libmesh-users — General information for libmesh users

Re: [Libmesh-users] normal vectors on surface meshes

[John P. <jwp...@gm...>]

On Tue, May 15, 2018 at 5:37 AM, Griffith, Boyce Eugene <
bo...@em...> wrote:

> Folks --
>
> Is there an easy way in the library to get normal vectors on surface
> meshes (e.g. 2D elements in 3D space, 1D elements in 2D space, etc)?  It
> seems like most of the support for this assumes that these are only needed
> for doing surface integrals on volumetric meshes, but I am sure I am
> overlooking something.
>

The "simplest" way is to build an FE object and only pre-request the
normals by calling:

const std::vector<Point> & face_normals = fe_face->get_normals();

(an example can be seen in adaptivity_ex4). The normals could of course be
computed using only geometric information, but this is not currently
implemented.

-- 
John

[Libmesh-users] normal vectors on surface meshes

[Griffith, B. E. <bo...@em...>]

Folks --

Is there an easy way in the library to get normal vectors on surface meshes (e.g. 2D elements in 3D space, 1D elements in 2D space, etc)?  It seems like most of the support for this assumes that these are only needed for doing surface integrals on volumetric meshes, but I am sure I am overlooking something.

(Of course, I know I can do this "by hand" if needed.)

Thanks!

-- Boyce

Re: [Libmesh-users] Variable groups to use blocked matrix (*BAIJ)

[Adriano C. <adr...@gm...>]

Dear John, Roy, David and Paul,

Many thanks for your return.
We found that using the option --enable-blocked-storage during the
configure step would automatically cast the BAIJ matrix representation, but
that is not the case.
Later we discovered that using the method
flow_system.identify_variable_groups(true);
after the .add_variables() made the job, that is confirmed by a -ksp_view
showing bs=4.
If we use a fixed grid with no AMR, then the code works pretty fine, but
with AMR turned on we are having the same issue as reported by David in the
mailing list thread pointed by Roy.
That is, there is a MatSetValue in a position that is not preallocated in
the BAIJ data structure.
Let us know if we could be of any help to fix this issue. The reported
error is bellow.

Best,
Adriano and Linda

---------------------------------------------------------------------
 Nonlinear solver converged at step 2
*** Warning, This code is deprecated, and likely to be removed in future
library versions!
/home1/05293/lindag/local/libmesh-block/include/libmesh/elem.h, line 2136,
compiled May 11 2018 at 06:08:00 ***
*** Warning, This code is deprecated, and likely to be removed in future
library versions!
/home1/05293/lindag/local/libmesh-block/include/libmesh/elem.h, line 1922,
compiled May 11 2018 at 06:08:00 ***

****************************************************
Mesh Refinement:
  Considering Transport Variable
  Number of elements before AMR step: 76800
  Number of elements after AMR step: 104226
  Nelem variation = 35.7109 %.

*********************************************************************
 Solving Navier-Stokes equation...
---------------------------------------------------------------------
Step L. Iter.  |b-AX|      |du|        |du|/|u|    C. R.
---------------------------------------------------------------------
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Argument out of range
[0]PETSC ERROR: New nonzero at (4372,4385) caused a malloc
Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn
off this check
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.9.1, unknown
[0]PETSC ERROR: ./sediment-opt on a  named
c455-011.stampede2.tacc.utexas.edu by lindag Fri May 11 07:29:20 2018
[0]PETSC ERROR: Configure options --prefix=/home1/05293/lindag/local/petsc
--with-blaslapack-dir=/opt/intel/compilers_and_libraries/linux/mkl
--with-debugging=0 --download-hypre --download-ml --download-mumps
--download-scalapack
[0]PETSC ERROR: #1 MatSetValues_MPIBAIJ() line 213 in
/home1/05293/lindag/src/petsc/src/mat/impls/baij/mpi/mpibaij.c
[0]PETSC ERROR: #2 MatSetValues() line 1312 in
/home1/05293/lindag/src/petsc/src/mat/interface/matrix.c
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

