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0000000..6051d31 --- /dev/null +++ b/_sources/basics.rst.txt @@ -0,0 +1,54 @@ +visualCaseGen Basics +==================== + +This section defines key concepts in visualCaseGen that will be referenced throughout the documentation. + + +Configuration Variable +----------------------- + +Configuration variables are essential CESM settings that must be defined before creating a case. +These include choices like the model, model physics, resolution, and grid options that are set in +CESM XML and user namelist files. visualCaseGen provides an intuitive, form-based interface for +configuring these variables, ensuring compatibility and completeness. Only the variables required +for case instantiation are included in visualCaseGen; other settings that can be adjusted after +case creation, such as simulation duration, are not included in the GUI. + +Stage +----- + +In visualCaseGen, a stage represents a group of related CESM configuration variables that can be +set together. Examples of stages include models, physics options, and resolutions. Stages introduce +a logical hierarchy, where those listed earlier hold higher precedence. For instance, model selection +is a prerequisite for defining model physics, so the model stage takes precedence. visualCaseGen +guides users through each stage in the proper order, ensuring that configurations are compatible +at each step. + +A stage is deemed complete when all of its configuration variables have been set. When a stage is +complete, visualCaseGen will automatically advance to the next stage. Users can also navigate +between stages by clicking the `Revert` button on the top bar of each Stage to return to the previous +stage or the `Proceed` button to advance to the next stage, but if there are any incomplete configuration +variables, visualCaseGen will prompt users to fill them in before proceeding. The `Defaults` button on +the top bar of each stage allows users to quickly set all configuration variables to their default +values, if available. The `Info` button provides additional information about the stage and its +configuration variables. + +Standard vs Custom +------------------ + +During configuration, users can choose between standard and custom options for certain settings, +like compsets, resolutions, and model grids. Standard options are predefined CESM configurations +that are generally easier and safer to use, while custom options allow for greater flexibility. +visualCaseGen assists users through the custom configuration process to maximize compatibility, +but custom setups may require additional troubleshooting. For any issues with custom configurations, +please refer to the Troubleshooting section of this guide. + + +Resolution vs Grid vs Model Grid +-------------------------------- + +In CESM terminology, *resolution* and *grid* are often used interchangeably, +both referring to the combination of model grids used in a CESM simulation. Unless +specifically noted as a *model grid* (i.e., a grid unique to a particular component, +such as the ocean grid), the term *grid* in the context of visualCaseGen should be understood as +*resolution*, meaning the full collection of *model grids* used in a particular CESM case. \ No newline at end of file diff --git a/_sources/compset.rst.txt b/_sources/compset.rst.txt new file mode 100644 index 0000000..972ba34 --- /dev/null +++ b/_sources/compset.rst.txt @@ -0,0 +1,121 @@ +Stage 1/3: Compset +================== + +In this stage, the component set (compset), i.e., the collection of models (`cam`, `clm`, `mom`, etc), physics +(`CAM70`, `CLM50`, `MOM6`, etc), and component options. e.g., `LT` (low top), `SP` (satellite phenology), `MARBL-BIO`, +etc. are determined. +You'll start by choosing between the `Standard` compset mode, which provides predefined and stable CESM configurations, +and the `Custom` compset mode, which allows for more tailored combinations for unique experiments. + +.. image:: assets/stage1_1.png + +Standard Compsets +------------------ + +- **Support Level:** You can select from a list of all standard compsets or only those that are scientifically + supported. `Supported` compsets have been validated by CESM developers, ensuring they produce + scientifically vetted results. These are typically recommended for production runs. The `All` option, + however, includes experimental compsets that may not be validated but can be useful for testing and + development. Selecting a supported compset ensures that you are working with configurations approved + for stability and accuracy, while the `All` option offers broader but potentially unstable options for + specialized needs. + + .. image:: assets/stage1_2.png + +- **Models to Include:** If you choose the `Supported` option, a list of scientifically validated + compsets will appear for you to choose from. However, if you choose the `All` option, you'll be + presented with a *model matrix* to refine the list of compsets displayed. This matrix allows you + to specify which model components you want to include. For instance, if you select `cam` as the + atmosphere model and `mom` as the ocean model, the list will filter down to include only those + compsets that incorporate both. If you're flexible with certain components, you can select `any` + for those classes, or click the `Defaults` button in the Stage top bar to apply typical defaults + for all components, streamlining your selection. This feature is particularly useful if you're + unsure about specific settings or wish to adhere to commonly used configurations. + + .. image:: assets/stage1_3.png + +- **Standard Compsets List:** After refining your options, visualCaseGen will display a list of + matching compsets. Each compset is labeled with an alias and incorporates an initialization time + and a short description of the included models, providing a snapshot of each configuration. + To narrow down the list further, you can use the search box above the list. Typing keywords + in the search box will display all compsets containing one or more of the search terms. For + precise filtering, use double quotes around terms for exact matches. This flexibility makes + it easy to locate specific compsets or explore different configurations to find the most + suitable one for your simulation needs. + + .. image:: assets/Stage1_4.png + +After selecting a compset, visualCaseGen will guide you to the next primary stage, `Grid`, where +you'll select a model resolution compatible with your chosen compset. + +Custom Compsets +------------------ + +.. note:: + If you initially selected the `Standard` compset mode, the `Custom` compset stages will not + display, and instead visualCaseGen will proceed directly to the `Grid` stage. To switch to the `Custom` + compset mode after already completing the `Standard` compset stages, you can click `Revert` + buttons to navigate back to the selection of configuration mode. + +If you prefer to build a custom compset, visualCaseGen provides a step-by-step process, +starting with the initialization time for your experiment. This choice impacts the initial +conditions and forcings for your simulation. You can choose from: + +- 1850: Represents pre-industrial conditions and is suitable for fixed-time-period runs, such as for model spin-ups. +- 2000: Represents modern-day conditions, also appropriate for fixed-period simulations. +- HIST: Represents a historical run setup, which covers transient simulations (e.g., from 1850 through 2015) that evolve with changing conditions over time. + + .. image:: assets/stage1_5.png + +Once you've selected the initialization time, visualCaseGen will prompt you to select the +models for each component class. You'll see options that include active models, data models +(prefixed with d, like `datm`), and stub models (prefixed with s, like `sice`). Data models +perform the basic function of reading preexisting forcing data, modifying that data, and then +sending it to active models via the coupler. Stub models act as placeholders required by the CESM +coupler infrastructure but have no impact on the simulation. This variety allows you to +configure a custom compset that includes as many or as few active components as desired, +depending on the specific goals of your simulation. + + .. image:: assets/Stage1_6.png + +As you make selections in this stage and elsewhere, visualCaseGen will guide you by crossing +out incompatible options, helping to prevent invalid configurations. For example, if you select +`cam` for the atmosphere and `mom` for the ocean, the GUI will disable several other model +options that are incompatible with this combination. This real-time feedback keeps your +configuration process streamlined and ensures that all selected options work together compatibly. + + .. image:: assets/Stage1_7.png + +At any stage, you can click on any crossed-out option to view a brief explanation of +why it's incompatible with your current selections for additional guidance. + + .. image:: assets/Stage1_8.png + +After choosing your models, you'll proceed to select the physics options for each. The physics +settings determine the complexity of each model component and impact computational requirements. +Higher version numbers indicate newer and more complex physics for a given model. Depending on +the model, you may have multiple physics options available. For example, `cam` and +`clm` have multiple physics options, while other models may offer only one, in