renaming mesh, part I

Author: pancetta

pySDC/implementations/datatype_classes/parallel_mesh.py renamed to pySDC/implementations/datatype_classes/mesh.py

@@ -8,7 +8,7 @@
     MPI = None
 
 
-class parallel_mesh(np.ndarray):
+class mesh(np.ndarray):
     """
     Numpy-based datatype for serial or parallel meshes.
     Can include a communicator and expects a dtype to allow complex data.
@@ -19,17 +19,17 @@ class parallel_mesh(np.ndarray):
 
     def __new__(cls, init, val=0.0, offset=0, buffer=None, strides=None, order=None):
         """
-        Instantiates new datatype. This ensures that even when manipulating data, the result is still a parallel_mesh.
+        Instantiates new datatype. This ensures that even when manipulating data, the result is still a mesh.
 
         Args:
-            init: either another parallel_mesh or a tuple containing the dimensions, the communicator and the dtype
+            init: either another mesh or a tuple containing the dimensions, the communicator and the dtype
             val: value to initialize
 
         Returns:
-            obj of type parallel_mesh
+            obj of type mesh
 
         """
-        if isinstance(init, parallel_mesh):
+        if isinstance(init, mesh):
             obj = np.ndarray.__new__(cls, shape=init.shape, dtype=init.dtype, buffer=buffer, offset=offset,
                                      strides=strides, order=order)
             obj[:] = init[:]
@@ -66,12 +66,12 @@ def __array_ufunc__(self, ufunc, method, *inputs, out=None, **kwargs):
         args = []
         comm = None
         for i, input_ in enumerate(inputs):
-            if isinstance(input_, parallel_mesh):
+            if isinstance(input_, mesh):
                 args.append(input_.view(np.ndarray))
                 comm = input_.comm
             else:
                 args.append(input_)
-        results = super(parallel_mesh, self).__array_ufunc__(ufunc, method, *args, **kwargs).view(parallel_mesh)
+        results = super(mesh, self).__array_ufunc__(ufunc, method, *args, **kwargs).view(mesh)
         if not method == 'reduce':
             results._comm = comm
         return results
@@ -147,8 +147,8 @@ class parallel_imex_mesh(object):
     This data type can be used to have RHS with 2 components (here implicit and explicit)
 
     Attributes:
-        impl (parallel_mesh.parallel_mesh): implicit part
-        expl (parallel_mesh.parallel_mesh): explicit part
+        impl (mesh.mesh): implicit part
+        expl (mesh.mesh): explicit part
     """
 
     def __init__(self, init, val=0.0):
@@ -164,12 +164,12 @@ def __init__(self, init, val=0.0):
         """
 
         if isinstance(init, type(self)):
-            self.impl = parallel_mesh(init.impl)
-            self.expl = parallel_mesh(init.expl)
+            self.impl = mesh(init.impl)
+            self.expl = mesh(init.expl)
         elif isinstance(init, tuple) and (init[1] is None or isinstance(init[1], MPI.Intracomm)) \
                 and isinstance(init[2], np.dtype):
-            self.impl = parallel_mesh(init, val=val)
-            self.expl = parallel_mesh(init, val=val)
+            self.impl = mesh(init, val=val)
+            self.expl = mesh(init, val=val)
         # something is wrong, if none of the ones above hit
         else:
             raise DataError('something went wrong during %s initialization' % type(self))
@@ -180,8 +180,8 @@ class parallel_comp2_mesh(object):
     RHS data type for meshes with 2 components
 
     Attributes:
-        comp1 (parallel_mesh.parallel_mesh): first part
-        comp2 (parallel_mesh.parallel_mesh): second part
+        comp1 (mesh.mesh): first part
+        comp2 (mesh.mesh): second part
     """
 
     def __init__(self, init, val=0.0):
@@ -196,12 +196,12 @@ def __init__(self, init, val=0.0):
         """
 
         if isinstance(init, type(self)):
-            self.comp1 = parallel_mesh(init.comp1)
-            self.comp2 = parallel_mesh(init.comp2)
+            self.comp1 = mesh(init.comp1)
+            self.comp2 = mesh(init.comp2)
         elif isinstance(init, tuple) and (init[1] is None or isinstance(init[1], MPI.Intracomm)) \
                 and isinstance(init[2], np.dtype):
-            self.comp1 = parallel_mesh(init, val=val)
-            self.comp2 = parallel_mesh(init, val=val)
+            self.comp1 = mesh(init, val=val)
+            self.comp2 = mesh(init, val=val)
         # something is wrong, if none of the ones above hit
         else:
             raise DataError('something went wrong during %s initialization' % type(self))

pySDC/implementations/datatype_classes/particles.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from pySDC.implementations.datatype_classes.parallel_mesh import parallel_mesh
+from pySDC.implementations.datatype_classes.mesh import mesh
 from pySDC.core.Errors import DataError
 
 try:
@@ -20,10 +20,10 @@ class particles(object):
         vel: contains the velocities of all particles
     """
 
