GtkTreeIter atom_level;
  k = 0;
  for (i=0; i< qm_proj -> nspec; i++)
  {
    gtk_tree_store_append (add_model, & spec_level, NULL);
    gtk_tree_store_set (add_model, & spec_level, 0, qm_proj -> chemistry -> label[i], 1, 0, 3, 0, 4, 0, -1);
    for (j=0; j< qm_proj -> natomes; j++)
    {
      if (qm_proj -> atoms[0][j].sp == i)
      {
        k ++;
        l = was_it_selected (therm, j);
        if (fixco)
        {
          if (is_cpmd)
          {
            if (tmp_cpmd -> fixat > 0)
            {
              for (m=0; m<tmp_cpmd -> fixat; m++)
              {
                if (qm_proj -> atoms[0][j].coord[2] == tmp_cpmd-> fixlist[m])
                {
                  l = 0;
                  break;
                }
              }
            }
          }
          else
          {
            if (tmp_cp2k -> fixat[1] > 0)
            {
              for (m=0; m<tmp_cp2k -> fixat[1]; m++)
              {
                if (qm_proj -> atoms[0][j].coord[2] == tmp_cp2k -> fixlist[1][m])
                {
                  l = 0;
                  break;
                }
              }
            }
          }
        }
        if (l)
        {
          gtk_tree_store_append (add_model, & atom_level, & spec_level);
          str = g_strdup_printf ("%s<sub>%d</sub>", exact_name(qm_proj -> chemistry -> label[i]), j+1);
          if (fixco)
          {
            gtk_tree_store_set (add_model, & atom_level, 0, 0, 1, k, 2, str, 3, old_thermo[j],
                                4, old_fixed[j][0], 5, old_fixed[j][1], 6, old_fixed[j][2], at_col, j+1, -1);
          }
          else
          {
            gtk_tree_store_set (add_model, & atom_level, 0, 0, 1, k, 2, str, 3, old_thermo[j], at_col, j+1, -1);
          }
          g_free (str);
        }
      }
    }
  }
}
 
#ifdef GTK4
G_MODULE_EXPORT void select_atoms_not_thermostated (GtkCheckButton * but, gpointer data)
#else
G_MODULE_EXPORT void select_atoms_not_thermostated (GtkToggleButton * but, gpointer data)
#endif
{
  int h, i, j, k, l, m;
  h = GPOINTER_TO_INT (data);
  j = button_get_status ((GtkWidget *)but);
  for (i=0; i<qm_proj -> natomes; i++)
  {
    m = 0;
    if (j)
    {
      k = l = m = 1;
      if (was_it_selected(h, i) != 1)
      {
        m = 0;
      }
    }
    else if (old_thermo[i])
    {
      k = -1;
      l = 0;
      m = 1;
    }
    if (m)
    {
      n_therm += k;
      old_thermo[i] = l;
      if (l) qm_view -> picked ++;
      qm_proj -> atoms[0][i].pick[0] = l;
      qm_proj -> atoms[0][i].label[0] = l;
    }
  }
  gtk_tree_store_clear (add_model);
  fill_thermo_atom_model (h);
  init_default_shaders (qm_view);
}
 
