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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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Oxygen number n type cannot be detected! #45

Closed ghost closed 3 years ago

ghost commented 3 years ago

Upon runnin the following command:

$ lammps-interface -ff MOF_FF HKUST-1.cif

With the attached file, the following output is produced:

fatal: ambiguous argument 'HEAD': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
No bonds reported in cif file - computing bonding..
totatomlen = 672
compute_topology_information()
func: cartesian_coordinates; Elps. 0.011s
func: min_img_distances; Elps. 2.995s
func: compute_bonding; Elps. 4.097s
func: init_typing; Elps. 4.293s
func: bond_typing; Elps. 4.304s
Detecting Inorganic clusters
Found Cu Paddlewheel
Found Cu Paddlewheel
<...>
Found Cu Paddlewheel
func: detect_clusters; Elps. 27.125s
func: angles; Elps. 27.129s
func: dihedrals; Elps. 27.134s
func: improper_dihedrals; Elps. 27.139s
Oxygen number 49 type cannot be detected!

First of all I am unsure why there is a Git fatality, even though Git has not been initiated in the respective folder. Nonetheless, other examples run until completion while also producing this error message, so I suspect this is not the issue.

The issue occurs with all of the structure files I have tried so far, including the one from http://www.crystallography.net/cod/2300380.html (after trimming a couple of irrelevant lines). Assistance would be much appreciated!

ghost commented 3 years ago

Apparently I was running the code with a .cif file which contained some oxygen from experimental data, but which one should not expect in the perfect HKUST-1. Silly me.