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Re: [HG DOLFIN] Add support for setting periodic boundary conditions.

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Matthew Knepley wrote:

On 7/9/07, Anders Logg <logg@xxxxxxxxx> wrote:

Good point, but I don't see how to do this in DOLFIN without a few major
changes. For example, we assume that each vertex is associated to
exactly one coordinate and the local-to-global mappings that FFC
generate are computed in terms of the global number of vertices, edges etc. 

I think we can preserve those. Imagine discretizing a cylinder, but with
Cartesian coordinates.The connectivity will give the correct assembly.


ok so far...


Our only problem is calculation of the Jacobian (I will ignore coordinate
functions for now). Since J only depends on coordinate differences, it
is enough to take differences mod L = \pi d. I have implemented this
for my thesis. It works well and I think its simpler to think about.
But what about when it's not a cylinder? Say a mesh of the unit square and its not embedded in 3D. 

/Anders



 Matt


Perhaps one could postprocess the system to remove the rows with a
single 1 on the diagonal (Dirichlet BCs) and the rows with a 1 and -1
(periodic BCs)?

/Anders


Matthew Knepley wrote:
> This seems weird to me. When I want periodic boundary conditions,
> I just make a periodic mesh. Anything else messes with the system
> too much. Making a periodic mesh from a flat one is simple surgery.
> I agree that you have to modify the computation of element geometry,
> but that seems to right place to me to account for the embedding.
>
>  Matt
>
> On 7/9/07, Garth N. Wells <g.n.wells@xxxxxxxxxx> wrote:
>>
>> Quoting DOLFIN <dolfin@xxxxxxxxxx>:
>>
>> > One or more new changesets pushed to the primary dolfin repository.
>> > A short summary of the last three changesets is included below.
>> >
>> > changeset:   3306:c70033cb881cb98ef8f177ebf0cb95348de96aa7
>> > tag:         tip
>> > user:        "Anders Logg <logg@xxxxxxxxx>"
>> > date:        Mon Jul 09 19:24:50 2007 +0200
>> > files:       Makefile.in aclocal.m4 configure src/Makefile.in
>> > src/bench/Makefile.in src/bench/fem/Makefile.in
>> src/bench/la/Makefile.in
>> > src/bench/ode/Makefile.in src/demo/Makefile.in src/greeting/Makefile.in 
>> > src/kernel/Makefile.in src/kernel/common/Makefile.in
>> > src/kernel/common/dolfin/Makefile.in src/kernel/elements/Makefile.in
>> > src/kernel/elements/dolfin/Makefile.in
>> src/kernel/fem/BoundaryCondition.cpp
>> > src/kernel/fem/Makefile.am src/kernel/fem/Makefile.in
>> > src/kernel/fem/PeriodicBoundaryCondition.cpp
>> > src/kernel/fem/dolfin/BoundaryCondition.h
>> src/kernel/fem/dolfin/Makefile.am
>> > src/kernel/fem/dolfin/Makefile.in
>> > src/kernel/fem/dolfin/PeriodicBoundaryCondition.h
>> > src/kernel/fem/dolfin/dolfin_fem.h src/kernel/function/Makefile.in
>> > src/kernel/function/dolfin/Makefile.in src/kernel/graph/Makefile.in
>> > src/kernel/graph/dolfin/Makefile.in src/kernel/io/Makefile.in
>> > src/kernel/io/dolfin/Makefile.in src/kernel/la/Makefile.in
>> > src/kernel/la/dolfin/Makefile.in src/kernel/log/Makefile.in src/kernel 
>> >  /log/dolfin/Makefile.in src/kernel/main/Makefile.in
>> > src/kernel/main/dolfin/Makefile.in src/kernel/math/Makefile.in
>> > src/kernel/math/dolfin/Makefile.in src/kernel/mesh/Makefile.in
>> > src/kernel/mesh/SubDomain.cpp src/kernel/mesh/dolfin/Makefile.in
>> > src/kernel/mesh/dolfin/SubDomain.h src/kernel/mf/Makefile.in
>> > src/kernel/mf/dolfin/Makefile.in src/kernel/nls/Makefile.in
>> > src/kernel/nls/dolfin/Makefile.in src/kernel/ode/Makefile.in
>> > src/kernel/ode/dolfin/Makefile.in src/kernel/parameter/Makefile.in
>> > src/kernel/parameter/dolfin/Makefile.in src/kernel/pde/Makefile.in
>> > src/kernel/pde/dolfin/Makefile.in src/kernel/plot/Makefile.in
>> > src/kernel/plot/dolfin/Makefile.in src/kernel/quadrature/Makefile.in
>> > src/kernel/quadrature/dolfin/Makefile.in src/lib/Makefile.in
>> > src/pydolfin/Makefile.in src/test/Makefile.in src/utils/Makefile.in
>> > src/utils/convert/Makefile.in src/utils/inp2dx/Makefile.in
>> > src/utils/swig/Makefile.in
>> > description:
>> > Add support for setting periodic boundary conditions.
>> >
>> > To set a periodic boundary condition, specify a pair of domains
>> > G and H by a SubDomain. The inside() function should specify the
>> > points of G and the map() function should specify a mapping F : H
>> --> G.
>> >
>> > Then create a PeriodicBoundaryCondition and apply() it to the linear
>> system.
>> >
>> > Bugs/features:
>> >
>> > 1. Only works for scalar subsystems, so it needs to be done once for 
>> >   each subsystem of a vector function.
>> >
>> >   2. Setting the entries in the matrix can perhaps be optimized.
>> >
>> > 3. PeriodicBoundaryCondition is not a subclass of BoundaryCondition, >> > so it does not work to give a PeriodicBoundaryCondition as argument 
>> >   to LinearPDE.
>> >
>> > To fix 3, should we rename BoundaryCondition --> DirichletBC
>> > and have PeriodicBC and DirichletBC as subclasses of BoundaryCondition? 
>> >
>>
>> Yes, sounds good.
>>
>> Garth
>>
>> >
>> > changeset:   3305:4564fa57c9159e7dbe287ba121324ec84afd4d00
>> > user:        "Garth N. Wells <g.n.wells@xxxxxxxxxx>"
>> > date:        Thu Jul 05 22:24:27 2007 +0200
>> > files:       src/kernel/la/PETScLUSolver.cpp
>> src/kernel/nls/NewtonSolver.cpp
>> > src/kernel/nls/dolfin/NewtonSolver.h src/kernel/pde/LinearPDE.cpp
>> > description:
>> > Fix use of PETSc with UMFPACK.
>> >
>> >
>> > changeset:   3304:1a95bb6095dd1b91e462f62a630035defd37c8c6
>> > parent:      3303:a324e9cb2c73b27ecd636fcee5b1a08cc01a0da8
>> > parent:      3302:cd19d9eeddaa68d14d8c6fafe4de490ff17c1f5a
>> > user:        "Garth N. Wells <g.n.wells@xxxxxxxxxx>"
>> > date:        Wed Jul 04 14:38:37 2007 +0200
>> > files:
>> > description:
>> > merge.
>> >
>> > ---------------------------------------------------------------------- 
>> > For more details, visit http://www.fenics.org/hg/dolfin
>> > _______________________________________________
>> > DOLFIN-dev mailing list
>> > DOLFIN-dev@xxxxxxxxxx
>> > http://www.fenics.org/mailman/listinfo/dolfin-dev
>> >
>> _______________________________________________
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>>
>
>

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