G_MODULE_EXPORT void run_select_atom_from_model (GtkDialog * dialog, gint response_id, gpointer data)
{
  int i, j;
  gboolean done = FALSE;
  gchar * str;
  switch (response_id)
  {
    case GTK_RESPONSE_APPLY:
      if (n_therm > 1)
      {
        str = g_strdup_printf ("%d atoms have been selected !", n_therm);
      }
      else if (n_therm)
      {
        str = g_strdup_printf ("A single atom has been selected !");
      }
      else
      {
        str = g_strdup_printf ("Not at single atom has been selected !");
      }
      str = g_strdup_printf ("%s\nis this correct ?", str);
      selection_confirmed = FALSE;
      field_question (str, G_CALLBACK(confirm_selection), NULL);
      g_free (str);
      if (selection_confirmed)
      {
        done = TRUE;
        if (fixco)
        {
          for (i=0; i<qm_proj -> natomes; i++)
          {
            if (old_thermo[i] && ! old_fixed[i][0] && ! old_fixed[i][1] && ! old_fixed[i][2])
            {
              str = g_strdup_printf ("Atom %d has been selected but not coordinates are frozen !\n"
                                     "Unselect atom %d or select coordinate(s) to freeze !", i+1, i+1);
              show_warning (str, qm_assistant);
              done = FALSE;
            }
          }
        }
      }
      thermostat * thermo;
      dummy_atom * dummy;
      if (done)
      {
        if (the_therm < -1)
        {
          dummy = get_active_dummy (-(the_therm+2));
          dummy -> natoms = n_therm;
          if (dummy -> list != NULL)
          {
            g_free (dummy -> list);
            dummy -> list = NULL;
          }
          if (n_therm > 0 && n_therm < qm_proj -> natomes)
          {
            dummy -> list = allocint (n_therm);
            j = -1;
            for (i=0; i< qm_proj -> natomes; i++)
            {
              if (old_thermo[i])
              {
                j ++;
                dummy -> list[j] = i;
              }
            }
          }
        }
        else if (the_therm == -1)
        {
          if (is_cpmd)
          {
            if (tmp_cpmd -> fixlist != NULL)
            {
              g_free (tmp_cpmd -> fixlist);
              tmp_cpmd -> fixlist = NULL;
              if (tmp_cpmd -> fixcoord != NULL)
              {
                g_free (tmp_cpmd -> fixcoord);
                tmp_cpmd -> fixcoord = NULL;
              }
            }
            if (n_therm > 0)
            {
              tmp_cpmd -> fixlist = allocint (n_therm);
              if (fixco) tmp_cpmd -> fixcoord = allocdint (n_therm, 3);
              tmp_cpmd -> fixat = n_therm;
              j = -1;
              for (i=0; i< qm_proj -> natomes; i++)
              {
                if (old_thermo[i])
                {
                  j ++;
                  tmp_cpmd -> fixlist[j] = i;
                  if (fixco)
                  {
                    tmp_cpmd -> fixcoord[j][0] = old_fixed[i][0];
                    tmp_cpmd -> fixcoord[j][1] = old_fixed[i][1];
                    tmp_cpmd -> fixcoord[j][2] = old_fixed[i][2];
                  }
                }
              }
            }
          }
          else
          {
            if (tmp_cp2k -> fixlist[0] != NULL)
            {
              g_free (tmp_cp2k -> fixlist[0]);
              tmp_cp2k -> fixlist[0] = NULL;
              if (tmp_cp2k -> fixcoord[0] != NULL)
              {
                g_free (tmp_cp2k -> fixcoord[0]);
                tmp_cp2k -> fixcoord[0] = NULL;
              }
            }
            if (n_therm > 0)
            {
              tmp_cp2k -> fixlist[0] = allocint (n_therm);
              tmp_cp2k -> fixcoord[0] = allocdint (n_therm, 3);
              tmp_cp2k -> fixat[0] = n_therm;
              j = -1;
              for (i=0; i< qm_proj -> natomes; i++)
              {
                if (old_thermo[i])
                {
                  j ++;
                  tmp_cp2k -> fixlist[0][j] = i;
                  tmp_cp2k -> fixcoord[0][j][0] = old_fixed[i][0];
                  tmp_cp2k -> fixcoord[0][j][1] = old_fixed[i][1];
                  tmp_cp2k -> fixcoord[0][j][2] = old_fixed[i][2];
                }
              }
            }
          }
        }
        else
        {
          thermo = get_active_thermostat (the_therm);
          thermo -> natoms = n_therm;
          if (thermo -> list != NULL)
          {
            g_free (thermo -> list);
            thermo -> list = NULL;
          }
          if (n_therm > 0)
          {
            thermo -> list = allocint (n_therm);
            j = -1;
            for (i=0; i< qm_proj -> natomes; i++)
            {
              if (old_thermo[i])
              {
                j ++;
                thermo -> list[j] = i;
              }
            }
          }
        }
      }
      break;
    case GTK_RESPONSE_CLOSE:
      done = TRUE;
      break;
  }
  if (done) destroy_this_dialog (dialog);
}
 