-    class position(parallel_mesh):
+    class position(mesh):
         pass
 
-    class velocity(parallel_mesh):
+    class velocity(mesh):
         pass
 
     def __init__(self, init=None, val=None):
@@ -204,7 +204,7 @@ def recv(self, source=None, tag=None, comm=None):
         return None
 
 
-class acceleration(parallel_mesh):
+class acceleration(mesh):
     pass
 
 
@@ -219,10 +219,10 @@ class fields(object):
         magn: contains the magnetic field
     """
 
-    class electric(parallel_mesh):
+    class electric(mesh):
         pass
 
-    class magnetic(parallel_mesh):
+    class magnetic(mesh):
         pass
 
     def __init__(self, init=None, val=None):

pySDC/implementations/problem_classes/AcousticAdvection_1D_FD_imex.py

@@ -3,7 +3,7 @@
 
 from pySDC.core.Errors import ParameterError
 from pySDC.core.Problem import ptype
-from pySDC.implementations.datatype_classes.parallel_mesh import parallel_mesh, parallel_imex_mesh
+from pySDC.implementations.datatype_classes.mesh import mesh, parallel_imex_mesh
 from pySDC.implementations.problem_classes.acoustic_helpers.buildWave1DMatrix import getWave1DMatrix, \
     getWave1DAdvectionMatrix
 
@@ -22,7 +22,7 @@ class acoustic_1d_imex(ptype):
 
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_imex_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=parallel_imex_mesh):
         """
         Initialization routine
 

pySDC/implementations/problem_classes/AdvectionDiffusionEquation_1D_FFT.py

@@ -2,7 +2,7 @@
 
 from pySDC.core.Errors import ParameterError, ProblemError
 from pySDC.core.Problem import ptype
-from pySDC.implementations.datatype_classes.parallel_mesh import parallel_mesh, parallel_imex_mesh
+from pySDC.implementations.datatype_classes.mesh import mesh, parallel_imex_mesh
 
 
 # noinspection PyUnusedLocal
@@ -19,7 +19,7 @@ class advectiondiffusion1d_imex(ptype):
         irfft_object: planned IFFT for backward transformation, real-valued output
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_imex_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=parallel_imex_mesh):
         """
         Initialization routine
 
@@ -134,7 +134,7 @@ class advectiondiffusion1d_implicit(advectiondiffusion1d_imex):
     fully-implicit time-stepping
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=mesh):
         """
         Initialization routine
 

pySDC/implementations/problem_classes/AdvectionEquation_1D_FD.py

@@ -4,7 +4,7 @@
 
 from pySDC.core.Errors import ParameterError, ProblemError
 from pySDC.core.Problem import ptype
-from pySDC.implementations.datatype_classes.parallel_mesh import parallel_mesh
+from pySDC.implementations.datatype_classes.mesh import mesh
 
 
 # noinspection PyUnusedLocal
@@ -18,7 +18,7 @@ class advection1d(ptype):
         dx: distance between two spatial nodes
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=mesh):
         """
         Initialization routine
 

pySDC/implementations/problem_classes/AdvectionEquation_1D_FD_dirichlet.py

@@ -4,7 +4,7 @@
 
 from pySDC.core.Errors import ParameterError, ProblemError
 from pySDC.core.Problem import ptype
-from pySDC.implementations.datatype_classes.parallel_mesh import parallel_mesh
+from pySDC.implementations.datatype_classes.mesh import mesh
 
 
 # noinspection PyUnusedLocal
@@ -18,7 +18,7 @@ class advection1d_dirichlet(ptype):
         dx: distance between two spatial nodes
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=mesh):
         """
         Initialization routine
 

pySDC/implementations/problem_classes/AdvectionEquation_ND_FD_periodic.py

@@ -4,7 +4,7 @@
 
 from pySDC.core.Errors import ParameterError, ProblemError
 from pySDC.core.Problem import ptype
-from pySDC.implementations.datatype_classes.parallel_mesh import parallel_mesh
+from pySDC.implementations.datatype_classes.mesh import mesh
 
