Added a hack that visualizes the a simple cubic unit cell when axis is clicked.

Author: avmarchenko

exatomic/algorithms/neighbors.py

@@ -174,6 +174,7 @@ def sorter(group, source_atom_idxs):
             nearest['frame'] = nearest['frame'].astype(int)
             nearest['molecule'] = nearest['molecule'].astype(int)
             dct['nearest'].append(nearest)
+            return uu
             for nn in sizes:
                 atm = []
                 for j, fdx in enumerate(nearest['frame'].unique()):

exatomic/widgets/traits.py

@@ -118,8 +118,9 @@ def two_traits(uni):
 
 def frame_traits(uni):
     """Get frame table traits."""
-    if not hasattr(uni, 'frame'): return {}
-    # TODO :: Implement me!!
+    # ASSUME SIMPLE CUBIC CELL this is a hack for now.
+    if 'xi' in uni.frame.columns:
+        return {'frame__a': uni.frame['xi'].max()}
     return {}
 
 def tensor_traits(uni):
@@ -133,6 +134,8 @@ def uni_traits(uni, atomcolors=None, atomradii=None, atomlabels=None):
     """Get Universe traits."""
     unargs = {}
     fields, tensors = [], None
+    if hasattr(uni, 'frame'):
+        unargs.update(frame_traits(uni))
     if hasattr(uni, 'atom'):
         unargs.update(atom_traits(uni.atom, atomcolors, atomradii, atomlabels))
     if hasattr(uni, 'atom_two'):

exatomic/widgets/widget_base.py

@@ -198,7 +198,7 @@ class UniverseScene(ExatomicScene):
     # Tensor traits
     tensor_d = Dict().tag(sync=True)
     # Frame traits
-
+    frame__a = Float(0.0).tag(sync=True)
     # Tensor traits
     tens = Bool(False).tag(sync=True)
     tensor_d = Dict().tag(sync=True)

js/src/appthree.js

@@ -518,6 +518,16 @@ class App3D {
                 meshes.push(mesh);
             };
         };
+        // Hack to also add unit cell if present
+        var a = this.view.model.get("frame__a");
+        if (a !== undefined) {
+            var _box = new THREE.BoxBufferGeometry(a, a, a);
+            var _edg = new THREE.EdgesGeometry(_box);
+            var _mat = new THREE.LineBasicMaterial({color: 0x808080});
+            var _lin = new THREE.LineSegments(_edg, _mat);
+            _lin.position.set(a/2, a/2, a/2);
+            meshes.push(_lin);
+        }
         return meshes;
     };
 

js/src/widgets.js

@@ -154,6 +154,7 @@ var UniverseSceneView = base.ExatomicSceneView.extend({
     },
 
     add_axis: function() {
+        // Additionally adds the unit cell
         this.app3d.clear_meshes("generic");
         if (this.model.get("axis")) {
             this.app3d.meshes["generic"] = this.app3d.add_unit_axis(