python3 script to read and modify Gaussian ONIOM input files
Command line arguments:
1. file name of an oniom input to read
2. name of the file to be produced (of type: oniom input, qm input, xyz)
3. string switch, one from the list given below
4. expected only for the switches: "rag", "rqg", "rqq" and "omod" - name of an additional input file
(of type: xyz (rag and rqg), qout (rqq) or input (omod))
Meaning of the switches:
eag - extract xyz coordinates of all atoms and write into the xyz file
eqg - extract xyz coordinates of H-layer atoms and write into the xyz file
ehmg - extract xyz coordinates of H- and M-layers atoms and write into the xyz file
rag - replace xyz coordinates of all atoms to those read from the xyz file
rqg - replace xyz coordinates of H-layer atoms to those read from the xyz file
rqq - replace H-layer atom charges to those read from the qout (RESP) file
z1 - prepare input for electronic embedding with the z1 charge model
z2 - prepare input for electronic embedding with the z2 charge model
z3 - prepare input for electronic embedding with the z3 charge model
rc - prepare input for electronic embedding with the rc charge model
rcd - prepare input for electronic embedding with the rcd charge model
cs - prepare input for electronic embedding with the cs charge model
wqm - write QM-only Gaussian input
wqm_z1/z2/z3/rc/rcd/cs - write QM-only Gaussian input for ESP(RESP) calculations
omod - modify oniom partitioning (2 or 3-layered) and/or frozen/optimized zone