Added STO supercell widget.

appendix.md

@@ -7,7 +7,11 @@ numbering:
 
 +++ {"part":"appendix"}
 (app:constants)=
-###  numerical values of constants
+
+### Unit conventions
+*ab*TEM and ASE uses the same [unit conventions](https://wiki.fysik.dtu.dk/ase/ase/units.html), as defined in the `ase.units` module. Thus, electron volts (eV), Ångström (Å), and atomic mass units are defined as 1.0. For convenience, user-defined input angles are in mrad.
+
+### Numerical values of constants
 
 The values of commonly used constants in SI units are
 

inputs.md

@@ -1,11 +1,48 @@
 ---
-title: Inputs and Simulation Parameters
+title: Simulation Inputs
 numbering:
   enumerator: 1.%s
 label : sim_inputs_page
 ---
 
 text
 
-(atomic-models)=
-### Building atomic models
+(specimen-models)=
+## Specimen models
+
+This chapter introduces the Atomic Simulation Environment ([ASE](https://wiki.fysik.dtu.dk/ase/)) for creating specimen models for use in TEM image simulation.
+
+ASE is a set of tools and Python modules for setting up, manipulating and visualizing atomic structures, which is used in conjunction with a large number of atomistic simulation codes, for example [GPAW](https://wiki.fysik.dtu.dk/gpaw/) for running DFT simulations. In this notebook, ASE is introduced in the context of running electron microscopy image simulations with [*ab*TEM](https://abtem.github.io/doc/intro.html).
+
+###  The `Atoms` object
+
+The `Atoms` object defines a collection of atoms. To define `Atoms` from scratch, we need to specify at least three things:
+
+* atomic positions,
+* atomic numbers (or chemical symbols),
+* a periodic cell.
+
+For example, to create a basic model of the N<sub>2</sub> molecule, we could define:
+
+`atoms = ase.Atoms("N2", positions=[(0.0, 0.0, 0.0), (1.0, 0.0, 0.0)], cell=[6, 6, 6])`
+
+All these attributes of the `Atoms` object are stored in underlying NumPy arrays,   which can be directly modified if desired. Convenient arithmetic operations also directly work for the `Atoms` object, so structures can be easily combined to create more complex specimens.
+
+#### Importing structures from files
+
+ASE can import all common atomic-structure formats (full list [here](https://wiki.fysik.dtu.dk/ase/ase/io/io.html)). Below we import a `.cif`-file defining a unit cell of strontium titanate (SrTiO<sub>3</sub>) that we provide with this text and will use in further examples.
+
+`srtio3 = ase.io.read("srtio3.cif")`
+
+### Manipulating atoms
+*ab*TEM always assumes that the imaging electrons propagate along the $z$-axis in the direction from _negative to positive_ coordinate values. Hence, to choose the zone axis, we need to manipulate the atoms so they are properly aligned.
+
+ASE has many tools for manipulating structures, but one particularly useful one is the `surface` function, which can be used for creating a periodic surface (aligned with the $z$-axis) for a given set of Miller indices.
+
+In the widget below, we have oriented the strontium titanate structure along the (110)-direction, and interactively create supercells out of it, with 2 Å of vacuum added at the top and bottom surfaces.
+
+```{figure} #app:sto_supercell
+:name: fig_sto_supercell
+:placeholder: ./static/sto_supercell.png
+**Interactive widget showing supercell construction for the STO(110) supercell.
+```

