move the 4th order reconstruction into mesh (#302)

this is consistent with the other reconstruction routines

Author: zingale

examples/mesh/bc_demo.py

@@ -1,9 +1,10 @@
 # test the boundary fill routine
 
 
+import numpy as np
+
 import pyro.mesh.boundary as bnd
 import pyro.mesh.patch as patch
-import numpy as np
 
 
 def doit():

pyro/advection_fv4/fluxes.py

@@ -1,5 +1,5 @@
 import pyro.mesh.array_indexer as ai
-from pyro.advection_fv4 import interface
+from pyro.mesh import fourth_order
 
 
 def fluxes(my_data, rp):
@@ -72,13 +72,13 @@ def fluxes(my_data, rp):
                              1./12.*(a.jp(-2, buf=1) + a.jp(1, buf=1))
 
     else:
-        a_l, a_r = interface.states(a, myg.ng, 1)
+        a_l, a_r = fourth_order.states(a, myg.ng, 1)
         if u > 0:
             a_x = ai.ArrayIndexer(d=a_l, grid=myg)
         else:
             a_x = ai.ArrayIndexer(d=a_r, grid=myg)
 
-        a_l, a_r = interface.states(a, myg.ng, 2)
+        a_l, a_r = fourth_order.states(a, myg.ng, 2)
         if v > 0:
             a_y = ai.ArrayIndexer(d=a_l, grid=myg)
         else:

pyro/compressible_fv4/fluxes.py

@@ -4,9 +4,8 @@
 
 import pyro.compressible as comp
 import pyro.mesh.array_indexer as ai
-from pyro.advection_fv4 import interface
 from pyro.compressible import riemann
-from pyro.mesh import reconstruction
+from pyro.mesh import fourth_order, reconstruction
 
 
 def flux_cons(ivars, idir, gamma, q):
@@ -104,7 +103,7 @@ def fluxes(myd, rp, ivars):
 
         else:
             for n in range(ivars.nq):
-                q_l[:, :, n], q_r[:, :, n] = interface.states(q_avg[:, :, n], myg.ng, idir)
+                q_l[:, :, n], q_r[:, :, n] = fourth_order.states(q_avg[:, :, n], myg.ng, idir)
 
             # apply flattening
             for n in range(ivars.nq):

pyro/mesh/__init__.py

@@ -3,7 +3,7 @@
 necessary to work with finite-volume data.
 """
 
-__all__ = ['patch', 'integration', 'reconstruction']
+__all__ = ['patch', 'fourth_order', 'integration', 'reconstruction']
 
 from .array_indexer import ArrayIndexer, ArrayIndexerFC
 from .boundary import BC, bc_is_solid, define_bc

pyro/advection_fv4/interface.py renamed to pyro/mesh/fourth_order.py

@@ -1,3 +1,5 @@
+"""Reconstruction routines for 4th order finite-volume methods"""
+
 import numpy as np
 from numba import njit
 
@@ -84,7 +86,7 @@ def states(a, ng, idir):
                 # this lives on the interface
                 d3a[i, j] = d2ac[i, j] - d2ac[i - 1, j]
 
-        # this is a look over cell centers, affecting
+        # this is a loop over cell centers, affecting
         # i-1/2,R and i+1/2,L
         for i in range(ilo - 1, ihi + 1):
             for j in range(jlo - 1, jhi + 1):