dolfin team mailing list archive

["Matthew Knepley" <knepley@xxxxxxxxx>]

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

Not sure what you mean here. Everything I said goes through for a
discretization of

  R^k \times S^{n-k}

So basically the product of a box and a torus. Do you have something
more complicated?

  Matt

> /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
> >> >> > _______________________________________________
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> >> >> > DOLFIN-dev@xxxxxxxxxx
> >> >> > http://www.fenics.org/mailman/listinfo/dolfin-dev
> >> >> >
> >> >> _______________________________________________
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> >> >>
> >> >
> >> >
> >>
> >>
> >
> >
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