notebooks/06.1_Atoms_STO-LTO.ipynb

@@ -13,7 +13,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 108,
    "id": "95c10e75-d7d3-40fa-a127-142d5f84438d",
    "metadata": {},
    "outputs": [],
@@ -36,7 +36,147 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 103,
+   "id": "95f90081-91d8-4eb2-9dd9-b56742137669",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib ipympl\n",
+    "from IPython.display import display\n",
+    "import ipywidgets\n",
+    "\n",
+    "# widget figure generation\n",
+    "with plt.ioff():\n",
+    "    dpi = 72\n",
+    "    fig, (ax1,ax2) = plt.subplots(1,2,figsize=(675/dpi, 300/dpi), dpi=dpi)\n",
+    "\n",
+    "supercell = srtio3_110.copy()\n",
+    "supercell.center(2, axis=2)\n",
+    "\n",
+    "top = abtem.show_atoms(supercell, ax=ax1, show_periodic=True)\n",
+    "beam = abtem.show_atoms(supercell, ax=ax2, plane='xz', show_periodic=True, legend=True)\n",
+    "ax1.set_title(\"Top view\")\n",
+    "ax2.set_title(\"Beam view\")\n",
+    "\n",
+    "fig.tight_layout()\n",
+    "\n",
+    "fig.canvas.resizable = False\n",
+    "fig.canvas.header_visible = False\n",
+    "fig.canvas.footer_visible = False\n",
+    "fig.canvas.toolbar_visible = True\n",
+    "fig.canvas.layout.width = '675px'\n",
+    "fig.canvas.layout.height = '330px'\n",
+    "fig.canvas.toolbar_position = 'bottom'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 104,
+   "id": "5d0aeebf-ee62-40fb-a9ed-80f18db8343c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def update_atoms(x, y, z):\n",
+    "    ax1.cla()\n",
+    "    ax2.cla()\n",
+    "    supercell = srtio3_110*(x,y,z)\n",
+    "    supercell.center(2, axis=2)\n",
+    "    top = abtem.show_atoms(supercell, ax=ax1, show_periodic=True)\n",
+    "    beam = abtem.show_atoms(supercell, ax=ax2, plane='xz', show_periodic=True, legend=True)\n",
+    "    fig.canvas.draw_idle()\n",
+    "    return None"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 105,
+   "id": "ad7fa665-3417-4c8d-ac8b-9a4f2cb445af",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "style = {\n",
+    "    'description_width': 'initial',\n",
+    "}\n",
+    "\n",
+    "sliderx = ipywidgets.IntSlider(\n",
+    "    orientation='horizontal',\n",
+    "    description='x repetitions: ',\n",
+    "    value=1,\n",
+    "    min=1,\n",
+    "    max=10,\n",
+    "    style = style,\n",
+    ")\n",
+    "\n",
+    "slidery = ipywidgets.IntSlider(\n",
+    "    orientation='horizontal',\n",
+    "    description='y repetitions: ',\n",
+    "    value=1,\n",
+    "    min=1,\n",
+    "    max=10,\n",
+    "    style = style,\n",
+    ")\n",
+    "\n",
+    "sliderz = ipywidgets.IntSlider(\n",
+    "    orientation='horizontal',\n",
+    "    description='z repetitions: ',\n",
+    "    value=1,\n",
+    "    min=1,\n",
+    "    max=10,\n",
+    "    style = style,\n",
+    ")\n",
+    "\n",
+    "ipywidgets.interactive_output(\n",
+    "    update_atoms, \n",
+    "    {\n",
+    "        'x':sliderx,\n",
+    "        'y':slidery,\n",
+    "        'z':sliderz,\n",
+    "    },\n",
+    ")\n",
+    "None"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 106,
+   "id": "f7da1ef3-9a6a-4726-b9b8-da3938e02a11",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "cb3eaaca2eb4430083cdee3cd89c6dcb",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "VBox(children=(Canvas(footer_visible=False, header_visible=False, layout=Layout(height='330px', width='675px')…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "#| label: app:sto_supercell\n",
+    "\n",
+    "widget = ipywidgets.VBox(\n",
+    "    [\n",
+    "        fig.canvas,\n",
+    "            ipywidgets.VBox([\n",
+    "                sliderx,\n",
+    "                slidery,\n",
+    "                sliderz,\n",
+    "            ]),\n",
+    "    ],\n",
+    ")\n",
+    "\n",
+    "display(widget);"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 107,
    "id": "ceddcd58-e901-4ad8-b599-2a616854d072",
    "metadata": {},
    "outputs": [],