which case it +will be selected by default. Since each physics option provides different levels of model complexity, +the selection should be based on the specific requirements of your simulation. Refer to +the individual model documentations for more information on the available physics options. + + .. image:: assets/Stage1_9.png + +The final part of custom compset creation is selecting optional physics modifiers. +Modifiers allow additional adjustments to physics and parameter settings, offering +further customization to meet modeling requirements and goals. Each component class +is represented in individual tabs within this stage. You can switch between tabs to +select modifiers or opt out of a modifier by choosing `(none)`. Tabs with available +modifiers will display a red question mark until a selection is made. While you can +select multiple modifiers for a single component class, be cautious: visualCaseGen +does not verify compatibility between multiple modifiers within a single component, +so it's advisable to consult CESM documentation or model experts if you're using complex +modifier combinations. + + .. image:: assets/Stage1_10.png + +Once you've completed the selection of models, physics, and optional modifiers, +visualCaseGen will automatically advance to the next main stage, `Grid`, where +you'll select a model resolution compatible with your chosen compset. + diff --git a/_sources/creating_case.rst.txt b/_sources/creating_case.rst.txt new file mode 100644 index 0000000..e1ec180 --- /dev/null +++ b/_sources/creating_case.rst.txt @@ -0,0 +1,10 @@ +Stages of Creating a Case +========================== + +The workflow for creating a CESM case using visualCaseGen is divided into three main stages: + +1. **Compset**: In this stage, the user will select the compset, i.e., the set of models, physics, and options that will be used in the simulation. +2. **Resolution**: In this stage, the user will select the resolution of the simulation, i.e., the collection of model grids. +3. **Launch**: In this final stage, the user will create and configure the case. + +Proceed to the following sections to learn more about each stage. diff --git a/_sources/fillindian.rst.txt b/_sources/fillindian.rst.txt new file mode 100644 index 0000000..4f056be --- /dev/null +++ b/_sources/fillindian.rst.txt @@ -0,0 +1,4 @@ +Fill Indian Ocean +================= + +Instructions coming soon... \ No newline at end of file diff --git a/_sources/grid.rst.txt b/_sources/grid.rst.txt new file mode 100644 index 0000000..f18cef4 --- /dev/null +++ b/_sources/grid.rst.txt @@ -0,0 +1,95 @@ +Stage 2/3: Grid +=============== + +The second major step in configuring your CESM case is choosing a resolution, which +is a specific set of grids for each active and data model in the compset. You may +select either a standard, out-of-the-box resolution or create a custom one by combining +existing model grids. In `Custom` mode, you can also generate custom model grids for CLM and/or MOM6 +using auxiliary tools included in visualCaseGen. Begin by selecting between `Standard` +and `Custom` grid modes. + +.. image:: assets/Stage2_1.png + +.. note:: In CESM terminology, *resolution* and *grid* are often used interchangeably, + both referring to the combination of model grids used in a CESM simulation. Unless + specifically noted as a *model grid* (i.e., a grid unique to a particular component, + such as the ocean grid), the term *grid* in this context should be understood as + *resolution*, meaning the full collection of *model grids* used in a particular CESM case. + +Standard Grids +------------------ + +Select from the available list of resolutions (combinations of model grids) below. +Resolutions known to be incompatible with your chosen compset have been omitted +from this list. Use the search box to refine the list further. For exact matches, +use double quotes; otherwise, the search will display all grids containing one +or more of the search terms. + +.. image:: assets/Stage2_2.png + +After selecting a grid, visualCaseGen will advance to the `Launch` stage, where +you can create your CESM case using the chosen compset and grid configuration. + +Custom Grids +------------------ + +In Custom Grid mode, you can build a custom grid by mixing and matching standard +model grids or generating new MOM6 and/or CLM grids with specialized tools that come with visualCaseGen. +Start by specifying a path to save the new grid files and a name to refer to this +new grid in the configuration process and beyond. + +.. image:: assets/Stage2_3.png + +After clicking `Select`, a file browser will open to help you locate your preferred +directory for saving the new grid files. Once the directory is selected, enter the +new grid name in the text box at the top right and click `Select` to proceed. + +.. image:: assets/Stage2_4.png + +Atmosphere Grid +~~~~~~~~~~~~~~~ + +Next, choose an atmosphere grid from the list of compatible options based on the +compset you selected in the `Compset` stage. Use the search box to filter options if needed. +This chosen atmosphere grid will be integrated with other model grids to form your custom CESM grid (resolution). + +.. image:: assets/Stage2_5.png + +Ocean Grid +~~~~~~~~~~ + +For the ocean grid, if MOM6 is selected as the ocean model, you can either select a standard +ocean grid or create a new MOM6 grid. When creating a new MOM6 grid, you'll specify parameters +such as grid extent and resolution, after which you'll be directed to a separate notebook that +uses the `mom6_bathy` tool to generate the new grid and bathymetry. + +If using a standard ocean grid, select one from the list compatible with your chosen compset +and atmosphere grid. If creating a new MOM6 grid, complete the required parameters, then proceed +to launch the `mom6_bathy` tool for final customization. + +.. image:: assets/Stage2_6.png + +After specifying all ocean grid parameters, click `Launch mom6_bathy`. This will open an +auto-generated Jupyter notebook where you can fine-tune the ocean grid bathymetry and generate +all necessary input files. For more details on mom6_bathy, refer to its documentation: https://ncar.github.io/mom6_bathy/ + +.. note:: If the `mom6_bathy` notebook doesn't open automatically, make sure that your browser allows + pop-ups from visualCaseGen. If the notebook still doesn't open, you can manually launch it by + navigating to the `mom6_bathy_notebooks/` directory in your visualCaseGen installation and opening + the notebook corresponding to your custom grid. + + +Land Grid +~~~~~~~~~ + +Following ocean grid selection or creation, you'll move to land grid selection. If CLM is chosen +as the land model, you can also modify an existing CLM grid. If so, select a base land grid for +customization. + +.. image:: assets/Stage2_7.png + +.. note:: Detailed instructions on customizing an existing CLM grid will be added here shortly. + +Once atmosphere, ocean, and land grids have been chosen or created, custom grid setup is complete. +visualCaseGen will guide you to the final stage, `Launch`, where you can create a CESM case based on +the specified compset and grid. \ No newline at end of file diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 0000000..e714c6c --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,62 @@ +.. visualCaseGen documentation master file, created by + sphinx-quickstart on Sun Oct 27 13:59:27 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to visualCaseGen! +========================================= + +visualCaseGen is a Jupyter-based graphical user interface (GUI) designed to streamline +the creation and configuration of Community Earth System Model v.3 (CESM3) cases. +The visualCaseGen GUI allows users to: + +- **Browse Standard CESM Configurations:** Easily explore and select from available CESM compsets + and resolutions. +- **Create Custom Configurations**: Rapidly customize CESM experiments with advanced options for component + selection, grid generation, and configuration. + +Key Features +------------ + +- **Easy Case Setup:** Intuitive interface for configuring experiments. +- **Hierarchical Modeling:** Combine different complexity levels across components. +- **Flexible Configurations:** Mix and match models and grids with compatibility guidance. +- **Automated Case Creation:** Generates input files and handles XML/namelist adjustments. +- **Modify CLM Inputs:** Easily adjust land masks and surface datasets with a form-based interface. +- **MOM6 Grid & Bathymetry Customization:** Create or modify grids and bathymetries with a point-and-click tool. + +.. image:: assets/demo3.gif + +Typical Workflow +---------------- + +- **Launch:** Open the visualCaseGen GUI within your Jupyter notebook environment. +- **Select Compset:** Choose from available standard CESM compsets or create a custom one by selecting + models, physics options, and other settings for each component (e.g., atmosphere, ocean, land, ice). +- **Define Resolution:** Select a compatible standard resolution or create a custom one by combining + different grids for each model component or generating new ones. +- **Generate Case:** Once your compset and resolution are set, visualCaseGen will create the CESM case, + automatically generating required input files and making all necessary modifications to CESM XML and + user namelist files. + +For more information on each step, please refer to the corresponding sections in this user guide. + +.. toctree:: + :maxdepth: 3 + :caption: User Manual: + + installation + open + basics + creating_case + compset + grid + launch + troubleshooting + +.. toctree:: + :maxdepth: 3 + :caption: Examples: + + ridge + fillindian \ No newline at end of file diff --git a/_sources/installation.rst.txt b/_sources/installation.rst.txt new file mode 100644 index 0000000..58c0b44 --- /dev/null +++ b/_sources/installation.rst.txt @@ -0,0 +1,74 @@ +Installation +====================================== + +visualCaseGen is presently bundled with a CESM distribution (fork) based on cesm3_0_beta03. The following +instructions guide you through obtaining and installing this specific CESM distribution with visualCaseGen. + +Prerequisite +------------- + +.. warning:: + The key prerequisite for installing visualCaseGen is that CESM cesm3_0_beta03 or a newer version is already + ported on your machine. If this version (or later) is not yet ported, follow the CESM documentation + instructions to port it first. Without this, visualCaseGen will not launch. + +- Verify CESM port: Ensure CESM cesm3_0_beta03 or newer is ported on your machine. If not, follow the CESM + documentation to port the required version. +- Conda Installation: Confirm that Conda is installed, either via Miniconda or Anaconda. You can install Miniconda + from the following link: + https://docs.conda.io/en/latest/miniconda.html + +Download CESM with visualCaseGen +-------------------------------- + +To download the specific CESM distribution bundled with visualCaseGen, clone the CESM GitHub repository and +use the `git-fleximod` script that comes with CESM as a package manager, as follows. Note that downloading +CESM may take some time. + +.. code-block:: bash + + git clone https://github.com/alperaltuntas/cesm.git -b cesm3_0_beta03_gui cesm3_0_beta03_gui + cd cesm3_0_beta03_gui + ./bin/git-fleximod update + +This will download the required CESM version, including visualCaseGen. + +Create the visualCaseGen conda environment +------------------------------------------ + +.. warning:: + If you are using a machine other than one of the supported systems (e.g., derecho, casper), you may need + to modify the ccs_config/machines XML files in the newly downloaded CESM distribution. This may be required + even if CESM cesm3_0_beta03 or a newer version is already ported on your machine. These modifications + should match the adjustments made previously for the ported CESM version. For guidance on updating the + ccs_config/machines XML files, refer to the CESM documentation, consult CESM support through the CESM forum, + or submit an issue on the visualCaseGen GitHub repository. Users on supported machines can ignore this warning, + as no changes are needed. + +To create the `visualCaseGen` conda environment, navigate to the `visualCaseGen` directory and run the following +commands: + +.. code-block:: bash + + cd visualCaseGen + conda env create -f environment.yml + +This will create the `visualCaseGen` conda environment. Activate the `visualCaseGen` conda environment by running +the following command: + +.. code-block:: bash + + conda activate visualCaseGen + +Verify Installation +------------------------------------------ + +To verify that visualCaseGen was installed correctly, run the test suite: + +.. code-block:: bash + + pytest tests/ + +If the test suite completes successfully, visualCaseGen is ready for use. If any tests fail, please open an +issue on the visualCaseGen GitHub repository, including error messages and the installation steps you followed. + diff --git a/_sources/launch.rst.txt b/_sources/launch.rst.txt new file mode 100644 index 0000000..15422b8 --- /dev/null +++ b/_sources/launch.rst.txt @@ -0,0 +1,56 @@ +Stage 3/3: Launch +================= + +The final main stage of visualCaseGen is the `Launch` stage, where you bring your CESM case to +life with the selected compset and grid configuration. In this stage, you'll find tools to +select the case directory, choose a target machine, and initiate case creation. + +.. image:: assets/Stage3_1.png + +Chosing the case directory +~~~~~~~~~~~~~~~~~~~~~~~~~~ + +To begin, open the file browser widget by clicking the `Select` button to set the directory for +the new case. Navigate to your desired location, then enter a unique name for the case in the +text box at the top right of the browser. Click `Select` to confirm your directory and case name. + +.. image:: assets/Stage3_2.png + +Selecting the target machine +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Next, choose the machine where the case will run. If CESM has already been ported to the machine, +this selection should populate automatically. If not, confirm that CESM is properly ported to the +machine you intend to use and that the correct machine is selected. For some systems, a PROJECT ID +is required; if so, you'll be prompted to enter it here. + +.. note:: + If you're using a machine that shares a file system with another, you have the flexibility + to select a different machine for running the case. For example, if you are working within + visualCaseGen on *casper* but intend to run the case on *derecho*, simply change the machine selection + to *derecho* at this stage. This allows you to configure the case on one machine while specifying + execution on another within the shared system environment. + +Creating the case +~~~~~~~~~~~~~~~~~ + +When all selections are finalized, you can click `Create Case` to initiate case creation or +`Show Commands` to view the terminal commands that will be executed. Below, you'll see an +example of the interface after clicking `Create Case`. Notice how visualCaseGen handles the +case setup process, including modifying CESM XML files, executing the create_newcase tool, +running the `case.setup` script, and applying any XML and namelist changes needed. + +.. image:: assets/Stage3_3.png + +The completion log provides confirmation of a successful case creation, including the path to +the new case directory, where you can proceed with case customization, building, and execution. + +Congratulations! +~~~~~~~~~~~~~~~~ + +You've successfully created a CESM case using visualCaseGen, bringing together the models, +grid, and configurations tailored to your scientific goals. With the case directory set up, +you're ready to move forward with any additional customizations, building, and executing your +case. Great job, and happy modeling! + + diff --git a/_sources/open.rst.txt b/_sources/open.rst.txt new file mode 100644 index 0000000..6b71b9e --- /dev/null +++ b/_sources/open.rst.txt @@ -0,0 +1,139 @@ +.. _Open: + +Opening the GUI +=============================== + +Once the conda environment is installed, you can launch visualCaseGen by opening the `GUI.ipynb` notebook +in the `visualCaseGen/` directory. Below are several common methods for launching the notebook. If you are +using NCAR machines, the JupyterHub interface is recommended. + +.. contents:: Launch Options: + :depth: 2 + :local: + + +From the Command Line +--------------------------------------- + +.. warning:: + The command-line launch is possible only if you’re running on a local machine or have SSH tunneling + enabled. For remote access, set up SSH tunneling (described in the next section). + +Ensure the `visualCaseGen` Conda environment is activated. If not, activate it with: + +.. code-block:: bash + + conda activate visualCaseGen + +Launch the notebook from the command line by navigating to the `visualCaseGen/` directory +where `GUI.ipynb` notebook is located and running: + +.. code-block:: bash + + jupyter-lab GUI.ipynb + +This will open the Jupyter notebook in your default web browser, displaying a cell with the following code: + +.. code-block:: python + + from visualCaseGen import gui; gui + +To start the GUI, execute the cell by clicking the **Run** button or pressing `Shift + Enter`. You should +see the following welcome dialog. Click **Start** to begin using the GUI: + +.. image:: assets/launch5.png + +- Once the `Start` button is clicked, a loadbar will appear, indicating that the GUI is initializing. When the + GUI is ready, the main interface will be displayed. If the loadbar hangs, click the `Help` button on the top + right corner of the welcome dialog to see if any error messages are displayed. If you encounter any issues, + please refer to the Troubleshooting section of this documentation. + +On a Remote Machine +------------------------------------- + +To access the GUI on a remote machine, set up SSH tunneling with port forwarding. + +- Establish an SSH connection with port forwarding (the exact command may vary depending on your system): + +.. code-block:: bash + + ssh -L 8888:localhost:8888 username@remote_host + +- After connecting, activate the `visualCaseGen` Conda environment, navigate to the `visualCaseGen/` directory, and run: + +.. code-block:: bash + + conda activate visualCaseGen + cd [PATH_TO_visualCaseGen] # e.g., ~/cesm3_0_beta03_gui/visualCaseGen + jupyter-lab GUI.ipynb --no-browser + +If the above steps are successful, the command line will display a URL that you can copy and paste into your web browser +to access the Jupyter notebook. The URL will look similar to: + +.. code-block:: bash + + http://localhost:8888/lab/?token=1234567890abcdef1234567890abcdef1234567890abcdef + +Paste the url **shown in your own terminal** into your web browser to access the visualCaseGen GUI. A Jupyter +notebook with the following cell will be displayed: + +.. code-block:: python + + from visualCaseGen import gui; gui + +To start the GUI, execute