Allow visualization of shapes in the structure viewer (#282)

* Enable visualization of shapes in the structure viewer Three kinds of shapes are available: ellipsoids, spheres and custom shape defined by a list of vertices and indices/simplices. Co-authored-by: Guillaume Fraux <[email protected]>
lab-cosmo · Jul 25, 2023 · fb96b04 · fb96b04
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diff --git a/.prettierrc.yml b/.prettierrc.yml
@@ -15,3 +15,4 @@ overrides:
       - '*.html.in'
     options:
       printWidth: 150
+      tabWidth: 3
diff --git a/docs/src/tutorial/input-reference.rst b/docs/src/tutorial/input-reference.rst
@@ -94,6 +94,32 @@ contains the following fields and values:
                 // a, b, and c are the unit cell vectors. All values are
                 // expressed in Angstroms.
                 "cell": [10, 0, 0, 0, 10, 0, 0, 0, 10],
+
+                // OPTIONAL: shapes to display on each site, if other than
+                // spheres. Multiple shapes groups with different names are
+                // supported.
+                //
+                // Each shape group should be an array of "size" elements,
+                // describing the different shapes.
+                "shapes": {
+                    <name>: [
+                        // Ellipsoid shapes, with the given `[ax, ay, az]` semi-axes
+                        {"kind": "ellipsoid", "semiaxes": [1, 1, 2]},
+                        // Each shape can contain an OPTIONAL "orientation",
+                        // given as a `[x, y, z, w]` quaternion. Defaults to
+                        // [0, 0, 0, 1]
+                        {"kind": "ellipsoid", "semiaxes": [1, 1, 2], "orientation": [0, 0, 0, 1]},
+                        // fully custom shape, from a list of vertices and
+                        // simplices (also called "indices" in WebGL)
+                        {
+                            "kind": "custom",
+                            "vertices": [[0, 0, 0], [1, 0, 0], [0, 1, 0]],
+                            "indices": [[0, 1, 2]],
+                        },
+                        // more shapes as needed
+                        ...
+                    ],
+                }
             },
             // other structures as needed
             ...

diff --git a/docs/src/tutorial/input.rst b/docs/src/tutorial/input.rst
@@ -55,6 +55,8 @@ generate an output in chemiscope format.
 
 .. autofunction:: chemiscope.librascal_atomic_environments
 
+.. autofunction:: chemiscope.extract_lammps_shapes_from_ase
+
 .. _ase: https://wiki.fysik.dtu.dk/ase/index.html
 .. _ASAP: https://github.com/BingqingCheng/ASAP
 

diff --git a/package-lock.json b/package-lock.json
diff --git a/python/chemiscope/__init__.py b/python/chemiscope/__init__.py
@@ -3,6 +3,7 @@
 from .structures import (  # noqa
     all_atomic_environments,
     composition_properties,
+    extract_lammps_shapes_from_ase,
     extract_properties,
     librascal_atomic_environments,
 )