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 ofresultsNAME.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