the cell by clicking the **Run** button or pressing `Shift + Enter`. You should +see the following welcome dialog. Click **Start** to begin using the GUI: + +.. image:: assets/launch5.png + +- Once the `Start` button is clicked, a loadbar will appear, indicating that the GUI is initializing. When the + GUI is ready, the main interface will be displayed. If the loadbar hangs, click the `Help` button on the top + right corner of the welcome dialog to see if any error messages are displayed. If you encounter any issues, + please refer to the Troubleshooting section of this documentation. + +NCAR JupyterHub +------------------------------------- + +.. warning:: + This method is available only to users with access to NCAR systems like `derecho` or `casper`. + +- Go to NCAR JupyterHub in your web browser: + +.. code-block:: bash + + https://jupyterhub.hpc.ucar.edu/ + +- Log in by selecting "Production" under "Available NCAR Resources," then enter your NCAR credentials. + +- Start a JupyterHub server by clicking the **"start"** button under the Actions column. + +.. image:: assets/launch1.png + +- When prompted, select a resource. Although any resource is acceptable, "Casper Login" is recommended, as visualCaseGen does not require significant computational power. + +.. image:: assets/launch2.png + +- After the resource starts, navigate to the `visualCaseGen/` directory from the File Browser tab on the left. + +.. tip:: + Create a symbolic link to your CESM directory in your home directory for easier access. + +- Open the `GUI.ipynb` notebook by double clicking on it, + +.. image:: assets/launch3.png + +- When prompted, select the visualCaseGen Conda kernel from the dropdown menu. (If not prompted, select the kernel by clicking + the kernel name in the top right corner of the notebook.) + +.. image:: assets/launch4.png + +- To start the GUI, execute the first cell (with `from visualCaseGen import gui; gui`) by clicking the **Run** button + or pressing `Shift + Enter`. You should see the following welcome dialog. Click **Start** to begin using the GUI: + +.. image:: assets/launch5.png + +- Once the `Start` button is clicked, a loadbar will appear, indicating that the GUI is initializing. When the + GUI is ready, the main interface will be displayed. If the loadbar hangs, click the `Help` button on the top + right corner of the welcome dialog to see if any error messages are displayed. If you encounter any issues, + please refer to the Troubleshooting section of this documentation. + diff --git a/_sources/ridge.rst.txt b/_sources/ridge.rst.txt new file mode 100644 index 0000000..6e7fad6 --- /dev/null +++ b/_sources/ridge.rst.txt @@ -0,0 +1,78 @@ +Ridge World +============================== + +This example provides step-by-step guidance on how to generate a coupled idealized +configuration that consists of an aquaplanet with land caps at the pole and a narrow +land ridge extending between the two poles, similar to the configuration used in `Wu et al (2021) `_ . +In the example given below, the visualCaseGen GUI is used to guide users through choosing +their CESM components, setting up all the ocean input files, setting up all the land input +files, and finally setting up and configuring their case. + +Here we are not running a standard case with CESM. We are modifying the configuration substantially by changing the ocean grid, ocean bathymetry, continental geometry and land surface properties, so you should select "Custom" here. + + +Stage 0: Open visualCaseGen +-------------------------- + +Follow the instructions in the :ref:`Open` to open visualCaseGen in your Jupyter notebook environment. + +Stage 1: Select Compset +---------------------- + +After having executed the cell with the command `from visualCaseGen import gui; gui`, +and clicking the **Start** button, you will see the main interface of visualCaseGen. + +Click the **Custom** button to proceed with creating a custom compset for our idealized +Ridge World configuration. + +.. image:: assets/stage1_1.png + +Initialization time +~~~~~~~~~~~~~~~~~~~ + +Once the `Custom` button is clicked, you will be prompted to select the initialization time. +For this example, we will select `1850`` as the initialization time. + +.. image:: assets/stage1_5.png + + +Models +~~~~~~ + +Once you've selected the initialization time, visualCaseGen will prompt you to select the +models for each component class. In this ridge world case we select the following component options: +`cam` as the atmosphere; +`clm`` as the land component; `cice`` as the ice component; `mom`` as the ocean component, `srof`` +(i.e., stub run off) as the river component; `sglc`` (i.e., stub land ice) as the land ice component; +and, `swav` (i.e. stub wave) as the wave component. After all the selections are made, the +model matrix should look like: + +.. image:: assets/ridge1.png + +Model Physics +~~~~~~~~~~~~~ + +Having selected the models, you will proceed to select the physics options for each. The physics +settings determine the complexity of each model component and impact computational requirements. +For this example, we will select the following physics options which are based on the selections +made in `Wu et al (2021) `_ : + +.. image:: assets/ridge2.png + +Component Options (Modifiers) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +We are now ready to finalize the compset by selecting optional physics modifiers. For this example, +we will select `(none)` for all the components except for the `clm` component where we will select +the satellite phenology (SP) mode for the land which means that aspects of the land model such as +leaf-area index are prescribed as opposed to being prognosed interactively by the land biogeochemistry. + +.. image:: assets/ridge3.png + +Stage 2: Grid +---------------------- +Having completed the compset configuration, you will now proceed to the `Grid` stage ... + +Further instructions will be added as the example is developed... + + diff --git a/_sources/troubleshooting.rst.txt b/_sources/troubleshooting.rst.txt new file mode 100644 index 0000000..ae6cc23 --- /dev/null +++ b/_sources/troubleshooting.rst.txt @@ -0,0 +1,30 @@ +Troubleshooting +====================================== + +Below are some common issues that users may encounter while using visualCaseGen and their solutions. +If the suggested solutions do not resolve the issue, or if you encounter a different problem, please +open an issue on the visualCaseGen GitHub repository: https://github.com/ESMCI/visualCaseGen/issues/new + +Commonly Encountered Issues +--------------------------- + +- **Error displaying widget: model not found:** + This message generally appears when a previously run + `GUI.ipynb` notebook is re-opened. This error message doesn't generally indicate a problem with the GUI, + and should dissapear after running the cell with the `from visualCaseGen import gui; gui` code. + +- **ModuleNotFoundError:** No module named `z3`, `ipyfilechooser`, etc.: This error indicates that either + the `visualCaseGen`` conda environment is not installed correctly, it was not chosen as the active environment, + or it was not chosen as the kernel in the Jupyter notebook. To resolve this issue, ensure that the `visualCaseGen` + conda environment is installed correctly and activated. If the issue persists, try restarting the Jupyter notebook + kernel and selecting the `visualCaseGen` environment as the kernel. + +- **Hanging Loadbar:** If the loadbar hangs after clicking the `Start` button, click the `Help` button on the top + right corner of the welcome dialog to see if any error messages are displayed. If so, submit an issue on the + visualCaseGen GitHub repository with the error messages. + +- **mom6_bathy notebook doesn't open automatically:** If the `mom6_bathy` notebook doesn't open automatically, + make sure that your browser allows + pop-ups from visualCaseGen. If the notebook still doesn't open, you can manually launch it by + navigating to the `mom6_bathy_notebooks/` directory in your visualCaseGen installation and opening + the notebook corresponding to your custom grid. \ No newline at end of file diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + 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+ document.dispatchEvent(event); + }); +}); \ No newline at end of file diff --git a/_static/language_data.js b/_static/language_data.js new file mode 100644 index 0000000..c7fe6c6 --- /dev/null +++ b/_static/language_data.js @@ -0,0 +1,192 @@ +/* + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, if available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; 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+ +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename, kind] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename, kind] = item; + + let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.setAttribute("role", "list"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + SearchResultKind.title, + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + SearchResultKind.index, + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + SearchResultKind.object, + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + SearchResultKind.text, + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/basics.html b/basics.html new file mode 100644 index 0000000..62af145 --- /dev/null +++ b/basics.html @@ -0,0 +1,171 @@ + + + + + + + + + visualCaseGen Basics — visualCaseGen 0.0.18 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

