dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

It looks to me like the (quad) cell which first has vertices 1-2-5-4 
after the surgery has vertices 1-(0)-(2)-3. What are then the 
coordinates of vertices (0) and (2)? Same as for 0 and 2, or same as 
original 2 and 5?

/Anders


Matthew Knepley wrote:
> Not quite. I am suggesting changing the grid. For instance, lets use
> the 3-lines mesh as an example. You start with
>
>  6--7--8
>  |    |    |
>  3--4--5
>  |    |    |
>  0--1--2
>
> and I suggest doing surgery to produce
>
>  4--5--(4)
>  |    |     |
>  2--3--(2)
>  |    |     |
>  0--1--(0)
>
> Notice that the edges on the far right are being shown twice. Thus, in the
> second mesh there are 6 vertices, 10 edges, and 8 triangles. Then we
> discretize on that mesh with my prescription for J.
>
>  Matt
>
> On 7/9/07, Anders Logg <logg@xxxxxxxxx> wrote:
> > Matthew Knepley wrote:
> > > 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
> >
> > I'm just thinking of the very simple case of the unit square and you
> > want u(0, y) = u(1, y). Then I think what you suggest is to let's number
> > the vertices vertices (and edges) at x = 0 with the same indices as the
> > vertices and edges at x = 1. Is this what you suggest?
> >
> > /Anders
> >
> >
> > >> /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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> > >> >> >> DOLFIN-dev@xxxxxxxxxx
> > >> >> >> http://www.fenics.org/mailman/listinfo/dolfin-dev
> > >> >> >>
> > >> >> >
> > >> >> >
> > >> >>
> > >> >>
> > >> >
> > >> >
> > >> _______________________________________________
> > >> DOLFIN-dev mailing list
> > >> DOLFIN-dev@xxxxxxxxxx
> > >> http://www.fenics.org/mailman/listinfo/dolfin-dev
> > >>
> > >
> > >
> > _______________________________________________
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