void select_atom_from_model (int therm)
{
  int i, j, k, l, m;
  the_therm = therm;
  GtkTreeViewColumn * ato_col[8];
  GtkCellRenderer * ato_cell[8];
  gchar * ato_title[2][8] = {{"Species", "Id (*)", "Atom", "Viz.3D & Select", " "},
                             {"Species", "Id (*)", "Atom", "Viz.3D & Select", "x", "y", "z", " "}};
  gchar * ctype[2][8] = {{"text", "text", "text", "active", "text", "active", "active", "active"},
                         {"text", "text", "text", "active", "active", "active", "active", "text"}};
  GType col_type[2][8] = {{G_TYPE_STRING, G_TYPE_INT, G_TYPE_STRING, G_TYPE_BOOLEAN, G_TYPE_INT},
                          {G_TYPE_STRING, G_TYPE_INT, G_TYPE_STRING, G_TYPE_BOOLEAN, G_TYPE_BOOLEAN, G_TYPE_BOOLEAN, G_TYPE_BOOLEAN, G_TYPE_INT}};
  gchar * str;
  at_col = 4;
 
  fixco = FALSE;
  qm_view -> picked = 0;
  if (! is_cpmd && the_therm == -1)
  {
    fixco = TRUE;
  }
  else if (is_cpmd)
  {
    if ((int)tmp_cpmd -> default_opts[DEFFI] == 2) fixco = TRUE;
  }
  if (the_therm < -1)
  {
    str = g_strdup_printf ("Select atom(s) to construct dummy N°%d", -(the_therm+1));
  }
  else if (the_therm == -1)
  {
    str = g_strdup_printf ("Select atom(s) to fix");
    if (fixco)
    {
      g_free (str);
      at_col = 7;
      str = g_strdup_printf ("Select atom(s) and coordinate(s) to fix");
    }
  }
  else
  {
    str = g_strdup_printf ("Add atom(s) to thermostat N°%d", the_therm+1);
  }
  GtkWidget * amol = dialogmodal (str, GTK_WINDOW(qm_assistant));
  g_free (str);
  gtk_dialog_add_button (GTK_DIALOG(amol), "Apply", GTK_RESPONSE_APPLY);
  n_therm = 0;
  i = (fixco) ? 1 : 0;
  j = (fixco) ? 8 : 5;
  add_model = gtk_tree_store_newv (j, col_type[i]);
  GtkWidget * add_tree = gtk_tree_view_new_with_model(GTK_TREE_MODEL(add_model));
  for (k=0; k<j-1; k++)
  {
    if (k < 3)
    {
      ato_cell[k] = gtk_cell_renderer_text_new ();
    }
    else
    {
      ato_cell[k] = gtk_cell_renderer_toggle_new ();
      if (k==3)
      {
        g_signal_connect (G_OBJECT(ato_cell[k]), "toggled", G_CALLBACK(cpmd_select_atom_id), & add_model);
      }
      else
      {
        g_signal_connect (G_OBJECT(ato_cell[k]), "toggled", G_CALLBACK(cp2k_select_coord_id), GINT_TO_POINTER(k));
      }
    }
    ato_col[k] = gtk_tree_view_column_new_with_attributes (ato_title[i][k], ato_cell[k], ctype[i][k], k, NULL);
    gtk_tree_view_append_column (GTK_TREE_VIEW(add_tree), ato_col[k]);
    gtk_tree_view_column_set_alignment (ato_col[k], 0.5);
    gtk_tree_view_column_set_cell_data_func (ato_col[k], ato_cell[k], atom_set_visible, GINT_TO_POINTER(k), NULL);
  }
  old_thermo = allocint (qm_proj -> natomes);
  if (fixco)
  {
    old_fixed = allocdint (qm_proj -> natomes, 3);
  }
  k = l = 0;
  for (i=0; i < qm_proj -> nspec; i++)
  {
    for (j=0; j < qm_proj -> natomes; j++)
    {
      if (qm_proj -> atoms[0][j].sp == i)
      {
        k ++;
        m = was_it_selected (the_therm, j);
        if (m)
        {
          l ++;
          n_therm += (m > 1) ? 1 : 0;
          old_thermo[j] = (m > 1) ? 1 : 0;
          qm_proj -> atoms[0][j].pick[0] = old_thermo[j];
          qm_view -> picked += old_thermo[j];
          if (fixco && m > 1)
          {
