[petsc-users] Testing DMPlex new functionalities

[Luc Berger-Vergiat]

Yeah I just got the compiler warning for (int) instead of (int *).
Final remark of the day, with GMSH you can do the following in the .geo:

Physical Line("bottom") = {line_id1};
Physical Line("right")     = {line_id2};
Physical Line("left")       = {line_id3};
Physical Line("top")       = {line_id4};

which in turns will get you something like this in the .msh:

$PhysicalNames
4
1 2 "bottom"
1 3 "right"
1 4 "left"
1 5 "top"
$EndPhysicalNames

It would be cool to catch these in order to define multiple label names 
to get a Petsc structure that looks like this:
Labels:
   bottom: 1 strata of sizes (12)
   right: 1 strata of sizes (12)
   top: 1 strata of sizes (12)
   left: 1 strata of sizes (12)
   depth: 3 strata of sizes (169, 312, 144)

instead of:
Labels:
   Face Sets: 4 strata of sizes (12, 12, 12, 12)
   depth: 3 strata of sizes (169, 312, 144)

Best,
Luc

On 01/22/2015 05:39 PM, Matthew Knepley wrote:
> On Thu, Jan 22, 2015 at 4:31 PM, Luc Berger-Vergiat 
> <lb2653 at columbia.edu <mailto:lb2653 at columbia.edu>> wrote:
>
>     Ok, I think what I will do is the following:
>
>     void top_bc(const PetscReal x[], PetscScalar *u, void *ctx)
>     {
>       *u = 0.2;
>     }
>     void bottom_bc(const PetscReal x[], PetscScalar *u, void *ctx)
>     {
>       *u = 0.0;
>     }
>
>
>     ierr = DMPlexAddBoundary(dm, PETSC_TRUE,"bottom","Face
>     Sets",0,(void (*)())bottom_bc,1,ids[0],&user);CHKERRQ(ierr);
>
>     ierr = DMPlexAddBoundary(dm, PETSC_TRUE,"top","Face Sets",0,(void
>     (*)())top_bc,1,ids[1],&user);CHKERRQ(ierr);
>
>
> You need &ids[0] and &ids[1].
>
>
>     Matt, have you started writing some documentation for these function?
>
>
> I thought I had, but I cannot find the branch.
>
>     If not I could probably get something started since I'm reading them.
>
>
> That would be great.
>
>     Another question, how do I explain to my DMPlex that I am solving
>     an elasticity problem and hence my solution field will be a 2
>     components vector and not a scalar? I haven't seen where you set
>     this info in snes example 12...
>
>
> Yes, ex12 is all scalar. In the call to PetscFECreateDefault() there 
> is a 1, which you would make 'dim'.
>
>   Thanks,
>
>     Matt
>
>     Best,
>     Luc
>
>     On 01/22/2015 05:19 PM, Matthew Knepley wrote:
>>     On Thu, Jan 22, 2015 at 4:17 PM, Luc Berger-Vergiat
>>     <lb2653 at columbia.edu <mailto:lb2653 at columbia.edu>> wrote:
>>
>>         Yes you are right, I corrected for the machine epsilon.
>>         I also looked deeper in Petsc's source code and I think I
>>         understand better how you implemented the GMSH reader.
>>         For instance the label I really care about is "Face Sets"
>>         since it detects automatically the BC's for me.
>>         An issue is that "Face Sets" contains 4 strata and I only
>>         care about two of these strata.
>>         How can I get the names of the Strata and how can I loop over
>>         the strata to assign my BCs?
>>
>>
>>     Instead of "marker" give "Face Sets"
>>
>>     Instead of 1, give 2
>>
>>     Instead of &id give ids, where PetscInt ids[2] = {stratumValue1,
>>     stratumValue2}
>>
>>       Thanks,
>>
>>         Matt
>>
>>         Best,
>>         Luc
>>
>>         On 01/22/2015 05:12 PM, Matthew Knepley wrote:
>>>         On Thu, Jan 22, 2015 at 12:08 PM, Luc Berger-Vergiat
>>>         <lb2653 at columbia.edu <mailto:lb2653 at columbia.edu>> wrote:
>>>
>>>             Hi all,
>>>             I'm trying to test some functionalities in DMPlex,
>>>             specifically I want to do a 2d fem simulation using a
>>>             mesh generated by GMSH.
>>>             At this point I am trying to understand how Dirichlet BC
>>>             can be applied.
>>>
>>>             Can you explain to me what arguments I have to pass to:
>>>             DMPlexAddBoundary()?
>>>
>>>
>>>           ierr = DMPlexAddBoundary(dm,
>>>         PETSC_TRUE,"wall","marker",(void
>>>         (*)())top_displacement,1,&id,user)
>>>
>>>         PETSC_TRUE means that these unknowns will be eliminated from
>>>         the global system
>>>
>>>         "wall" is the name of the BC
>>>
>>>         "marker" is the name of the DMLabel that you want to use to
>>>         identify the mesh points
>>>
>>>         1 is the number of label IDs that identify constrained mesh
>>>         points
>>>
>>>         id is the label ID which identifies constrained mesh points
>>>
>>>         top_displacement is the function used to set boundary values
>>>
>>>             I am attaching a little bit of c code and my mesh.geo
>>>             and mesh.msh so that you understand the context.
>>>             The BCs I want to apply are displacement of 0.2 in the y
>>>             direction if y==1.0
>>>             0.0 in the x direction if y==0.0
>>>
>>>
>>>         I might do this:
>>>
>>>         void top_displacement(const PetscReal x[], PetscScalar *u,
>>>         void *ctx)
>>>         {
>>>           *u = x[1] < PETSC_MACHINE_EPSILON ? 0.0 : 0.2;
>>>         }
>>>
>>>           Thanks,
>>>
>>>              Matt
>>>
>>>
>>>             -- 
>>>             Best,
>>>             Luc
>>>
>>>
>>>
>>>
>>>         -- 
>>>         What most experimenters take for granted before they begin
>>>         their experiments is infinitely more interesting than any
>>>         results to which their experiments lead.
>>>         -- Norbert Wiener
>>
>>
>>
>>
>>     -- 
>>     What most experimenters take for granted before they begin their
>>     experiments is infinitely more interesting than any results to
>>     which their experiments lead.
>>     -- Norbert Wiener
>
>
>
>
> -- 
> What most experimenters take for granted before they begin their 
> experiments is infinitely more interesting than any results to which 
> their experiments lead.
> -- Norbert Wiener

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