JKCS3_run

JKCS3_run utilizes 3rd-party programs to optimize clusters and evaluate their properties (e.g., electronic energy or free energies). The script either uses the output structures in the folder from previous step (e.g., XTB, ABC, DFT_opt) or those listed in a file (e.g., resultsXTB.dat).

Hint

For help use:

JKCS3_run -help

For instance, if you want to run XTB calculations on structures from ABC folder, you run (of = old folder):

JKCS3_run -of ABC
JKCS3_run          #this would do the same

If you did collect (and filter) structures into a file (e.g., resultsXTB.dat), to use those run (rf = results file):

#JKCS4_collect XTB
JKCS3_run -p G16 -m "# wb97xd 6-31++g** opt=verytight" -nf DFT_opt -rf XTB
JKCS3_run -p G16 -m "# wb97xd 6-31++g** opt=verytight" -nf DFT_opt -rf resultsXTB.dat #this would do the same

If you did extra-filter the data and resultsXXX_FILTERED.dat exists, it will be used instead of resultsXXX.dat:

#JKCS4_collect XTB
#JKCS5_filter -d 10  #selects only the 10 lowest kcal/mol
JKCS3_run -p G16 -m "# wb97xd 6-31++g** opt=verytight" -nf DFT_opt -rf XTB
JKCS3_run -p G16 -m "# wb97xd 6-31++g** opt=verytight" -nf DFT_opt -rf resultsXTB_FILTERED.dat #this would do the same

Hint

You can check if your calculations are still running by using:

JKcheck
JKcheck XTB

Note

Charges and multiplicities are handled by JKCS based on parameters.txt

XTB examples

After ABC exploration, you can directly run XTB by:

JKCS3_run
JKCS3_run       -p XTB        -of ABC        -nf XTB      -m "-opt vtight" #this would do the same
JKCS3_run -program XTB -oldfolder ABC -newfolder XTB -method "-opt vtight" #this would do the same

Some other options:

JKCS3_run -p XTB -of ABC -nf XTB      -m "-opt vtight --gfn 1"
JKCS3_run -p XTB -rf XTB -nf XTB_freq -m "-ohess -temp 298.15"

Note

If you did pickle structures after ABC exploration, you should use -JKQC command also now:

#JKCS2_explore -gen 200 -pop 1000 -lm 3000 -JKQC
JKCS3_run -JKQC

Gaussian examples

JKCS is well working with Gaussian16 = G16. Although, it should work with other versions as well. The commands are similar to those in XTB. Examples:

JKCS3_run -p G16 -rf XTB     -nf DFT_sp   -m "# HF 6-31+g*"
JKCS3_run -p G16 -rf XTB     -nf DFT_opt  -m "# wb97xd 6-31++g** opt=verytight"
JKCS3_run -p G16 -rf DFT_opt -nf DFT_freq -m "# wb97xd 6-31++g** freq"
JKCS3_run -p G16 -rf XTB     -nf DFT      -m "# wb97xd GEN Pseudo=Read Opt Int=UltraFine Freq MaxDisk=32GB" -bc I -mem 12GB -cpu 16

ORCA examples

This is not that well tested as people usually use their own scripts for ORCA, however, you should be able to run it as well. Examples:

JKCS3_run -p ORCA -rf XTB      -nf OPT   -m "! PBE0 def2-TZVP TIGHTSCF Opt D3BJ"
JKCS3_run -p ORCA -rf DFT_freq -nf DLPNO -m "! DLPNO-CCSD(T) aug-cc-pvtz aug-cc-pvtz/C GRID4 nofinalgrid TightPNO TightSCF NOPOP NOPRINTMOS"

Arguments

-JKQC

after the run, the structures are pickled into a single file (database.pkl, see JKQC for more details). This saves memory and significantly reduces number of files.

-nf, -newfolder <string>

name of the new (calculation) folder. [default = “XTB”]

-of, -oldfolder <string>

name of the old (calculation) folder. Do not combine with -rf. [default = “ABC”]

-rf, -resultsfile <string>

name of the results file (e.g., XTB, resultsXTB.dat, resultsXTB_FILTERED.dat) containing list of structures for further calculation. When -rf “NAME” is used and resultsNAME_FILTERED.dat is available, it is used instead of resultsNAME.dat. Do not combine with -of.

-m, -method <string>

method used by 3rd-party program [default for XTB = “-opt vtight”]

-bs, -add, -addbase <atom>

insert basis set for heavy atoms to the end of file (only for Gaussian) and yet only for atoms like I or Br