visualCaseGen Basics

+

This section defines key concepts in visualCaseGen that will be referenced throughout the documentation.

+
+

Configuration Variable

+

Configuration variables are essential CESM settings that must be defined before creating a case. +These include choices like the model, model physics, resolution, and grid options that are set in +CESM XML and user namelist files. visualCaseGen provides an intuitive, form-based interface for +configuring these variables, ensuring compatibility and completeness. Only the variables required +for case instantiation are included in visualCaseGen; other settings that can be adjusted after +case creation, such as simulation duration, are not included in the GUI.

+
+
+

Stage

+

In visualCaseGen, a stage represents a group of related CESM configuration variables that can be +set together. Examples of stages include models, physics options, and resolutions. Stages introduce +a logical hierarchy, where those listed earlier hold higher precedence. For instance, model selection +is a prerequisite for defining model physics, so the model stage takes precedence. visualCaseGen +guides users through each stage in the proper order, ensuring that configurations are compatible +at each step.

+

A stage is deemed complete when all of its configuration variables have been set. When a stage is +complete, visualCaseGen will automatically advance to the next stage. Users can also navigate +between stages by clicking the Revert button on the top bar of each Stage to return to the previous +stage or the Proceed button to advance to the next stage, but if there are any incomplete configuration +variables, visualCaseGen will prompt users to fill them in before proceeding. The Defaults button on +the top bar of each stage allows users to quickly set all configuration variables to their default +values, if available. The Info button provides additional information about the stage and its +configuration variables.

+
+
+

Standard vs Custom

+

During configuration, users can choose between standard and custom options for certain settings, +like compsets, resolutions, and model grids. Standard options are predefined CESM configurations +that are generally easier and safer to use, while custom options allow for greater flexibility. +visualCaseGen assists users through the custom configuration process to maximize compatibility, +but custom setups may require additional troubleshooting. For any issues with custom configurations, +please refer to the Troubleshooting section of this guide.

+
+
+

Resolution vs Grid vs Model Grid

+

In CESM terminology, resolution and grid are often used interchangeably, +both referring to the combination of model grids used in a CESM simulation. Unless +specifically noted as a model grid (i.e., a grid unique to a particular component, +such as the ocean grid), the term grid in the context of visualCaseGen should be understood as +resolution, meaning the full collection of model grids used in a particular CESM case.

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Stage 1/3: Compset

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In this stage, the component set (compset), i.e., the collection of models (cam, clm, mom, etc), physics +(CAM70, CLM50, MOM6, etc), and component options. e.g., LT (low top), SP (satellite phenology), MARBL-BIO, +etc. are determined. +You’ll start by choosing between the Standard compset mode, which provides predefined and stable CESM configurations, +and the Custom compset mode, which allows for more tailored combinations for unique experiments.

+_images/stage1_1.png +
+

Standard Compsets

+
    +

  • Support Level: You can select from a list of all standard compsets or only those that are scientifically +supported. Supported compsets have been validated by CESM developers, ensuring they produce +scientifically vetted results. These are typically recommended for production runs. The All option, +however, includes experimental compsets that may not be validated but can be useful for testing and +development. Selecting a supported compset ensures that you are working with configurations approved +for stability and accuracy, while the All option offers broader but potentially unstable options for +specialized needs.

    +_images/stage1_2.png +
    • +

  • Models to Include: If you choose the Supported option, a list of scientifically validated +compsets will appear for you to choose from. However, if you choose the All option, you’ll be +presented with a model matrix to refine the list of compsets displayed. This matrix allows you +to specify which model components you want to include. For instance, if you select cam as the +atmosphere model and mom as the ocean model, the list will filter down to include only those +compsets that incorporate both. If you’re flexible with certain components, you can select any +for those classes, or click the Defaults button in the Stage top bar to apply typical defaults +for all components, streamlining your selection. This feature is particularly useful if you’re +unsure about specific settings or wish to adhere to commonly used configurations.

    +_images/stage1_3.png +
    • +

  • Standard Compsets List: After refining your options, visualCaseGen will display a list of +matching compsets. Each compset is labeled with an alias and incorporates an initialization time +and a short description of the included models, providing a snapshot of each configuration. +To narrow down the list further, you can use the search box above the list. Typing keywords +in the search box will display all compsets containing one or more of the search terms. For +precise filtering, use double quotes around terms for exact matches. This flexibility makes +it easy to locate specific compsets or explore different configurations to find the most +suitable one for your simulation needs.

    +_images/Stage1_4.png +
    • +
+

After selecting a compset, visualCaseGen will guide you to the next primary stage, Grid, where +you’ll select a model resolution compatible with your chosen compset.

+
+
+

Custom Compsets

+
+

Note

+

If you initially selected the Standard compset mode, the Custom compset stages will not +display, and instead visualCaseGen will proceed directly to the Grid stage. To switch to the Custom +compset mode after already completing the Standard compset stages, you can click Revert +buttons to navigate back to the selection of configuration mode.

+
+

If you prefer to build a custom compset, visualCaseGen provides a step-by-step process, +starting with the initialization time for your experiment. This choice impacts the initial +conditions and forcings for your simulation. You can choose from:

+
    +

  • 1850: Represents pre-industrial conditions and is suitable for fixed-time-period runs, such as for model spin-ups.

    • +

  • 2000: Represents modern-day conditions, also appropriate for fixed-period simulations.

    • +

  • HIST: Represents a historical run setup, which covers transient simulations (e.g., from 1850 through 2015) that evolve with changing conditions over time.

    +_images/stage1_5.png +
    • +
+

Once you’ve selected the initialization time, visualCaseGen will prompt you to select the +models for each component class. You’ll see options that include active models, data models +(prefixed with d, like datm), and stub models (prefixed with s, like sice). Data models +perform the basic function of reading preexisting forcing data, modifying that data, and then +sending it to active models via the coupler. Stub models act as placeholders required by the CESM +coupler infrastructure but have no impact on the simulation. This variety allows you to +configure a custom compset that includes as many or as few active components as desired, +depending on the specific goals of your simulation.

+
+
_images/Stage1_6.png +
+

As you make selections in this stage and elsewhere, visualCaseGen will guide you by crossing +out incompatible options, helping to prevent invalid configurations. For example, if you select +cam for the atmosphere and mom for the ocean, the GUI will disable several other model +options that are incompatible with this combination. This real-time feedback keeps your +configuration process streamlined and ensures that all selected options work together compatibly.

+
+
_images/Stage1_7.png +
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At any stage, you can click on any crossed-out option to view a brief explanation of +why it’s incompatible with your current selections for additional guidance.

+
+
_images/Stage1_8.png +
+

After choosing your models, you’ll proceed to select the physics options for each. The physics +settings determine the complexity of each model component and impact computational requirements. +Higher version numbers indicate newer and more complex physics for a given model. Depending on +the model, you may have multiple physics options available. For example, cam and +clm have multiple physics options, while other models may offer only one, in which case it +will be selected by default. Since each physics option provides different levels of model complexity, +the selection should be based on the specific requirements of your simulation. Refer to +the individual model documentations for more information on the available physics options.

+
+
_images/Stage1_9.png +
+

The final part of custom compset creation is selecting optional physics modifiers. +Modifiers allow additional adjustments to physics and parameter settings, offering +further customization to meet modeling requirements and goals. Each component class +is represented in individual tabs within this stage. You can switch between tabs to +select modifiers or opt out of a modifier by choosing (none). Tabs with available +modifiers will display a red question mark until a selection is made. While you can +select multiple modifiers for a single component class, be cautious: visualCaseGen +does not verify compatibility between multiple modifiers within a single component, +so it’s advisable to consult CESM documentation or model experts if you’re using complex +modifier combinations.

+
+
_images/Stage1_10.png +
+

Once you’ve completed the selection of models, physics, and optional modifiers, +visualCaseGen will automatically advance to the next main stage, Grid, where +you’ll select a model resolution compatible with your chosen compset.

