new package releases: bim 1.1.0 and msh 1.0.5

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new package releases: bim 1.1.0 and msh 1.0.5

c.-2
Hi all,

New versions of the Forge packages bim (1.1.0) and msh (1.0.5) have been uploaded to the package release forum,
and will soon be available for download from Octave-Forge.

BIM provides functions to solve Advection-Diffusion-Reaction Partial Differential Equations in 1, 2 and 3
spatial dimensions on structured or unstructured triangular/tetrahedral meshes.

MSH provides functions to generate and manage triangular and tetrahetral meshes in Octave.

See this page http://wiki.octave.org/Bim_package on the wiki for usage examples.

Enjoy,
cdf.




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Re: new package releases: bim 1.1.0 and msh 1.0.5

c.-2

On 22 Oct 2012, at 16:39, [hidden email] wrote:

>> BIM provides functions to solve Advection-Diffusion-Reaction Partial Differential Equations in 1, 2 and 3
>> spatial dimensions on structured or unstructured triangular/tetrahedral meshes.
>
> Pointers to literature on the theory and implementation behind BIM
> would be very much appreciated.

The method used for the discretization of symmetric elliptic operators is a piecewise linear continuos
Finite Element method with mass-lumpig, which is described in many elementary textbooks on numerical
methods for PDEs as, for example, this one: http://www.springer.com/math/book/978-88-470-1070-3

For stabilization of Advection dominated problems the Exponential Fitting approach is used.
The description of this method can be found in the same book mentioned above for the 1D case,
for references to papers about the 2d and 3d case you can have a look at chapter 5 my PHD thesis
(http://mox.polimi.it/it/progetti/pubblicazioni/tesi/de_falco.pdf).

For 3D there is also functions that implement the computation of the stiffness matrix with the
Orthogonal Subdomain Collocation method described here: http://dx.doi.org/10.1137/S1064827595290711.


> This link
> http://agora.octave.org/snippet/1bqV
> to the example source code doesn't seem to work.

Thanks for noting this.

That's probably because the Agora database
was flushed during the latest update and all snippets were lost :(
Sorry for that, Agora is starting to look good but it is still work
in progress.

I commented out that line on the wiki page for the moment.

c.




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Re: new package releases: bim 1.1.0 and msh 1.0.5

Rafael Laboissière
In reply to this post by c.-2
* c. <[hidden email]> [2012-10-22 12:21]:

> New versions of the Forge packages bim (1.1.0) and msh (1.0.5) have
> been uploaded to the package release forum, and will soon be available
> for download from Octave-Forge.
>
> [snip]

Thanks for this new release.  I noticed a problem in it: the unit
testing in the file msh3m_structured_mesh.m does not work.  The patch
attached below fixes the problem (there were two issues: tests were
preceded by "%" instead of "%!" and there were spurious "=" signs after
"assert").  However, the test fails with the following error message:

      octave:1> test msh3m_structured_mesh
      ***** test
       x = y = z = linspace (0,1,2);
       [mesh] = msh3m_structured_mesh (x, y, z, 1, 1:6);
       assert (columns (mesh.p), 8);
       assert (columns (mesh.t), 6);
       assert (columns (mesh.e), 12);
      !!!!! test failed
      `p' undefined near line 145 column 10

It seems that several variables (x, y, z, p, and sides) that used inside
the subfunction __t6_connections__ are only locally defined in
msh3m_structured_mesh.

This bug also affects the bim package.

