Adjust Simulation constructor (#170)

* Adjust Simulation constructor

* Make sure all "input variables" from the scheme docs can be passed into the constructor.
* Organize arguments into a column for readability.

* Update docs

doc/docs/Python_User_Interface.md

@@ -33,7 +33,17 @@ class Simulation(object):
                  extra_materials=[],
                  material_function=None,
                  epsilon_func=None,
-                 epsilon_input_file=''):
+                 epsilon_input_file='',
+                 progress_interval=4,
+                 subpixel_tol=1e-4,
+                 subpixel_maxeval=100000,
+                 ensure_periodicity=False,
+                 num_chunks=0,
+                 courant=0.5,
+                 accurate_fields_near_cylorigin=False,
+                 filename_prefix='',
+                 output_volume=None,
+                 output_single_precision=False):
 ```
 
 All `Simulation` attributes are described in further detail here. In brackets after each variable is the type of value that it should hold. The classes, complex datatypes like `GeometricObject`, are described in a later subsection. The basic datatypes, like `integer`, `boolean`, `complex`, and `string` are defined by Python. `Vector3` is a `meep` class.

python/simulation.py

@@ -231,10 +231,34 @@ def _harm(sim):
 
 class Simulation(object):
 
-    def __init__(self, cell_size, resolution, geometry=[], sources=[], eps_averaging=True,
-                 dimensions=2, boundary_layers=[], symmetries=[], verbose=False,
-                 force_complex_fields=False, default_material=mp.Medium(), m=0, k_point=False,
-                 extra_materials=[], material_function=None, epsilon_func=None, epsilon_input_file=''):
+    def __init__(self,
+                 cell_size,
+                 resolution,
+                 geometry=[],
+                 sources=[],
+                 eps_averaging=True,
+                 dimensions=2,
+                 boundary_layers=[],
+                 symmetries=[],
+                 verbose=False,
+                 force_complex_fields=False,
+                 default_material=mp.Medium(),
+                 m=0,
+                 k_point=False,
+                 extra_materials=[],
+                 material_function=None,
+                 epsilon_func=None,
+                 epsilon_input_file='',
+                 progress_interval=4,
+                 subpixel_tol=1e-4,
+                 subpixel_maxeval=100000,
+                 ensure_periodicity=False,
+                 num_chunks=0,
+                 courant=0.5,
+                 accurate_fields_near_cylorigin=False,
+                 filename_prefix='',
+                 output_volume=None,
+                 output_single_precision=False):
 
         self.cell_size = cell_size
         self.geometry = geometry
@@ -245,32 +269,31 @@ def __init__(self, cell_size, resolution, geometry=[], sources=[], eps_averaging
         self.symmetries = symmetries
         self.geometry_center = Vector3()
         self.eps_averaging = eps_averaging
-        self.subpixel_tol = 1e-4
-        self.subpixel_maxeval = 100000
-        self.ensure_periodicity = False
+        self.subpixel_tol = subpixel_tol
+        self.subpixel_maxeval = subpixel_maxeval
+        self.ensure_periodicity = ensure_periodicity
         self.extra_materials = extra_materials
         self.default_material = default_material
         self.epsilon_input_file = epsilon_input_file
-        self.num_chunks = 0
-        self.courant = 0.5
+        self.num_chunks = num_chunks
+        self.courant = courant
         self.global_d_conductivity = 0
         self.global_b_conductivity = 0
         self.special_kz = False
         self.k_point = k_point
         self.fields = None
         self.structure = None
-        self.accurate_fields_near_cylorigin = False
+        self.accurate_fields_near_cylorigin = accurate_fields_near_cylorigin
         self.m = m
         self.force_complex_fields = force_complex_fields
         self.verbose = verbose
-        self.progress_interval = 4
+        self.progress_interval = progress_interval
         self.init_fields_hooks = []
-        self.progress_interval = 4
         self.run_index = 0
         self.filename_prefix = ''
         self.output_append_h5 = None
-        self.output_single_precision = False
-        self.output_volume = None
+        self.output_single_precision = output_single_precision
+        self.output_volume = output_volume
         self.last_eps_filename = ''
         self.output_h5_hook = lambda fname: False
         self.interactive = False