            if (is_cpmd)
            {
              old_fixed[j][0] = tmp_cpmd -> fixcoord[m-2][0];
              old_fixed[j][1] = tmp_cpmd -> fixcoord[m-2][1];
              old_fixed[j][2] = tmp_cpmd -> fixcoord[m-2][2];
            }
            else
            {
              old_fixed[j][0] = tmp_cp2k -> fixcoord[0][m-2][0];
              old_fixed[j][1] = tmp_cp2k -> fixcoord[0][m-2][1];
              old_fixed[j][2] = tmp_cp2k -> fixcoord[0][m-2][2];
            }
          }
        }
      }
    }
  }
  fill_thermo_atom_model (the_therm);
  init_default_shaders (qm_view);
  num_cpmd_objects = l;
  g_object_unref (add_model);
  i = ((qm_proj -> nspec + l)*37 < 500) ? (qm_proj -> nspec + l)*37 : 500;
  //GtkWidget * scrollsets = create_scroll (NULL, -1, -1, GTK_SHADOW_ETCHED_IN, 0);
  GtkWidget * scrollsets = create_scroll (dialog_get_content_area (amol), 320, i, GTK_SHADOW_ETCHED_IN);
  add_container_child (CONTAINER_SCR, scrollsets, add_tree);
  str = g_strdup_printf (" <b>(*)</b> Order of appearance in the input file");
  GtkWidget * vbox = dialog_get_content_area (amol);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, markup_label(str, -1, -1, 0.0, 0.5), FALSE, FALSE, 0);
  g_free (str);
  if (the_therm != -1)
  {
    if (get_num_thermo() > 1 || the_therm < -1)
    {
      add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, gtk_separator_new (GTK_ORIENTATION_HORIZONTAL), FALSE, FALSE, 0);
      GtkWidget * hbox = create_hbox (0);
      gchar * lab[2] = {"All non-thermostated atom(s)", "All atom(s)"};
      add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox,
                          check_button (lab[(the_therm > -1) ? 0 : 1], -1, -1,
                          FALSE, G_CALLBACK(select_atoms_not_thermostated), GINT_TO_POINTER(the_therm)),
                          FALSE, FALSE, 50);
      add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 0);
    }
  }
  run_this_gtk_dialog (amol, G_CALLBACK(run_select_atom_from_model), & fixco);
  proj_unselect_all_atoms ();
  if (the_therm > -1) set_going_forward ();
  g_free (old_thermo);
  fixco = FALSE;
}
 
G_MODULE_EXPORT void atom_selection_button (GtkButton * but, gpointer data)
{
  int num, id;
  int i = GPOINTER_TO_INT(data);
  select_atom_from_model (i);
  if (i < -1)
  {
    id = 2;
    num = get_active_dummy (-(i+2)) -> natoms;
  }
  else if (i == -1)
  {
    id = 1;
    num = (is_cpmd) ? tmp_cpmd -> fixat : tmp_cp2k -> fixat[0];
  }
  else
  {
    id = 0;
    thermostat * thermo = get_active_thermostat (i);
    num = thermo -> natoms;
  }
  gchar * stra, * strb;
  if (num  == 0)
  {
    stra = g_strdup_printf ("Not picked yet !");
    strb = g_strdup_printf (DELETEB);
  }
  else
  {
    stra = g_strdup_printf ("%d atom(s)", num);
    strb = g_strdup_printf (APPLY);
  }
  set_image_from_icon_name (sel_img[id], strb);
  gtk_button_set_label (but, stra);
  g_free (stra);
  g_free (strb);
  if (is_cpmd)
  {
    // CPMD
    if (i < -1)
    {
      print_the_section (8, 0, qmbuffer[8]);
    }
    else if (i == -1)
    {
      print_the_section (8, 0, qmbuffer[8]);
    }
    else
    {
      for (i=1; i<4; i++) print_the_section (i, 0, qmbuffer[i]);
    }
  }
  else
  {
    // CP2K
  }
}
 