2018-05-10 11:30 GMT-03:00 Paul T. Bauman <ptb...@gm...>:

> The last time I talked to @benkirk (which was a long time ago...) he'd
> indicated they used this feature very regularly. It may have been for only
> a single variable group, but I can't say for sure. We definitely need to
> exercise this more I think (and I'm also guilty of not really doing it when
> really I should be).
>
> On Thu, May 10, 2018 at 9:44 AM, David Knezevic <
> dav...@ak...> wrote:
>
>> On Thu, May 10, 2018 at 9:38 AM, Roy Stogner <roy...@ic...>
>> wrote:
>>
>> >
>> > On Wed, 9 May 2018, John Peterson wrote:
>> >
>> > On Wed, May 9, 2018 at 11:56 AM, Linda G <li...@na...> wrote:
>> >>
>> >> Dear Libmesh Users,
>> >>>
>> >>> We are trying to figure out how to set up a Stabilized NS FEM
>> formulation
>> >>> to work
>> >>> in a blocked matrix fashion. After reading the documentation we
>> realized
>> >>> that this boils down to define a
>> >>> variable group, but we could not find any example (even the Elasticity
>> >>> ones) that uses the
>> >>> block matrix (*BAIJ) feature.
>> >>> Please remember that our formulation is stabilized, so we are using
>> P1P1
>> >>> and P2P2 for velocity and pressure.
>> >>> Is the function to define variables groups a member of System class or
>> >>> DofMap class?
>> >>> Please if anyone has a working example, or teach us how to do it, we
>> >>> really
>> >>> appreciate.
>> >>>
>> >>>
>> >> If I understand correctly, this should happen automatically if you
>> have a
>> >> System with 1 variable group that contains more than 1 var, provided
>> that
>> >> you configure libmesh with --enable-blocked-storage. The default is
>> >> --disable-blocked-storage since I believe we ran into some issues while
>> >> using this option in the past.
>> >>
>> >
>> > https://github.com/libMesh/libmesh/issues/703 is the only concrete
>> > issue I can find, thanks to SourceForge mailing list changes breaking
>> > old archive links.
>> >
>> > We should probably track this down soon so we can at least upgrade
>> > blocked-storage from "enable only explicitly" to "enable with
>> > --enable-everything".  I haven't been testing --enable-blocked-storage
>> > for a long time so it may have regressed even further.
>> > ---
>> > Roy
>>
>>
>>
>> Should we re-open #703 then? I agree that we never got to the bottom of
>> what was going on there, we just avoided the issue by disabling some
>> examples.
>>
>> David
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Libmesh-users mailing list
>> Lib...@li...
>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>
>
>


-- 
Adriano Côrtes
=================================================
*NUMPEX-COMP / Campus Duque de Caxias and*
*High-performance Computing Center (NACAD/COPPE)*
Federal University of Rio de Janeiro (UFRJ)

[Libmesh-users] libMesh performance evaluation?

[Junchao Z. <jun...@gm...>]

Hello,
   Does anyone know libMesh performance evaluation papers or libMesh
benchmarks? It is even better that the code and input are publicly
accessible so that I can repeat the experiments.  I am particularly
interested in libMesh performance on multicore clusters when multithreading
is turned on.
  Thank you

--Junchao Zhang

[Libmesh-users] computing lift and drag forces

[Bin L. <ken...@ho...>]

I am a new user and still not very familiar with libmesh library functionality. May I know how do I compute the drag and lift traction forces along a submerged solid wall in libmesh? Is there an example code for demonstration? Particularly, I need the nodal global coordinates, the shape function and shape function gradient values at the nodes along the boundary of  the solid wall.


Thank you

Ken

Re: [Libmesh-users] Variable groups to use blocked matrix (*BAIJ)

[Paul T. B. <ptb...@gm...>]

The last time I talked to @benkirk (which was a long time ago...) he'd
indicated they used this feature very regularly. It may have been for only
a single variable group, but I can't say for sure. We definitely need to
exercise this more I think (and I'm also guilty of not really doing it when
really I should be).

