Cleaned up and added some new information

advection_nonuniform/__init__.py

@@ -4,4 +4,4 @@
 """
 
 __all__ = ['simulation']
-from .simulation import *
+from .simulation import Simulation

advection_nonuniform/advective_fluxes.py

@@ -78,27 +78,27 @@ def unsplit_fluxes(my_data, rp, dt, scalar_name):
 
     for index, vel in np.ndenumerate(u.v(buf=1)):
         if vel < 0:
-            a_x.v(buf=1)[index] = a.ip(shift_x.v(buf=1)[index], buf=1)[index] - \
-                0.5 * (1.0 + cx.v(buf=1)[index]) * \
-                ldelta_ax.ip(shift_x.v(buf=1)[index], buf=1)[index]
+            a_x.v(buf=1)[index] = a.ip(shift_x.v(buf=1)[index], buf=1)[index] \
+                - 0.5*(1.0 + cx.v(buf=1)[index]) \
+                * ldelta_ax.ip(shift_x.v(buf=1)[index], buf=1)[index]
         else:
-            a_x.v(buf=1)[index] = a.ip(shift_x.v(buf=1)[index], buf=1)[index] + \
-                0.5 * (1.0 - cx.v(buf=1)[index]) * \
-                ldelta_ax.ip(shift_x.v(buf=1)[index], buf=1)[index]
+            a_x.v(buf=1)[index] = a.ip(shift_x.v(buf=1)[index], buf=1)[index] \
+                + 0.5*(1.0 - cx.v(buf=1)[index]) \
+                * ldelta_ax.ip(shift_x.v(buf=1)[index], buf=1)[index]
 
     # upwind in y-direction
     a_y = myg.scratch_array()
     shift_y = my_data.get_var("y-shift").astype(int)
 
     for index, vel in np.ndenumerate(v.v(buf=1)):
         if vel < 0:
-            a_y.v(buf=1)[index] = a.jp(shift_y.v(buf=1)[index], buf=1)[index] - \
-                0.5 * (1.0 + cy.v(buf=1)[index]) * \
-                ldelta_ay.jp(shift_y.v(buf=1)[index], buf=1)[index]
+            a_y.v(buf=1)[index] = a.jp(shift_y.v(buf=1)[index], buf=1)[index] \
+                - 0.5*(1.0 + cy.v(buf=1)[index]) \
+                * ldelta_ay.jp(shift_y.v(buf=1)[index], buf=1)[index]
         else:
-            a_y.v(buf=1)[index] = a.jp(shift_y.v(buf=1)[index], buf=1)[index] + \
-                0.5 * (1.0 - cy.v(buf=1)[index]) * \
-                ldelta_ay.jp(shift_y.v(buf=1)[index], buf=1)[index]
+            a_y.v(buf=1)[index] = a.jp(shift_y.v(buf=1)[index], buf=1)[index] \
+                + 0.5*(1.0 - cy.v(buf=1)[index]) \
+                * ldelta_ay.jp(shift_y.v(buf=1)[index], buf=1)[index]
 
     # compute the transverse flux differences.  The flux is just (u a)
     # HOTF
@@ -110,17 +110,18 @@ def unsplit_fluxes(my_data, rp, dt, scalar_name):
 
     # the zone where we grab the transverse flux derivative from
     # depends on the sign of the advective velocity
-    dtdx2 = 0.5 * dt / myg.dx
-    dtdy2 = 0.5 * dt / myg.dy
+    dtdx2 = 0.5*dt/myg.dx
+    dtdy2 = 0.5*dt/myg.dy
 
     for index, vel in np.ndenumerate(u.v(buf=1)):
-        F_x.v(buf=1)[index] = vel * (a_x.v(buf=1)[index] -
-                                     dtdy2 * (F_yt.ip_jp(shift_x.v(buf=1)[index], 1, buf=1)[index] -
-                                              F_yt.ip(shift_x.v(buf=1)[index], buf=1)[index]))
+        F_x.v(buf=1)[index] = vel * (a_x.v(buf=1)[index] - dtdy2
+               * (F_yt.ip_jp(shift_x.v(buf=1)[index], 1, buf=1)[index]
+               - F_yt.ip(shift_x.v(buf=1)[index], buf=1)[index]))
 
     for index, vel in np.ndenumerate(v.v(buf=1)):
-        F_y.v(buf=1)[index] = vel * (a_y.v(buf=1)[index] -
-                                     dtdx2 * (F_xt.ip_jp(1, shift_y.v(buf=1)[index], buf=1)[index] -
-                                              F_xt.jp(shift_y.v(buf=1)[index], buf=1)[index]))
+        F_y.v(buf=1)[index] = vel * (a_y.v(buf=1)[index] - dtdx2
+               * (F_xt.ip_jp(1, shift_y.v(buf=1)[index], buf=1)[index]
+               - F_xt.jp(shift_y.v(buf=1)[index], buf=1)[index]))
 
     return F_x, F_y
+

advection_nonuniform/problems/_slotted.defaults

@@ -1,3 +1,3 @@
 [slotted]
-omega = 0.5     ;angular velocity
-offset = 0.25   ;offset of the slot center from domain center
+omega = 0.5   ;angular velocity
+offset = 0.25 ;offset of the slot center from domain center

docs/source/advection_nonuniform.problems.rst

@@ -15,28 +15,4 @@ advection\_nonuniform\.problems\.slotted module
 .. automodule:: advection_nonuniform.problems.slotted
     :members:
     :undoc-members:
-    :show-inheritance:
-
-advection\_nonuniform\.problems\.smooth module
-----------------------------------------------
-
-.. automodule:: advection_nonuniform.problems.smooth
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-advection\_nonuniform\.problems\.test module
---------------------------------------------
-
-.. automodule:: advection_nonuniform.problems.test
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-advection\_nonuniform\.problems\.tophat module
-----------------------------------------------
-
-.. automodule:: advection_nonuniform.problems.tophat
-    :members:
-    :undoc-members:
-    :show-inheritance:
+    :show-inheritance:

docs/source/advection_nonuniform_defaults.inc

@@ -28,3 +28,12 @@
   | particle_generator               | ``grid``       |                                                    |
   +----------------------------------+----------------+----------------------------------------------------+
 
+* section: [slotted]
+
+  +----------------------------------+----------------+----------------------------------------------------+
+  | option                           | value          | description                                        |
+  +==================================+================+====================================================+
+  | omega                            | ``0.5``        | angular velocity                                   |
+  +----------------------------------+----------------+----------------------------------------------------+
+  | offset                           | ``0.25``       | offset of the slot's center from domain's center   |
+  +----------------------------------+----------------+----------------------------------------------------+

paper/paper.md

@@ -18,12 +18,16 @@ authors:
 - name: Ian Hawke
   orcid: 0000-0003-4805-0309
   affiliation: 2
-
+- name: Taher Chegini
+  orcid: 0000-0002-5430-6000
+  affiliation: 3
 affiliations:
 - name: Department of Physics and Astronomy, Stony Brook University
   index: 1
 - name: University of Southampton
   index: 2
+- name: University of Houston
+  index: 3
 
 date: 10 August 2018