Tutorial for Input Processing with cclib¶
This tutorial shows how to use the cclib Python program package to process quantum chemical output files together with ORBKIT. It is prerequisite to install a current version cclib (>=1.3.1) beforehand by following the installation guide:
Note
Currently, the cclib interface is only tested for Gaussian .log files. If you find any incompatibilities, please do not hesitate to contact us!
Table of Contents:
General Aspects¶
In order to parse a quantum chemical output file with cclib, ORBKIT follows the standard procedure described in cclib’s tutorial, e.g. for a Gaussian output file:
from cclib.parser import Gaussian
p = Gaussian('mycalc.log')
ccData = p.parse()
Afterwards, ORBKIT converts the ccData data set to ORBKIT’s QCinfo class
(cf. Central Variables), i.e.:
from orbkit import read
qc = read.convert_cclib(ccData)
Usage via the Terminal¶
For the standard ORBKIT terminal interface you have to specify two options:
--itype=cclib and --cclib_parser=CCLIB_PARSER. The first tells ORBKIT
to use cclib for parsing the output and the latter specifies which
cclib.parser has to be imported. (The available parser may be found on the
cclib website.)
Thus, to process the Gaussian output file mycalc.log, you have to call:
$ orbkit -i mycalc.log --itype=cclib --cclib_parser=Gaussian
Attention
The option --cclib_parser is case sensitive!
ORBKIT’s High-Level Interface¶
Again, to use the cclib paser, two options have to be called:
import orbkit as ok
ok.options.filename = 'mycalc.log'
ok.options.itype = 'cclib'
ok.options.cclib_parser = 'Gaussian'
data = ok.run_orbkit()
Attention
The option ok.options.cclib_parser is case sensitive!
ORBKIT’s Low-Level Interface¶
For ORBKIT’s low-level interface, there are two possible ways to use cclib.
You can either tell ORBKIT, that it should use the cclib.parser
from orbkit import read
qc = read.main_read(filename,itype='cclib',all_mo=False,cclib_parser='Gaussian')
# This is basically the same as
qc = read.read_with_cclib(filename, cclib_parser='Gaussian', all_mo=False)
or you can do the parsing by yourself and let ORBKIT only convert the data:
from orbkit import read
from cclib.parser import Gaussian
p = Gaussian('mycalc.log')
ccData = p.parse()
qc = read.convert_cclib(ccData)