dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

On 3 September 2012 09:06, Marie E. Rognes <meg@xxxxxxxxx> wrote:
> On 09/02/2012 12:23 PM, Garth N. Wells wrote:
>>
>> On 2 September 2012 11:10, Anders Logg <logg@xxxxxxxxx> wrote:
>>>
>>> On Sat, Sep 01, 2012 at 03:09:42PM +0100, Garth N. Wells wrote:
>>>>
>>>> The logic around how we handle integration over domains is confusing.
>>>> I'm trying to fix a small problem which is opening a can of worms.
>>>> Subdomain data can be optionally passed to the assembler, attached to
>>>> a Form or attached to a Mesh (the latter being particularly confusing
>>>> because it's mixing concepts). I suggest that we have just one to do
>>>> things, and I think the most logical and user friendly is to attach
>>>> subdomain data to Forms. Opinions?
>
>
> Agree!
>
>
>>> I agree that the logic is complex, but it is there for a reason.
>>>
>>> There are three ways to specify subdomains, by order of increasing
>>> priority.
>>>
>>> First, it can be specified as part of the mesh. This is a good thing
>>> since it allows markers to be stored as part of Mesh XML files. Very
>>> useful for Mesh generators and tools like VMTK.
>>>
>> I think that this is very clumsy and mixes concepts. Say I have one
>> mesh but want to perform two different simulations with different bcs.
>> It's opaque. What happens if I have markers in a Mesh and markers
>> attached to a Form -> ambiguous.
>>
>> Better would be to store the markers as part of the mesh, but pull
>> them out and attach them to a form. I was already planning to have
>> mesh markers in a mesh file that are identified by strings (e.g.
>> "top", "inner sphere", etc) rather than  integers (which are error
>> prone because they convey no meaning). A user could query which
>> markers a mesh has (via a set of identifier strings), and attach the
>> right ones.
>
>
> Yes, I would find this less confusing and more useful.
>

Yes, I was getting confused. Also, I was trying convert a common 3rd
party format the uses names for sub-domains.

>
>>> Second, it can be specified as part of a Form. This is useful for
>>> assembling several forms on the same mesh but with different domains.
>>>
>> This is nice.
>>
>>> Third, it can be specified explicitly as an argument to the assembler.
>>>
>>> If we should cut any of these, I would suggest cutting the third one,
>>> but I think it is widely used as part of both user code and examples
>>> so I'm not sure we should cut it.
>>>
>
> I think in order to cut the third one, there needs to be a reliable and
> flexible way of replacing subdomains in a given form cf Johan's comment.
> This might exist today, but I'm not entirely sure.
>

Should be easy via shared pointers.

>
>
>> We have a bug that I'm more interested in fixing simply and robustly
>> than in preserving a clumsy interface, so I'd cut it. Users can update
>> their code.
>
>
> Cutting this interface is a significant change, so I would suggest
> adding a deprecation warning and making a release before doing so.
>

Could be tricky because the interface is the bug, due to ambiguities
with all the default arguments.

Garth

> --
> Marie
>>
>> Garth
>>
>>> The logic for extracting which domains could be moved to a special
>>> function that takes care of extracting the correct MeshFunction from
>>> either Mesh, Form or explicit arguments. With some extra diagnostics
>>> and careful error checking, it can be made more robust and
>>> user-friendly.
>>>
>>> --
>>> Anders
>>
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>
>
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