Skip to content

Commit

Permalink
Update documentation
Browse files Browse the repository at this point in the history
  • Loading branch information
cecilehannay committed Aug 8, 2024
0 parents commit 931ba91
Show file tree
Hide file tree
Showing 583 changed files with 161,618 additions and 0 deletions.
4 changes: 4 additions & 0 deletions .buildinfo
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 08c226f57982fca33cc7beee8c87c901
tags: 645f666f9bcd5a90fca523b33c5a78b7
Empty file added .nojekyll
Empty file.
753 changes: 753 additions & 0 deletions README.html

Large diffs are not rendered by default.

Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CAMchem_compsets.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_CIME_Infrastructure.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_Code_Components_List.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_Create_Newcase_Command.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_Create_Newcase_Compset.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_Create_Newcase_Resolution.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_Discuss.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_Events.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_MCT_Coupling.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_Porting.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_Workspaces_Code.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_Workspaces_Detail.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_case_build.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_case_setup.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_case_submit.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_create_newcase.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_github_CESM.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_github_ESCOMP.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_github_main.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_short_term_archive.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM2_xml_files.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM_NUOPC_Coupling.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM_directories_and_SourceMods.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/CESM_directories_and_log_files.png
Binary file added _images/CESM_directories_and_namelists.png
Binary file added _images/CESM_exp_1.png
Binary file added _images/CESM_exp_2.png
Binary file added _images/CESM_exp_3.png
Binary file added _images/CESM_github.png
Binary file added _images/Diagnostics_1.png
Binary file added _images/Diagnostics_2.png
Binary file added _images/Diagnostics_3.png
Binary file added _images/Diagnostics_4.png
Binary file added _images/Diagnostics_5.png
Binary file added _images/Diagnostics_6.png
Binary file added _images/Diagnostics_7.png
Binary file added _images/Diagnostics_8.png
Binary file added _images/Diagnostics_duo_pcode.png
Binary file added _images/Fcompset.png
Binary file added _images/NCVIEW_App_Window.png
Binary file added _images/NCVIEW_Jan0001_PRECC.png
Binary file added _images/NCVIEW_Jan0001_PRECL.png
Binary file added _images/NCVIEW_Jan0001_TS.png
Binary file added _images/Precip_isotope_Cartoon.jpg
Binary file added _images/WACCM_compsets1.png
Binary file added _images/WACCM_compsets2.png
Binary file added _images/advanced_plot_1.png
Binary file added _images/advanced_plot_11.png
Binary file added _images/advanced_plot_12.png
Binary file added _images/advanced_plot_2.png
Binary file added _images/advanced_plot_21.png
Binary file added _images/advanced_plot_3.png
Binary file added _images/advanced_plot_4.png
Binary file added _images/advanced_plot_5.png
Binary file added _images/advanced_plot_6.png
Binary file added _images/basics_plot_1.png
Binary file added _images/basics_plot_10.png
Binary file added _images/basics_plot_101.png
Binary file added _images/basics_plot_11.png
Binary file added _images/basics_plot_12.png
Binary file added _images/basics_plot_13.png
Binary file added _images/basics_plot_14.png
Binary file added _images/basics_plot_2.png
Binary file added _images/basics_plot_21.png
Binary file added _images/basics_plot_22.png
Binary file added _images/basics_plot_23.png
Binary file added _images/basics_plot_24.png
Binary file added _images/basics_plot_3.png
Binary file added _images/basics_plot_31.png
Binary file added _images/basics_plot_32.png
Binary file added _images/basics_plot_33.png
Binary file added _images/basics_plot_34.png
Binary file added _images/basics_plot_4.png
Binary file added _images/basics_plot_41.png
Binary file added _images/basics_plot_42.png
Binary file added _images/basics_plot_43.png
Binary file added _images/basics_plot_44.png
Binary file added _images/basics_plot_5.png
Binary file added _images/basics_plot_51.png
Binary file added _images/basics_plot_52.png
Binary file added _images/basics_plot_53.png
Binary file added _images/basics_plot_6.png
Binary file added _images/basics_plot_61.png
Binary file added _images/basics_plot_62.png
Binary file added _images/basics_plot_63.png
Binary file added _images/basics_plot_7.png
Binary file added _images/basics_plot_71.png
Binary file added _images/basics_plot_72.png
Binary file added _images/basics_plot_8.png
Binary file added _images/basics_plot_81.png
Binary file added _images/basics_plot_82.png
Binary file added _images/basics_plot_9.png
Binary file added _images/basics_plot_91.png
Binary file added _images/bgc_table_1.png
Binary file added _images/bgc_table_2.png
Binary file added _images/cam_SST_diff.png
Binary file added _images/cam_topo_diff.png
Binary file added _images/cape.png
Binary file added _images/chemistry-mechanism-example.png
Binary file added _images/chemistry-ozone-reaction.png
Binary file added _images/chemistry-ozone-reaction_orig.png
Binary file added _images/chemistry-preprocessor-info.png
Binary file added _images/chemistry-rundir-example.png
Binary file added _images/cice_rsnw2.png
Binary file added _images/clim_data_gateway.png
Binary file added _images/clim_data_guide.png
Binary file added _images/dcs.png
Binary file added _images/gcase.png
Binary file added _images/gecocase.png
Binary file added _images/geov-2files.png
Binary file added _images/geov-difference.png
Binary file added _images/geov-openingfile.png
Binary file added _images/i2000.png
Binary file added _images/ihist.png
Binary file added _images/light_dark_mode.png
Binary file added _images/modules.png
Binary file added _images/namelist_var_search.png
Binary file added _images/ncdump_example.png
Binary file added _images/ncview.png
Binary file added _images/ncview_T750-T500.png
Binary file added _images/ncview_diff_dcs.png
Binary file added _images/nhtfrq.png
Binary file added _images/overflows.png
Binary file added _images/term_jupyter_1.png
Binary file added _images/term_jupyter_2.png
Binary file added _images/term_mac.png
Binary file added _images/term_pc.png
Binary file added _images/transport_sections_mom6.png
33 changes: 33 additions & 0 deletions _sources/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@

