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revise quickview guides
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‎docs/.vitepress/config.mjs‎

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@@ -17,7 +17,7 @@ export default defineConfig({
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{ text: "Home", link: "/" },
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{ text: "News", link: "/news" },
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{ text: "Gallery", link: "/gallery/" },
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{ text: "User's Guide", link: "/guides/data" },
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{ text: "User's Guide", link: "/guides/reminders" },
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{ text: "At NERSC", link: "/nersc/login" },
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{ text: "Repo", link: "https://github.com/Kitware/QuickView" },
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{ text: "Bugs and Requests", link: "https://github.com/Kitware/QuickView/issues" },
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{
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text: "Introduction",
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items: [
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{ text: "Key Reminders", link: "/guides/reminders" },
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{ text: "Connecitiviy Files", link: "/guides/connectivity" },
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{ text: "Data Format", link: "/guides/data" },
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{ text: "Installation", link: "/guides/installation" },
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],
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text: "QuickView",
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items: [
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{ text: "Getting started", link: "/guides/quickview" },
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{ text: "Toolbar", link: "/guides/quickview/toolbar" },
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{ text: "Resources", link: "/guides/quickview/resources" },
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],
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},

‎docs/guides/connectivity.md‎

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# Connectivity files
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::: tip "Tip: Connecitivity File Download"
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A collection of connectivity files can
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be found on [Zenodo](https://doi.org/10.5281/zenodo.16908566). The archive is
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continually updated as more users inform us about the grids their data files
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use.
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:::
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The horizontal grids used by EAM are cubed spheres. Since these are unstructed
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grids, QuickView needs to know how to map data to the globe. Therefore, for each
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simulation data file, a "connectivity file" needs to be provided.
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In EAMv2, v3, and v4, most of the variables (physical quantities) are written
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out on a "physics grid" (also referred to as "physgrid", "FV grid", or "control
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volume mesh") described in
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[Hannah et al. (2021)](https://doi.org/10.1029/2020MS002419). The naming
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convention for such grids is `ne*pg2`, with `*` being a number, e.g., 4, 30,
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120, 256. Further details about EAM's cubed-sphere grids can be found in EAM's
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documentation, for example in
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[this overview](https://e3sm.atlassian.net/wiki/spaces/DOC/pages/34113147/SE+Atmosphere+Grid+Overview+EAM+CAM)
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and
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[this description](https://e3sm.atlassian.net/wiki/spaces/DOC/pages/872579110/Running+E3SM+on+New+Atmosphere+Grids).
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Future versions of QuickView will also support the cubed-sphere meshes used by
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EAM's dynamical core, i.e., the `ne*np4` grids (also referred to as "native
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grids" or "GLL grids").
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## Generate connectivity files
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Users can generate connectivity files with
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[`TempestRemap`](https://github.com/ClimateGlobalChange/tempestremap)
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([Ullrich and Taylor, 2015](https://doi.org/10.1175/MWR-D-14-00343.1);
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[Ullrich et al., 2016](https://doi.org/10.1175/MWR-D-15-0301.1)) using
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[this script](https://github.com/mt5555/remap-ncl/blob/master/makeSE.sh) shared
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by Mark A. Taylor at Sandia National Laboratories. (`TempestRemap` is available
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as a part of the [`E3SM-Unified`](https://github.com/E3SM-Project/e3sm-unified)
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conda environment. It can also be installed following the instructions provided
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in its [repo](https://github.com/ClimateGlobalChange/tempestremap).)
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For example, using Mark's script, the command
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```
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./makeSE.sh 30
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```
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will generate several different files for the `ne30pg2` grid, including, e.g.,
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- `TEMEPST_NE30pg2.g` (Exodus format),
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- `TEMPEST_ne30pg2.scrip.nc` (SCRIP format).
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QuickView uses the **SCRIP** format.

