Fixing ticket:491, renaming parallel and serial communicators.

The names `parallel` and `serial` for the communicator instances are
not descriptive enough. Renamed to `parallelComm` and `serialComm`.

 * Maintaining `serial` and `parallel` for backwards
   compatibility. These are not deprecated as they are not functions
   or classes, but just instances.

examples/diffusion/anisotropy.py

@@ -83,7 +83,7 @@
 Import a mesh previously created using :term:`Gmsh`.
 
 >>> import os
->>> mesh = Gmsh2D(os.path.splitext(__file__)[0] + '.msh', communicator=serial) # doctest: +GMSH
+>>> mesh = Gmsh2D(os.path.splitext(__file__)[0] + '.msh', communicator=serialComm) # doctest: +GMSH
 
 Set the centermost cell to have a value.
 

examples/levelSet/advection/mesh1D.py

@@ -67,8 +67,8 @@
 
 .. index:: Grid1D
 
->>> from fipy.tools import serial
->>> mesh = Grid1D(dx=dx, nx=nx, communicator=serial)
+>>> from fipy.tools import serialComm
+>>> mesh = Grid1D(dx=dx, nx=nx, communicator=serialComm)
 
 Construct a `distanceVariable` object.
 

examples/levelSet/advection/trench.py

@@ -56,8 +56,8 @@
 >>> timeStepDuration = cfl * dx / velocity
 >>> steps = 200
 
->>> from fipy.tools import serial
->>> mesh = Grid2D(dx = dx, dy = dx, nx = nx, ny = ny, communicator=serial)
+>>> from fipy.tools import serialComm
+>>> mesh = Grid2D(dx = dx, dy = dx, nx = nx, ny = ny, communicator=serialComm)
 
 >>> var = DistanceVariable(name = 'level set variable',
 ...                        mesh = mesh,

examples/levelSet/distanceFunction/circle.py

@@ -59,8 +59,8 @@
 
 .. index:: Grid2D
 
->>> from fipy.tools import serial
->>> mesh = Grid2D(dx=dx, dy=dy, nx=nx, ny=ny, communicator=serial)
+>>> from fipy.tools import serialComm
+>>> mesh = Grid2D(dx=dx, dy=dy, nx=nx, ny=ny, communicator=serialComm)
 
 Construct a `distanceVariable` object.
 

examples/levelSet/distanceFunction/interior.py

@@ -81,8 +81,8 @@
 Lx = nx * dx
 Ly = ny * dy
 
-from fipy.tools import serial
-mesh = Grid2D(dx = dx, dy = dy, nx = nx, ny = ny, communicator=serial)
+from fipy.tools import serialComm
+mesh = Grid2D(dx = dx, dy = dy, nx = nx, ny = ny, communicator=serialComm)
 
 var = DistanceVariable(
     name = 'level set variable',

examples/levelSet/distanceFunction/mesh1D.py

@@ -58,8 +58,8 @@
 
 .. index:: Grid2D
 
->>> from fipy.tools import serial
->>> mesh = Grid1D(dx=dx, nx=nx, communicator=serial)
+>>> from fipy.tools import serialComm
+>>> mesh = Grid1D(dx=dx, nx=nx, communicator=serialComm)
 
 Construct a `distanceVariable` object.
 