# Welcome to the [CESM Tutorial](https://ncar.github.io/CESM-Tutorial/README.html)

<br>

In 1983 NCAR created the _Community Climate Model_ (CCM) as a freely available global atmosphere model for use by the climate research community. The scope of CCM development continued to expand and in 1994 NCAR scientists released the _Climate System Model_ (CSM), a global model that included component models for the atmosphere, land surface, ocean, and sea-ice, communicating through a central coupler component. To recognize the broad community of users and sponsors contributing to this effort, the CSM was renamed the _Community Climate System Model_ (CCSM). The CCSM model evolved to include ice sheet and biogeochemical modeling and was renamed the _Community Earth System Model_ (CESM) in 2013.

This repository includes materials designed to be an introduction to running the CESM. The materials were developed to support the CESM tutorial and serve as reference documentation for all CESM users.

## Goals of This Tutorial

**Through this online tutorial you will learn how to run the CESM model, modify the model experiments, and use the model output. These tutorial materials are designed for the CESM version 2 (CESM2)**

## Yearly In-Person Tutorials

The CESM tutorial was started in 2010 and is typically offered as an in-person summer workshop. If you are interested in attending the tutorial, please see the [CESM webpage](https://www.cesm.ucar.edu/events/tutorials) for the most up to date information about when the tutorial will next be offered in Boulder, Colorado and the timeline for applying.

## CESM Project Funding

This material is based upon work supported by the National Center for Atmospheric Research (NCAR), which is a major facility sponsored by the National Science Foundation (NSF) under Cooperative Agreement No. 1852977. Staff time on this project was also supported by the Climate and Global Dynamics (CGD) laboratory.

## Acknowledgements

A number of people have been critical to this effort, including:
- Cecile Hannay, David Bailey, Peter Lawrence, Hui Li, Sophia Macarewich, Jesse Nusbaumer, Adam Phillips, and Kate Thayer-Calder who serve on the CESM tutorial committee and put together the tutorial materials.
- Alice DuVivier, Brian Dobbins, Gunter Leguy, and Gustavo Marques, who helped test materials and have contributed substantially.
- Elizabeth Faircloth, who supports the CESM program administratively and without whom everything would probably fall apart.
- David Lawrence, who supported this effort as CESM chief scientist.
- Testers, others...