‎docs/guides/data.md‎

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is converted to NaN and ignored in the calculation of global averages and for
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the visualization.
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# Connectivity files
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::: tip Tip: Connecitivity File Download A collection of connectivity files can
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be found on [Zenodo](https://doi.org/10.5281/zenodo.16908566). The archive is
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continually updated as more users inform us about the grids their data files
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use.
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:::
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The horizontal grids used by EAM are cubed spheres. Since these are unstructed
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grids, QuickView needs to know how to map data to the globe. Therefore, for each
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simulation data file, a "connectivity file" needs to be provided.
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In EAMv2, v3, and v4, most of the variables (physical quantities) are written
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out on a "physics grid" (also referred to as "physgrid", "FV grid", or "control
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volume mesh") described in
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[Hannah et al. (2021)](https://doi.org/10.1029/2020MS002419). The naming
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convention for such grids is `ne*pg2`, with `*` being a number, e.g., 4, 30,
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120, 256. Further details about EAM's cubed-sphere grids can be found in EAM's
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documentation, for example in
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[this overview](https://e3sm.atlassian.net/wiki/spaces/DOC/pages/34113147/SE+Atmosphere+Grid+Overview+EAM+CAM)
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and
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[this description](https://e3sm.atlassian.net/wiki/spaces/DOC/pages/872579110/Running+E3SM+on+New+Atmosphere+Grids).
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Future versions of QuickView will also support the cubed-sphere meshes used by
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EAM's dynamical core, i.e., the `ne*np4` grids (also referred to as "native
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grids" or "GLL grids").
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## Generate connectivity files
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Users can generate connectivity files with
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[`TempestRemap`](https://github.com/ClimateGlobalChange/tempestremap)
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([Ullrich and Taylor, 2015](https://doi.org/10.1175/MWR-D-14-00343.1);
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[Ullrich et al., 2016](https://doi.org/10.1175/MWR-D-15-0301.1)) using
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[this script](https://github.com/mt5555/remap-ncl/blob/master/makeSE.sh) shared
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by Mark A. Taylor at Sandia National Laboratories. (`TempestRemap` is available
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as a part of the [`E3SM-Unified`](https://github.com/E3SM-Project/e3sm-unified)
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conda environment. It can also be installed following the instructions provided
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in its [repo](https://github.com/ClimateGlobalChange/tempestremap).)
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For example, using Mark's script, the command
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```
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./makeSE.sh 30
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```
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will generate several different files for the `ne30pg2` grid, including, e.g.,
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- `TEMEPST_NE30pg2.g` (Exodus format),
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- `TEMPEST_ne30pg2.scrip.nc` (SCRIP format).
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EAM QuickView uses the **SCRIP** format.

‎docs/guides/quickview/toolbar.md‎

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## Toolbar

‎docs/guides/reminders.md‎

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## Key reminders for using QuickView and other tools in the family
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::: tip "Two modes of use"
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QuickView can be used in two modes:
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a ^^new-viz^^ mode (for starting a new visualization) or
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a ^^resume^^ mode (for resuming an analysis). Further details can be found on
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the [toolbar description page](/guides/quickview/toolbar.md).
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:::
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::: tip "Connectivity Files"
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Since E3SM's horizontal grids are unstructured meshes from ParaView's perspective,
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connectivity files are needed in addition to the simulation data files.
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Further details can be found on the documentation pages
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describing the [connectivity files](/guides/connectivity.md) and the
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[toolbar](/guides/quickview/toolbar.md).
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:::
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::: tip "The `LOAD VARIABLES` Button"
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Most buttons, sliders, and selection boxes in the GUI apply their effects
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immediately upon user interaction. The only exception is the variable
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selection: After variables are chosen for the first time following file load
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or after the selection is changed, the user ^^must^^ click the `LOAD VARIABLES`
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button in the [toolbar](/guides/quickview/toolbar.md) for the new selection to take effect.
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:::
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::: tip "Viewport Layout"
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The QuickView app is designed to present multiple variables simultaneously
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in an informative way. Users can ^^rearrange^^ the individual views
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(i.e., contour plots) in the [viewport](/guides/quickview/viewport.md)
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and ^^resize^^ each view.
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Furthermore, if a user saves a state file after these
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adjustments, they can later resume their analysis with the customized
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arrangement.
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:::

‎docs/index.md‎

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name: "QuickView"
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text: "for Earth system models"
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tagline:
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Intuitive and interative exploration of simulation data.
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Intuitive and interactive exploration of simulation data.
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image: /banner.png
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actions:
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- theme: brand

‎docs/old-to-delete/userguide/reminders.md‎

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