dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Sun, Mar 30, 2008 at 02:28:35PM +0200, Joachim B Haga wrote:
> 
> The attached patches (one for each of dolfin, ffc, viper) reduce the number of
> attributes from 546 to 137. The ugliest bit is the swig import, which I ended
> up cherry-picking from in __init__.py. All the swigged functions are still
> available through dolfin.dolfin.

Nice!

> A few comments:
> 
> [Anders]
> > If you want to make a patch (hg export) or bundle, that would be
> > excellent. Remove as much as you can, as long as it's possible to
> > run the demos.
> 
> I have tested those that I can (I don't have petsc, slepc, scotch, gts). Two of
> them fail, but I don't think it's my fault:
>
> - convection-diffusion fails with some Vector/GenericVector
> confusion.

This is Kent's "fault"... ;-) More about that in a separate post.

> - periodic
>     Traceback (most recent call last):
>     File "demo.py", line 68, in ?
>       u = pde.solve()
>     File "/home/jbh/src/fenics/dolfin/site-packages/dolfin/assemble.py", line 193, in solve
>       cpp_DirichletBC.apply(bc, A, b, self.dof_maps.sub(1), compiled_form)
>     TypeError: unbound method apply() must be called with cpp_DirichletBC instance as first argument (got PeriodicBC instance instead)
> 
> > Sounds good. Be very aggressive when pruning the namespace. We can
> > always add back the things that are missing one by one.
> 
> I took the opportunistic approach: fix the simple majority first, makes it
> easier to get an overview and do the rest (which requires more thought or work)
> in smaller increments later. Still, after reading this comment I went back and
> commented out (in __init__) the swig classes that weren't being used by demos,
> but haven't done the same for ffc, assembler etc.
> 
> > I'm not sure we need to modularize the namespace, so let's keep it
> > flat until it's really necessary. My reason for wanting to keep it
> > flat is:
> >
> > 1. There aren't (or shouldn't be) that many things in the namespace
> > anyway. Basically, we have a few classes:
> >
> >     Vector, Matrix, Mesh, FiniteElement, Function, DirichletBC
> >
> > and a few free functions:
> >
> >     assemble, solve, plot
> 
> I made one submodule (logger). Feel free to remove it, it's not used by any
> current code. But I do think that to make it as simple as above, it requires
> splitting up the namespace (quadrature, graph, mesh, linalg, etc). That doesn't
> mean that the most common stuff (like Mesh) cannot also be present at
> top-level.
> 
> [Joachim]
> > - A number of functions seem to be "leaked" from c++. Examples: ios, ios_base,
> >   ios_base_sync_with_stdio, ios_base_xalloc, iostream, istream, istringstream,
> >   endl_cb_ptr, ends, ends_cb_ptr.
> 
> These are now removed from the namespace, but they are still generated
> (unnecessarily?) by swig with resulting longer compile time etc. Should be
> filtered higher up?

Anything that can be made to reduce the compile time of the wrapper
code is good.

> [Joachim]
> > - Some non-obvious names. Examples: dolfin_{add,get,set} which could perhaps be
> >   called {add,get,set}_parameter. I was actually looking for this functionality
> >   but didn't find it before compiling this list :)
> 
> I didn't touch this, since they have the same names in c++.

ok.

