Updated.

docs/api.rst

@@ -0,0 +1,48 @@
+API Reference
+==============
+
+
+Geometry Module
+---------------------------
+
+.. autoclass:: morpho.geometry.Geometry
+   :members: 
+   :show-inheritance:
+
+BrillouinZone Module
+---------------------------
+
+.. autoclass:: morpho.brillouinzone.SymmetryPoint
+   :members: 
+   :show-inheritance:
+
+.. autoclass:: morpho.brillouinzone.BrillouinZonePath
+   :members: 
+   :show-inheritance:
+
+Solver Module
+---------------------------
+.. autoclass:: morpho.solver.Solver
+   :members: run
+   :show-inheritance:
+
+.. autoclass:: morpho.solver.Solver2D
+   :members: run
+   :show-inheritance:
+
+
+Utils Module
+---------------------------
+.. autofunction:: morpho.utils.convmat
+
+
+Exceptions Module
+------------------------
+
+.. automodule:: morpho.exceptions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+==============
+
+

docs/index.rst

@@ -4,17 +4,13 @@
    contain the root `toctree` directive.
 
 Welcome to morpho.py's documentation!
-==================================
+======================================
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
 
+   quickstart
+   introduction
+   api
+   references
 
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

docs/introduction.rst

@@ -0,0 +1,3 @@
+Introduction
+==============
+

docs/quickstart.rst

@@ -0,0 +1,66 @@
+QuickStart
+==============
+
+
+Installation
+---------------------------
+The package can be installed by:
+
+.. code-block:: bash
+
+   pip install morpho.py
+
+Examples
+---------------------------
+
+.. code-block:: python
+
+   """2D example."""
+   import matplotlib.pyplot as plt
+   import numpy as np
+   from morpho import BrillouinZonePath as BZPath
+   from morpho import Geometry, Solver2D
+   from morpho import SymmetryPoint as SPoint
+
+   Nx, Ny = 64, 64
+   P, Q = 5, 5
+   a = 1
+   eps_r = 9.8
+   mu_r = 1.0
+
+   # Define the symmetry points
+   G = SPoint((0, 0), "Γ")
+   X = SPoint((1 / 2, 0), "X")
+   M = SPoint((1 / 2, 1 / 2), "M")
+
+   t1, t2, t3 = (a, 0, 0), (0, a, 0), (0, 0, a)
+
+   # Construct the bloch wave path
+   bz_path = BZPath([G, X, M, G], t1, t2, n_points=100)
+
+   # Construct the geometry
+   geo = Geometry(t1, t2, None, Nx, Ny, 1)
+
+
+   # Define the permitivity profile
+   @geo.set_epsr_f
+   def epsr_f():
+       """Define eps_r profile function."""
+       mask = geo.x**2 + geo.y**2 <= 0.2**2
+       geo.eps_r[mask] = eps_r
+
+
+   # Define the permeability profile
+   @geo.set_mur_f
+   def mur_f():
+       """Define mu_r profile function."""
+
+
+   # Solve
+   solver_tm = Solver2D(geometry=geo, path=bz_path, P=P, Q=Q, pol="TM")
+   solver_tm.run()
+
+   solver_te = Solver2D(geometry=geo, path=bz_path, P=P, Q=Q, pol="TE")
+   solver_te.run()
+
+

docs/references.rst

@@ -0,0 +1,4 @@
+References
+==============
+
+[1] J. D. Joannopoulos, Ed., Photonic crystals: molding the flow of light, 2nd ed. Princeton: Princeton University Press, 2008.

examples/example_2d.py

@@ -1,40 +1,43 @@
-"""3D example."""
+"""2D example."""
 import matplotlib.pyplot as plt
 import numpy as np
 from morpho import BrillouinZonePath as BZPath
 from morpho import Geometry, Solver2D
 from morpho import SymmetryPoint as SPoint
 
-Nx, Ny = 64, 64
-P, Q = 5, 5
-a = 1
-eps_r = 9.8
-mu_r = 1.0
+# Input parameters
+N1, N2 = 64, 64  # discretization
+P, Q = 7, 7  # number of fourier terms
+a = 1  # normalized lattice length
+r = 0.2 * a  # cylinder radius
+eps_r = 9.8  # permittivity
+mu_r = 1.0  # permeability
 
 # Define the symmetry points
 G = SPoint((0, 0), "Γ")
 X = SPoint((1 / 2, 0), "X")
 M = SPoint((1 / 2, 1 / 2), "M")
 
-t1, t2, t3 = (a, 0, 0), (0, a, 0), (0, 0, a)
+# Lattice vectors
+t1, t2 = (a, 0), (0, a)
 
 # Construct the bloch wave path
 bz_path = BZPath([G, X, M, G], t1, t2, n_points=100)
 
 # Construct the geometry
-geo = Geometry(t1, t2, None, Nx, Ny, 1)
+geo = Geometry(t1=t1, t2=t2, N1=N1, N2=N2)
 
 
 # Define the permitivity profile
-@geo.set_epsr_f
+@geo.set_eps_rf
 def epsr_f():
     """Define eps_r profile function."""
     mask = geo.x**2 + geo.y**2 <= 0.2**2
     geo.eps_r[mask] = eps_r
 
