Geometry tutorial and remove clickable stripe between images on the website

docs/_static/custom.css

@@ -5,4 +5,14 @@ html[data-theme="dark"] .navbar-brand img {
 
 .headerlink {
     display: none;
+}
+
+.side-by-side-images {
+   display: flex;
+   gap: 5%;
+}
+
+.side-by-side-images img {
+   display: block;
+   width: 100%;
 }

docs/tutorial.rst

@@ -11,6 +11,7 @@ started!
    :maxdepth: 1
 
    tutorial/magnetization
+   tutorial/geometry
    tutorial/shapes
    tutorial/regions
    tutorial/stdp4

docs/tutorial/geometry.rst

@@ -0,0 +1,145 @@
+:nosearch:
+
+Geometry
+========
+
+This tutorial will teach you how to set your geometry for your magnets. The ``geometry`` parameter can accept numpy arrays and functions.
+
+.. code-block:: python
+
+    import numpy as np
+    from mumaxplus import Ferromagnet, Grid, World
+    import mumaxplus.util.shape as shape
+    import matplotlib.pyplot as plt
+
+We will first define the constants of our world and grid. The grid is comprised of 128 x 64 x 1 cells of each 1 x 1 x 1 nm³.
+
+.. code-block:: python
+
+    nx, ny, nz = 128, 64, 1
+    cx, cy, cz = 1e-9, 1e-9, 1e-9
+    center = cx*(nx-1)/2, cy*(ny-1)/2, cz*(nz-1)/2
+
+Now we create a function to visualise the geometry. In the final images empty space will be shown as white while the magnetic material will be gray.
+
+.. code-block:: python
+
+    def show_2D_geom(magnet):
+        geom = magnet.geometry[0,...]
+        im_extent = (-0.5*cx * 1e9, (nx*cx - 0.5*cx) * 1e9, -0.5*cy * 1e9, (ny*cy - 0.5*cy) * 1e9)
+        plt.imshow(geom, cmap="Greys", origin="lower", extent=im_extent, vmin=0, vmax=2)
+        plt.xlabel("x (nm)")
+        plt.ylabel("y (nm)")
+        plt.show()
+
+1. Numpy arrays
+---------------
+Here we will be looking at setting the geometry with a numpy array. The array should have the same dimensions as our grid and should contain booleans.
+
+1.1 The full grid
+^^^^^^^^^^^^^^^^^
+If we want our magnet to be the entire grid we do not have to specify a geometry.
+
+.. code-block:: python
+
+    world = World(cellsize=(cx, cy, cz))
+    grid  = Grid((nx, ny, nz))
+
+    magnet = Ferromagnet(world=world, grid=grid)
+
+    show_2D_geom(magnet)
+
+.. image:: ../images/magnet_full.png
+   :align: center
+   :width: 600px
+
+1.2 Eliminating pixels
+^^^^^^^^^^^^^^^^^^^^^^
+If we want to remove some pixels from the magnet we can create an array as big as our grid and set some values to 0 (or ``False``). Note that the array should have a shape of (nz, ny, nx).
+Let's now remove a row of cells at the center of the magnet.
+
+.. code-block:: python
+
+    world = World(cellsize=(cx, cy, cz))
+    grid  = Grid((nx, ny, nz))
+
+    geom_array = np.ones(shape=(nz,ny,nx))
+    geom_array[:,ny//2,:] = np.zeros(shape=(nz,nx))
+
+    magnet = Ferromagnet(world=world, grid=grid, geometry=geom_array)
+
+    show_2D_geom(magnet)
+
+.. image:: ../images/magnet_remove_line.png
+   :align: center
+   :width: 600px
+
+2. Functions
+------------
+We can also create our own functions to form geometries. The input of every function should be (x,y,z) where x, y and z are real space coordinates. The output of the function should be a boolean.
+
+2.1 Circle
+^^^^^^^^^^
+Here we create a circle with a radius of 20nm at the center of the grid.
+
+.. code-block:: python
+
+    world = World(cellsize=(cx, cy, cz))
+    grid  = Grid((nx, ny, nz))
+
+    geomfunc = lambda x, y, z: (x - center[0])**2 + (y - center[1])**2 < (20e-9)**2
+
+    magnet = Ferromagnet(world=world, grid=grid, geometry=geomfunc)
+
+    show_2D_geom(magnet)
+
+.. image:: ../images/magnet_cylinder.png
+   :align: center
+   :width: 600px
+
+2.2 Sawtooth
+^^^^^^^^^^^^
+Here we will cut a sawtooth pattern out of a magnet.
+
+.. code-block:: python
+
+    world = World(cellsize=(cx, cy, cz))
+    grid  = Grid((nx, ny, nz))
+
+    p = 25e-9
+    a = 20e-9
+
+    def saw(x,y,z):
+        func = a*(x/p - np.floor(0.5 + x/p)) + a/2-cy
+        return y > func
+
+    magnet = Ferromagnet(world=world, grid=grid, geometry=saw)
+
+    show_2D_geom(magnet)
+
+.. image:: ../images/magnet_sawtooth.png
+   :align: center
+   :width: 600px
+
+3. Shapes
+---------
+Let's end this tutoial by using the ``Shape`` class to generate a geometry. For more information on different shapes and shape manipulations see :doc:`Shapes <shapes>`.
+
+3.1 Sphere
+^^^^^^^^^^
+Here we create a spherical magnet with a diameter of 60nm.
+
+.. code-block:: python
+
+    world = World(cellsize=(cx, cy, cz))
+    grid  = Grid((nx, ny, nz))
+
+    circ = shape.Sphere(diam=20e-9)
+    circ.translate(*center)
+    magnet = Ferromagnet(world=world, grid=grid, geometry=circ)
+
+    show_2D_geom(magnet)
+
+.. image:: ../images/magnet_sphere.png
+   :align: center
+   :width: 600px

docs/tutorial/plot_field.rst

@@ -88,11 +88,13 @@ Or look along a different out-of-plane axis.
     plot_field(mag, out_of_plane_axis="x")
     plot_field(mag, out_of_plane_axis="y")
 
-.. image:: ../images/plot_field/plot_field_OoP_x.png
-   :width: 45%
+.. container:: side-by-side-images
 
-.. image:: ../images/plot_field/plot_field_OoP_y.png
-   :width: 45%
+    .. image:: ../images/plot_field/plot_field_OoP_x.png
+        :width: 100%
+
+    .. image:: ../images/plot_field/plot_field_OoP_y.png
+        :width: 100%
 
 A few things to note:
 

docs/tutorial/regions.rst

@@ -81,11 +81,13 @@ Now one can set parameter values in each region seperately.
 
     plot_field(magnet.magnetization, arrow_size=1)
 
-.. image:: ../images/regions_1.png
-   :width: 45%
+.. container:: side-by-side-images
 
-.. image:: ../images/regions_2.png
-   :width: 45%
+   .. image:: ../images/regions_1.png
+      :width: 100%
+
+   .. image:: ../images/regions_2.png
+      :width: 100%
 
 Likewise, the antiferromagnetic nearest-neighbour exchange constant, ``afmex_nn``,
 can be set in the same way.