On Thu, May 10, 2018 at 9:44 AM, David Knezevic <dav...@ak...>
wrote:

> On Thu, May 10, 2018 at 9:38 AM, Roy Stogner <roy...@ic...>
> wrote:
>
> >
> > On Wed, 9 May 2018, John Peterson wrote:
> >
> > On Wed, May 9, 2018 at 11:56 AM, Linda G <li...@na...> wrote:
> >>
> >> Dear Libmesh Users,
> >>>
> >>> We are trying to figure out how to set up a Stabilized NS FEM
> formulation
> >>> to work
> >>> in a blocked matrix fashion. After reading the documentation we
> realized
> >>> that this boils down to define a
> >>> variable group, but we could not find any example (even the Elasticity
> >>> ones) that uses the
> >>> block matrix (*BAIJ) feature.
> >>> Please remember that our formulation is stabilized, so we are using
> P1P1
> >>> and P2P2 for velocity and pressure.
> >>> Is the function to define variables groups a member of System class or
> >>> DofMap class?
> >>> Please if anyone has a working example, or teach us how to do it, we
> >>> really
> >>> appreciate.
> >>>
> >>>
> >> If I understand correctly, this should happen automatically if you have
> a
> >> System with 1 variable group that contains more than 1 var, provided
> that
> >> you configure libmesh with --enable-blocked-storage. The default is
> >> --disable-blocked-storage since I believe we ran into some issues while
> >> using this option in the past.
> >>
> >
> > https://github.com/libMesh/libmesh/issues/703 is the only concrete
> > issue I can find, thanks to SourceForge mailing list changes breaking
> > old archive links.
> >
> > We should probably track this down soon so we can at least upgrade
> > blocked-storage from "enable only explicitly" to "enable with
> > --enable-everything".  I haven't been testing --enable-blocked-storage
> > for a long time so it may have regressed even further.
> > ---
> > Roy
>
>
>
> Should we re-open #703 then? I agree that we never got to the bottom of
> what was going on there, we just avoided the issue by disabling some
> examples.
>
> David
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>

Re: [Libmesh-users] Variable groups to use blocked matrix (*BAIJ)

[David K. <dav...@ak...>]

On Thu, May 10, 2018 at 9:38 AM, Roy Stogner <roy...@ic...>
wrote:

>
> On Wed, 9 May 2018, John Peterson wrote:
>
> On Wed, May 9, 2018 at 11:56 AM, Linda G <li...@na...> wrote:
>>
>> Dear Libmesh Users,
>>>
>>> We are trying to figure out how to set up a Stabilized NS FEM formulation
>>> to work
>>> in a blocked matrix fashion. After reading the documentation we realized
>>> that this boils down to define a
>>> variable group, but we could not find any example (even the Elasticity
>>> ones) that uses the
>>> block matrix (*BAIJ) feature.
>>> Please remember that our formulation is stabilized, so we are using P1P1
>>> and P2P2 for velocity and pressure.
>>> Is the function to define variables groups a member of System class or
>>> DofMap class?
>>> Please if anyone has a working example, or teach us how to do it, we
>>> really
>>> appreciate.
>>>
>>>
>> If I understand correctly, this should happen automatically if you have a
>> System with 1 variable group that contains more than 1 var, provided that
>> you configure libmesh with --enable-blocked-storage. The default is
>> --disable-blocked-storage since I believe we ran into some issues while
>> using this option in the past.
>>
>
> https://github.com/libMesh/libmesh/issues/703 is the only concrete
> issue I can find, thanks to SourceForge mailing list changes breaking
> old archive links.
>
> We should probably track this down soon so we can at least upgrade
> blocked-storage from "enable only explicitly" to "enable with
> --enable-everything".  I haven't been testing --enable-blocked-storage
> for a long time so it may have regressed even further.
> ---
> Roy



Should we re-open #703 then? I agree that we never got to the bottom of
what was going on there, we just avoided the issue by disabling some
examples.

