Merge pull request #46 from Avogadro/fixup-build

Added images and tweaked user docs
Avogadro · Oct 29, 2023 · 60154bb · 60154bb
2 parents 2c93200 + 396c024
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diff --git a/source/_images/spectra.png b/source/_images/spectra.png
diff --git a/source/_images/start-with-a-generated-crystal-surface.png b/source/_images/start-with-a-generated-crystal-surface.png
diff --git a/source/_images/start-with-a-wfn-file.png b/source/_images/start-with-a-wfn-file.png
diff --git a/source/_images/start-with-your-molecule-of-interest.png b/source/_images/start-with-your-molecule-of-interest.png
diff --git a/source/_images/stick.png b/source/_images/stick.png
diff --git a/source/_images/surfaces.png b/source/_images/surfaces.png
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diff --git a/source/api/index.md b/source/api/index.md
@@ -2,7 +2,30 @@
 
 # Develop
 
-Avogadro libraries can be used from both C++ and Python interfaces.
+Avogadro can be extended from both C++ and Python interfaces.
+
+In many cases,
+
+## Script Plugins
+
+Many features in Avogadro can be extended with Python scripts, including:
+
+- menu commands
+- electrostatic models
+- force fields
+- input generators
+
+For more details, see the [script plugin](../scripts/index) documentation.
+
+## External Scripting
+
+Avogadro supports sending messages from external scripts, through
+remote procedure call (RPC) JSON. This can be very helpful for rendering
+images of molecules, generating orbitals, etc.
+
+For more details, see the [RPC](rpc) documentation.
+
+## Libraries
 
 The Avogadro libraries are developed to support the Avogadro2 application, and
 provide liberally BSD-licensed, open-source reusable components for both C++ and Python. At its core it is a platform for developing molecular visualization, editing and interactive simulation applications. This is achieved using a collection of libraries, along with a plugin interface allowing the platform to be easily extended and used in a variety of environments.
@@ -44,6 +67,7 @@ maxdepth: 2
 hidden: true
 ---
 