void create_selection_button (GtkWidget * box, int num, int id, gpointer data)
{
  int i = GPOINTER_TO_INT(data);
  GtkWidget * hbox = cpmd_box (box, "Atom(s) selection: ", 5, 20, (i < -1) ? 120 : 220);
  gchar * str;
  if (num == 0)
  {
    str = g_strdup_printf ("Not picked yet !");
    sel_img[id] = stock_image (DELETEB);
  }
  else
  {
    str = g_strdup_printf ("%d atom(s)", (int)num);
    sel_img[id] = stock_image (APPLY);
  }
  sel_but[id] = gtk_button_new_with_label (str);
  gtk_widget_set_size_request (sel_but[id], 150, -1);
  g_free (str);
  g_signal_connect (G_OBJECT(sel_but[id]), "clicked", G_CALLBACK(atom_selection_button), data);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, sel_but[id], FALSE, FALSE, 0);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, sel_img[id], FALSE, FALSE, 30);
}
 
void create_nose_thermo_param_box (int therm_id)
{
  gchar * str;
  nose_id_box[1] = destroy_this_widget (nose_id_box[1]);
  str = g_strdup_printf ("Configuration for thermostat N°<b>%d</b>: ", therm_id+1);
  nose_id_box[1] = create_vbox (BSEP);
  cpmd_box (nose_id_box[1], str, 5, 5, 220);
  g_free (str);
  thermostat * thermo = get_active_thermostat (therm_id);
  create_selection_button (nose_id_box[1], thermo -> natoms, 0, GINT_TO_POINTER(therm_id));
  nose_parameters (nose_id_box[1], therm_id,
                   v_thermo[!is_cpmd][thermo->type],
                   c_thermo[!is_cpmd][thermo->type],
                   u_thermo[!is_cpmd][thermo->type]);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, nose_id_box[0], nose_id_box[1], FALSE, FALSE, 0);
  show_the_widgets (nose_id_box[1]);
}
 
G_MODULE_EXPORT void changed_nose_thermo_id_box (GtkComboBox * box, gpointer data)
{
  int i;
  i = combo_get_active ((GtkWidget *)box);
  create_nose_thermo_param_box (i);
}
 
void create_selection_combo (int id, int num, int type, GCallback handler)
{
  int i, j;
  gchar * str;
  gchar * lab[2]={"Thermostat", "Dummy atom"};
  combo_id_box[id] = destroy_this_widget (combo_id_box[id]);
  combo_id_box[id] = create_combo ();
  for (i=0; i<num; i++)
  {
    str = g_strdup_printf ("%s N°%d", lab[id], i+1);
    combo_text_append (combo_id_box[id], str);
    g_free (str);
  }
  j = type;
  if (num > 0)
  {
    combo_set_active (combo_id_box[id], 0);
    if (id == 0)
    {
      create_nose_thermo_param_box (0);
    }
    else
    {
      create_dummy_param_box (0);
    }
  }
  else
  {
    combo_set_active (combo_id_box[id], -1);
    widget_set_sensitive (combo_id_box[id], FALSE);
  }
  g_signal_connect (G_OBJECT (combo_id_box[id]), "changed", handler, GINT_TO_POINTER(j));
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, combo_id[id], combo_id_box[id], FALSE, FALSE, 0);
  show_the_widgets (combo_id[id]);
}
 