-- 
Anders


> -j.
> 

Content-Description: Patch for dolfin
> # HG changeset patch
> # User "Joachim B Haga <jobh@xxxxxxxxx>"
> # Date 1206879405 -7200
> # Node ID f55c4da693e090c8a0bac52f23dcf7eb488bc469
> # Parent  cb9afa68c89cfc8492a25ed849586b1679eebdcd
> Reduce clutter in dolfin namespace.
> 
> diff -r cb9afa68c89c -r f55c4da693e0 demo/pde/poisson1D/python/demo.py
> --- a/demo/pde/poisson1D/python/demo.py	Sat Mar 29 16:12:04 2008 +0100
> +++ b/demo/pde/poisson1D/python/demo.py	Sun Mar 30 14:16:45 2008 +0200
> @@ -51,8 +51,8 @@ pde = LinearPDE(a, L, mesh, bc)
>  pde = LinearPDE(a, L, mesh, bc)
>  u = pde.solve()
>  
> -# Viper can't plot in 1D yet
> -# plot(u)
> +# Plot solution
> +plot(u)
>  
>  # Save solution to file
>  file = File("poisson.pvd")
> diff -r cb9afa68c89c -r f55c4da693e0 site-packages/dolfin/__init__.py
> --- a/site-packages/dolfin/__init__.py	Sat Mar 29 16:12:04 2008 +0100
> +++ b/site-packages/dolfin/__init__.py	Sun Mar 30 14:16:45 2008 +0200
> @@ -1,9 +1,50 @@
>  # Import DOLFIN wrapper module as well as additional utility entities
>  
> +from ffc import *
>  from constants import *
>  from assemble import *
>  from norm import *
>  from plot import *
> -from dolfin import *
> +
> +import dolfin
> +from dolfin import dolfin_get, dolfin_add, dolfin_set, tic, toc, tocd
> +#from dolfin import GenericTensor, GenericMatrix, GenericVector
> +from dolfin import Matrix, Vector, Scalar
> +#from dolfin import LinearSolver, KrylovSolver, LUSolver, GMRES, LU
> +from dolfin import solve, residual
> +#from dolfin import ElementLibrary, InvMeshSize
> +#from dolfin import Graph, GraphEditor, GraphPartition
> +#from dolfin import UndirectedClique, DirectedClique
> +from dolfin import File
> +#from dolfin import Lagrange, Legendre
> +#from dolfin import Quadrature, Variable
> +from dolfin import GaussianQuadrature, GaussQuadrature
> +from dolfin import RadauQuadrature, LobattoQuadrature
> +from dolfin import Mesh, MeshEditor, MeshFunction
> +#from dolfin import MeshEntity, MeshTopology, MeshGeometry
> +#from dolfin import MeshConnectivity, MPIMeshCommunicator, BoundaryMesh
> +from dolfin import Vertex, Edge, Face, Facet, Cell, Point
> +from dolfin import vertices, edges, faces, facets, cells
> +from dolfin import SubDomain
> +from dolfin import UnitCube, UnitInterval, UnitSquare
> +#from dolfin import IntersectionDetector, DofMap, DofMapSet
> +from dolfin import SubSystem
> +from dolfin import BoundaryCondition, PeriodicBC
> +#from dolfin import Form, Assembler
> +#from dolfin import MatrixFactory
> +from dolfin import NewtonSolver, NonlinearProblem
> +from dolfin import TimeDependent, ODE, ComplexODE, Homotopy
> +
> +try: # optional package petsc
> +    from dolfin import PETScMatrix, PETScVector
> +except:
> +    pass
> +
> +try: # optional package slepc
> +    from dolfin import SLEPcEigenValueSolver
> +except:
> +    pass
>  
>  from numpy import sin, cos, exp
> +
> +import logger
> diff -r cb9afa68c89c -r f55c4da693e0 site-packages/dolfin/assemble.py
> --- a/site-packages/dolfin/assemble.py	Sat Mar 29 16:12:04 2008 +0100
> +++ b/site-packages/dolfin/assemble.py	Sun Mar 30 14:16:45 2008 +0200
> @@ -12,6 +12,9 @@ __date__ = "2007-08-15 -- 2008-02-11"
>  __date__ = "2007-08-15 -- 2008-02-11"
>  __copyright__ = "Copyright (C) 2007-2008 Anders Logg"
>  __license__  = "GNU LGPL Version 2.1"
> +
> +__all__ = ['assemble', 'Function', 'FacetNormal', 'MeshSize', 'AvgMeshSize',
> +           'LinearPDE', 'DirichletBC']
>  
>  from ffc import *
>  from dolfin import *
> diff -r cb9afa68c89c -r f55c4da693e0 site-packages/dolfin/logger.py
> --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
> +++ b/site-packages/dolfin/logger.py	Sun Mar 30 14:16:45 2008 +0200
> @@ -0,0 +1,1 @@
> +from dolfin import warning, error, message, begin, end, debug, Event, Progress
> diff -r cb9afa68c89c -r f55c4da693e0 site-packages/dolfin/norm.py
> --- a/site-packages/dolfin/norm.py	Sat Mar 29 16:12:04 2008 +0100
> +++ b/site-packages/dolfin/norm.py	Sun Mar 30 14:16:45 2008 +0200
> @@ -5,6 +5,8 @@ __date__ = "2008-03-19 -- 2008-03-19"
>  __date__ = "2008-03-19 -- 2008-03-19"
>  __copyright__ = "Copyright (C) 2008 Anders Logg"
>  __license__  = "GNU LGPL Version 2.1"
> +
> +__all__ = ['norm']
>  
>  from assemble import assemble
>  from ffc import dot, grad, div, curl, dx

