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jkcs2.1

Jammy Key framework

https://github.com/kubeckaj/jkcs2.1

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
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    Scientific vocabulary similarity
    Low similarity (10.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Jammy Key framework

Basic Info
  • Host: GitHub
  • Owner: kubeckaj
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 4.6 MB
Statistics
  • Stars: 7
  • Watchers: 1
  • Forks: 5
  • Open Issues: 0
  • Releases: 0
Created almost 7 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

JKCS (=JKCS2.1)

Jammy Key for Configurational Sampling

HOW TO SETUP:

(INSTALLATION: https://youtu.be/9mw45tbj1G4)

git clone https://github.com/kubeckaj/JKCS2.1.git #copy JKCS (JKCS folder is created)
cd JKCS2.1
sh setup.sh                                       #run basic "setup" (installation)
source ~/.bashrc                                  #required after the first "setup"

ADJUST USER SETUP:

(H.Vehkamäki group: Puhti users do not have to adjust it)

vim/nano/emacs ~/.JKCSusersetup.txt               #adjust user setup
#     CHANGE:
# ABCluster: rigidmoloptimizer path
# XTB: xtb path
# PYTHON: please setup how to use python2.0 (python 3.0 is just for GoodVibes in JKCS4)
# Gaussian: G16 path and module
# Orca: Orca path and modules

sh test.sh                                        #test that all your paths#       are set correctly

Simple TEST (on local computer):

(VERY FAST SHOW OF JKCS: https://youtu.be/xKKWZrO-EmU)

(USING JKCS: https://youtu.be/C4dAkhU7O8E)

cd $WRKDIR                 #go to your working directory
mkdir TESTING_JKCS         #create a new forder 
cd TESTING_JKCS            #and enter it
JKCS0_copy --help          #CHECKING POINT:This fail if instal. wasn't succesful or you didn't source ~/.bashrc  
JKCS0_copy SA A            #create input.txt for sulphuric acid and ammonia cluster
ls
#Here you can adjust the input.txt file [vim input.txt]
JKCS1_prepare --help       #explains what is doing this script
JKCS1_prepare              #prepare folders and some files based on input.txt
ls                         #list files and folders
JKCS2_runABC --help        #explains what is doing this script
JKCS2_runABC -gen 10 -lm 10 -pop 10  -loc
                           #CHECK POINT:This fail if you didn't setup rigidmoloptimizer
                           #run 10 bee colony for 10 generations and save 10 best struc.
                           #enter each folder and perform ABCluster exploration
JKcheck                    #check that all calculations were finished
#optional: you can perform [JKCS4_collect ABC -loc] to collect ABC results
JKCS3_runXTB --help        #shows help
JKCS3_runXTB -loc          #CHECKING POINT:This fail if you didn't setup xtb paths in programs.txt properly
JKCS4_collect XTB -loc     #CHECKING POINT:This fail if you didn't setup python properly
                           #this script collect semi-empirically(xtb) optimized structures
cd SYS_1SA_1A              #Enter folder with cluster 1sa1a
cat resultsXTB.dat         #see results [structure | gyration rad. | energy]
molden movieXTB.xyz        #visualize molecules

#######################
# If everything worked, continue, otherwise, contact Jakub Kubecka (ja-kub-ecka@chem.au.dk).
# adjust the rest of file ~/.JKCSusersetup.txt:
# QUEING, QUANTUM CHEMISTRY PROGRAMS etc.

and the rest, you have to consult with manual

Owner

  • Login: kubeckaj
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Kubecka"
  given-names: "Jakub"
  orcid: "https://orcid.org/0000-0002-8002-0911"
title: "Jammy Key for Configurational Sampling"
version: 2.1
doi: 10.1021/acs.jpca.9b03853
date-released: 2019
url: "https://github.com/kubeckaj/JKCS2.1"

GitHub Events

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  • Watch event: 3
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  • Pull request event: 11
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Last Year
  • Watch event: 3
  • Issue comment event: 1
  • Push event: 113
  • Pull request review event: 4
  • Pull request event: 11
  • Fork event: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 5
  • Average time to close issues: N/A
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  • Total pull request authors: 3
  • Average comments per issue: 0
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  • Merged pull requests: 3
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Past Year
  • Issues: 0
  • Pull requests: 5
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 days
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
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