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peteboyd / lammps_interface

automatic generation of LAMMPS input files for molecular dynamics simulations of MOFs
MIT License
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Undesired atom type assignment of aluminium with UFF4MOF #46

Closed greigcs closed 3 years ago

greigcs commented 3 years ago

Thanks a lot for this tool, very useful!

There is however, one MOF is giving me problems: MFM-300(Al), taking the cleaned up cif from the CoRe MOF database, XUPSAE_clean.

I passed it through Lammps Interface using the command "lammps-interface -ff UFF4MOF XUPSAE_clean.cif" and it seems it couldn't decide an atom type for aluminium as it returns the following:

WARNING: Could not find an appropriate UFF4MOF type for Al. Assigning Al3 WARNING: Could not find an appropriate UFF4MOF type for Al. Assigning Al6+3 WARNING: Could not find an appropriate UFF4MOF type for Al. Assigning Al3f2 WARNING: Could not find an appropriate UFF4MOF type for Al. Assigning Al3 WARNING: Could not find an appropriate UFF4MOF type for Al. Assigning Al6+3 WARNING: Could not find an appropriate UFF4MOF type for Al. Assigning Al3f2 ................................................................................................................................................................

This sequence repeats several times and in the end, it chooses Al3f2, which is for tetrahedrally coordinated aluminium, rather than the expected octahedral Al6+3.