[ase-users] Wrong atom number reading cif files

[Landi, 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"


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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