by Pasquale Pavone for exciting neon
Purpose: Here, it will be given fundamental information on how to set exciting before starting with the calculation performed in the hands-on tutorials.
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Table of Contents
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1. Setting environment variables
The next instructions have to be executed only once before starting your first tutorial!
For a correct installation of exciting neon, users need to set some important environment variables:
- EXCITINGROOT = Full path of the directory in which the exciting neon code can be found. For "IMPRS 2023" participants this path is fixed to /data/scratch/how-exciting-2023/exciting-git .
The above variable is used to define other environment variables
- EXCITINGTOOLS = Directory where the tutorial scripts are located, defined as $EXCITINGROOT/tools/tutorial_scripts .
- TIMEFORMAT = Output format for writing on the screen the running elapsed time, used in some script.
The setting of these variables can be done in a bash shell by appending to the ~/.bashrc file in your $HOME directory the following shell snippet.
#=====================================================================================
# The following shell variables are needed for executing scripts in exciting tutorials
#
export EXCITINGROOT=/data/scratch/how-exciting-2023/exciting-git
export EXCITINGTOOLS=$EXCITINGROOT/tools/tutorial_scripts
#-------------------------------------------------------------------------------------
export TIMEFORMAT=" Elapsed time = %0lR"
#-------------------------------------------------------------------------------------
export WRITEMINMAX="1"
ulimit -s unlimited
module purge
module load intel-oneapi
export OMP_NUM_THREADS=4
#-------------------------------------------------------------------------------------
export PYTHONPATH=$PYTHONPATH:$EXCITINGTOOLS/stm
export PATH=$PATH:$EXCITINGTOOLS:$EXCITINGROOT/bin:$EXCITINGTOOLS/stm
alias xcrysden=/usr/global/xcrysden-1.5.24/xcrysden
#=====================================================================================A shell script to add this snippet to your $HOME/.bashrc file is the script UPDATE-bashrc.sh that you can find in the directory /data/scratch/how-exciting-2023 . It can be executed as following (from now on and for the whole tutorials the symbol $ will indicate the shell prompt)
$ /data/scratch/how-exciting-2023/UPDATE-bashrc.shIn order to activate the changes in $HOME/.bashrc, you must use the commands
$ source $HOME/.bashrcYou can check if everything went well by typing
$ echo $EXCITINGROOT
/data/scratch/how-exciting-2023/exciting-gitEverything is ok if you get /data/scratch/how-exciting-2023/exciting-git as a replay.
2. Download and compile exciting
Contrary to general users of exciting, you do not have to download and compile exciting.
A shared-memory version of exciting, exciting_smp compiled with ifort (intel-2019), is available for you in /data/scratch/how-exciting-2023/exciting-git/bin
($EXCITINGROOT/bin). You can check this by typing on the command line the following command
$ ls $EXCITINGROOT/bin
exciting_smp3. Tutorial scripts
All the scripts used in the exciting tutorials are stored in the directory $EXCITINGROOT/tools/tutorial_scripts .
4. Work directory
Before starting the calculations of the hands-on tutorial, a work directory has to be created.
- We strongly suggest to create this directory as $HOME/IMPRS.
$ mkdir $HOME/IMPRS- Move to the work directory $HOME/IMPRS and start the tutorial Graphene: From ground state to excitations (link).
$ cd $HOME/IMPRS5. Tips for Linux beginners
i) Useful commands for our workstations (as implemented in the standard $HOME/.bashrc file)
- For editing a file named NAMEFILE, the suggested editor command (using kwrite) is
$ g NAMEFILE- For visualizing PNG, JPEG, and PDF files, use the command okular. A useful short cut is oku, as shown in the following.
$ oku NAMEFILE.png- For visualizing specifically the file PLOT.png, you can use the simple command opng :
$ opng