examples/levelSet/electroChem/adsorbingSurfactantEquation.py

@@ -85,8 +85,8 @@ class AdsorbingSurfactantEquation():
     >>> c = 0.2
     
     >>> from fipy.meshes import Grid2D
-    >>> from fipy import serial
-    >>> mesh = Grid2D(dx = dx, dy = dy, nx = 5, ny = 1, communicator=serial)
+    >>> from fipy import serialComm
+    >>> mesh = Grid2D(dx = dx, dy = dy, nx = 5, ny = 1, communicator=serialComm)
     >>> distanceVar = DistanceVariable(mesh = mesh, 
     ...                                value = (-dx*3/2, -dx/2, dx/2, 
     ...                                          3*dx/2,  5*dx/2),
@@ -121,7 +121,7 @@ class AdsorbingSurfactantEquation():
     >>> c0 = 1.
     >>> c1 = 1.
     >>> totalSteps = 10
-    >>> mesh = Grid2D(dx = dx, dy = dy, nx = 5, ny = 1, communicator=serial)
+    >>> mesh = Grid2D(dx = dx, dy = dy, nx = 5, ny = 1, communicator=serialComm)
     >>> distanceVar = DistanceVariable(mesh = mesh, 
     ...                                value = dx * (numerix.arange(5) - 1.5),
     ...                                hasOld = 1)
@@ -196,7 +196,7 @@ class AdsorbingSurfactantEquation():
     >>> ny = 5
     >>> dx = 1.
     >>> dy = 1.
-    >>> mesh = Grid2D(dx=dx, dy=dy, nx = nx, ny = ny, communicator=serial)
+    >>> mesh = Grid2D(dx=dx, dy=dy, nx = nx, ny = ny, communicator=serialComm)
     >>> x, y = mesh.cellCenters
 
     >>> disVar = DistanceVariable(mesh=mesh, value=1., hasOld=True)

examples/levelSet/electroChem/adsorption.py

@@ -115,8 +115,8 @@
 ## build the mesh
 
 dx = L / (nx - 1.5)
-from fipy.tools import serial
-mesh = Grid1D(nx = nx, dx = dx, communicator=serial)
+from fipy.tools import serialComm
+mesh = Grid1D(nx = nx, dx = dx, communicator=serialComm)
 
 ## build the distance variable
 

examples/levelSet/electroChem/gapFillMesh.py

@@ -49,8 +49,8 @@
 
 from fipy.meshes import Gmsh2D
 from fipy.meshes import Grid2D
-from fipy.tools import serial
-from fipy.tools import parallel
+from fipy.tools import serialComm
+from fipy.tools import parallelComm
 
 class GapFillMesh(Gmsh2D):
     """
@@ -64,7 +64,7 @@ class GapFillMesh(Gmsh2D):
 
     >>> import fipy.tools.dump as dump
     >>> (f, filename) = dump.write(mesh) # doctest: +GMSH 
-    >>> if parallel.Nproc == 1:
+    >>> if parallelComm.Nproc == 1:
     ...     mesh = dump.read(filename, f) # doctest: +GMSH
 
     >>> print 136 < mesh.globalNumberOfCells < 300 # doctest: +GMSH
@@ -104,7 +104,7 @@ def __init__(self,
                  desiredDomainHeight=None,
                  desiredFineRegionHeight=None,
                  transitionRegionHeight=None,
-                 communicator=parallel):
+                 communicator=parallelComm):
 
         """
         Arguments:
@@ -133,7 +133,7 @@ def __init__(self,
         numberOfBoundaryLayerCells = int(boundaryLayerHeight / actualDomainWidth)
 
         # Build the fine region mesh.
-        self.fineMesh = Grid2D(nx=nx, ny=ny, dx=cellSize, dy=cellSize, communicator=serial)
+        self.fineMesh = Grid2D(nx=nx, ny=ny, dx=cellSize, dy=cellSize, communicator=serialComm)
 
         eps = cellSize / nx / 10
 

examples/levelSet/electroChem/howToWriteAScript.py

@@ -142,12 +142,12 @@
 >>> from metalIonDiffusionEquation import buildMetalIonDiffusionEquation
 >>> from adsorbingSurfactantEquation import AdsorbingSurfactantEquation
 
->>> from fipy import serial
+>>> from fipy import serialComm
 >>> mesh = Grid2D(dx=cellSize,
 ...               dy=cellSize,
 ...               nx=xCells,
 ...               ny=yCells,
-...               communicator=serial)
+...               communicator=serialComm)
 
 A ``distanceVariable`` object,
 :math:`\phi`, is  required to store  the  position of the interface.

examples/levelSet/electroChem/metalIonDiffusionEquation.py

@@ -94,8 +94,8 @@ def buildMetalIonDiffusionEquation(ionVar = None,
     >>> from fipy.meshes import Grid1D
     >>> nx = 11
     >>> dx = 1.
-    >>> from fipy.tools import serial
-    >>> mesh = Grid1D(nx = nx, dx = dx, communicator=serial)
+    >>> from fipy.tools import serialComm
+    >>> mesh = Grid1D(nx = nx, dx = dx, communicator=serialComm)
     >>> x, = mesh.cellCenters
     >>> from fipy.variables.cellVariable import CellVariable
     >>> ionVar = CellVariable(mesh = mesh, value = 1.)
@@ -131,8 +131,8 @@ def buildMetalIonDiffusionEquation(ionVar = None,
     Testing the interface source term
 