 
 # Define the permeability profile
-@geo.set_mur_f
+@geo.set_mu_rf
 def mur_f():
     """Define mu_r profile function."""
 
@@ -50,13 +53,14 @@ def mur_f():
 beta_len = bz_path.beta_vec_len
 wn_tm = np.vstack(solver_tm.wn)
 wn_te = np.vstack(solver_te.wn)
-fig, ax = plt.subplots()
+
+fig, ax = plt.subplots(figsize=(5, 4))
 ax.set_xticklabels(bz_path.symmetry_names)
 ax.set_xticks(bz_path.symmetry_locations)
 ax.set_xlim(0, bz_path.symmetry_locations[-1])
-ax.set_ylim(0, 1)
+ax.set_ylim(0, 0.8)
 ax.set_xlabel(r"Bloch Wave Vector $\beta$")
-ax.set_ylabel(r"Frequency $\frac{\omega a}{2\pi c}$")
+ax.set_ylabel(r"Frequency ${\omega a}/{2\pi c}$")
 ax.plot(beta_len, wn_tm * a / (2 * np.pi), "b-", label="TM")
 ax.plot(beta_len, wn_te * a / (2 * np.pi), "r-", label="TE")
 handles, labels = ax.get_legend_handles_labels()

examples/example_3d.py

@@ -3,7 +3,7 @@
 from morpho import Geometry, Solver
 from morpho import SymmetryPoint as SPoint
 
-Nx, Ny, Nz = 128, 128, 128
+N1, N2, N3 = 128, 128, 128
 P, Q, R = 3, 3, 3
 
 a = 1
@@ -24,11 +24,11 @@
 bz_path = BZPath([D, Z, G, Z, T, X], t1, t2, t3, 200)
 
 # Construct the geometry
-geo = Geometry(t1, t2, t3, Nx, Ny, Nz)
+geo = Geometry(t1, t2, t3, N1, N2, N3)
 
 
 # Define the permitivity profile
-@geo.set_epsr_f
+@geo.set_eps_rf
 def epsr_f():
     """Define eps_r profile function."""
     mask1 = (abs(geo.x) >= a/2 - w/2) & (abs(geo.y) >= a/2 - w/2)
@@ -38,7 +38,7 @@ def epsr_f():
 
 
 # Define the permeability profile
-@geo.set_mur_f
+@geo.set_mu_rf
 def mur_f():
     """Define mu_r profile function."""
 

morpho/brillouinzone.py

@@ -7,7 +7,15 @@
 
 
 class SymmetryPoint:
-    """Model of a symmetry point at the brillouinzone."""
+    """Model of a symmetry point at the brillouinzone.
+
+    Parameters
+    ----------
+    point : Tuple[float, ...]
+        A point in the reciprocal domain.
+    name : str
+        A label to describe the point.
+    """
 
     def __init__(self, point: Tuple[float, ...], name: str):
         """Initialize a SymmetryPoint."""
@@ -16,15 +24,29 @@ def __init__(self, point: Tuple[float, ...], name: str):
 
 
 class BrillouinZonePath:
-    """Model of a path at the brillouinzone."""
+    """Model of a path at the brillouinzone.
+
+    Parameters
+    ----------
+    path : List[SymmetryPoint]
+        A List of symmetry points.
+    t1 : Tuple[float, ...]
+        Direct vector t1. Ex: (0.5, 0.5, 0.5) | (0.5, 0.5) | (0.5,)
+    t2 : Optional[Tuple[float, ...]]
+        Direct vector t2. Ex: (0.5, 0.5, 0.5) | (0.5, 0.5)
+    t3 : Optional[Tuple[float, ...]]
+        Direct vector t3. Ex: (0.5, 0.5, 0.5)
+    n_points : int
+        Number of points in the path.
+    """
 
     def __init__(
         self,
         path: List[SymmetryPoint],
         t1: Tuple[float, ...],
         t2: Optional[Tuple[float, ...]] = None,
         t3: Optional[Tuple[float, ...]] = None,
-        n_points: int = 5,
+        n_points: int = 50,
     ):
         """Initialize a BrillouinZonePath."""
         self.path_points = path
@@ -53,32 +75,32 @@ def __init__(
 
     @property
     def t1(self):
-        """Return vector t1."""
+        """Return the direct vector t1."""
         return self._t1[:self.dim]
 
     @property
     def t2(self):
-        """Return vector t2."""
+        """Return the direct vector t2."""
         return self._t2[:self.dim]
 
     @property
     def t3(self):
-        """Return vector t3."""
+        """Return the direct vector t3."""
         return self._t3[:self.dim]
 
     @property
     def T1(self):
-        """Return vector T1."""
+        """Return the reciprocal vector T1."""
         return self._T1[:self.dim]
 
     @property
     def T2(self):
-        """Return vector T2."""
+        """Return the reciprocal vector T2."""
         return self._T2[:self.dim]
 
     @property
     def T3(self):
-        """Return vector T3."""
+        """Return the reciprocal vector T3."""
         return self._T3[:self.dim]
 
     def _calculate_beta(self):