JKCS4_collect

After JKCS2_explore or JKCS3_run submitted jobs are finished, JKCS4_collect script collects all data within the calculation folder.

JKCS4_collect utilises JKQC to go through all the output files within specified calculation folder.

JKCS4_collect XTB
JKCS4_collect DFT_freq

The main outcome of the JKCS4_collect is, e.g., collectionXTB.pkl file. However, some other readable files are produced, too: collectionXTB.txt (list of files, gyration radii Rg, and energies E), resultsXTB.dat (the same file but after filtering based on [Rg,E] with thresholds of [0.01,0.001], and structures are sorted with respect to energy), and movieXTB.xyz (list of xyz concatenated within one file). For instance, the collectionXTB.txt could contain:

/path/SYS_2sa_2am/XTB_2_2_0_0_0_0_2_1_0/2sa2am-220000_1_0.xyz        2.675910073831769   -56.7011189
/path/SYS_2sa_2am/XTB_2_2_0_0_0_0_2_1_0/2sa2am-220000_1_100.xyz      2.4146549048885455  -56.6972184
/path/SYS_2sa_2am/XTB_2_2_0_0_0_0_2_1_0/2sa2am-220000_1_101.xyz      2.643341483522292   -56.6990367
...

Note

When collecting data with vibrational frequency calculations, the structures in, e.g., resultsDFT_freq.dat will be then sorted with respect to the 4th column = Gibbs free energy.

Hint

The movieXTB.xyz can be easily visualized with Molden:

molden movieXTB.xyz

If you find the collectionXTB.txt, resultsXTB.dat, and movieXTB.xyz files unnecessary, you can only collect (-oc) the pickle:

JKCS4_collect XTB -oc

Hint

I strongly recommend checking JKQC manual for structure post-processing and manipulation of, e.g., collectionXTB.pkl file.

The JKCS4_collect is a submission script. If you used JKCS2_explore or JKCS3_run with the -of argument, then X+1 jobs will be submitted, i.e. one for each subfolder and one for collecting all pickles into one with post-processing (unless the -oc argument (only collect) is used). In other case, 1+1 jobs are submitted. You can use all submission arguments to control the submission (see the submission section), e.g.:

JKCS4_collect XTB -oc -tpj 2 -cleanfull
JKCS4_collect DFT_freq -loc
JKCS4_collect ABC -par q64 -cpu 1 -time 1-00:00:00 -arraymax 2
JKCS4_collect DLPNO -oc -par qtest -time 10:00

API

<string>

name of the folder which should be analysed (e.g. XTB)

-clean

after collecting, removes all unnecessary files (.xyz|.log|.out|.com|.cmd). This saves memory and significantly reduces number of files.

-cleanfull

after collecting, completely removes the analysed folder. This saves memory and significantly reduces number of files.

-JKQCrecollect

if it happens that something fails, or you did collect folder when the jobs were still running, then the pickle files in subfolders are already created and you must force to recollect the QC outputs by this argument. (Equivalent to rm XTB/*/*/*.pkl XTB/*/*.pkl on init.)