     >>> from fipy.meshes import Grid2D
-    >>> from fipy import numerix, serial
-    >>> mesh = Grid2D(dx = 1., dy = 1., nx = 2, ny = 2, communicator=serial)
+    >>> from fipy import numerix, serialComm
+    >>> mesh = Grid2D(dx = 1., dy = 1., nx = 2, ny = 2, communicator=serialComm)
     >>> from fipy.variables.distanceVariable import DistanceVariable
     >>> distance = DistanceVariable(mesh = mesh, value = (-.5, .5, .5, 1.5))
     >>> ionVar = CellVariable(mesh = mesh, value = (1, 1, 1, 1))

examples/levelSet/electroChem/simpleTrenchSystem.py

@@ -198,12 +198,12 @@ def runSimpleTrenchSystem(faradaysConstant=9.6e4,
 
     xCells = int(trenchSpacing / 2 / cellSize)
 
-    from fipy.tools import serial
+    from fipy.tools import serialComm
     mesh = Grid2D(dx = cellSize,
                   dy = cellSize,
                   nx = xCells,
                   ny = yCells,
-                  communicator=serial)
+                  communicator=serialComm)
 
     narrowBandWidth = numberOfCellsInNarrowBand * cellSize
 

examples/levelSet/electroChem/trenchMesh.py

@@ -37,7 +37,7 @@
 
 from fipy.tools import numerix
 from fipy.variables.cellVariable import CellVariable
-from fipy.tools import parallel
+from fipy.tools import parallelComm
 from gapFillMesh import GapFillMesh
 
 class TrenchMesh(GapFillMesh):
@@ -58,7 +58,7 @@ class TrenchMesh(GapFillMesh):
 
     >>> import fipy.tools.dump as dump 
     >>> (f, filename) = dump.write(mesh) # doctest: +GMSH 
-    >>> if parallel.Nproc == 1:
+    >>> if parallelComm.Nproc == 1:
     ...     mesh = dump.read(filename, f) # doctest: +GMSH 
     >>> print mesh.globalNumberOfCells - len(numerix.nonzero(mesh.electrolyteMask)[0]) # doctest: +GMSH, +SERIAL
     150
@@ -99,7 +99,7 @@ def __init__(self,
                  cellSize=None,
                  aspectRatio=None,
                  angle=0.,
-                 communicator=parallel):
+                 communicator=parallelComm):
         """
 
         `trenchDepth` - Depth of the trench.
@@ -135,7 +135,7 @@ def __init__(self,
                                          desiredDomainHeight=domainHeight,
                                          desiredFineRegionHeight=fineRegionHeight,
                                          transitionRegionHeight=transitionHeight,
-                                         communicator=parallel)
+                                         communicator=parallelComm)
 
         trenchWidth = trenchDepth / aspectRatio
 

examples/levelSet/surfactant/expandingCircle.py

@@ -100,8 +100,8 @@
 dx = L / nx
 steps = 20
 
-from fipy.tools import serial
-mesh = Grid2D(dx = dx, dy = dx, nx = nx, ny = nx, communicator=serial)
+from fipy.tools import serialComm
+mesh = Grid2D(dx = dx, dy = dx, nx = nx, ny = nx, communicator=serialComm)
 
 x, y = mesh.cellCenters
 distanceVariable = DistanceVariable(

examples/parallel.py

@@ -11,13 +11,13 @@
 trilinos_info = "PyTrilinos: processor %d of %d" % (epcomm.MyPID(),
                                                     epcomm.NumProc())
 
