save_mol.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) 2022-2026 by CNRS and University of Strasbourg */

 
/*
* This file: 'save_mol.c'
*
* Contains:
*
 
 - The functions to save molecules information in the atomes project file format
 
*
* List of functions:
 
  int save_atom_m (FILE * fp, project * this_proj, int s, int a);
  int save_this_mol (FILE * fp, project * this_proj, molecule * tmp);
  int save_mol (FILE * fp, project * this_proj);
 
*/
 
#include "global.h"
#include "project.h"
 
/*molecule {
  int id;                                 // Molecule id number
  int md;                                 // MD step
  int multiplicity;                       // Multiplicity
  int * fragments;                        // Fragments list
  int natoms;                             // Number of atoms
  int nspec;                              // Number of chemical species
  int * species;                          // Number of atom by species
  atom ** atoms;                          // The list of all atoms
  int nbonds;                             // Number of chemical bonds
  int ** pbonds;                          // Number of chemical bonds by geometries
  int nangles;                            // Number of bond angles
  int *** pangles;                        // Number of bond angles by geometries
  int ** lgeo;                            // list of coordination spheres (by species)
  molecule * next;
  molecule * prev;
};*/

int save_atom_m (FILE * fp, project * this_proj, int s, int a)
{
  if (fwrite (& this_proj -> atoms[s][a].coord[2], sizeof(int), 1, fp) != 1) return signal_error (__FILE__, __func__, __LINE__, signal_error (__FILE__, __func__, __LINE__, ERROR_MOL));
  if (fwrite (& this_proj -> atoms[s][a].coord[3], sizeof(int), 1, fp) != 1) return signal_error (__FILE__, __func__, __LINE__, signal_error (__FILE__, __func__, __LINE__, ERROR_MOL));
  return OK;
}

int save_this_mol (FILE * fp, project * this_proj, molecule * tmp)
{
  if (fwrite (& tmp -> id, sizeof(int), 1, fp) != 1) return signal_error (__FILE__, __func__, __LINE__, signal_error (__FILE__, __func__, __LINE__, ERROR_MOL));
  if (fwrite (& tmp -> md, sizeof(int), 1, fp) != 1) return signal_error (__FILE__, __func__, __LINE__, signal_error (__FILE__, __func__, __LINE__, ERROR_MOL));;
  if (fwrite (& tmp -> multiplicity, sizeof(int), 1, fp) != 1) return signal_error (__FILE__, __func__, __LINE__, signal_error (__FILE__, __func__, __LINE__, ERROR_MOL));
  if (fwrite (tmp -> fragments, sizeof(int), tmp -> multiplicity, fp) != tmp -> multiplicity) return signal_error (__FILE__, __func__, __LINE__, signal_error (__FILE__, __func__, __LINE__, ERROR_MOL));
  if (fwrite (& tmp -> natoms, sizeof(int), 1, fp) != 1) return signal_error (__FILE__, __func__, __LINE__, signal_error (__FILE__, __func__, __LINE__, ERROR_MOL));
  if (fwrite (& tmp -> nspec, sizeof(int), 1, fp) != 1) return signal_error (__FILE__, __func__, __LINE__, signal_error (__FILE__, __func__, __LINE__, ERROR_MOL));
  if (fwrite (tmp -> species, sizeof(int), this_proj -> nspec, fp) != this_proj -> nspec) return signal_error (__FILE__, __func__, __LINE__, signal_error (__FILE__, __func__, __LINE__, ERROR_MOL));
  return OK;
}

int save_mol (FILE * fp, project * this_proj)
{
  int i, j;
  i = 0;
  if (! this_proj -> modelfc)
  {
    if (fwrite (& i, sizeof(int), 1, fp) != 1) return signal_error (__FILE__, __func__, __LINE__, ERROR_MOL);
    return OK;
  }
  i = 1;
  if (fwrite (& i, sizeof(int), 1, fp) != 1) return signal_error (__FILE__, __func__, __LINE__, ERROR_MOL);
  for (i=1; i<4; i++)
  {
    if (fwrite (& this_proj -> coord -> totcoord[i], sizeof(int), 1, fp) != 1) return signal_error (__FILE__, __func__, __LINE__, ERROR_MOL);
  }
  if (fwrite (this_proj -> modelfc -> mol_by_step, sizeof(int), this_proj -> steps, fp) != this_proj -> steps) return signal_error (__FILE__, __func__, __LINE__, ERROR_MOL);
  for (i=0; i<this_proj -> steps; i++)
  {
    for (j=0; j<this_proj -> modelfc -> mol_by_step[i]; j++)
    {
      if (save_this_mol (fp, this_proj, & this_proj -> modelfc -> mols[i][j]) != OK)
      {
        update_error_trace (__FILE__, __func__, __LINE__-2);
        return ERROR_MOL;
      }
    }
  }
  for (i=0; i<this_proj -> steps; i++)
  {
    for (j=0; j< this_proj -> natomes; j++)
    {
      if (save_atom_m (fp, this_proj, i, j) != OK)
      {
        update_error_trace (__FILE__, __func__, __LINE__-2);
        return ERROR_MOL;
      }
    }
  }
  return OK;
}