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+ + + + \ No newline at end of file diff --git a/creating_case.html b/creating_case.html new file mode 100644 index 0000000..65027d1 --- /dev/null +++ b/creating_case.html @@ -0,0 +1,128 @@ + + + + + + + + + Stages of Creating a Case — visualCaseGen 0.0.18 documentation + + + + + + + + + + + + + + + + + +
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Stages of Creating a Case

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The workflow for creating a CESM case using visualCaseGen is divided into three main stages:

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    +

  1. Compset: In this stage, the user will select the compset, i.e., the set of models, physics, and options that will be used in the simulation.

    2. +

  2. Resolution: In this stage, the user will select the resolution of the simulation, i.e., the collection of model grids.

    3. +

  3. Launch: In this final stage, the user will create and configure the case.

    4. +
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Proceed to the following sections to learn more about each stage.

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Fill Indian Ocean

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Instructions coming soon…

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  • Index
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Index

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© Copyright 2024, Alper Altuntas.

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+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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Stage 2/3: Grid

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The second major step in configuring your CESM case is choosing a resolution, which +is a specific set of grids for each active and data model in the compset. You may +select either a standard, out-of-the-box resolution or create a custom one by combining +existing model grids. In Custom mode, you can also generate custom model grids for CLM and/or MOM6 +using auxiliary tools included in visualCaseGen. Begin by selecting between Standard +and Custom grid modes.

+_images/Stage2_1.png +
+

Note

+

In CESM terminology, resolution and grid are often used interchangeably, +both referring to the combination of model grids used in a CESM simulation. Unless +specifically noted as a model grid (i.e., a grid unique to a particular component, +such as the ocean grid), the term grid in this context should be understood as +resolution, meaning the full collection of model grids used in a particular CESM case.

+
+
+

Standard Grids

+

Select from the available list of resolutions (combinations of model grids) below. +Resolutions known to be incompatible with your chosen compset have been omitted +from this list. Use the search box to refine the list further. For exact matches, +use double quotes; otherwise, the search will display all grids containing one +or more of the search terms.

+_images/Stage2_2.png +

After selecting a grid, visualCaseGen will advance to the Launch stage, where +you can create your CESM case using the chosen compset and grid configuration.

+
+
+

Custom Grids

+

In Custom Grid mode, you can build a custom grid by mixing and matching standard +model grids or generating new MOM6 and/or CLM grids with specialized tools that come with visualCaseGen. +Start by specifying a path to save the new grid files and a name to refer to this +new grid in the configuration process and beyond.

+_images/Stage2_3.png +

After clicking Select, a file browser will open to help you locate your preferred +directory for saving the new grid files. Once the directory is selected, enter the +new grid name in the text box at the top right and click Select to proceed.

+_images/Stage2_4.png +
+

Atmosphere Grid

+

Next, choose an atmosphere grid from the list of compatible options based on the +compset you selected in the Compset stage. Use the search box to filter options if needed. +This chosen atmosphere grid will be integrated with other model grids to form your custom CESM grid (resolution).

+_images/Stage2_5.png +
+
+

Ocean Grid

+

For the ocean grid, if MOM6 is selected as the ocean model, you can either select a standard +ocean grid or create a new MOM6 grid. When creating a new MOM6 grid, you’ll specify parameters +such as grid extent and resolution, after which you’ll be directed to a separate notebook that +uses the mom6_bathy tool to generate the new grid and bathymetry.

+

If using a standard ocean grid, select one from the list compatible with your chosen compset +and atmosphere grid. If creating a new MOM6 grid, complete the required parameters, then proceed +to launch the mom6_bathy tool for final customization.

+_images/Stage2_6.png +

After specifying all ocean grid parameters, click Launch mom6_bathy. This will open an +auto-generated Jupyter notebook where you can fine-tune the ocean grid bathymetry and generate +all necessary input files. For more details on mom6_bathy, refer to its documentation: https://ncar.github.io/mom6_bathy/

+
+

Note

+

If the mom6_bathy notebook doesn’t open automatically, make sure that your browser allows +pop-ups from visualCaseGen. If the notebook still doesn’t open, you can manually launch it by +navigating to the mom6_bathy_notebooks/ directory in your visualCaseGen installation and opening +the notebook corresponding to your custom grid.

+
+
+
+

Land Grid

+

Following ocean grid selection or creation, you’ll move to land grid selection. If CLM is chosen +as the land model, you can also modify an existing CLM grid. If so, select a base land grid for +customization.

+_images/Stage2_7.png +
+

Note

+

Detailed instructions on customizing an existing CLM grid will be added here shortly.

+
+

Once atmosphere, ocean, and land grids have been chosen or created, custom grid setup is complete. +visualCaseGen will guide you to the final stage, Launch, where you can create a CESM case based on +the specified compset and grid.

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Welcome to visualCaseGen!

+

visualCaseGen is a Jupyter-based graphical user interface (GUI) designed to streamline +the creation and configuration of Community Earth System Model v.3 (CESM3) cases. +The visualCaseGen GUI allows users to:

+
    +

  • Browse Standard CESM Configurations: Easily explore and select from available CESM compsets +and resolutions.

    • +

  • Create Custom Configurations: Rapidly customize CESM experiments with advanced options for component +selection, grid generation, and configuration.

    • +
+
+

Key Features

+
    +

  • Easy Case Setup: Intuitive interface for configuring experiments.

    • +

  • Hierarchical Modeling: Combine different complexity levels across components.

    • +

  • Flexible Configurations: Mix and match models and grids with compatibility guidance.

    • +

  • Automated Case Creation: Generates input files and handles XML/namelist adjustments.

    • +

  • Modify CLM Inputs: Easily adjust land masks and surface datasets with a form-based interface.

    • +

  • MOM6 Grid & Bathymetry Customization: Create or modify grids and bathymetries with a point-and-click tool.

    • +
+_images/demo3.gif +
+
+

Typical Workflow

+
    +

  • Launch: Open the visualCaseGen GUI within your Jupyter notebook environment.

    • +

  • Select Compset: Choose from available standard CESM compsets or create a custom one by selecting +models, physics options, and other settings for each component (e.g., atmosphere, ocean, land, ice).

    • +

  • Define Resolution: Select a compatible standard resolution or create a custom one by combining +different grids for each model component or generating new ones.

    • +

  • Generate Case: Once your compset and resolution are set, visualCaseGen will create the CESM case, +automatically generating required input files and making all necessary modifications to CESM XML and +user namelist files.

    • +
+

For more information on each step, please refer to the corresponding sections in this user guide.

+
+

User Manual:

+ +
+
+

Examples:

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Installation

+

visualCaseGen is presently bundled with a CESM distribution (fork) based on cesm3_0_beta03. The following +instructions guide you through obtaining and installing this specific CESM distribution with visualCaseGen.

+
+

Prerequisite

+
+

Warning

+

The key prerequisite for installing visualCaseGen is that CESM cesm3_0_beta03 or a newer version is already +ported on your machine. If this version (or later) is not yet ported, follow the CESM documentation +instructions to port it first. Without this, visualCaseGen will not launch.

+
+
    +

  • Verify CESM port: Ensure CESM cesm3_0_beta03 or newer is ported on your machine. If not, follow the CESM +documentation to port the required version.

    • +

  • Conda Installation: Confirm that Conda is installed, either via Miniconda or Anaconda. You can install Miniconda +from the following link: +https://docs.conda.io/en/latest/miniconda.html

    • +
+
+
+

Download CESM with visualCaseGen

+

To download the specific CESM distribution bundled with visualCaseGen, clone the CESM GitHub repository and +use the git-fleximod script that comes with CESM as a package manager, as follows. Note that downloading +CESM may take some time.

+
git clone https://github.com/alperaltuntas/cesm.git -b cesm3_0_beta03_gui cesm3_0_beta03_gui
+cd cesm3_0_beta03_gui
+./bin/git-fleximod update
+
+
+

This will download the required CESM version, including visualCaseGen.

