[ase-users] Wrong atom number reading cif files

[Gaël Donval]

Hi Alessandro,
> Hello everyone.
> 
> 
> I am a PhD student in chemistry at the University of Liverpool and a
> new user of ASE.
> 
> 
> Unfortunately, I am having problems when I try to read the cif of
> TIPS-pentacene (attached) that I downloaded from the Cambridge
> Cristallographic Data Centre.
> 
> 
> As you can see from the attached cif file, TIPS-pentacene has
> chemical formula "C44 H54 Si2"
> 
> 
> However when I use "atoms=ase.io.read(cif_file)", the actual chemical
> formula changes, as I checked by printing "atoms"

I am no CIF expert so someone might come after me and prove me wrong
but it seems that your CIF provides atoms with partial occupancies to
represent disorder while retaining a maximum number of symmetries.

If you don't care about disorder, you could edit the CIF file to remove
the extra atoms (either manually or using a program that can do that).
There are ways to make the overlapping atom check more strict (so that
ASE would get rid of the copies), but this is not going to work here
for a couple of hydrogens. You could also use ASE GUI, and manually
select and delete copies (using backspace).

Basically just remove all the primed atomes (C20', etc.) and the D, E,
F variants of hydrogen in the CIF file and it'll work with ASE.

Cheers,
Gaël

> 
> 
> Atoms(symbols='C48H68Si2', pbc=True, cell=[[7.565, 0.0, 0.0],
> [0.8598515049547191, 7.702152646463657, 0.0], [3.3793900993103994,
> -0.1259731853643117, 16.49184884460357]])
> 
> Is it possible that it is due to the disorder in the cif file?
> 
> 
> In any case, how can I avoid this problem and read (or get after some
> manipulations) only the atoms constituting the actual molecule? (I
> don't care about the disorder since I only need a reasonable
> structure to do some QM computations on it)
> 
> 
> Thanks in advance.
> 
> 
> Best regards,
> 
> Alessandro
> 
> 
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