Author Topic: Generating framework.def and labeling cif by atom type  (Read 94 times)


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Generating framework.def and labeling cif by atom type
« on: May 17, 2023, 09:28:39 PM »

I have a question about utilizing flexible frameworks in a GCMC simulation in Raspa:

Is there an easy way to generate a cif which is labeled by atom types such that each atom type can be uniquely defined in bonds/angles/dihedrals/impropers a framework.def file? I hope to write my own framework.def file for UFF atom types, I see that there are some example framework.def files in the examples directory in the RASPA install, but they don't seem to have all the types in UFF e.g. C atoms in rings C_R.

One approach I was thinking of using was taking a cif -> lammps datafile generated from the lammps_interface from Boyd et al. ( since it determines the hybridizations and identifies atom types corresponding to UFF, and then using that to re-generate a cif file which has unique atom names (e.g. C_3, C_R, C_R, C_R...  from the original cif of just C, C, C, C...), from which I can then write the framework.def file of every unique grouping for bonds/angles/dihedrals/impropers.

Is there a better or more conventional way to do this than going through the hassle of using lammps_interface to do this?

Thanks in advance!