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evaleev committed Sep 12, 2023
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Expand Up @@ -9,23 +9,29 @@ This directory contains various utilities:

## `MRAMeshOrbitalPlot3D.wl`

- if you have [https://www.wolfram.com/wolframscript/](WolframScript) installed (yes by default on Windows/Linux; on a Mac need to [https://www.wolfram.com/wolframscript/](download/install manually)) to plot from command-line or shell script. See a quick example in `h2-no1.wsl`; to try out execute `./h2-no1.wsl > h2-no1.pdf`
- if you have [WolframScript](https://www.wolfram.com/wolframscript/) installed (it is bundled with Mathematica by default on Windows/Linux; on a Mac need to [download/install manually](https://www.wolfram.com/wolframscript/) to plot from command-line or shell script. See a quick example in `h2-no1.wsl`; to try out execute `./h2-no1.wsl > h2-no1.pdf`
- more elaborate plotting is best done from a Mathematica notebook. Here's a brief example:
```Wolfram
<< "/path/to/madness/source/dir/src/madness/mra/tools/MRAMeshOrbitalPlot3D.wl"
(* this assumes that data.cube (produced by madness::plot_cubefile) and data.tree.json (produced by madness::print_tree_jsonfile) exist in /path/to/data
MRAMeshOrbitalPlot3D["/path/to/data"]
```
You can even pull the module and data remotely, e.g.:
```Wolfram
<< "https://raw.githubusercontent.com/m-a-d-n-e-s-s/madness/evaleev/feature/wolfram-orbital-plotting/src/madness/mra/tools/MRAMeshOrbitalPlot3D.wl"
MRAMeshOrbitalPlot3D["https://raw.githubusercontent.com/m-a-d-n-e-s-s/madness/evaleev/feature/wolfram-orbital-plotting/src/madness/mra/tools/h2-no1"]
```

###
The only function `MRAMeshOrbitalPlot3D.wl` provides is `MRAMeshOrbitalPlot3D`. `MRAMeshOrbitalPlot3D[fp,opts]` returns a plot of the orbital stored via `madness::plot_cubefile` and `madness::print_json_treefile` in files `fp.cube` and `fp.tree.json`, respectively. `MRAMeshOrbitalPlot3D` accepts all options recognized by `Graphics3D` and `ListContourPlot3D` functions, as well as the following additional options:

| Option | Default | Description |
|-----------------------------|---------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `Zoom` | `1` | Can be used to produce a plot in a zoomed-in section of the simulation cell. This does not need to match the zoom value given to plot_cubefile (that only affects the resolution/extent of the Gaussian Cube mesh) |
| `MRAMeshCuboidDirectives` | `{EdgeForm[Thick]}` | Specifies how the Cuboid objects comprising the MRA mesh are drawn. All Graphics3D directives that are applicable to Cuboid (except Opacity) can be specified. |
| `MaxLevel` | `Infinity` | Controls the highest refinement level of displayed mesh elements. |
| `MinLevel` | `0` | Controls the lowest refinement level of displayed mesh elements. |
The only function `MRAMeshOrbitalPlot3D.wl` provides is `MRAMeshOrbitalPlot3D`. `MRAMeshOrbitalPlot3D[fp,opts]` returns a plot of the orbital stored via `madness::plot_cubefile` and `madness::print_json_treefile` in files `fp.cube` and `fp.tree.json`, respectively. `MRAMeshOrbitalPlot3D` accepts all options recognized by [`Graphics3D`](https://reference.wolfram.com/language/ref/Graphics3D.html]) and [`ListContourPlot3D`](https://reference.wolfram.com/language/ref/ListContourPlot3D.html) functions, as well as the following additional options:

| Option | Default | Description |
|-----------------------------|---------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `Zoom` | `1` | Can be used to produce a plot in a zoomed-in section of the simulation cell. This does not need to match the zoom value given to plot_cubefile (that only affects the resolution/extent of the Gaussian Cube mesh) |
| `MRAMeshCuboidDirectives` | `{EdgeForm[Thick]}` | Specifies how the Cuboid objects comprising the MRA mesh are drawn. All [`Graphics3D`](https://reference.wolfram.com/language/ref/Graphics3D.html) directives that are applicable to [`Cuboid`](https://reference.wolfram.com/language/ref/Cuboid.html) (except [`Opacity`](https://reference.wolfram.com/language/ref/Opacity.html)) can be specified. |
| `MaxLevel` | `Infinity` | Controls the highest refinement level of displayed mesh elements. |
| `MinLevel` | `0` | Controls the lowest refinement level of displayed mesh elements. |


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