Re: [Eidors Help] Is it possible to add face numbers to fwd_model?

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Hi Russel and Bartek,

I agree with this. Let's add mat_idx and fc to the models that come
out of the ng*models functions. Now we need to decide what to call
them: How about
   material_idx,
and
   boundary_numbers

Russell, do you have svn commit priveledges?
--
Andy Adler <ad...@sc...> +1-613-520-2600x8785

On 3 June 2011 06:27, Russell Miller
<rus...@ma...> wrote:
> Hi Bartek,
>
> This sounds good. We would also need to add fc as an output argument to any
> function that calls ng_mk_fwd_model (I have actually been calling
> ng_mk_gen_models to create my finite forward model).
>
> Best,
>
> Russell
>
>
> On Friday 03 Jun 2011 11:20:57 Bartek Grychtol wrote:
>> Hi All,
>>
>> Once we're discussing ng_mk_fwd_model it's worth having a look at the
>> mat_indices too. At the moment, the signature is
>>
>> [fwd_mdl, mat_indices] = ng_mk_fwd_model(...);
>>
>> But if there is more than one material in the model, it makes sense to
>> put them into fwd_mdl.mat_idx and this is what the recent mk_GREIT_model
>> function does.
>> I presume the original argument for not doing it this way was not to
>> inflate the size of the fmdl structure unnecessary. (But what about
>> conditional inclusion?)
>>
>> Following the same argument, we should only put the face numbers in the
>> fmdl if they are useful, so I think the best way would be for
>> ng_mk_fwd_model to pass 'fc' out as an output (like mat_indices is now)
>> and to request and handle them as needed in the calling functions.
>>
>> On the other hand, mat_indices are always useful if there's more than
>> one material, so I would advocate including them in the fmdl structure
>> in that case, but we would probably have to keep it in the output as
>> well to avoid breaking a lot of code.
>>
>> Best,
>>
>> Bartek
>>
>> On 03/06/2011 12:01, Russell Miller wrote:
>> > Hi Andy,
>> >
>> > I don't think my last post was clear, sorry. As far as I am aware,
>> > netgen does not have infinite elements but I have been working on some
>> > code that adds them to a simple EIDORS forward model after the simple
>> > model has been meshed by netgen.
>> >
>> > The main problem is defining which boundaries need the infinite
>> > elements (i.e. for a half-space this would be all boundaries except
>> > the top surface). I think the best way to define which boundaries need
>> > infinite elements is to have a number for each boundary (or
>> > face/surface) and then the modeller can choose which faces require
>> > infinite elements (I am also in the process of writing a function that
>> > builds a half-space model using netgen then automatically adds
>> > infinite elements on the correct faces).
>> >
>> > Fortunately, I have found that netgen numbers the surfaces of a given
>> > object and these are the numbers that are stored in the variable "fc"
>> > in construct_fwd_model. I just need this variable fc to be assigned as
>> > a field of the fwd_model structure in the mg_mk_fwd_model function so
>> > that when I build my initial (finite) model using ng_mk_gen_models I
>> > can then append infinite elements to the correct boundaries.
>> >
>> > I have made a local copy of ng_mk_fwd_model.m in which I have added to
>> > the following lines (additions in bold):
>> >
>> > [srf,vtx,fc,bc,simp,edg,mat_ind] = ng_read_mesh(ng_vol_filename);
>> >
>> > ...
>> >
>> > fwd_mdl= construct_fwd_model(srf,vtx,simp,bc, name, ...
>> >
>> > stim_pattern, centres, z_contact,fc);
>> >
>> > ...
>> >
>> > mdl.nodes = vtx;
>> >
>> > mdl.elems = simp;
>> >
>> > mdl.boundary = srf;
>> >
>> > mdl.boundary_numbers = fc;
>> >
>> > mdl.gnd_node= find_centre_node(vtx);
>> >
>> > mdl.np_fwd_solve.perm_sym = '{n}';
>> >
>> > mdl.name = name;
>> >
>> > ...
>> >
>> > My question is: can you add these same lines of code to the svn
>> > version of EIDORS so that I can access the surface numbers in order to
>> > append the infinite elements to the correct surfaces? Adding an extra
>> > field to the fwd_model structure shouldn't cause any bugs in existing
>> > code if the field has never been used before.
>> >
>> > Thanks,
>> >
>> > Russell
>> >
>> > Hi Russell,
>> > I didn't even know that netgen does infinite elements. To start us off
>> > discussing how to do it, could you send an example (ie. a netgen geo
>> > file that makes infinite elements).
>> > This is definitely useful stuff. We just need to figure out how to
>> > do it most easily, without breaking older code.
>> > Thanks
>> > --
>> > Andy Adler <adler@...> +1-613-520-2600x8785
>> > On 2 June 2011 07:47, Russell Miller
>> >
>> > <russell.miller@...> wrote:
>> > > Hi Andy,
>> > >
>> > > I've been working code to introduce infinite elements to solve forward
>> > > problems in half-space domains. I think the best way to choose on which
>> > > boundary faces I need to "append" the infinite elements is to have the
>> > > face numbers (or surfnr) as they are called in the NETGEN .vol output
>> > > files. I have noticed that the function ng_read_mesh.m does get these
>> > > values and stores them in a variable called fc but then
>> > > ng_mk_fwd_model does not pass these values to construct_fwd_model.
>> > >
>> > > Basically, my question is: Can we modify ng_mk_fwd_model so that the
>> > > fwd_model structure has a field that store the face numbers so that
>> > > they can be cross- referenced with the fwd_model.boundary field?
>> > >
>> > > Best regards,
>> > >
>> > > Russell Miller
>> >
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