David

Re: [Libmesh-users] Variable groups to use blocked matrix (*BAIJ)

[Roy S. <roy...@ic...>]

On Wed, 9 May 2018, John Peterson wrote:

> On Wed, May 9, 2018 at 11:56 AM, Linda G <li...@na...> wrote:
>
>> Dear Libmesh Users,
>>
>> We are trying to figure out how to set up a Stabilized NS FEM formulation
>> to work
>> in a blocked matrix fashion. After reading the documentation we realized
>> that this boils down to define a
>> variable group, but we could not find any example (even the Elasticity
>> ones) that uses the
>> block matrix (*BAIJ) feature.
>> Please remember that our formulation is stabilized, so we are using P1P1
>> and P2P2 for velocity and pressure.
>> Is the function to define variables groups a member of System class or
>> DofMap class?
>> Please if anyone has a working example, or teach us how to do it, we really
>> appreciate.
>>
>
> If I understand correctly, this should happen automatically if you have a
> System with 1 variable group that contains more than 1 var, provided that
> you configure libmesh with --enable-blocked-storage. The default is
> --disable-blocked-storage since I believe we ran into some issues while
> using this option in the past.

https://github.com/libMesh/libmesh/issues/703 is the only concrete
issue I can find, thanks to SourceForge mailing list changes breaking
old archive links.

We should probably track this down soon so we can at least upgrade
blocked-storage from "enable only explicitly" to "enable with
--enable-everything".  I haven't been testing --enable-blocked-storage
for a long time so it may have regressed even further.
---
Roy

Re: [Libmesh-users] Variable groups to use blocked matrix (*BAIJ)

[John P. <jwp...@gm...>]

On Wed, May 9, 2018 at 11:56 AM, Linda G <li...@na...> wrote:

> Dear Libmesh Users,
>
> We are trying to figure out how to set up a Stabilized NS FEM formulation
> to work
> in a blocked matrix fashion. After reading the documentation we realized
> that this boils down to define a
> variable group, but we could not find any example (even the Elasticity
> ones) that uses the
> block matrix (*BAIJ) feature.
> Please remember that our formulation is stabilized, so we are using P1P1
> and P2P2 for velocity and pressure.
> Is the function to define variables groups a member of System class or
> DofMap class?
> Please if anyone has a working example, or teach us how to do it, we really
> appreciate.
>

If I understand correctly, this should happen automatically if you have a
System with 1 variable group that contains more than 1 var, provided that
you configure libmesh with --enable-blocked-storage. The default is
--disable-blocked-storage since I believe we ran into some issues while
using this option in the past.

-- 
John

[Libmesh-users] Variable groups to use blocked matrix (*BAIJ)

[Linda G <li...@na...>]

Dear Libmesh Users,

We are trying to figure out how to set up a Stabilized NS FEM formulation
to work
in a blocked matrix fashion. After reading the documentation we realized
that this boils down to define a
variable group, but we could not find any example (even the Elasticity
ones) that uses the
block matrix (*BAIJ) feature.
Please remember that our formulation is stabilized, so we are using P1P1
and P2P2 for velocity and pressure.
Is the function to define variables groups a member of System class or
DofMap class?
Please if anyone has a working example, or teach us how to do it, we really
appreciate.

Many thanks in advance.
Sincerely,
Linda and Adriano.

-- 

Linda Gesenhues
=================================================
PhD Student
High-performance Computing Center (NACAD)
Federal University of Rio de Janeiro (UFRJ)

Re: [Libmesh-users] Adding a variable group

[Harshad S. <hsa...@pu...>]

Hi Roy,

Thank you very much for your reply. I do have a single VariableGroup.