void add_thermostat (int extra)
{
  int i, j;
  thermostat * thermo = get_thermo ();
  j = get_num_thermo ();
  while (thermo -> next != NULL) thermo = thermo -> next;
  for (i=0; i<extra; i++)
  {
    thermo -> next = init_thermo (i+j, thermo -> type, thermo -> sys);
    thermo -> next -> prev = thermo;
    if (i < extra-1) thermo = thermo -> next;
  }
 
  if (is_cpmd)
  {
    tmp_cpmd -> thermostats += extra;
  }
  else
  {
    tmp_cp2k -> thermostats += extra;
  }
  // finally update the combobox
  create_selection_combo (0, get_num_thermo (), get_thermo() -> type, G_CALLBACK(changed_nose_thermo_id_box));
}
 
G_MODULE_EXPORT void add_or_remove_thermostat (GtkSpinButton * res, gpointer data)
{
  int id = gtk_spin_button_get_value_as_int(res);
  int i, j, k;
  gchar * str;
  gboolean add_thermo = TRUE;
  thermostat * thermo = get_thermo();
  if (id != get_num_thermo ())
  {
    if (id > get_num_thermo ())
    {
      // adding thermostats
      // ok if: 1) all atoms do not already have a thermostat assigned
      //        2) number of thermostat(s) to create < number of atoms that do have a thermostat assigned
      j = 0;
      for (i=0; i<get_num_thermo (); i++)
      {
        j += thermo -> natoms;
        if (thermo -> next != NULL) thermo = thermo -> next;
      }
      if (j < qm_proj -> natomes)
      {
        // Number of thermostat to create
        k = id - get_num_thermo ();
        if (k < (qm_proj -> natomes - j))
        {
          if (k > 1)
          {
            str = g_strdup_printf ("Do you really want to add %d thermostat(s) ?", k);
            add_thermo = ask_yes_no ("Adding thermostat(s) ?", str, GTK_MESSAGE_QUESTION, qm_assistant);
            g_free (str);
          }
          if (add_thermo)
          {
            add_thermostat (k);
          }
          else
          {
            // Set value back to the number of ionic thermostats
            gtk_spin_button_set_value (GTK_SPIN_BUTTON(res), (double)get_num_thermo ());
          }
        }
        else
        {
          show_warning ("It is not possible to create so many thermostats", qm_assistant);
          gtk_spin_button_set_value (GTK_SPIN_BUTTON(res), (double)get_num_thermo ());
        }
      }
      else
      {
        show_warning ("All atoms arleady have a thermostat assigned", qm_assistant);
        gtk_spin_button_set_value (GTK_SPIN_BUTTON(res), (double)get_num_thermo ());
      }
    }
    else
    {
      // removing thermostats
      remove_nose_thermostat (get_num_thermo () - id);
    }
  }
  gtk_spin_button_set_value (GTK_SPIN_BUTTON(res), (double)(get_num_thermo ()));
  if (is_cpmd) for (i=1; i<4; i++) print_the_section (i, 0, qmbuffer[i]);
}
 
G_MODULE_EXPORT void update_thermo_parameter (GtkEntry * res, gpointer data)
{
  int i, j;
  i = GPOINTER_TO_INT(data);
  const gchar * m = entry_get_text (res);
  double v = string_to_double ((gpointer)m);
  if (i < 0)
  {
    if (tmp_cpmd -> elec_thermostat -> params[i+2] != v)
    {
      tmp_cpmd -> elec_thermostat -> params[i+2] = v;
      update_entry_double (res, v);
    }
  }
  else
  {
    if (get_num_thermo () > 1)
    {
      j = combo_get_active (combo_id_box[0]);
    }
    else
    {
      j = 0;
    }
    thermostat * thermo = get_active_thermostat (j);
    if (i < 2)
    {
      if (thermo -> params[i] != v)
      {
        thermo -> params[i] = v;
        update_entry_double (res, v);
      }
    }
    else
    {
      if ((int)thermo -> params[i] != (int)v)
      {
        thermo -> params[i] = v;
        update_entry_int (res, (int)v);
      }
    }
  }
  if (is_cpmd) for (i=1; i<4; i++) print_the_section (i, 0, qmbuffer[i]);
}
 