Content-Description: Patch for ffc
> # HG changeset patch
> # User "Joachim B Haga <jobh@xxxxxxxxx>"
> # Date 1206878601 -7200
> # Node ID 38ee98ce8631cb46bd85bc99171918bad5fb54b1
> # Parent  e7a1ca641486c424e91b813267ce7953a1f99f3a
> Reduce clutter in main ffc namespace.
> 
> diff -r e7a1ca641486 -r 38ee98ce8631 src/ffc/__init__.py
> --- a/src/ffc/__init__.py	Tue Mar 25 12:00:30 2008 +0100
> +++ b/src/ffc/__init__.py	Sun Mar 30 14:03:21 2008 +0200
> @@ -22,10 +22,11 @@ except:
>  
>  # Import finite elements and dof map
>  from ffc.fem.finiteelement import FiniteElement
> -from ffc.fem.vectorelement import *
> +from ffc.fem.vectorelement import VectorElement, VectorQuadratureElement
>  from ffc.fem.mixedelement import MixedElement
>  from ffc.fem.mixedfunctions import TestFunctions, TrialFunctions, Functions
>  from ffc.fem.dofmap import DofMap
> +from ffc.fem.projection import Projection
>  
>  # Import compiler
>  from ffc.compiler.compiler import compile
> @@ -39,4 +40,4 @@ from ffc.compiler.language.builtins impo
>  from ffc.compiler.language.builtins import *
>  
>  # Import constants
> -from ffc.common.constants import *
> +#from ffc.common.constants import *
> diff -r e7a1ca641486 -r 38ee98ce8631 src/ffc/compiler/language/operators.py
> --- a/src/ffc/compiler/language/operators.py	Tue Mar 25 12:00:30 2008 +0100
> +++ b/src/ffc/compiler/language/operators.py	Sun Mar 30 14:03:21 2008 +0200
> @@ -5,6 +5,10 @@ __date__ = "2005-09-07 -- 2007-12-30"
>  __date__ = "2005-09-07 -- 2007-12-30"
>  __copyright__ = "Copyright (C) 2005-2007 Anders Logg"
>  __license__  = "GNU GPL version 3 or any later version"
> +
> +__all__ = ['Identity', 'value_rank', 'vec', 'dot', 'cross', 'trace', 'transp',
> +           'mult', 'outer', 'D', 'grad', 'div', 'rot', 'curl', 'mean', 'avg',
> +           'jump', 'sqrt', 'modulus', 'lhs', 'rhs']
>  
>  # Modified by Ola Skavhaug, 2005
>  # Modified by Dag Lindbo, 2006

Content-Description: Patch for viper
> # HG changeset patch
> # User "Joachim B Haga <jobh@xxxxxxxxx>"
> # Date 1206878801 -7200
> # Node ID ea089fb991441eaf96bebb98df7cb1309d9838fe
> # Parent  33a776fbc3ff4c3da4ee3846a8f32c5a5a11d5d8
> Change in dolfin import of MeshFunction*.
> 
> Viper is the only user of the MeshFunctionUInt etc names
> (as opposed to MeshFunction("uint") etc). Those are now
> removed fram toplevel dolfin namespace. Change import so
> that these are now imported from the "private" namespace
> dolfin.dolfin.
> 
> diff -r 33a776fbc3ff -r ea089fb99144 src/viper/viper_dolfin.py
> --- a/src/viper/viper_dolfin.py	Fri Mar 28 14:09:44 2008 +0100
> +++ b/src/viper/viper_dolfin.py	Sun Mar 30 14:06:41 2008 +0200
> @@ -21,9 +21,9 @@ Citation: %s
>  """ % (__copyright__, __license__, __cite__)
>  
>  from viper import Viper as ViperBase
> -from dolfin import Mesh, MeshFunctionInt, MeshFunctionUInt, MeshFunctionBool, MeshFunctionReal
> -from dolfin import cpp_Function as Function
>  import dolfin
> +from dolfin.dolfin import Mesh, MeshFunctionInt, MeshFunctionUInt, MeshFunctionBool, MeshFunctionReal
> +from dolfin.dolfin import cpp_Function as Function
>  import numpy
>  import vtk
>  

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