Best,
Harshad

On Mon, May 7, 2018 at 5:45 PM, Roy Stogner <roy...@ic...>
wrote:

>
> On Mon, 7 May 2018, Harshad Sahasrabudhe wrote:
>
> I need to add a group of variables to my CondensedEigenSystem. My current
>> code handles a single variable. What would be the shortest way to update
>> my
>> code to accommodate the variable group? I would like the PetscMatrix to be
>> block sparse with a node major ordering. What should I set in DofMap in
>> the
>> code to get this done without using the " --node_major_dofs " command line
>> option?
>>
>
> If you add variables which are all of the exact same FE type and
> subdomain restriction, and you add them consecutively without any
> variables of different types in between, and if you haven't manually
> disabled System::identify_variable_groups(), then libMesh should put
> them all in the same VariableGroup.  If you *only* have one
> VariableGroup after everything is added, then the matrix ordering ends
> up looking like node_major_dofs.
>
> If you have different variable types or subdomain restrictions, then
> right now I believe the only way to get node_major_dofs ordering is
> --node_major_dofs.  A patch adding a programmatic control option would
> certainly be appreciated.
> ---
> Roy
>

Re: [Libmesh-users] Adding a variable group

[Roy S. <roy...@ic...>]

On Mon, 7 May 2018, Harshad Sahasrabudhe wrote:

> I need to add a group of variables to my CondensedEigenSystem. My current
> code handles a single variable. What would be the shortest way to update my
> code to accommodate the variable group? I would like the PetscMatrix to be
> block sparse with a node major ordering. What should I set in DofMap in the
> code to get this done without using the " --node_major_dofs " command line
> option?

If you add variables which are all of the exact same FE type and
subdomain restriction, and you add them consecutively without any
variables of different types in between, and if you haven't manually
disabled System::identify_variable_groups(), then libMesh should put
them all in the same VariableGroup.  If you *only* have one
VariableGroup after everything is added, then the matrix ordering ends
up looking like node_major_dofs.

If you have different variable types or subdomain restrictions, then
right now I believe the only way to get node_major_dofs ordering is
--node_major_dofs.  A patch adding a programmatic control option would
certainly be appreciated.
---
Roy

[Libmesh-users] Adding a variable group

[Harshad S. <hsa...@pu...>]

Hello,

I need to add a group of variables to my CondensedEigenSystem. My current
code handles a single variable. What would be the shortest way to update my
code to accommodate the variable group? I would like the PetscMatrix to be
block sparse with a node major ordering. What should I set in DofMap in the
code to get this done without using the " --node_major_dofs " command line
option?

Thanks!
Harshad

Re: [Libmesh-users] [RB] Find the minimum eigenvalue using A_q and B_q in the RB system.

[David K. <dav...@ak...>]

On Mon, May 7, 2018 at 8:20 AM, <ss...@pu...> wrote:

> Hello, all.
>
>
>
> I try to solve an eigenproblem with the linear elasticity and find the
> minimum eigenvalue in the RB system
>
> Of course, I may create another libMesh code that solve only the
> eigenproblem, but I want to utilize A_q and B_q already made by the RB
> system. First of all, I referred to the libMesh code, "RBSCMConstruction,"
> however, I do not know how to load the matrices and solve the eigenproblem
> in my RB code.
>
>
>
> My questions are as follows:
>
> 1.      Given the specific(constant) parameter, is there any simple
> way(code) to find the minimum eigenvalue in the RB system?
> 2.      How to obtain matrices, A_q and B_q, including theta for the
> specific parameter? In other words, how to get the full matrices, A and B
> used in the RB system?
>
>
>
> It would be greatly appreciated if you could give me some examples or codes
> for reference.
>


I don't have any examples of this kind of thing, I haven't tried to do that
myself. I don't think there's any simple way to do it, so you would have to
write the necessary code to do it yourself based on the reduced basis code
in libMesh. It should be possible (all the data is available) but it may
take a lot of work.

Regards,
David

[Libmesh-users] [RB] Find the minimum eigenvalue using A_q and B_q in the RB system.

[<ss...@pu...>]

Hello, all.

 

I try to solve an eigenproblem with the linear elasticity and find the
minimum eigenvalue in the RB system

Of course, I may create another libMesh code that solve only the
eigenproblem, but I want to utilize A_q and B_q already made by the RB
system. First of all, I referred to the libMesh code, "RBSCMConstruction,"
however, I do not know how to load the matrices and solve the eigenproblem
in my RB code.

