3. KIMERA format

The goal of a Kimera file is to enhance the efficiency of succesive simulations with the same system. The data in a kimera file is as follows:

1- Cells and their corresponding atoms forming the box of the system. Next code in applied in the format of type_atom:

1:  NORMAL
-1: INSOLUBLE
-2: REVOMED_ATOM (it is already dissolved)

2- Neighbours of each atom and the distance to each one.

3- Affected atoms for every atom. An affected atom dissolves as soon as the father does.

4- Linked atoms, related with the neighbour by the order that they follow in this file. The contribution of one neighbour is only considered if the linked atom exist. Next code in applied in the format of type_link:

0:  NOT LINKED
1:  LINKED
-1: LINKED TO A DISSOLVED ATOM

---

CELL 0
0   Si   1   2.505   0   0
1   Si   1   -1.2525   2.16939   3.64667
2   Si   1   1.2525   2.16939   1.82333
CELL 1
9   Si   1   2.505   -9.79754e-013   5.47
10   Si   1   -1.2525   2.16939   9.11667
11   Si   1   1.2525   2.16939   7.29333
12   O   1   1.59543   0.92112   6.38167
CELL (int)cell_id
(int)atom_id    (text)element   (int)type_atom   (double)position_x  (double)position_y  (double)position_z  
(int)atom_id    (text)element   (int)type_atom   (double)position_x  (double)position_y  (double)position_z  
(int)atom_id    (text)element   (int)type_atom   (double)position_x  (double)position_y  (double)position_z  
(int)atom_id    (text)element   (int)type_atom   (double)position_x  (double)position_y  (double)position_z  
...   ...   ...   ...   ...   ...
...   ...   ...   ...   ...   ...
CELL (int)cell_id
(int)atom_id    (text)element   (int)type_atom   (double)position_x  (double)position_y  (double)position_z  
(int)atom_id    (text)element   (int)type_atom   (double)position_x  (double)position_y  (double)position_z  
...   ...   ...   ...   ...   ...
...   ...   ...   ...   ...   ...
NEIGHBORS 
0   2   3.09832   407   3.09832   405   5.01   45   5.01   1   5.66774   856   5.66774   406   4.42416   451   4.42416   
1   2   3.09832   4052   3.09832   54   3.09832   4059   3.09832   4051   5.01   451   5.01   496   5.01   4456   5.01   0   5.66774   
2   0   3.09832   1   3.09832   45   3.09832   451   3.09832   407   5.01   47   5.01   4052   5.01   452   5.01   4059   5.66774
(int)atom_id  (int)neighbour_id  (double)distance_atom_neighbour  (int)neighbour_id  (double)distance_atom_neighbour  ...   ... 
(int)atom_id  (int)neighbour_id  (double)distance_atom_neighbour  (int)neighbour_id  (double)distance_atom_neighbour  ...   ... 
(int)atom_id  (int)neighbour_id  (double)distance_atom_neighbour  (int)neighbour_id  (double)distance_atom_neighbour  ...   ... 
...   ...   ...   ...   ...   ...   ...
...   ...   ...   ...   ...   ...   ...
...   ...   ...   ...   ...   ...   ...
AFFECTED
0   3   411   
1   7   8   4054   4055   
2   3   5   6   8   
(int)atom_id    (int)affected_id    (int)affected_id    ...   ...
(int)atom_id    (int)affected_id    (int)affected_id    ...   ...
...   ...   ...   ...   ...   ...  
...   ...   ...   ...   ...   ...  
LINKED 
0  L  0  L  0  L  1   407  L  1   2  L  1   2  L  1   407  L  1   407  L  1   2
1  L  0  L  0  L  0  L  0  L  1   4052  L  1   2  L  1   54  L  1   4059  L  1   2  L  1   4052  L  1   54
2  L  0  L  0  L  0  L  0  L  1   0  L  1   45  L  1   1  L  1   451  L  1   1  L  1   451  L  1   451  L  1   1
(int)atom_id  L (int)type_link  (int)linked_id  (int)linked_id   ...    L (int)type_link  (int)linked_id  (int)linked_id   ...
(int)atom_id  L (int)type_link  (int)linked_id  (int)linked_id   ...    L (int)type_link  (int)linked_id  (int)linked_id   ...
...  ... ...  ...  ...   ...    ... ...  ...  ...   ...
...  ... ...  ...  ...   ...    ... ...  ...  ...   ...