Setup & Installation

Note

In order to install and use JKQC and JKML you need to install JKCS!

Requirements

git
Python >3.8 but <4.0

Depending on your need other programs are required too (e.g. ABCluster, XTB, Gaussian, ORCA)

JKCS

Clone the JKCS from github, (modify setup [see the hint below first]), and run setup.sh (this might take a while):

git clone https://github.com/kubeckaj/JKCS2.1.git
cd JKCS2.1
sh setup.sh -help  #see the help first
sh setup.sh -r     #-r = rewrites your current ~/.JKCSusersetup.txt setup
#or: sh setup.sh -r -python python3.9 -module "module load python-data/3.9"

Once you modify all paths in ~/.JKCSusersetup.txt, you can check if everything that you need is set properly by:

sh test.sh

If something fails, you must modify ~/.JKCSusersetup.txt in order to use the JKCS features.

Hint

Users of some clusters (Puhti, Mahti, Grendel) can use predefined paths and python modules by typing:

sh setup.sh puhti -r   #for Puhti users
sh setup.sh grendel -r #for Grendel users
sh setup.sh mahti -r   #for Mahti users

Note

If you need to resetup the JKCS use -r or -r2, e.g.:

sh setup.sh -r grendel   #reinstall all python libs and rewrites ~/.JKCSusersetup.txt
sh setup.sh -r2 grendel  #only rewrites ~/.JKCSusersetup.txt

JKQC

All features are automatically installed with JKCS, yeay :-D

JKML

In order to use JKML, you must install some Python packages:

Note

-qml will install all libraries for quantum machine learning (QML)

-nn will install all libraries for neural network modelling (SchNetPack)

-descriptors will install dscribe library for some JKML extra features (-sampleeach)

3rd-party programs

ABCluster

ABCluster can be obtained from http://www.zhjun-sci.com/software-abcluster-download.php The online manual is available at http://www.zhjun-sci.com/abcluster/doc/ Modify the following lines in the ~/.JKCSusersetup.txt:

PATH_ABC="[-ABCluster-folder-path-]"      #e.g.: "/users/kubeckaj/ABCluster-2.0-Linux/"
MODULE_ABC="module load gcc"              #e.g.: "module load gcc/8.2.0" || "module load GCC/8.2.0-2.31.1"

If you want to use the ABCluster program by yourself, put the following lines to your ~/.bashrc file:

export PATH=$PATH:[-ABCluster-folder-path-]
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:[-ABCluster-folder-path-]

then you should be able to use ABCluster, e.g.:

#source ~/.bashrc
module load gcc
bee
...

XTB

The Linux version can be obtained from https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/xtb/xtb The online manual is available at https://xtb-docs.readthedocs.io/en/latest/contents.html Modify the following line in the ~/.JKCSusersetup.txt:

PATH_XTB="[-XTB-folder-path-]"            #e.g.: "/user/kubeckaj/XTB6.4"

If you want to use the XTB program by yourself, either use the full path directory to the executables or put the following lines to your ~/.bashrc file:

export PATH=[-XTB-folder-path-]/bin:$PATH #e.g.: "/user/kubeckaj/XTB6.4/bin"
export XTBHOME=[-XTB-folder-path-]        #e.g.: "/user/kubeckaj/XTB6.4"

then you should be able to run XTB, e.g.:

#source ~/.bashrc
xtb file.xyz --opt vtight

Gaussian

I hope that you know how to call Gaussian jobs. If not ask a blessed person around you how to do it. Usually you load Gaussian from a module, e.g.:

module load gaussian

then you can figure out where are located Gaussian executables, e.g.:

$USER: > which g16
/appl/soft/chem/gaussian/G16RevC.01_new/g16/g16

based on that modify the following lines in the ~/.JKCSusersetup.txt:

PATH_G16="/appl/soft/chem/gaussian/G16RevC.01/"
MODULE_G16="module load gaussian/G16RevC.01"    #"module load Gaussian"

If you want to run Gaussian by yourself, use some predefined scripts (something like subg16 etc.)

How to setup Jupyter

Activate JKCS-python environment for Jupyter

(.venv) $ pip install --user ipykernel
(.venv) $ python -m ipykernel install --user --name=jkcs