 

My questions are as follows:

1.	Given the specific(constant) parameter, is there any simple
way(code) to find the minimum eigenvalue in the RB system?
2.	How to obtain matrices, A_q and B_q, including theta for the
specific parameter? In other words, how to get the full matrices, A and B
used in the RB system?

 

It would be greatly appreciated if you could give me some examples or codes
for reference.

 

I look forward to your reply.

 

Thank you.

 

Regards,

SKang

 

Re: [Libmesh-users] DG and boundary conditions

[Roy S. <roy...@ic...>]

On Thu, 3 May 2018, Renato Poli wrote:

>>> you might as well add manual constraint equations between
>>> your solution triangles and the desired boundary values directly.
>
> Could you elaborate a little on that?
> Do you mean adding scalar variables with Lagrangian multipliers?
> Or "DofMap->add_constraint_row"?

DofMap::add_constraint_row(), yes.

> Any example to refer?

I wish.  I'm not sure we even have any raw test coverage other than in
tests/base/dof_map_test.C

We also use that API in dof_map_constraints.C, but in an indirect
functor-filled threading way that's probably even less instructional.
---
Roy

Re: [Libmesh-users] DG and boundary conditions

[Renato P. <re...@gm...>]

>> you might as well add manual constraint equations between
>> your solution triangles and the desired boundary values directly.

Could you elaborate a little on that?
Do you mean adding scalar variables with Lagrangian multipliers?
Or "DofMap->add_constraint_row"?
Any example to refer?

Thanks,
Renato

On Thu, May 3, 2018 at 12:28 PM, Roy Stogner <roy...@ic...> wrote:
>
> On Wed, 2 May 2018, Renato Poli wrote:
>
>> Well, I am working with fracture creation in between mesh elements. In
>> this case I believe it sort of makes sense to have 'strong' BCs and
>> internal discontinuous DOFs being tied together by interior
>> penalties... (not sure though)
>
>
> I think strong BCs will hurt your convergence rates, but you should
> still converge, so it couldn't hurt to try and see if I'm wrong.
>
>> I was considering to duplicate the DOFs myself during topology
>> creation: I would add triangles sharing vertices _coordinates_ but not
>> vertex _references_. Then I map the neighbors and tie them together
>> during assembly.
>>
>> Would that be sound?
>
>
> Gah.  At that point you'd have to add manual constraint equations
> between your solution triangles and the duplicate triangles the
> constrained boundary DoFs, so you might as well add manual constraint
> equations between your solution triangles and the desired boundary
> values directly.
> ---
> Roy

Re: [Libmesh-users] new libmeshdm fails with newtonrsls

[Ata M. <a.m...@gm...>]

Hi Roy,

You can simply regenerate the error if you pass:

./example-opt --verbose dim=1 N=1024 initial_state=strip initial_center=0.5 initial_width=0.1 dt=1e-10 max_time=.5e-8 -snes_type vinewtonssls --use-petsc-dm

This generates a seg fault on my mac with the PETSc and libMesh revisions I provided before.

My guess is the seg fault happens probably because the solution vector is not initiated correctly. So the VecDuplicate generates an error at

>> src/snes/impls/vi/vi.c: 383


Ata

> On May 3, 2018, at 11:29 AM, Roy Stogner <roy...@ic...> wrote:
> 
> 
> On Mon, 30 Apr 2018, gmail wrote:
> 
>> The new implementation of the libMeshDM unfortunately fails when
>> using variational inequality solvers VINEWTONRSLS or VINEWTONSSLS
>> (for example miscellaneous/ex7). This happens when PETSc tries to
>> VecDuplicate the solution vector for lower bound in
>> src/snes/impls/vi/vi.c: 383 ?!
>> 
>> I pulled the latest libMesh (48bd50d4a) this morning and compiled it
>> with PETSc 3.8 (756c7f9f8).  I’m attaching my config log for
>> libMesh.
> 
> Sorry, the config log doesn't go through on the mailing list.
> 
> Could you either try bisecting the problem, or give us instructions
> (run misc ex7 manually with different command line options?) for
> replicating it?
> 
> Thanks,
> ---
> Roy

