atom_species.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) 2022-2024 by CNRS and University of Strasbourg */
 
/*
* This file: 'atom_species.c'
*
* Contains:
*
 
 - The functions to look for new chemical species and modify the chemical information accordingly
 
*
* List of functions:
 
  int find_spec_id (int s, int z, double * list_z);
  int search_for_new_spec (atom_edition * edit, atomic_object * object);
 
  chemical_data * duplicate_chemical_data (int spec, chemical_data * chem);
 
*/
 
#include "atom_edit.h"
 
chemical_data * duplicate_chemical_data (int spec, chemical_data * chem)
{
  chemical_data * newchem = g_malloc0 (sizeof*chem);
  newchem -> label = g_malloc (spec*sizeof*newchem -> label);
  newchem -> element = g_malloc (spec*sizeof*newchem -> element);
  int i, j;
  for (i=0; i<spec; i++)
  {
    newchem -> label[i] = g_strdup_printf ("%s", chem -> label[i]);
    newchem -> element[i] = g_strdup_printf ("%s", chem -> element[i]);
  }
  newchem -> nsps = duplicate_int (spec, chem -> nsps);
  newchem -> formula = duplicate_int (spec, chem -> formula);
  newchem -> cutoffs = allocddouble (spec, spec);
  newchem -> grtotcutoff = chem -> grtotcutoff;
  newchem -> chem_prop = allocddouble (CHEM_PARAMS, spec);
  for (i=0; i<spec; i++)
  {
    for (j=0; j<spec; j++) newchem -> cutoffs[i][j] = chem -> cutoffs[i][j];
    for (j=0; j<CHEM_PARAMS; j++) newchem -> chem_prop[j][i] = chem -> chem_prop[j][i];
  }
  return newchem;
}
 
int find_spec_id (int s, int z, double * list_z)
{
  int i;
  if (list_z)
  {
    for (i=0; i<s; i++)
    {
      if (list_z[i] == (double)z)
      {
        return i;
      }
    }
  }
  return -1;
}
 
int search_for_new_spec (atom_edition * edit, atomic_object * object)
{
  coord_info * coord = edit -> coord;
  int i, j, k, l, m;
  i = 0;
  for (j=0; j<object -> species; j++)
  {
    if (object -> old_z[j] > 0)
    {
      k = find_spec_id (coord -> species, object -> old_z[j], edit -> new_z);
      if (k < 0)
      {
        i ++;
        edit -> new_z = g_realloc (edit -> new_z, (coord -> species+i)*sizeof*edit -> new_z);
        edit -> new_z[coord -> species+i-1] = (double)object -> old_z[j];
       }
    }
  }
 
  if (i)
  {
    coord_info * tmp = duplicate_coord_info (edit -> coord);
    for (j=0; j<2; j++)
    {
      if (coord -> species)
      {
        g_free (coord -> ntg[j]);
        g_free (coord -> geolist[j]);
      }
      coord -> ntg[j] = allocint (coord -> species + i);
      coord -> geolist[j] = g_malloc0 ((coord -> species + i)*sizeof* coord -> geolist[j]);
      if (j)
      {
        if (coord -> species) g_free (coord -> partial_geo);
        coord -> partial_geo = g_malloc0 ((coord -> species + i)*sizeof*coord -> partial_geo);
      }
      for (k=0; k<coord -> species; k++)
      {
        coord -> ntg[j][k] = tmp -> ntg[j][k];
        coord -> geolist[j][k] = duplicate_int (tmp -> ntg[j][k], tmp -> geolist[j][k]);
        if (j)
        {
          coord -> partial_geo[k] = allocdint (coord -> ntg[j][k], coord -> species + i);
          for (l=0; l<tmp -> ntg[j][k]; l++)
          {
            for (m=0; m<coord -> species; m++)
            {
              coord -> partial_geo[k][l][m] = tmp -> partial_geo[k][l][m];
            }
          }
        }
      }
    }
    coord -> species += i;
    g_free (tmp);
  }
  return i;
}