Merge pull request #2 from osscar-org/develop

Prepare for version 0.1.0a3

.github/workflows/python-publish.yml

@@ -4,6 +4,12 @@
 name: Upload Python Package
 
 on:
+  workflow_dispatch:
+    inputs:
+      name:
+        description: 'Publish on PyPi'
+        required: true
+        default: 'Publish on PyPi'
   release:
     types: [created]
 
@@ -22,6 +28,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel twine
+        pip install jupyterlab
     - name: Build and publish
       env:
         TWINE_USERNAME: __token__

example/bzvisualizer-example.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "hindu-movement",
+   "id": "agreed-accreditation",
    "metadata": {},
    "source": [
     "## **A Jupyter widget to visualize the 1st Brillouin zone**\n",
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "particular-companion",
+   "id": "valued-worry",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -24,7 +24,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "great-number",
+   "id": "fluid-heavy",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -34,7 +34,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "constant-techno",
+   "id": "figured-palestinian",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -45,7 +45,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "north-moisture",
+   "id": "powered-gardening",
    "metadata": {},
    "outputs": [],
    "source": []

js/lib/BZVisualizer.js

@@ -739,8 +739,8 @@ var BZVisualizer = function (showAxes, showBVectors, showPathpoints, useSVGRende
 
         }
         else {
-            var widthHalf = 0.5 * renderer.context.canvas.width / devicePixelRatio;
-            var heightHalf = 0.5 * renderer.context.canvas.height / devicePixelRatio;
+            var widthHalf = 0.5 * renderer.getContext().canvas.width / devicePixelRatio;
+            var heightHalf = 0.5 * renderer.getContext().canvas.height / devicePixelRatio;
             vector2D.x = (vector2D.x * widthHalf) + widthHalf;
             vector2D.y = - (vector2D.y * heightHalf) + heightHalf;
         }

js/lib/example.js

@@ -56,6 +56,7 @@ var BrillouinZoneView = widgets.DOMWidgetView.extend({
         this.model.on('change:kpts', this.kpts_changed, this);
         this.model.on('change:face_color', this.faceColor_changed, this);
         this.model.on('change:path_vectors', this.vectors_changed, this);
+        this.model.on('change:update_structure', this.reloadBZ, this);
 
         this.el.innerHTML = '<div class="BZ-widget" id="' + this.canvasID + '"></div>'
             + '<div id="' + this.infoID + '"></div>';
@@ -70,6 +71,14 @@ var BrillouinZoneView = widgets.DOMWidgetView.extend({
         });
     },
 
+    reloadBZ: function () {
+        var jsondata = this.model.get('jsondata');
+        var faceColor = this.model.get('face_color');
+
+        this.BZVisualizer.loadBZ(canvasID = this.canvasID, infoID = this.infoID, jsondata = jsondata);
+        this.BZVisualizer.set_visibility(faceColor);
+    },
+
     toggle_faceColor: function () {
         const faceColor = this.model.get('face_color');
         this.model.set('face_color', !faceColor);

requirements.txt

@@ -1,3 +1,5 @@
+pip==21.0.1
 voila==0.2.7 
 voila-osscar-template==0.2.8
-widget-bzvisualizer==0.1.0a1
+widget-bzvisualizer==0.1.0a2
+scipy

widget_bzvisualizer/_version.py

@@ -1,5 +1,5 @@
 # Module version
-version_info = (0, 1, 0, 'alpha', 2)
+version_info = (0, 1, 0, 'alpha', 3)
 
 # Module version stage suffix map
 _specifier_ = {'alpha': 'a', 'beta': 'b', 'candidate': 'rc', 'final': ''}

widget_bzvisualizer/example.py

@@ -1,5 +1,5 @@
 import ipywidgets as widgets
-from traitlets import Unicode, Dict, List, Bool
+from traitlets import Unicode, Dict, List, Bool, Int, observe
 import seekpath
 from seekpath.brillouinzone.brillouinzone import get_BZ
 import numpy as np
@@ -49,6 +49,9 @@ class BZVisualizer(widgets.DOMWidget):
     # The path vectors
     path_vectors = List().tag(sync=True)
 
+    # Singal to update the structure
+    update_structure = Int().tag(sync=True)
+
     def __init__(self, cell, positions, numbers, face_color=True):
         if type(cell) == np.ndarray:
             cell = cell.tolist()
@@ -107,4 +110,54 @@ def __init__(self, cell, positions, numbers, face_color=True):
 
         self.jsondata = response
         self.kpts = self.jsondata['explicit_kpoints_abs']
-        self.path_vectors = self.jsondata['path']
+        self.path_vectors = self.jsondata['path']
+        self.update_structure = 0
+
+    @observe('cell')
+    def _cell_change(self, change):
+        system = (np.array(change['new']), np.array(self.positions), np.array(self.numbers))
+        res = seekpath.getpaths.get_path(system, with_time_reversal=False)
+
+        real_lattice = res["primitive_lattice"]
+        rec_lattice = np.array(seekpath.hpkot.tools.get_reciprocal_cell_rows(real_lattice))
+        b1, b2, b3 = rec_lattice
+
+        faces_data = get_BZ(b1=b1, b2=b2, b3=b3)
+
+        response = {}
+        response["faces_data"] = faces_data
+        response["b1"] = b1.tolist()
+        response["b2"] = b2.tolist()
+        response["b3"] = b3.tolist()
+        ## Convert to absolute
+        response["kpoints"] = {
+            k: (v[0] * b1 + v[1] * b2 + v[2] * b3).tolist()
+            for k, v in res["point_coords"].items()
+        }
+        response["kpoints_rel"] = {
+            k: [v[0], v[1], v[2]] for k, v in res["point_coords"].items()
+        }
+        response["path"] = res["path"]
+
+        # It should use the same logic, so give the same cell as above
+        res_explicit = seekpath.get_explicit_k_path(system, with_time_reversal=False)
+        for k in res_explicit:
+            if k == "segments" or k.startswith("explicit_"):
+                if isinstance(res_explicit[k], np.ndarray):
+                    response[k] = res_explicit[k].tolist()
+                else:
+                    response[k] = res_explicit[k]
+
+        if (
+            np.sum(
+                np.abs(
+                    np.array(res_explicit["reciprocal_primitive_lattice"])
+                    - np.array(res["reciprocal_primitive_lattice"])
+                )
+            )
+            > 1.0e-7
+        ):
+            raise AssertionError("Got different reciprocal cells...")
+
+        self.jsondata = response
+        self.update_structure += 1