+
+
+

Create the visualCaseGen conda environment

+
+

Warning

+

If you are using a machine other than one of the supported systems (e.g., derecho, casper), you may need +to modify the ccs_config/machines XML files in the newly downloaded CESM distribution. This may be required +even if CESM cesm3_0_beta03 or a newer version is already ported on your machine. These modifications +should match the adjustments made previously for the ported CESM version. For guidance on updating the +ccs_config/machines XML files, refer to the CESM documentation, consult CESM support through the CESM forum, +or submit an issue on the visualCaseGen GitHub repository. Users on supported machines can ignore this warning, +as no changes are needed.

+
+

To create the visualCaseGen conda environment, navigate to the visualCaseGen directory and run the following +commands:

+
cd visualCaseGen
+conda env create -f environment.yml
+
+
+

This will create the visualCaseGen conda environment. Activate the visualCaseGen conda environment by running +the following command:

+
conda activate visualCaseGen
+
+
+
+
+

Verify Installation

+

To verify that visualCaseGen was installed correctly, run the test suite:

+
pytest tests/
+
+
+

If the test suite completes successfully, visualCaseGen is ready for use. If any tests fail, please open an +issue on the visualCaseGen GitHub repository, including error messages and the installation steps you followed.

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Stage 3/3: Launch

+

The final main stage of visualCaseGen is the Launch stage, where you bring your CESM case to +life with the selected compset and grid configuration. In this stage, you’ll find tools to +select the case directory, choose a target machine, and initiate case creation.

+_images/Stage3_1.png +
+

Chosing the case directory

+

To begin, open the file browser widget by clicking the Select button to set the directory for +the new case. Navigate to your desired location, then enter a unique name for the case in the +text box at the top right of the browser. Click Select to confirm your directory and case name.

+_images/Stage3_2.png +
+
+

Selecting the target machine

+

Next, choose the machine where the case will run. If CESM has already been ported to the machine, +this selection should populate automatically. If not, confirm that CESM is properly ported to the +machine you intend to use and that the correct machine is selected. For some systems, a PROJECT ID +is required; if so, you’ll be prompted to enter it here.

+
+

Note

+

If you’re using a machine that shares a file system with another, you have the flexibility +to select a different machine for running the case. For example, if you are working within +visualCaseGen on casper but intend to run the case on derecho, simply change the machine selection +to derecho at this stage. This allows you to configure the case on one machine while specifying +execution on another within the shared system environment.

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+
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Creating the case

+

When all selections are finalized, you can click Create Case to initiate case creation or +Show Commands to view the terminal commands that will be executed. Below, you’ll see an +example of the interface after clicking Create Case. Notice how visualCaseGen handles the +case setup process, including modifying CESM XML files, executing the create_newcase tool, +running the case.setup script, and applying any XML and namelist changes needed.

+_images/Stage3_3.png +

The completion log provides confirmation of a successful case creation, including the path to +the new case directory, where you can proceed with case customization, building, and execution.

+
+
+

Congratulations!

+

You’ve successfully created a CESM case using visualCaseGen, bringing together the models, +grid, and configurations tailored to your scientific goals. With the case directory set up, +you’re ready to move forward with any additional customizations, building, and executing your +case. Great job, and happy modeling!

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+ + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000..9e5675b --- /dev/null +++ b/objects.inv @@ -0,0 +1,5 @@ +# Sphinx inventory version 2 +# Project: visualCaseGen +# Version: +# The remainder of this file is compressed using zlib. +xڅRN0+[TjŢcOK;D/Ic7-7OU‚ur-6%Tv!2Lr%ӫ5nM™;GƜ 6# BvRDJKu>bFad{\WtoBkg{}XjA6٬#/+ﲎ.3>F|Т ɣB?΋Hg#qua)ܓl߅jp }7+//_ή|ua"/;$ ;J7\o6ߕMA%[ of \ No newline at end of file diff --git a/open.html b/open.html new file mode 100644 index 0000000..3d7e9db --- /dev/null +++ b/open.html @@ -0,0 +1,253 @@ + + + + + + + + + Opening the GUI — visualCaseGen 0.0.18 documentation + + + + + + + + + + + + + + + + + +
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Opening the GUI

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Once the conda environment is installed, you can launch visualCaseGen by opening the GUI.ipynb notebook +in the visualCaseGen/ directory. Below are several common methods for launching the notebook. If you are +using NCAR machines, the JupyterHub interface is recommended.

+ +
+

From the Command Line

+
+

Warning

+

The command-line launch is possible only if you’re running on a local machine or have SSH tunneling +enabled. For remote access, set up SSH tunneling (described in the next section).

+
+

Ensure the visualCaseGen Conda environment is activated. If not, activate it with:

+
conda activate visualCaseGen
+
+
+

Launch the notebook from the command line by navigating to the visualCaseGen/ directory +where GUI.ipynb notebook is located and running:

+
jupyter-lab GUI.ipynb
+
+
+

This will open the Jupyter notebook in your default web browser, displaying a cell with the following code:

+
from visualCaseGen import gui; gui
+
+
+

To start the GUI, execute the cell by clicking the Run button or pressing Shift + Enter. You should +see the following welcome dialog. Click Start to begin using the GUI:

+_images/launch5.png +
    +

  • Once the Start button is clicked, a loadbar will appear, indicating that the GUI is initializing. When the +GUI is ready, the main interface will be displayed. If the loadbar hangs, click the Help button on the top +right corner of the welcome dialog to see if any error messages are displayed. If you encounter any issues, +please refer to the Troubleshooting section of this documentation.

    • +
+
+
+

On a Remote Machine

+

To access the GUI on a remote machine, set up SSH tunneling with port forwarding.

+
    +

  • Establish an SSH connection with port forwarding (the exact command may vary depending on your system):

    • +
+
ssh -L 8888:localhost:8888 username@remote_host
+
+
+
    +

  • After connecting, activate the visualCaseGen Conda environment, navigate to the visualCaseGen/ directory, and run:

    • +
+
conda activate visualCaseGen
+cd [PATH_TO_visualCaseGen] # e.g., ~/cesm3_0_beta03_gui/visualCaseGen
+jupyter-lab GUI.ipynb --no-browser
+
+
+

If the above steps are successful, the command line will display a URL that you can copy and paste into your web browser +to access the Jupyter notebook. The URL will look similar to:

+
http://localhost:8888/lab/?token=1234567890abcdef1234567890abcdef1234567890abcdef
+
+
+

Paste the url shown in your own terminal into your web browser to access the visualCaseGen GUI. A Jupyter +notebook with the following cell will be displayed:

+
from visualCaseGen import gui; gui
+
+
+

To start the GUI, execute the cell by clicking the Run button or pressing Shift + Enter. You should +see the following welcome dialog. Click Start to begin using the GUI:

+_images/launch5.png +
    +

  • Once the Start button is clicked, a loadbar will appear, indicating that the GUI is initializing. When the +GUI is ready, the main interface will be displayed. If the loadbar hangs, click the Help button on the top +right corner of the welcome dialog to see if any error messages are displayed. If you encounter any issues, +please refer to the Troubleshooting section of this documentation.

    • +
+
+
+

NCAR JupyterHub

+
+

Warning

+

This method is available only to users with access to NCAR systems like derecho or casper.

+
+
    +

  • Go to NCAR JupyterHub in your web browser:

    • +
+
https://jupyterhub.hpc.ucar.edu/
+
+
+
    +

  • Log in by selecting “Production” under “Available NCAR Resources,” then enter your NCAR credentials.

    • +

  • Start a JupyterHub server by clicking the “start” button under the Actions column.

    • +
+_images/launch1.png +
    +

  • When prompted, select a resource. Although any resource is acceptable, “Casper Login” is recommended, as visualCaseGen does not require significant computational power.

    • +
+_images/launch2.png +
    +

  • After the resource starts, navigate to the visualCaseGen/ directory from the File Browser tab on the left.

