"Total oxidation state (cif): nan" & "Error:Group has no unique connection"

[orex]

"Total oxidation state (cif): nan" & "Error:Group has no unique connection"

[orex]

Dear PheLiBoP,
Thank you very much for the detailed request.
The answer to your first issue is simple. Change here

loop_
_atom_type_symbol
_atom_type_oxidation_number
Mg2+ 2
Al3+ 3
O2- -2
C4+ 4
H1+ 1

atom type to atom labels (Mg2+ to Mg1 for example). I understand that it can be quite confusing, but some cif files can use "type_symbol" like yours, but some of them can use labels to set an atomic charge. If you don't want to edit the file, you can set charges from supercell command line explicitly. More information you can find in the

1. supercell tutorial http://orex.github.io/supercell/doc/supercell_tutorial.pdf ("Basic functionality section" for relevant cif file structure and "Permutations in ice" for command line charge change).
2. supercell manual http://orex.github.io/supercell/doc/supercell_man.html#section_3 for charge setting options.
3. Please also check the issue #6 (comment). The second problem there is the same as yours first issue.

I need some time to answer to the second question. I will come soon.

P. S. To be clear
Total charge oxidation state (cif): calculated by cif oxidation stated, but in the next steps only charges from column "Used" is proceed.
Total charge cell calculated by sum of <cif_occupancy>*<cif_multiplicity>*<used_charge>. The charge is almost zero. The value comes from rounding error. if you calculate the value by yourself and you get the same nonzero value.

[orex]

The second issue looks more complex.

First of all, I would like to say, that there are absolutely no reasons to increase tolerance ("-t") value so much. Such huge increase breaks supercell algorithms logic. Please see the "Stage 1" of the "Algorithm implementations in the supercell program" section in supercell paper. https://jcheminf.biomedcentral.com/articles/10.1186/s13321-016-0129-3#Sec5
Shortly, the tolerance value should be less than the distance between distinct crystallographic sites. Let's say value 1.5 Å is absolute maximum.

Another good thing before using supercell with such complex structure is to visually check the structure (see image below).

In the picture you can clearly see that 6 O2 atoms make a ring with interatomic distance is around 0.5 Å. Obviously this ring can by occupied only by one oxygen atom (typical O-O distance is more than 2.0 Å). Please also note that O2 atom occupancy is 0.167. 0.167*6(atoms in ring) = 1.0. That means that it is always one O atom in the position. Therefore this site is not "occupancy" disordered, but "displacement" disordered. Simply speaking the O2 atoms move from central position to one of the positions on the ring because of another sites disorder. Your case is similar to case of PZT ceramics (described in supercell tutorial) where Pb atoms moves from high symmetry position because of Zr-Ti site disorder. In case of PZT the Pb atoms displacement are small. Therefore it can be combined to one group without problems. In your case the displacement is too much to be group automatically. Therefore you should put the O2 atom to high symmetry position manually.
First of all O2 site has a multiplicity 18. The "central" position should have a multiplicity 18/6(atoms in O2 ring)=3. Checking crystallography data for the spacegroup (http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list?gnum=166&grha=hexagonal) you can see two special positions with multiplicity 3: 3a and 3b. The relevant position is 3b (almost the same z coordinate as O2 original position). Therefore just change the O2 line to

O2 O2- 3 b 0.0 0.0 0.5 0.0198(22) 1.0 0

The result you can see below

O2old - the old 18h position, O2 - new "central" position.

If you have doubts that the new structure is not the same that the initial one, don't worry. During the MD simulation the O2 atom will move to more energetically preferable position.

Feel free to ask any questions. When the problems are solved, please close the issue. If you have another questions, not related to this topic, don't hesitate to open another issue. I'm also happy to receive any feedback about supercell program.
Kirill.

[PheLiBoP]

Dear Kirill,
Thank you very much for your help. The issues have been solved ^ ^
The first one by changing the labels and the second by using the suggested position. I will proceed with the creation of a bigger supercell. I hope you have a nice week.

-----------------------------------------------------
-               Supercell program                   -
-----------------------------------------------------
-      Authors:   * Kirill Okhotnikov               -
-                  ([email protected])    -
-                 * Sylvian Cadars                  -
-                  ([email protected])     -
-                 * Thibault Charpentier            -
-                  ([email protected])    -
-----------------------------------------------------
-  please cite:                                     -
-    K. Okhotnikov, T. Charpentier and S. Cadars    -
-    J. Cheminform. 8 (2016) 17 – 33.               -
-----------------------------------------------------

Initial system:
  Chemical Formula: Al0.99 C0.498 H9 Mg2.01 O9

Supercell system (1x1x1):
  Size a=3.04535, b=3.04535, c=22.701

Current charge balance option is "try"
Total charge oxidation state (cif):  -0.0179999
Total charge cell:   -0.0179999
Charge balancing:   yes
----------------------------------------------------------------
| Atom Label	| 	charge  	| mult	| occup x mult
| 		| Ox. state	| Used	| (cif)	|		 
----------------------------------------------------------------
|  Al1		|  3		|  3	|  3	|  0.99
|  C1		|  4		|  4	|  6	|  0.498
|  H1		|  1		|  1	|  6	|  6
|  H2		|  1		|  1	|  6	|  3
|  Mg1		|  2		|  2	|  3	|  2.01
|  O1		|  -2		|  -2	|  6	|  6
|  O2		|  -2		|  -2	|  3	|  3
----------------------------------------------------------------

Chemical formula of the supercell: Al1 C0 H11 Mg2 O9
Total charge of supercell: 0

----------------------------------------------------
 Identification of groups of crystallographic sites 
----------------------------------------------------

 Group 1 (3 atomic positions in supercell):
  * Site #1: Mg1 (occ. 0.67) -> distributed over 2 positions out of 3 (actual occ.: 0.667).
  * Site #2: Al1 (occ. 0.33) -> distributed over 1 positions out of 3 (actual occ.: 0.333).
  Number of combinations for the group is 3

 Group 2 (6 atomic positions in supercell):
  * Site #1: C1 (occ. 0.083) -> distributed over 0 positions out of 6 (actual occ.: 0.000).
  * Site #2: H2 (occ. 0.5) -> distributed over 5 positions out of 6 (actual occ.: 0.833).
  Crystallographic sites with different positions found for this group.
  Maximum distance within the group: 0.0068103 A.
  Number of combinations for the group is 6

 Group 3 (6 atomic positions in supercell):
  * Site #1: H1 (occ. 1) -> FIXED with occupancy 1.000.

 Group 4 (6 atomic positions in supercell):
  * Site #1: O1 (occ. 1) -> FIXED with occupancy 1.000.

 Group 5 (3 atomic positions in supercell):
  * Site #1: O2 (occ. 1) -> FIXED with occupancy 1.000.

Minimal distance between atoms of two distinct groups: 1.03721 A.

-------------------------------------------------
The total number of combinations is 18
-------------------------------------------------