Unhandled Exception reached the top of main: single data block expected, got 2, application will now exit

[orex]

Unhandled Exception reached the top of main: single data block expected, got 2, application will now exit

[orex]

CIF file contains several structures, but supercell can work with only one at time.

[Hcx99]

Thank you very much for your reply! The problem has been solved, thank you very much!

[orex]

Awesome! Don't hesitate to contact me in case of any problem.

[Hcx99]

Sorry to bother you again! I have a question: I now have a crystal structure with fractional occupancy, and I want to create a fractional occupancy doping structure by doping the structure with elements. Can supercell implement this? Thank you very much!

[orex]

Yes. Sure supercell can do this. Probably you will need to edit cif file to add the doping elements. Check tutorial for more details
https://orex.github.io/supercell/docs/tutorial/

[Hcx99]

Do you mean "edit cif file" by adding doping elements and occupancy numbers directly to cif file? I have seen many examples in the toturial file before, but I am not quite clear which example is about doping elements. Could you please kindly inform me?

[orex]

Please provide more information for doping? Which kind of defect and how you want to introduce to your compounds.

[Hcx99]

There are two kinds of Li in my structure, Li1 and Li2 are both fractional occupied, I want to doping Ga element at the Li site, the proportion of Ga doping in Li1 and Li2 is not evenly distributed.

It looks something like this：
loop_
_atom_site_label
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_adp_type
_atom_site_U_iso_or_equiv
_atom_site_type_symbol
Li1 0.9620 0.375000 0.000000 0.250000 Uiso 0.033000 Li
Ga1 0.0380 0.375000 0.000000 0.250000 Uiso 0.033000 Ga
Li2 0.2804 0.687400 0.581500 0.098700 Uiso 0.012670 Li
Ga2 0.0113 0.687400 0.581500 0.098700 Uiso 0.012670 Ga

[orex]

Everything looks OK. What is the problem?

[Hcx99]

No, this example I found from the database, its doping concentration does not meet my requirements, so I want to find a way to doping other concentrations.

[orex]

Such cases are descibed in tutorial. You can change either _atom_site_occupancy values in cif file, or use -p option. Check manual also.

[Hcx99]

It's like you said change _atom_site_occupancy values in cif file,doping Li site with Ga elements, Li1 and Li2 are available, so how should occupancy from Li1 and Li2 be determined?

[Hcx99]

I'm sorry to bother you! I have a problem. I can filter The original structure by supercell, but when I mixed the elements, The total number of combinations is 12223933875394560(~1.2e+16).

ERROR: The Number of total combinations is too high to work with.

[orex]

Yes. It is really to high number to process. There is some tricks that you can use to reduce such number. Please check
https://orex.github.io/supercell/docs/tutorial/
Section "Application of supercell program to Rb-PST-1 zeolite".

[Hcx99]

I'm sorry I can't understand the -p "rb2’s much-publicised: p = 0" -p "r (Si1 | Ga1) : fixed" this phrase, p = 0 mean? i have two Li sites in my structure, both fractional occupied, and Zr/Sb sites. If I want to fix Li sites first, command supercell -i Sb0.5.cif -q -p "r (Li1) : fixed" -p "r (Li2) : fixed" -m -v 2-n l10-o Sb05_out/LLZO Is this correct?

[orex]

I would run
supercell -i Sb0.5.cif -q -p "Li*:fixed" -m -v 2-n l10-o Sb05_out/LLZO
In this case Li sites will be excluded from permutations and as a result you will get a set of structures with fractional Li sites.