    • +
+
+

Tip

+

Create a symbolic link to your CESM directory in your home directory for easier access.

+
+
    +

  • Open the GUI.ipynb notebook by double clicking on it,

    • +
+_images/launch3.png +
    +

  • When prompted, select the visualCaseGen Conda kernel from the dropdown menu. (If not prompted, select the kernel by clicking +the kernel name in the top right corner of the notebook.)

    • +
+_images/launch4.png +
    +

  • To start the GUI, execute the first cell (with from visualCaseGen import gui; gui) by clicking the Run button +or pressing Shift + Enter. You should see the following welcome dialog. Click Start to begin using the GUI:

    • +
+_images/launch5.png +
    +

  • Once the Start button is clicked, a loadbar will appear, indicating that the GUI is initializing. When the +GUI is ready, the main interface will be displayed. If the loadbar hangs, click the Help button on the top +right corner of the welcome dialog to see if any error messages are displayed. If you encounter any issues, +please refer to the Troubleshooting section of this documentation.

    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ridge.html b/ridge.html new file mode 100644 index 0000000..f53fa94 --- /dev/null +++ b/ridge.html @@ -0,0 +1,189 @@ + + + + + + + + + Ridge World — visualCaseGen 0.0.18 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Ridge World

+

This example provides step-by-step guidance on how to generate a coupled idealized +configuration that consists of an aquaplanet with land caps at the pole and a narrow +land ridge extending between the two poles, similar to the configuration used in Wu et al (2021) . +In the example given below, the visualCaseGen GUI is used to guide users through choosing +their CESM components, setting up all the ocean input files, setting up all the land input +files, and finally setting up and configuring their case.

+

Here we are not running a standard case with CESM. We are modifying the configuration substantially by changing the ocean grid, ocean bathymetry, continental geometry and land surface properties, so you should select “Custom” here.

+
+

Stage 0: Open visualCaseGen

+

Follow the instructions in the Opening the GUI to open visualCaseGen in your Jupyter notebook environment.

+
+
+

Stage 1: Select Compset

+

After having executed the cell with the command from visualCaseGen import gui; gui, +and clicking the Start button, you will see the main interface of visualCaseGen.

+

Click the Custom button to proceed with creating a custom compset for our idealized +Ridge World configuration.

+_images/stage1_1.png +
+

Initialization time

+

Once the Custom button is clicked, you will be prompted to select the initialization time. +For this example, we will select 1850` as the initialization time.

+_images/stage1_5.png +
+
+

Models

+

Once you’ve selected the initialization time, visualCaseGen will prompt you to select the +models for each component class. In this ridge world case we select the following component options: +cam as the atmosphere; +clm` as the land component; cice` as the ice component; mom` as the ocean component, srof` +(i.e., stub run off) as the river component; sglc` (i.e., stub land ice) as the land ice component; +and, swav (i.e. stub wave) as the wave component. After all the selections are made, the +model matrix should look like:

+_images/ridge1.png +
+
+

Model Physics

+

Having selected the models, you will proceed to select the physics options for each. The physics +settings determine the complexity of each model component and impact computational requirements. +For this example, we will select the following physics options which are based on the selections +made in Wu et al (2021) :

+_images/ridge2.png +
+
+

Component Options (Modifiers)

+

We are now ready to finalize the compset by selecting optional physics modifiers. For this example, +we will select (none) for all the components except for the clm component where we will select +the satellite phenology (SP) mode for the land which means that aspects of the land model such as +leaf-area index are prescribed as opposed to being prognosed interactively by the land biogeochemistry.

+_images/ridge3.png +
+
+
+

Stage 2: Grid

+

Having completed the compset configuration, you will now proceed to the Grid stage …

+

Further instructions will be added as the example is developed…

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/search.html b/search.html new file mode 100644 index 0000000..41ef2a0 --- /dev/null +++ b/search.html @@ -0,0 +1,132 @@ + + + + + + + + Search — visualCaseGen 0.0.18 documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Search
    • +
  • +
    • +
+
+
+
+
+ + + + +
+ +
+ +
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+ +
+

© Copyright 2024, Alper Altuntas.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + + + + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 0000000..8507721 --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"Atmosphere Grid": [[4, "atmosphere-grid"]], "Chosing the case directory": [[7, "chosing-the-case-directory"]], "Commonly Encountered Issues": [[10, "commonly-encountered-issues"]], "Component Options (Modifiers)": [[9, "component-options-modifiers"]], "Configuration Variable": [[0, "configuration-variable"]], "Congratulations!": [[7, "congratulations"]], "Create the visualCaseGen conda environment": [[6, "create-the-visualcasegen-conda-environment"]], "Creating the case": [[7, "creating-the-case"]], "Custom Compsets": [[1, "custom-compsets"]], "Custom Grids": [[4, "custom-grids"]], "Download CESM with visualCaseGen": [[6, "download-cesm-with-visualcasegen"]], "Examples:": [[5, null]], "Fill Indian Ocean": [[3, null]], "From the Command Line": [[8, 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to visualCaseGen!", "Installation", "Stage 3/3: Launch", "Opening the GUI", "Ridge World", "Troubleshooting"], "titleterms": {"0": 9, "1": [1, 9], "2": [4, 9], "3": [1, 4, 7], "On": 8, "atmospher": 4, "basic": 0, "case": [2, 7], "cesm": 6, "chose": 7, "command": 8, "commonli": 10, "compon": 9, "compset": [1, 9], "conda": 6, "configur": 0, "congratul": 7, "creat": [2, 6, 7], "custom": [0, 1, 4], "directori": 7, "download": 6, "encount": 10, "environ": 6, "exampl": 5, "featur": 5, "fill": 3, "from": 8, "grid": [0, 4, 9], "gui": 8, "indian": 3, "initi": 9, "instal": 6, "issu": 10, "jupyterhub": 8, "kei": 5, "land": 4, "launch": [7, 8], "line": 8, "machin": [7, 8], "manual": 5, "model": [0, 9], "modifi": 9, "ncar": 8, "ocean": [3, 4], "open": [8, 9], "option": [8, 9], "physic": 9, "prerequisit": 6, "remot": 8, "resolut": 0, "ridg": 9, "select": [7, 9], "stage": [0, 1, 2, 4, 7, 9], "standard": [0, 1, 4], "target": 7, "time": 9, "troubleshoot": 10, "typic": 5, "user": 5, "v": 0, "variabl": 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Troubleshooting

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Below are some common issues that users may encounter while using visualCaseGen and their solutions. +If the suggested solutions do not resolve the issue, or if you encounter a different problem, please +open an issue on the visualCaseGen GitHub repository: https://github.com/ESMCI/visualCaseGen/issues/new

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Commonly Encountered Issues

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  • Error displaying widget: model not found: +This message generally appears when a previously run +GUI.ipynb notebook is re-opened. This error message doesn’t generally indicate a problem with the GUI, +and should dissapear after running the cell with the from visualCaseGen import gui; gui code.

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  • ModuleNotFoundError: No module named z3, ipyfilechooser, etc.: This error indicates that either +the visualCaseGen` conda environment is not installed correctly, it was not chosen as the active environment, +or it was not chosen as the kernel in the Jupyter notebook. To resolve this issue, ensure that the visualCaseGen +conda environment is installed correctly and activated. If the issue persists, try restarting the Jupyter notebook +kernel and selecting the visualCaseGen environment as the kernel.

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  • Hanging Loadbar: If the loadbar hangs after clicking the Start button, click the Help button on the top +right corner of the welcome dialog to see if any error messages are displayed. If so, submit an issue on the +visualCaseGen GitHub repository with the error messages.

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  • mom6_bathy notebook doesn’t open automatically: If the mom6_bathy notebook doesn’t open automatically, +make sure that your browser allows +pop-ups from visualCaseGen. If the notebook still doesn’t open, you can manually launch it by +navigating to the mom6_bathy_notebooks/ directory in your visualCaseGen installation and opening +the notebook corresponding to your custom grid.

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