GtkWidget * create_nose_box (int n)
{
  GtkWidget * vbox = create_vbox (BSEP);
  GtkWidget * hbox;
  GtkWidget * widg;
  if (n > GLOBAL)
  {
    hbox = cpmd_box (vbox, "Number of thermostat(s): ", 5, 5, 220);
    widg = spin_button (G_CALLBACK(add_or_remove_thermostat),
                        (double)(get_num_thermo ()), 1.0, (double)qm_proj -> natomes, 1.0, 0, 100, NULL);
    add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, widg, FALSE, FALSE, 0);
    combo_id[0] = cpmd_box (vbox, "Thermostat to configure: ", 5, 5, 220);
    nose_id_box[0] = create_vbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, nose_id_box[0], FALSE, FALSE, 10);
    create_selection_combo (0, get_num_thermo (), get_thermo () -> type, G_CALLBACK(changed_nose_thermo_id_box));
    create_nose_thermo_param_box (0);
  }
  else
  {
    nose_parameters (vbox, 0,
                     v_thermo[!is_cpmd][get_thermo()->type],
                     c_thermo[!is_cpmd][get_thermo()->type],
                     u_thermo[!is_cpmd][get_thermo()->type]);
  }
  return vbox;
}
 
G_MODULE_EXPORT void changed_thermo_box_nose (GtkComboBox * box, gpointer data)
{
  int i;
  i = combo_get_active ((GtkWidget *)box);
  if (i != get_thermo () -> sys)
  {
    clean_thermostat (get_thermo () -> type);
    clean_nose_widgets ();
    get_thermo () -> sys = i;
    nose_box = create_nose_box (get_thermo () -> sys);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, therm_param_ions, nose_box, FALSE, FALSE, 0);
    int j;
    if (is_cpmd) for (j=1; j<4; j++) print_the_section (j, 0, qmbuffer[j]);
    show_the_widgets (therm_param_ions);
  }
  set_going_forward ();
}
 
void prepare_therm_ions ()
{
  int i, j, k;
  GtkWidget * hbox;
  GtkWidget * tbox;
  gchar * str;
  clean_nose_widgets ();
  therm_param_ions = destroy_this_widget (therm_param_ions);
  therm_param_ions = create_vbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, therm_ions, therm_param_ions, FALSE, FALSE, 0);
  i = (is_cpmd) ? 1 : 0;
  //if (is_cpmd)
  {
    if (get_thermo () -> type > i)
    {
      hbox = cpmd_box (therm_param_ions, "Thermostat type: ", 5, 5, 220);
      tbox = create_combo ();
      j = 2; // For QM-MM: qm_view -> bonding + 2;
      for (k=0; k<j; k++)
      {
        str = g_strdup_printf ("%s", nosetype[k]);
        combo_text_append (tbox, str);
        g_free (str);
      }
      add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, tbox, FALSE, FALSE, 0);
      combo_set_active (tbox, get_thermo () -> sys);
      g_signal_connect (G_OBJECT (tbox), "changed", G_CALLBACK(changed_thermo_box_nose), NULL);
    }
  }
  nose_box = create_nose_box (get_thermo () -> sys);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, therm_param_ions, nose_box, FALSE, FALSE, 0);
  show_the_widgets (therm_param_ions);
  if (is_cpmd) for (i=1; i<4; i++) print_the_section (i, 0, qmbuffer[i]);
}
 
void prepare_therm_elec ()
{
  therm_param_elec = destroy_this_widget (therm_param_elec);
  therm_param_elec = create_vbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, therm_elec, therm_param_elec, FALSE, FALSE, 0);
  int i;
  nose_parameters (therm_param_elec, -2,
                   v_thermo[0][tmp_cpmd -> elec_thermostat -> type],
                   c_thermo[0][tmp_cpmd -> elec_thermostat -> type],
                   ue_thermo[tmp_cpmd -> elec_thermostat -> type]);
  show_the_widgets (therm_param_elec);
  for (i=1; i<4; i++) print_the_section (i, 0, qmbuffer[i]);
}
 