Rafael








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test-msh3m_structured_mesh.patch (1K) Download Attachment
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Re: new package releases: bim 1.1.0 and msh 1.0.5

c.-2

On 23 Oct 2012, at 17:27, Rafael Laboissiere wrote:

> * c. <[hidden email]> [2012-10-22 12:21]:
>
>> New versions of the Forge packages bim (1.1.0) and msh (1.0.5) have been uploaded to the package release forum, and will soon be available for download from Octave-Forge.
>>
>> [snip]
>
> Thanks for this new release.  I noticed a problem in it: the unit testing in the file msh3m_structured_mesh.m does not work.  The patch attached below fixes the problem (there were two issues: tests were preceded by "%" instead of "%!" and there were spurious "=" signs after "assert").  However, the test fails with the following error message:
>
>     octave:1> test msh3m_structured_mesh
>     ***** test
>      x = y = z = linspace (0,1,2);
>      [mesh] = msh3m_structured_mesh (x, y, z, 1, 1:6);
>      assert (columns (mesh.p), 8);
>      assert (columns (mesh.t), 6);
>      assert (columns (mesh.e), 12);
>     !!!!! test failed
>     `p' undefined near line 145 column 10
>
> It seems that several variables (x, y, z, p, and sides) that used inside the subfunction __t6_connections__ are only locally defined in msh3m_structured_mesh.
Rafael,
Thank you very much for testing the package!

I just uploaded a new version of the package in the release forum, could you please check if the problem is solved there?

> This bug also affects the bim package.

is this because of the dependency or is there similar bugs in bim?

> Rafael

c.
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Re: new package releases: bim 1.1.0 and msh 1.0.5

Carlo de Falco-3

On 23 Oct 2012, at 20:34, c. wrote:

> I just uploaded a new version of the package in the release forum, could you please check if the problem is solved there?
this is a direct link:
https://sourceforge.net/p/octave/package-releases/9/attachment/msh-1.0.5.tar.gz

c.
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Re: new package releases: bim 1.1.0 and msh 1.0.5

Rafael Laboissière
In reply to this post by c.-2

* c. <[hidden email]> [2012-10-23 20:34]:
>
> On 23 Oct 2012, at 17:27, Rafael Laboissiere wrote:
>>
>> This bug also affects the bim package.
>
> is this because of the dependency or is there similar bugs in bim?

Because of the dependency.  All functions in the bim package that call
msh3m_structured_mesh are broken, because the later is broken.

Rafael


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Re: new package releases: bim 1.1.0 and msh 1.0.5

Rafael Laboissière
In reply to this post by Carlo de Falco-3
* c. <[hidden email]> [2012-10-23 20:35]:

>
> On 23 Oct 2012, at 20:34, c. wrote:
>
>> I just uploaded a new version of the package in the release forum,
>> could you please check if the problem is solved there?
>
> this is a direct link:
> https://sourceforge.net/p/octave/package-releases/9/attachment/msh-1.0.5.tar.gz

This tarball seems to work.

Thanks,

Rafael




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Re: new package releases: bim 1.1.0 and msh 1.0.5

Rafael Laboissière
In reply to this post by Rafael Laboissière
* Rafael Laboissiere <[hidden email]> [2012-10-25 01:33]:

>
> * c. <[hidden email]> [2012-10-23 20:34]:
>>
>> On 23 Oct 2012, at 17:27, Rafael Laboissiere wrote:
>>>
>>> This bug also affects the bim package.
>>
>> is this because of the dependency or is there similar bugs in bim?
>
> Because of the dependency.  All functions in the bim package that call
> msh3m_structured_mesh are broken, because the later is broken.

Ok, this does not seem to be an issue anymore.

However, the test of bim3c_tri_to_nodes fails with:

    ***** test
   msh = bim3c_mesh_properties (msh2m_structured_mesh (linspace (0, 1, 31), linspace (0, 1, 13), linspace (0, 1, 13), 1, 1:6));
   nel  = columns (msh.t);
   nnod = columns (msh.p);
   u_tri = randn (nel, 1);
   un1 = bim3c_tri_to_nodes (msh, u_tri);
   [un2, m] = bim3c_tri_to_nodes (msh, u_tri);
   assert (un1, un2, 1e-10)
  !!!!! test failed
  msh2m_structured_mesh: REGION must be a valid scalar.


Rafael




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Re: new package releases: bim 1.1.0 and msh 1.0.5

c.-2

On 25 Oct 2012, at 08:31, Rafael Laboissiere wrote:

> Ok, this does not seem to be an issue anymore.
>
> However, the test of bim3c_tri_to_nodes fails with:
>
>    ***** test
>   msh = bim3c_mesh_properties (msh2m_structured_mesh (linspace (0, 1, 31), linspace (0, 1, 13), linspace (0, 1, 13), 1, 1:6));
>   nel  = columns (msh.t);
>   nnod = columns (msh.p);
>   u_tri = randn (nel, 1);
>   un1 = bim3c_tri_to_nodes (msh, u_tri);
>   [un2, m] = bim3c_tri_to_nodes (msh, u_tri);
>   assert (un1, un2, 1e-10)
>  !!!!! test failed
>  msh2m_structured_mesh: REGION must be a valid scalar.
>
>
> Rafael


Rafael,

I posted a new version of bim here:

https://sourceforge.net/p/octave/package-releases/9/#5b7d

testing is welcome as usual
c.
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Re: new package releases: bim 1.1.0 and msh 1.0.5

Rafael Laboissière
* c. <[hidden email]> [2012-10-26 01:02]:
>
> I posted a new version of bim here:
>
> https://sourceforge.net/p/octave/package-releases/9/#5b7d

This tarball works fine, thanks.

Rafael


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Re: new package releases: bim 1.1.0 and msh 1.0.5

Rafael Laboissière
* Rafael Laboissiere <[hidden email]> [2012-10-26 13:43]:

> * c. <[hidden email]> [2012-10-26 01:02]:
>>
>> I posted a new version of bim here:
>>
>> https://sourceforge.net/p/octave/package-releases/9/#5b7d
>
> This tarball works fine, thanks.

Well, when testing functions bim3a_osc_advection_diffusion and
bim3a_osc_laplacian, I get lots of this message:

     warning: product: automatic broadcasting operation applied

I guess they are harmless.

Rafael


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Re: new package releases: bim 1.1.0 and msh 1.0.5

Juan Pablo Carbajal-2
On Sat, Oct 27, 2012 at 10:31 AM, Rafael Laboissiere
<[hidden email]> wrote:

> * Rafael Laboissiere <[hidden email]> [2012-10-26 13:43]:
>
>> * c. <[hidden email]> [2012-10-26 01:02]:
>>>
>>> I posted a new version of bim here:
>>>
>>> https://sourceforge.net/p/octave/package-releases/9/#5b7d
>>
>> This tarball works fine, thanks.
>
> Well, when testing functions bim3a_osc_advection_diffusion and
> bim3a_osc_laplacian, I get lots of this message:
>
>      warning: product: automatic broadcasting operation applied
>
> I guess they are harmless.
>
> Rafael
>
>
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The warning is just telling the user that broadcast was applied.
Whether Carlo wants that or not I do not know.
@Carlo: In the latest Octave you will be able to deactivate the
warnings locally to each function.

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Re: new package releases: bim 1.1.0 and msh 1.0.5

c.-2
In reply to this post by Rafael Laboissière

On 27 Oct 2012, at 10:31, Rafael Laboissiere wrote:

> Well, when testing functions bim3a_osc_advection_diffusion and
> bim3a_osc_laplacian, I get lots of this message:
>
>     warning: product: automatic broadcasting operation applied
>
> I guess they are harmless.
>
> Rafael

Yes, they are.
c.

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Re: new package releases: bim 1.1.0 and msh 1.0.5

c.-2
In reply to this post by Juan Pablo Carbajal-2

On 27 Oct 2012, at 10:36, Juan Pablo Carbajal wrote:

> The warning is just telling the user that broadcast was applied.
> Whether Carlo wants that or not I do not know.
It is expected and actually gives a great improvement in performance in the specific case.

> @Carlo: In the latest Octave you will be able to deactivate the
> warnings locally to each function.
I know, I am working with the development version, but I was not sure it would work with the 3.6 release

c.
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