-from fipy import parallel, Grid1D
+from fipy import parallelComm, Grid1D
 
 mesh = Grid1D(nx=10)
 
 fipy_info = "FiPy: %d cells on processor %d of %d" % (mesh.numberOfCells,
-                                                      parallel.procID,
-                                                      parallel.Nproc)
+                                                      parallelComm.procID,
+                                                      parallelComm.Nproc)
 
 print " :: ".join((mpi4py_info, trilinos_info, fipy_info))
 

fipy/__init__.py

@@ -68,11 +68,11 @@ def _getVersion():
     input = input
     input_original = input
 
-    if parallel.Nproc > 1:
+    if parallelComm.Nproc > 1:
         def mpi_input(prompt=""):
-            parallel.Barrier()
+            parallelComm.Barrier()
             sys.stdout.flush() 
-            if parallel.procID == 0:
+            if parallelComm.procID == 0:
                 sys.stdout.write(prompt)
                 sys.stdout.flush()
                 return sys.stdin.readline()
@@ -85,11 +85,11 @@ def mpi_input(prompt=""):
     raw_input = raw_input
     raw_input_original = raw_input
 
-    if parallel.Nproc > 1:
+    if parallelComm.Nproc > 1:
         def mpi_raw_input(prompt=""):
-            parallel.Barrier()
+            parallelComm.Barrier()
             sys.stdout.flush()
-            if parallel.procID == 0:
+            if parallelComm.procID == 0:
                 sys.stdout.write(prompt)
                 sys.stdout.flush()
                 return sys.stdin.readline()
@@ -115,14 +115,14 @@ def doctest_raw_input(prompt):
     This routine attempts to be savvy about running in parallel.
     """
     try:
-        from fipy.tools import parallel
-        parallel.Barrier()
+        from fipy.tools import parallelComm
+        parallelComm.Barrier()
         _saved_stdout.flush()
-        if parallel.procID == 0:
+        if parallelComm.procID == 0:
             txt = _serial_doctest_raw_input(prompt)
         else:
             txt = ""
-        parallel.Barrier()
+        parallelComm.Barrier()
     except ImportError:
         txt = _serial_doctest_raw_input(prompt)
 #     return txt

fipy/boundaryConditions/boundaryCondition.py

@@ -108,8 +108,8 @@ class in this manner. This is merely a test.
 
         >>> from fipy.meshes import Grid1D
         >>> mesh = Grid1D(nx = 2)
-        >>> from fipy.tools import parallel
-        >>> if parallel.procID == 0:
+        >>> from fipy.tools import parallelComm
+        >>> if parallelComm.procID == 0:
         ...     bc = __BoundaryCondition(mesh.interiorFaces, 0)
         ... else:
         ...     raise IndexError("Face list has interior faces")

fipy/matrices/pysparseMatrix.py

@@ -355,8 +355,8 @@ def asTrilinosMeshMatrix(self):
 
     @property
     def numpyArray(self):
-        from fipy.tools import parallel
-        if parallel.Nproc == 1:
+        from fipy.tools import parallelComm
+        if parallelComm.Nproc == 1:
             return super(_PysparseMeshMatrix, self).numpyArray
         else:
             return self.asTrilinosMeshMatrix().numpyArray
@@ -417,8 +417,8 @@ def __init__(self, mesh):
         """Create a sparse matrix associated with a `Mesh` with '1' in the diagonal
         
             >>> from fipy import Grid1D
-            >>> from fipy.tools import serial
-            >>> mesh = Grid1D(nx=3, communicator=serial)
+            >>> from fipy.tools import serialComm
+            >>> mesh = Grid1D(nx=3, communicator=serialComm)
             >>> print _PysparseIdentityMeshMatrix(mesh=mesh)
              1.000000      ---        ---    
                 ---     1.000000      ---    

fipy/matrices/scipyMatrix.py

@@ -407,8 +407,8 @@ def __init__(self, mesh):
         Create a sparse matrix associated with a `Mesh` with '1' in the diagonal
         
             >>> from fipy import Grid1D
-            >>> from fipy.tools import serial
-            >>> mesh = Grid1D(nx=3, communicator=serial)
+            >>> from fipy.tools import serialComm
+            >>> mesh = Grid1D(nx=3, communicator=serialComm)
             >>> print _ScipyIdentityMeshMatrix(mesh=mesh)
              1.000000      ---        ---    
                 ---     1.000000      ---