G_MODULE_EXPORT void changed_thermo_box (GtkComboBox * box, gpointer data)
{
  int i, j;
  i = combo_get_active ((GtkWidget *)box);
  j = GPOINTER_TO_INT (data);
  if (j == 0 && i != get_thermo () -> type)
  {
    clean_thermostat (i);
    thermostat * thermo = get_thermo();
    thermo -> sys = GLOBAL;
    prepare_therm_ions ();
  }
  else if (j == -1)
  {
    if (i != tmp_cpmd -> elec_thermostat -> type)
    {
      g_free (tmp_cpmd -> elec_thermostat);
      tmp_cpmd -> elec_thermostat = init_thermo (-1, i, 0);
      tmp_cpmd -> elec_thermostat -> sys = 0;
      prepare_therm_elec ();
    }
  }
  set_going_forward ();
}
 
void thermo_type_box (GtkWidget * vbox, gchar * str, int id)
{
  int i;
  GtkWidget * hbox = create_hbox (0);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, hbox, FALSE, FALSE, 5);
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, markup_label(str, 250, -1, 0.0, 0.5), FALSE, FALSE, 5);
  GtkWidget * tbox = create_combo ();
  for (i=0; i<num_thermo[!is_cpmd]; i++)
  {
    str = g_strdup_printf ("%s", thermo_name[!is_cpmd][i]);
    combo_text_append (tbox, str);
    g_free (str);
  }
  if (id == -1)
  {
    combo_set_active (tbox, tmp_cpmd -> elec_thermostat -> type);
  }
  else
  {
    thermostat * thermo = get_thermo();
    combo_set_active (tbox, thermo -> type);
  }
  g_signal_connect (G_OBJECT (tbox), "changed", G_CALLBACK(changed_thermo_box), GINT_TO_POINTER(id));
  add_box_child_start (GTK_ORIENTATION_HORIZONTAL, hbox, tbox, FALSE, FALSE, 0);
}
 
GtkWidget * thermo_box ()
{
  gchar * thermo_info[2] = {"<u>Ionic subsystem thermostat:</u> ", "Thermostat: "};
  GtkWidget * vbox = create_vbox (BSEP);
  GtkWidget * vvbox;
  nose_id_box[0] = nose_id_box[1] = NULL;
  therm_param_ions = NULL;
  therm_param_elec = NULL;
  nose_box = NULL;
  combo_id_box[0] = NULL;
  combo_id[0] = NULL;
  if (get_num_thermo() == 0) init_thermostats (0, 1);
  // Thermostat type ions
  vvbox = create_vbox (BSEP);
  gtk_widget_set_size_request (vvbox, (is_cpmd) ? 525 : -1, (is_cpmd) ? 350 : 260);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, vvbox, FALSE, FALSE, 0);
  thermo_type_box (vvbox, thermo_info[!is_cpmd], 0);
  therm_ions = create_vbox (BSEP);
  add_box_child_start (GTK_ORIENTATION_VERTICAL, vvbox, therm_ions, FALSE, FALSE, (is_cpmd) ? 0 : 20);
  prepare_therm_ions ();
  // Thermostat type electrons
  if (is_cpmd)
  {
    electron_box = create_vbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, vbox, electron_box, FALSE, FALSE, 5);
    thermo_type_box (electron_box, "<u>Fictitious electronic subsystem:</u> ", -1);
    therm_elec = create_vbox (BSEP);
    add_box_child_start (GTK_ORIENTATION_VERTICAL, electron_box, therm_elec, FALSE, FALSE, 0);
    prepare_therm_elec ();
  }
  return vbox;
}