 
 # noinspection PyUnusedLocal
@@ -17,7 +17,7 @@ class advectionNd_periodic(ptype):
         A: FD discretization of the ND grad operator
         dx: distance between two spatial nodes (here: being the same in all dimensions)
     """
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=mesh):
         """
         Initialization routine
 

pySDC/implementations/problem_classes/AllenCahn_1D_FD.py

@@ -5,7 +5,7 @@
 
 from pySDC.core.Errors import ParameterError, ProblemError
 from pySDC.core.Problem import ptype
-from pySDC.implementations.datatype_classes.parallel_mesh import parallel_mesh, parallel_imex_mesh, parallel_comp2_mesh
+from pySDC.implementations.datatype_classes.mesh import mesh, parallel_imex_mesh, parallel_comp2_mesh
 
 
 class allencahn_front_fullyimplicit(ptype):
@@ -18,7 +18,7 @@ class allencahn_front_fullyimplicit(ptype):
         dx: distance between two spatial nodes
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=mesh):
         """
         Initialization routine
 
@@ -197,7 +197,7 @@ class allencahn_front_semiimplicit(allencahn_front_fullyimplicit):
         dx: distance between two spatial nodes
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_imex_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=parallel_imex_mesh):
         """
         Initialization routine
 
@@ -384,7 +384,7 @@ class allencahn_periodic_fullyimplicit(ptype):
         dx: distance between two spatial nodes
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=mesh):
         """
         Initialization routine
 
@@ -549,7 +549,7 @@ class allencahn_periodic_semiimplicit(allencahn_periodic_fullyimplicit):
     with driving force, 0-1 formulation (Bayreuth example)
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_imex_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=parallel_imex_mesh):
         """
         Initialization routine
 
@@ -620,7 +620,7 @@ class allencahn_periodic_multiimplicit(allencahn_periodic_fullyimplicit):
     with driving force, 0-1 formulation (Bayreuth example)
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_comp2_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=parallel_comp2_mesh):
         """
         Initialization routine
 

pySDC/implementations/problem_classes/AllenCahn_2D_FD.py

@@ -5,7 +5,7 @@
 
 from pySDC.core.Errors import ParameterError, ProblemError
 from pySDC.core.Problem import ptype
-from pySDC.implementations.datatype_classes.parallel_mesh import parallel_mesh, parallel_imex_mesh, parallel_comp2_mesh
+from pySDC.implementations.datatype_classes.mesh import mesh, parallel_imex_mesh, parallel_comp2_mesh
 
 
 # http://www.personal.psu.edu/qud2/Res/Pre/dz09sisc.pdf
@@ -21,7 +21,7 @@ class allencahn_fullyimplicit(ptype):
         dx: distance between two spatial nodes (same for both directions)
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=mesh):
         """
         Initialization routine
 
@@ -187,7 +187,7 @@ class allencahn_semiimplicit(allencahn_fullyimplicit):
     Example implementing the Allen-Cahn equation in 2D with finite differences, SDC standard splitting
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_imex_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=parallel_imex_mesh):
         """
         Initialization routine
 
@@ -258,7 +258,7 @@ class allencahn_semiimplicit_v2(allencahn_fullyimplicit):
     Example implementing the Allen-Cahn equation in 2D with finite differences, AC splitting
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_imex_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=parallel_imex_mesh):
         """
         Initialization routine
 
@@ -352,7 +352,7 @@ class allencahn_multiimplicit(allencahn_fullyimplicit):
     Example implementing the Allen-Cahn equation in 2D with finite differences, SDC standard splitting
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_comp2_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=parallel_comp2_mesh):
         """
         Initialization routine
 
@@ -479,7 +479,7 @@ class allencahn_multiimplicit_v2(allencahn_fullyimplicit):
     Example implementing the Allen-Cahn equation in 2D with finite differences, AC splitting
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_comp2_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=parallel_comp2_mesh):
         """
         Initialization routine
 

pySDC/implementations/problem_classes/AllenCahn_2D_FFT.py

@@ -2,7 +2,7 @@
 
 from pySDC.core.Errors import ParameterError, ProblemError
 from pySDC.core.Problem import ptype
-from pySDC.implementations.datatype_classes.parallel_mesh import parallel_mesh, parallel_imex_mesh
+from pySDC.implementations.datatype_classes.mesh import mesh, parallel_imex_mesh
 
 
 # noinspection PyUnusedLocal
@@ -18,7 +18,7 @@ class allencahn2d_imex(ptype):
         irfft_object: planned IFFT for backward transformation
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_imex_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=parallel_imex_mesh):
         """
         Initialization routine
 
@@ -147,7 +147,7 @@ class allencahn2d_imex_stab(allencahn2d_imex):
         irfft_object: planned IFFT for backward transformation
     """
 
-    def __init__(self, problem_params, dtype_u=parallel_mesh, dtype_f=parallel_imex_mesh):
+    def __init__(self, problem_params, dtype_u=mesh, dtype_f=parallel_imex_mesh):
         """
         Initialization routine