+../scripts/index
 rpc
 classlist
 ```
diff --git a/source/conf.py b/source/conf.py
@@ -49,7 +49,7 @@
     'sphinx.ext.viewcode',
     'sphinx_design',
     'sphinx_copybutton',
-    #'breathe',
+    'breathe',
     'myst_parser',
 ]
 
@@ -74,6 +74,7 @@
 myst_substitutions = {
   "release": release,
   "macurl": f"https://github.com/OpenChemistry/avogadrolibs/releases/download/{version}/Avogadro2-{version}-Darwin.dmg",
+  "macarmurl": f"https://github.com/OpenChemistry/avogadrolibs/releases/download/{version}/Avogadro2-{version}-Darwin-arm64.dmg",
   "winurl": f"https://github.com/OpenChemistry/avogadrolibs/releases/download/{version}/Avogadro2-{version}-win64.exe",
   "appurl": f"https://github.com/OpenChemistry/avogadrolibs/releases/download/{version}/Avogadro2-x86_64.AppImage"
 }

diff --git a/source/docs/building-materials/building-a-crystal-slab.md b/source/docs/building-materials/building-a-crystal-slab.md
@@ -4,27 +4,27 @@ Build up a crystal surface, e.g., Pt  for a defined Miller Plane.
 
 ## Import the appropriate crystal structure.
 
-![](../.gitbook/assets/import-the-appropriate-crystal-structure.png)
+![](../../_images/import-the-appropriate-crystal-structure.png)
 
 Either open a CIF file with the crystal structure needed, or import one from the built-in Avogadro crystal library. The tutorial will assume you import a structure from the Avogadro library. Choose File &gt; Import &gt; Crystal to bring up the library.
 
-![](../.gitbook/assets/media_1332447195630.png)
+![](../../_images/media_1332447195630.png)
 
 Either browse through the crystals, or type a filter -- by element or name. Click "Insert" to import the selected structure.
 
-![](../.gitbook/assets/media_1332447360825.png)
+![](../../_images/media_1332447360825.png)
 
 Importing a crystal will show the asymmetric unit cell \(e.g., one atom for Silver here\).
 
-![](../.gitbook/assets/media_1332448938642.png)
+![](../../_images/media_1332448938642.png)
 
 To build a specified surface \(e.g., Ag \) choose Crystallography &gt; Build &gt; Slab... to bring up the slab builder settings. Future crystal builders \(e.g., nanoparticles, supercells\) will also appear in this menu.
 
-![](../.gitbook/assets/3d1781c8-d8ba-45ce-af85-65625a1c4d24.png)
+![](../../_images/3d1781c8-d8ba-45ce-af85-65625a1c4d24.png)
 
 Specify the indices of the Miller plane desired \(for hexagonal unit cells, all 4 indices will appear\), and choose the dimensions in either distances or repeating cells of the resulting surface. The generated surface is aligned in the XY plane, and a specified thickness will be cleaved in the z-axis below the XY plane. This feature allows easy alignment between a new surface and a molecule for surface interaction calculations. Click "Build" to start the surface generation.
 
-![](../.gitbook/assets/media_1332468285179.png)
+![](../../_images/media_1332468285179.png)
 
 After clicking "Build," Avogadro will generate a large supercell, align, rotate, and cleave the designated surface. This may take some time, depending on the size of the crystal cell. Here translucent van der Waals spheres are used to illustrate the corrugation of the Ag  surface. The resulting surface is a 2x2 supercell, with a large spacing \(40 Å\) in the z-axis.
 
diff --git a/source/docs/building-materials/building-a-polymer-unit-cell.md b/source/docs/building-materials/building-a-polymer-unit-cell.md
@@ -2,51 +2,51 @@
 
 A walk-through on creating a unit cell \(of a polymer\) using Avogadro and the Align tool. This specific example uses Gaussian, but translation vectors for other programs can be performed similarly.
 
-![](../.gitbook/assets/media_1260118979959.png)
+![](../../_images/media_1260118979959.png)
 
 Build out the molecule for the unit cell. Notice that while the repeat unit here is 2 rings, we have built 3 rings. This way, we will properly model the bond which spans two unit cells.
 
-![](../.gitbook/assets/media_1260119377141.png)
+![](../../_images/media_1260119377141.png)
 
 Optimize the geometry of the molecule.
 
-![](../.gitbook/assets/media_1260119456591.png)
+![](../../_images/media_1260119456591.png)
 
 Switch to the Align tool to translate and orient the unit cell coordinates.
 
-![](../.gitbook/assets/media_1260119601872.png)
+![](../../_images/media_1260119601872.png)
 
 Make sure to open the Tool Settings window, which will allow you to work with the Align tool.
 
-![](../.gitbook/assets/media_1260119685502.png)
+![](../../_images/media_1260119685502.png)
 
 First click on the "start" atom of the polythiophene. This atom will be translated to the origin \(0, 0, 0\). Then click on the corresponding atom in the "next" unit cell. The distance between these two atoms will define one axis in the unit cell.
 
-![](../.gitbook/assets/media_1260119852731.png)
+![](../../_images/media_1260119852731.png)
 
 In the "Align Settings" window, define an axis for the unit cell. Then click the Align button. This will change the coordinate set to have atom \#1 at the origin, and atom \#2 \(from the step above\) projected onto the x-axis.
 
-![](../.gitbook/assets/media_1260120107101.png)
+![](../../_images/media_1260120107101.png)
 
 Open the Cartesian Editor window to verify the results of the Align operation.
 
-![](../.gitbook/assets/Screen-shot-2009-12-06-at-12.23.01-PM.png)
+![](../../_images/Screen-shot-2009-12-06-at-12.23.01-PM.png)
 
 Notice that atom \#1 is at the origin, and atom \#11 is projected onto the X-axis. The size of the unit cell is 7.806Å -- the distance between atom \#1 and atom \#11.
 
-![](../.gitbook/assets/media_1260120454671.png)
+![](../../_images/media_1260120454671.png)
 
 Now delete "extra" atoms which should not be included in the unit cell calculations. This includes the third ring \(including atom 11\) and the "end" hydrogen atoms. For example, you can use the select tool and drag over the atoms to be deleted to pick them.
 
-![](../.gitbook/assets/media_1260120552391.png)
+![](../../_images/media_1260120552391.png)
 
 Once selected, you can use the "Clear" menu command to delete the atoms.
 
-![](../.gitbook/assets/media_1260120773167.png)
+![](../../_images/media_1260120773167.png)
 
 If you wish to submit the unit cell to Gaussian, pick the Gaussian input extension.
 
-![](../.gitbook/assets/Screen-shot-2009-12-06-at-12.36.05-PM.png)
+![](../../_images/Screen-shot-2009-12-06-at-12.36.05-PM.png)
 
 Set options as you desire. Make sure to add a "TV 7.806 0.0 0.0" line at the bottom of the preview text. This will enable the unit cell calculation by setting the translation vector for the unit cell.