Manipulation

Hint

Use JKQC help to get idea what everything it can do:

JKQC -help

Generally, use JKQC in one of the following formats:

JKQC <File(s)> <Database(s)> <Options/Parameters>

However, I would first recommend to keep the file names in the below suggested format (automatically done within JKCS).

File names

To get full functionality of JKQC, keep the file names in the following format:

>> ls
1sa.log 1am.log 2am3sa-1conf.log 2am3sa-2conf.log 2sa-12_23.log
1sa.xyz 1am.xyz 2am3sa-1conf.xyz 2am3sa-2conf.xyz 2sa-12_23.xyz

This means that name has of formation of enumerated monomers composition and any additional comments are separated by a hyphen.

These are strong recommendations for your file names:

Nomenclature for molecules

neutral

positive

negative

1sa = sulfuric acid

1b = bisulphate

1msa = methanesulfonic acid

1mb = methanebisulphate

1nta = nitric acid

1nt = nitrate

1am = ammonia

1am1p = ammonium

1ma = methylamine

1ma1p = methylammonium

1dma = dimethylamine

1dma1p = dimethylammonium

1tma = trimethylamine

1tma1p = trimethylammonium

1eda = ethylendiamine

1eda1p = ethylendiammonium

1gd = guanidine

1gd1p = guanidium

1w = water

1w1p = hydronium

1oh = hydroxide

Hint

If you work with molecules and want to calculate, e.g., atomization energies, use the following naming:

>> ls
1H.log 1C.log 3C8H.log 3C8H-stretched.log
1H.xyz 1C.xyz 3C8H.xyz 3C8H-stretched.xyz

Do not forget to use correct spin multiplicities, e.g.: H=2, C,O,S=3, N=4.

Note

By default, it is assumed that structures are saved in *.xyz file, the Gaussian/XTB output is saved in *.log files, and ORCA outputs in *.out files. You can however modify that by, e.g.:

JKQC -collect log -orcaext log -out collectedorca.pkl

Database manipulation

Input

<Files>

input files can be any .log, .out, and .xyz files. However, if you specify, e.g., *.log, it will collect information from all files with the same name.

database.pkl

loads database.pkl file. You can load several databases into one

Input data

Specified

Description

NOTHING

takes in all .log files working in folder

FILES

takes in all specified .log, .out, .xyz files

DATABASES

takes in all specified (-in) .pkl databases

COMBINED

FILES and DATABASES combined
–folder <PATH>

collects data from a given folder

–collect <string>

collects data for

Output

–out database.pkl

output database.pkl pickled file

Output database

Specified

Description

NOTHING

in classified conditions: mydatabase.out

DATABASE

saves all input data into -out specified .pkl database

You can print various properties (see the section below), e.g.:

JKQC *.log -b -el    #[basename] [electronic_energy]

You can print various other files:

-xyz

creates xyz files for all pickled files

-movie

concatenate all xyz into movie.xyz

-imos_xlsx

Excel sheet input for IMoS

Printing properties

See JKQC help JKQC -help for all various properties. For instance, you can print (name and) electronic energy from files/database:

JKQC *.log -b -el        #[basename] [electronic_energy]
JKQC database.pkl -b -el #significantly faster

Processing

You can extract (name and) electronic energy for a specific cluster(s):

JKQC in.pkl -extract 1sa2w -b -el
JKQC in.pkl -extract 3sa,1sa0-10w -b -el

You sort your data with respect to el = electronic_energy/g = gibbs_free_energy

JKQC in.pkl -sort el -b -el
JKQC in.pkl -sort g -out out.pkl

Certainly utilize some filtering techniques (see JKQC help for greater detail):

  • Uniqueness: -uniq rg,el or -arbalign 0.38 (CITE ArbAlign)

  • Low/High cutoff: -pass lf 0 (removes structures with negative/imaginary frequencies), -cut rg 10 (select structures with Rg less than 10 Angstrom), -cutr el 10 (selects only 10 lowest kcal/mol structures)

  • Reacted: -reacted (compares all conformers and tries to remove some reacted/exploded structures)

Post-processing

This an example how to print binding free energies in kcal/mol while taking only the global free energy minimum

JKQC clusters.pkl monomers.pkl -ct -g -glob -formation -unit -noex

and now with using treatment for low vibrational frequencies and anharmonicity correction (CITE Grimme):

JKQC clusters.pkl monomers.pkl -ct -g -glob -fc 100 -v 0.996 -formation -unit -noex

and now, assuming that the *.log files (Gaussian) were accompanied with *.out (ORCA) single-point corrections:

JKQC clusters.pkl monomers.pkl -ct -gout -globout -fc 100 -v 0.996 -formation -unit -noex

and now, at different temperature:

JKQC clusters.pkl monomers.pkl -ct -gout -globout -fc 100 -v 0.996 -formation -unit -noex -temp 270