<br>

<div>
109 changes: 109 additions & 0 deletions _sources/notebooks/basics/basics_overview.ipynb
Original file line number Diff line number Diff line change
@@ -0,0 +1,109 @@
{
"cells": [
{
"cell_type": "markdown",
"id": "b2cd974a-dfbb-4937-8ed0-ab87ab60f1ef",
"metadata": {},
"source": [
"# Basics"
]
},
{
"cell_type": "markdown",
"id": "9db9d54e-ef78-44ef-a003-4ddd8a416317",
"metadata": {},
"source": [
"The CESM Model is developed around a structured workflow. The first step of this workflow is to set up your workspace, which is usually a one-time task. After setting up your workspace, a basic CESM simulation can be run with only four commands. This section will cover these steps and enable you to complete your first CESM run."
]
},
{
"cell_type": "markdown",
"id": "e2abf5cb-c507-408e-8f2a-2fd12934873d",
"metadata": {},
"source": [
"## Workflow Elements"
]
},
{
"cell_type": "markdown",
"id": "acfe09a5-e3ee-457a-a328-bde665cfe761",
"metadata": {
"jp-MarkdownHeadingCollapsed": true,
"tags": []
},
"source": [
"<div class=\"alert alert-info\" style=\"text-align: left;\">\n",
"\n",
"- Set up workspace (one time setup)\n",
" - **``Download``** the CESM code\n",
" - **``Create or Locate ``** an **``Input Data``** Root Directory\n",
" - Possibly **``Porting``** if not on a setup machine\n",
"- Creating, Running and Reviewing a Case\n",
" - **``Create``** a new case\n",
" - **``Invoke``** `case.setup`\n",
" - **``Build``** the executable with `case.build`\n",
" - **``Run``** the model with `case.submit`\n",
" - **``Review``** output data\n",
"\n",
"</div>"
]
},
{
"cell_type": "markdown",
"id": "0c07b51d-f999-4737-9739-3ea989f20802",
"metadata": {},
"source": [
"## Setting up your environment"
]
},
{
"cell_type": "markdown",
"id": "9d6954eb-3505-4a58-b6fa-bea7047c63cf",
"metadata": {},
"source": [
"Every time you log onto the NCAR HPC you want to ensure you have the correct modules loaded. Please refer to the NCAR supercomputer section under Resources to make sure you are setting up your environment properly. \n",
"\n",
"**YOU SHOULD ENSURE YOU CHECK THIS EVERY TIME YOU ARE BUILDING A NEW CASE**\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "523165e7-728b-4305-b9f7-4e6ee530a27d",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "715674b2-a858-49ae-b044-7f7fc61a750c",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.13"
},
"toc-showcode": false
},
"nbformat": 4,
"nbformat_minor": 5
}
92 changes: 92 additions & 0 deletions _sources/notebooks/basics/cesm_workflow.ipynb
Original file line number Diff line number Diff line change
@@ -0,0 +1,92 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# CESM Workflow"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"CESM has been designed to be easy to use. Once you have downloaded the CESM code, a CESM `case` can be run with a set of 4 commands. \n",
"\n",
"*Note: In CESM jargon, a case refers to a specific instance of a model simulation.*"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<div class=\"alert alert-info\" style=\"text-align: left;\">\n",
"\n",
"1) Create a new case using `create_newcase`\n",
"2) Set up the case by invoking `case.setup`\n",
"3) Build the executable using `case.build`\n",
"4) Run your case using `case.submit`\n",
" \n",
"</div>\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The following sections will go into more detail about these 4 commands and also provide information about how to check your job status or create a clone of a previous case."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### More information"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"More detailed information on the CESM2 Workflow is documented in the following links and can be read in detail at a later time."
]
},
{
"cell_type": "markdown",
"metadata": {
"tags": []
},
"source": [
"<div class=\"alert alert-info\" style=\"text-align: center;\">\n",
"\n",
"[CESM2 release](https://escomp.github.io/CESM/release-cesm2/)\n",
" \n",
"[CIME](https://esmci.github.io/cime/versions/master/html/index.html)\n",
"\n",
"</div>"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Bash",
"language": "bash",
"name": "bash"
},
"language_info": {
"codemirror_mode": "shell",
"file_extension": ".sh",
"mimetype": "text/x-sh",
"name": "bash"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
Loading

0 comments on commit 931ba91

Please sign in to comment.