README.md

-# bccr_icesm_workshop
+## Tutorial to work with iCESM water isotope output on NIRD infrastructure
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/git/https%3A%2F%2Fgit.app.uib.no%2FGFI-public%2Fbccr_icesm_workshop/HEAD?labpath=bccr_icesm_tutorial%2FiCESM%2FBCCR_notebook_final.ipynb)
-
-## Getting started
-
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
-
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
-
-## Add your files
-
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-
-```
-cd existing_repo
-git remote add origin https://git.app.uib.no/GFI-public/bccr_icesm_workshop.git
-git branch -M main
-git push -uf origin main
-```
-
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://git.app.uib.no/GFI-public/bccr_icesm_workshop/-/settings/integrations)
-
-## Collaborate with your team
 
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-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
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-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
+## Description
+This project contains the material from the Bjerknes Centre Fast-track initiative focused on introducing water-isotope enabled climate model simulation data to Bjerknes Centre scientists.
 
-## Suggestions for a good README
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
+Two simulations have been run with iCESM1.2 and iCESM2.0. We provide a fully documented jupyter notebook that allows to easily plot and analyze data from these model simulations.
 
-## Name
-Choose a self-explaining name for your project.
+A more detailed documentation is available in the [project Wiki](https://git.app.uib.no/GFI-public/bccr_icesm_workshop/-/wikis/home)
 
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
+The project documentation will be detailed further in the future.
 
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/git/https%3A%2F%2Fgit.app.uib.no%2FGFI-public%2Fbccr_icesm_workshop/HEAD?labpath=bccr_icesm_tutorial%2FiCESM%2FBCCR_notebook_final.ipynb)
 
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 ## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
 
 ## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
 
 ## License
-For open source projects, say how it is licensed.
+ This project is licensed under the GNU General Public License v3.0 or later. [[ Learn more | https://git.app.uib.no/GFI-public/bccr_icesm_workshop/-/blob/main/LICENSE]]
 
 ## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.

bccr_icesm_tutorial/iCESM/environment.yml

-name: icesm_work
+name: CHESS_WS2024
 channels:
     - conda-forge
     - defaults

icesm_high_frequency_setup.sh

+#!/bin/sh
+
+#Execute the script in cluster/home/user
+
+#Fill in your username and project number below!
+USER="username"
+PROJECT="nn9555k"
+	
+CASE_NAME="test_icesm_high_frequency3"
+
+#echo $PROJECT
+##Script stops and  shoots an error message if command fails
+#set -e
+
+files_dir=$(pwd)
+
+
+##GO INTO SCRIPTS
+cd /cluster/home/$USER/$PROJECT/progs/iCESM1.2/iCESM1.2/scripts/
+
+
+##CREATE THE CASE
+./create_newcase -case $CASE_NAME -res f19_g16 -compset B1850CN -mach fram
+
+
+##GO INTO THE CASE
+cd $CASE_NAME
+
+
+##RUN THE SETUP 
+./cesm_setup
+
+
+##COPY DIAGNOSTIC FILE FROM MODEL BASE TO CASE
+cp /cluster/home/$USER/$PROJECT/progs/iCESM1.2/iCESM1.2/models/atm/cam/src/physics/cam/cam_diagnostics.F90 SourceMods/src.cam/
+
+##MAKE SOFT LINK TO GET FILES
+ln -s /cluster/work/users/hso039/noresm/ncar_reference/ /cluster/home/$USER/$PROJECT/progs/iCESM1.2/iCESM1.2/scripts/$CASE_NAME/work
+
+
+##GO BACK TO HOME DIRECTORY
+cd $files_dir
+
+
+##MOVE THE MODIFIED FILES TO CASE
+cp -i user_nl_cam /cluster/home/$USER/$PROJECT/progs/iCESM1.2/iCESM1.2/scripts/$CASE_NAME
+cp -i env_run.xml /cluster/home/$USER/$PROJECT/progs/iCESM1.2/iCESM1.2/scripts/$CASE_NAME
+cp -i icesm_high_frequency.run /cluster/home/$USER/$PROJECT/progs/iCESM1.2/iCESM1.2/scripts/$CASE_NAME/$CASE_NAME.run
+
+
+echo "The case icesm_high_frequency has been set up in scripts"
+
+
+########DOWNLOAD NECESSARY RESTART FILES
+
+#Move to directory where restart files will be downloaded
+
+#cd /cluster/projects/$PROJECT/work/iCESM1.2
+
+#echo "Start downloading reastart files"
+
+##Downloading list of startup files
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.cam.h0.1849-12.nc 
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.cam.h1.1850-01-01-00000.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.cam.i.1850-01-01-00000.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.cam.rs.1850-01-01-00000.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.cice.r.1850-01-01-00000.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.clm2.h0.1849-12.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.clm2.h1.1850-01-01-00000.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.clm2.r.1850-01-01-00000.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.clm2.rh0.1850-01-01-00000.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.clm2.rh1.1850-01-01-00000.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.cpl.r.1850-01-01-00000.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.pop.r.1850-01-01-00000.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.pop.ro.1850-01-01-00000
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.rtm.h0.1849-12.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.rtm.r.1850-01-01-00000.nc
+#wget -nc https://zenodo.org/record/3553753/files/b.ie12.B1850C5CN.f19_g16.LME.002.rtm.rh0.1850-01-01-00000.nc
+#wget -nc https://zenodo.org/record/3553753/files/rpointer.atm
+#wget -nc https://zenodo.org/record/3553753/files/rpointer.drv
+#wget -nc https://zenodo.org/record/3553753/files/rpointer.ice
+#wget -nc https://zenodo.org/record/3553753/files/rpointer.lnd
+#wget -nc https://zenodo.org/record/3553753/files/rpointer.ocn.ovf
+#wget -nc https://zenodo.org/record/3553753/files/rpointer.ocn.restart
+#wget -nc https://zenodo.org/record/3553753/files/rpointer.rof
+#wget -nc https://zenodo.org/record/3553753/files/surfdata_1.9x2.5_simyr1850_c140303.nc
+
+echo "All restart files downloaded"
+
+
+
+echo "Script finished successfully"
+
+
+
+