From 0c4017f4a2b4867c54ac4982c1aa305bd109faff Mon Sep 17 00:00:00 2001 From: Jesse Nusbaumer Date: Tue, 15 Oct 2024 10:45:27 -0600 Subject: [PATCH] Add new CAM-SIMA 'directory structure' section. --- docs/design/directory-structure.md | 131 +++++++++++++++++++++++++++++ mkdocs.yml | 3 +- 2 files changed, 133 insertions(+), 1 deletion(-) create mode 100644 docs/design/directory-structure.md diff --git a/docs/design/directory-structure.md b/docs/design/directory-structure.md new file mode 100644 index 0000000..6b7b78d --- /dev/null +++ b/docs/design/directory-structure.md @@ -0,0 +1,131 @@ +# CAM-SIMA directory structure + +This page lists out the directory structure for CAM-SIMA, and what the general purpose of each directory and subdirectory is. + +## Top-level external directories + +These directories contain external repository source code, libraries, or tools, and usually are only present after `bin/git-fleximod update` has been run. + +Please note that any modifications to the source code in these directories should generally be made outside of CAM-SIMA and instead in the associated external repository listed below. + +### bin + +Contains the `git-fleximmod` tool for downloading needed source code and software from external repositories. More information on `git-fleximod` can be found [here](https://github.com/ESMCI/git-fleximod). + +### ccpp_framework + +Contains the core [CCPP-framework](https://github.com/NCAR/ccpp-framework) source code and tools. + +### ccs_config + +Contains the configuration files used by CIME to properly configure and build a CAM-SIMA (or CESM) case. The Github repository associated with this directory can be found [here](https://github.com/ESMCI/ccs_config_cesm). + +### cime + +Contains the [Common Infrastructure for Modeling the Earth (CIME)](https://github.com/ESMCI/cime) tools and associated libraries. Used by CAM-SIMA and CESM for the general configuration and building of a simulation (or "case"). + +### components + +Contains the following other CESM components: +- [Community Data Models for Earth Prediction Systems (CDEPS)](https://github.com/ESCOMP/CDEPS) +- [CICE sea ice model](https://github.com/ESCOMP/CESM_CICE) +- [Community Ice Sheet Model (CISM)](https://github.com/ESCOMP/CISM-wrapper) +- [Community Terrestrial Systems Model (CTSM/CLM)](https://github.com/ESCOMP/CTSM) +- [Community Mediator for Earth Prediction Systems (CMEPS)](https://github.com/ESCOMP/CMEPS) +- [mizuRoute](https://github.com/ESCOMP/mizuRoute) +- [MOdel for Scale Adaptive River Transport (MOSART)](https://github.com/ESCOMP/MOSART) +- [River Transport Model (RTM)](https://github.com/ESCOMP/RTM) + + +### libraries + +Contains the following external libraries: +- [Flexible Modeling System (FMS)](https://github.com/ESCOMP/FMS_interface.git) +- [Parallel IO (PIO)](https://github.com/NCAR/ParallelIO) + +### share + +Contains source code [shared across all CESM components](https://github.com/ESCOMP/CESM_share). + +## Top-level CAM-SIMA directories + +These directories represent code and tools that is solely contained within the CAM-SIMA repository. If there is a sub-directory that is also an external submodule or repository it will be marked with the "(external)" label. + +### cime_config + +Contains the SIMA-specific python and XML configuration routines used by CIME and the CCPP-framework to properly configure and build a CAM-SIMA simulation, including the CCPP-generated caps and namelist files. + +**Subdirectories**: + +- testdefs - Location of the CAM-SIMA regression test list and associated files used by CIME during regression (system) testing. + - testmods_dirs/cam - Location of CAM-SIMA case configuration files used during CIME regression testing. + +### docker + +Contains files needed to run certain CAM-SIMA configurations in a docker container. + +### src + +Contains all of the SIMA-specific source code needed to run the model. Additional details can be found below in the "Source directories" section. + +### test + +Contains everything needed to perform software testing and validation of CAM-SIMA source code. + +**Subdirectories**: + +- system - Includes scripts needed to run CIME (integration) regression tests. +- unit - Includes scripts and source code needed to run CAM-SIMA unit tests. + - sample_files - Contains files that are used to validate the unit test results. + +### tools + +Contains non-required scripts and source code that may be useful for CAM-SIMA development. + +## Source (src) directories + +This section lists all of the directories underneath the "src" top-level directory. + +### control + +Contains all of the source code needed for general model configuration, organization, and workflow, i.e. all of the "control" systems. + +### cpl + +Contains all of the source code needed for SIMA to interact with a coupler + +**Subdirectories**: + +- nuopc - Contains the source code needed to interact with the [NUOPC](https://earthsystemmodeling.org/nuopc/) coupler, which is brought in via the CMEPS external. + +### data + +Contains all of the source code needed to manage internal model data. This includes auto-generated registry and initial conditions files code, physical constants, and atmospheric composition and thermodynamic properties. + +### dynamics + +Contains all of the dynamical core (dycore) source code. + +**Subdirectories**: + +- mpas - Contains all of the source code needed for SIMA to properly couple to the [MPAS dynamical core](https://github.com/MPAS-Dev/MPAS-Model). + - dycore (external) - External submodule that contains the MPAS dycore code. +- none - Contains the "null" dycore source code, which allows physics and chemistry routines to be forced with atmospheric data coming directly from input files as opposed to dycore calculations. +- se - Contains all of the source code needed for SIMA to properly couple to the [Spectral Element dynamical core](https://ncar.github.io/CAM/doc/build/html/cam5_scientific_guide/dynamics.html#spectral-element-dynamical-core). + - dycore - Contains the internal SE dycore source code files. +- tests - Contains the source code needed to configure analytic initial conditions for dycores. + - initial_conditions - Contains source code needed to configure specific analytic initial conditions formulations. +- utils - Contains utility code used by all dycores in SIMA. + +### physics + +Contains all of the SIMA physics and chemistry source code. + +**Subdirectories**: + +- ncar_ccpp (external) - External submodule that contains all of the code in the [atmospheric_physics](https://github.com/ESCOMP/atmospheric_physics) repo. +- utils - Contains SIMA-specific utility routines for working with the CCPP-framework and CCPP-ized physics routines. + +### utils + +Contains source code for generic SIMA utility routines that can be used throughout the model. diff --git a/mkdocs.yml b/mkdocs.yml index 5c614bb..decbd98 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -18,6 +18,7 @@ nav: - design/cam-run-process.md - design/ccpp-in-cam-sima.md - design/constituents.md + - design/directory-structure.md - design/history.md - design/sima-design-goals.md - Development: @@ -46,7 +47,7 @@ theme: name: Switch to light mode # Palette toggle for light mode - media: "(prefers-color-scheme: light)" - scheme: default + scheme: default toggle: