fpl and msh

[thomas.l.scofield]

I will be teaching introductory pdes in the fall at my institution (Calvin College).  I have done so before, about 3 years ago, and used Octave as the software package for the course.  At that time, there was a "package" (don't recall if it was available through the octave-forge site, but think probably not) which, though out of date at the time and requiring a separate executable to generate the mesh, was adequate for teaching rudimentary finite element methods.

I was excited to see that there are packages, namely fpl and msh, now available through octave-forge, which may be more up-to-date and easier to use.  I installed both by first downloading the zipped tarballs and then running

   > pkg install ...

I had not first noted the dependence upon gmsh.  Anyway, the "pkg install" command above produced no errors for either package, so I thought everything was fine.  Even with the dependence upon gmsh, I am unsure why things like

   > help MSH3Mgmsh

produce the message

   help: `MSH3Mgmsh' not found

I have since gone and got gmsh.  Since I am working on a Mac, the best way seemed via a disk image (.dmg) file which, when mounted, gave me Gmsh.app, which I could drag into my applications folder.  Now I can run Gmsh.  What I do not have, however, is the ability to run gmsh from a terminal (could probably set that up with an alias), if that matters.  Is there some "switch", amounting to "which gmsh", that is checked at the time these packages are installed and, when it fails, keeps the package from being installed?  That would seem quite strange in light of the fact that

   > pkg list

lists both fpl and msh as 'installed'.

Thomas L. Scofield

--------------------------------------------------------

Associate Professor

Department of Mathematics and Statistics

Calvin College

--------------------------------------------------------

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[Carlo de Falco-2]

On 17 Jun 2009, at 20:02, Thomas L. Scofield wrote:

>
> I will be teaching introductory pdes in the fall at my institution  
> (Calvin College).  I have done so before, about 3 years ago, and  
> used Octave as the software package for the course.  At that time,  
> there was a "package" (don't recall if it was available through the  
> octave-forge site, but think probably not) which, though out of date  
> at the time and requiring a separate executable to generate the  
> mesh, was adequate for teaching rudimentary finite element methods.
>
> I was excited to see that there are packages, namely fpl and msh,  
> now available through octave-forge, which may be more up-to-date and  
> easier to use.

You might also want to have a look at "bim" which can be used to solve  
simple elliptic equatioons in 1, 2 and 3d with piece-wise linear  
continuous finite elements

>  I installed both by first downloading the zipped tarballs and then  
> running
>
>    > pkg install ...
>
> I had not first noted the dependence upon gmsh.  Anyway, the "pkg  
> install" command above produced no errors for either package, so I  
> thought everything was fine.  Even with the dependence upon gmsh, I  
> am unsure why things like
>
>    > help MSH3Mgmsh
>
> produce the message
>
>    help: `MSH3Mgmsh' not found

To avoid crowding up Octave's name space some packages are configured  
to not be loaded automatically at startup, 'msh' 'fpl' and 'bim' are  
among those.
Before you can use the functions from msh you need to do

pkg load msh

> I have since gone and got gmsh.  Since I am working on a Mac, the  
> best way seemed via a disk image (.dmg) file which, when mounted,  
> gave me Gmsh.app, which I could drag into my applications folder.  
> Now I can run Gmsh.  What I do not have, however, is the ability to  
> run gmsh from a terminal (could probably set that up with an alias),  
> if that matters.

Yes, it does matter the command 'gmsh' must be in the path for Octave  
to be able to use it.
If you have installed version 2.3.1 of Gmsh.app in /Applications you  
can achieve this by adding the line:

PATH="${PATH}:/Applications/gmsh-2.3.1/Gmsh.app/Contents/MacOS/"

to the file .bash_login (or .bashrc) in your home directory

>  Is there some "switch", amounting to "which gmsh", that is checked  
> at the time these packages are installed and, when it fails, keeps  
> the package from being installed?  That would seem quite strange in  
> light of the fact that

No, if gmsh is not available msh can still be used for other things,  
e.g. to create structured meshes and to apply some simple mesh  
transformations, try for example

demo MSH2Mjigglemesh

therefore msh does not refuse to install or run if gmsh is not  
available.

>    > pkg list
>
> lists both fpl and msh as 'installed'.

as I said before these packages need not only be installed but also  
loaded,
when they are loaded they will show a '*' beside their name:

 >> pkg list
Package Name  | Version | Installation directory
--------------+---------+-----------------------
          bim  |   0.1.1 | /Users/carlo/octave/bim-0.1.1
          fpl  |   0.1.6 | /Users/carlo/octave/fpl-0.1.6
  integration  |   1.0.7 | /Users/carlo/octave/integration-1.0.7
          msh  |   0.1.1 | /Users/carlo/octave/msh-0.1.1
        nurbs  |   1.0.1 | /Users/carlo/octave/nurbs-1.0.1
      splines  |   1.0.7 | /Users/carlo/octave/splines-1.0.7
 >> pkg load msh
 >> pkg list
Package Name  | Version | Installation directory
--------------+---------+-----------------------
          bim  |   0.1.1 | /Users/carlo/octave/bim-0.1.1
          fpl  |   0.1.6 | /Users/carlo/octave/fpl-0.1.6
  integration  |   1.0.7 | /Users/carlo/octave/integration-1.0.7
          msh *|   0.1.1 | /Users/carlo/octave/msh-0.1.1
        nurbs  |   1.0.1 | /Users/carlo/octave/nurbs-1.0.1
      splines *|   1.0.7 | /Users/carlo/octave/splines-1.0.7
 >>



> Thomas L. Scofield

HTH,
c.



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[thomas.l.scofield]

Thanks.  I hadn't known that some packages need to be explicitly loaded even after they are installed.  Once I loaded them, I got results from

   > demo MSH2Mjigglemesh

I also added gmsh to my path.  Now, as I understood the previous note, the demo above does not use gmsh.  So, if I look over the commands in that demo, I will not be seeing examples of what is possible using gmsh.  Are there examples/demos for full-blown use of msh/fpl?  Is there documentation available somewhere?

Thanks.

Thomas Scofield

On Jun 17, 2009, at 3:55 PM, Carlo de Falco wrote:

On 17 Jun 2009, at 20:02, Thomas L. Scofield wrote:

I will be teaching introductory pdes in the fall at my institution (Calvin College).  I have done so before, about 3 years ago, and used Octave as the software package for the course.  At that time, there was a "package" (don't recall if it was available through the octave-forge site, but think probably not) which, though out of date at the time and requiring a separate executable to generate the mesh, was adequate for teaching rudimentary finite element methods.

I was excited to see that there are packages, namely fpl and msh, now available through octave-forge, which may be more up-to-date and easier to use.

You might also want to have a look at "bim" which can be used to solve simple elliptic equatioons in 1, 2 and 3d with piece-wise linear continuous finite elements

 I installed both by first downloading the zipped tarballs and then running

   > pkg install ...

I had not first noted the dependence upon gmsh.  Anyway, the "pkg install" command above produced no errors for either package, so I thought everything was fine.  Even with the dependence upon gmsh, I am unsure why things like

   > help MSH3Mgmsh

produce the message

   help: `MSH3Mgmsh' not found

To avoid crowding up Octave's name space some packages are configured to not be loaded automatically at startup, 'msh' 'fpl' and 'bim' are among those.

Before you can use the functions from msh you need to do

pkg load msh

I have since gone and got gmsh.  Since I am working on a Mac, the best way seemed via a disk image (.dmg) file which, when mounted, gave me Gmsh.app, which I could drag into my applications folder.  Now I can run Gmsh.  What I do not have, however, is the ability to run gmsh from a terminal (could probably set that up with an alias), if that matters.

Yes, it does matter the command 'gmsh' must be in the path for Octave to be able to use it.

If you have installed version 2.3.1 of Gmsh.app in /Applications you can achieve this by adding the line:

PATH="${PATH}:/Applications/gmsh-2.3.1/Gmsh.app/Contents/MacOS/"

to the file .bash_login (or .bashrc) in your home directory

 Is there some "switch", amounting to "which gmsh", that is checked at the time these packages are installed and, when it fails, keeps the package from being installed?  That would seem quite strange in light of the fact that

No, if gmsh is not available msh can still be used for other things, e.g. to create structured meshes and to apply some simple mesh transformations, try for example

demo MSH2Mjigglemesh

therefore msh does not refuse to install or run if gmsh is not available.

   > pkg list

lists both fpl and msh as 'installed'.

as I said before these packages need not only be installed but also loaded,

when they are loaded they will show a '*' beside their name:

>> pkg list

Package Name  | Version | Installation directory

--------------+---------+-----------------------

         bim  |   0.1.1 | /Users/carlo/octave/bim-0.1.1

         fpl  |   0.1.6 | /Users/carlo/octave/fpl-0.1.6

 integration  |   1.0.7 | /Users/carlo/octave/integration-1.0.7

         msh  |   0.1.1 | /Users/carlo/octave/msh-0.1.1

       nurbs  |   1.0.1 | /Users/carlo/octave/nurbs-1.0.1

     splines  |   1.0.7 | /Users/carlo/octave/splines-1.0.7

>> pkg load msh

>> pkg list

Package Name  | Version | Installation directory

--------------+---------+-----------------------

         bim  |   0.1.1 | /Users/carlo/octave/bim-0.1.1

         fpl  |   0.1.6 | /Users/carlo/octave/fpl-0.1.6

 integration  |   1.0.7 | /Users/carlo/octave/integration-1.0.7

         msh *|   0.1.1 | /Users/carlo/octave/msh-0.1.1

       nurbs  |   1.0.1 | /Users/carlo/octave/nurbs-1.0.1

     splines *|   1.0.7 | /Users/carlo/octave/splines-1.0.7

>>

Thomas L. Scofield

HTH,

c.

Thomas L. Scofield

--------------------------------------------------------

Associate Professor

Department of Mathematics and Statistics

Calvin College

--------------------------------------------------------

------------------------------------------------------------------------------
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royalty-free distribution of the report engine for externally facing
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[Carlo de Falco-2]

On 17 Jun 2009, at 22:50, Thomas L. Scofield wrote:

>
> Thanks.  I hadn't known that some packages need to be explicitly  
> loaded even after they are installed.  Once I loaded them, I got  
> results from
>
>    > demo MSH2Mjigglemesh
>
> I also added gmsh to my path.  Now, as I understood the previous  
> note, the demo above does not use gmsh.  So, if I look over the  
> commands in that demo, I will not be seeing examples of what is  
> possible using gmsh.  Are there examples/demos for full-blown use of  
> msh/fpl?  Is there documentation available somewhere?

There is a short tutorial in the "doc" directory inside the "bim"  
package:
http://octave.svn.sourceforge.net/viewvc/octave/trunk/octave-forge/extra/bim/doc/tutorial.html?revision=5177

Of course the documentation could use some improvement, if you use  
these packages for your course and
produce some lecture notes that would be a very valuable contribution...

> Thanks.
> Thomas Scofield

c.

P.S. FPL depends on openDX, be sure to have it installed and in your  
path to be able to run the visualization section of the tutorial

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