Re: [Libmesh-users] new libmeshdm fails with newtonrsls

[Roy S. <roy...@ic...>]

On Mon, 30 Apr 2018, gmail wrote:

> The new implementation of the libMeshDM unfortunately fails when
> using variational inequality solvers VINEWTONRSLS or VINEWTONSSLS
> (for example miscellaneous/ex7). This happens when PETSc tries to
> VecDuplicate the solution vector for lower bound in
> src/snes/impls/vi/vi.c: 383 ?!
>
> I pulled the latest libMesh (48bd50d4a) this morning and compiled it
> with PETSc 3.8 (756c7f9f8).  I’m attaching my config log for
> libMesh.

Sorry, the config log doesn't go through on the mailing list.

Could you either try bisecting the problem, or give us instructions
(run misc ex7 manually with different command line options?) for
replicating it?

Thanks,
---
Roy

Re: [Libmesh-users] DG and boundary conditions

[Roy S. <roy...@ic...>]

On Wed, 2 May 2018, Renato Poli wrote:

> Well, I am working with fracture creation in between mesh elements. In
> this case I believe it sort of makes sense to have 'strong' BCs and
> internal discontinuous DOFs being tied together by interior
> penalties... (not sure though)

I think strong BCs will hurt your convergence rates, but you should
still converge, so it couldn't hurt to try and see if I'm wrong.

> I was considering to duplicate the DOFs myself during topology
> creation: I would add triangles sharing vertices _coordinates_ but not
> vertex _references_. Then I map the neighbors and tie them together
> during assembly.
>
> Would that be sound?

Gah.  At that point you'd have to add manual constraint equations
between your solution triangles and the duplicate triangles the
constrained boundary DoFs, so you might as well add manual constraint
equations between your solution triangles and the desired boundary
values directly.
---
Roy

Re: [Libmesh-users] Question regarding Subdivision Implementation in libMesh

[Lee, J. H. <jae...@li...>]

I used -ksp_type cg -pc_type icc -pc_factor_shift_type positive_definite, but this takes ~300 iterations.

> On May 2, 2018, at 12:52 PM, Roy Stogner <roy...@ic...> wrote:
> 
> 
> On Tue, 1 May 2018, Lee, Jae Ho wrote:
> 
>> Actually, this issue is now resolved. The problem was that the
>> default linear solver was not converging. This issue can be resolved
>> by using a stronger linear solver.
> 
> Thanks for the update!
> 
> You had me worried at first - I don't think any of the most active
> developers are currently doing anything with subdivision elements,
> which is exactly the sort of situation where regressions are a risk.
> Good to hear that wasn't the case.
> 
> How far in the "stronger linear solver" direction did you have to go?
> Stronger tolerance(s); stronger preconditioner; direct instead of
> iterative?
> ---
> Roy

Re: [Libmesh-users] ExodusII and AMR

[Derek G. <fri...@gm...>]

Also: name you should name your files like:

something.e
something.e-0002
something.e-0003

Then Paraview will pick up the series automatically simply by opening
"something.e".

Derek

On Wed, May 2, 2018 at 12:20 PM John Peterson <jwp...@gm...> wrote:

> On Wed, May 2, 2018 at 11:56 AM, Daniel Vasconcelos <
> dan...@ou...
> > wrote:
>
> > ​Dear libMesh users,
> >
> > I have been using Paraview to visualize outputs generated by my code. So
> > far I have been using VTK to write the solutions however, recently, I
> have
> > started testing Exodus II due to some issues with the available VTK
> > installation. With a fixed mesh no problem at all, even with a time
> series.
> > My problem starts when I add mesh adaptivity.
> >
> > Is there any available example on how to use Exodus II with a transient
> > system and AMR and still be able to visualize the results with Paraview?
> >
>
> This is possible, the key is that each timestep must be written to a
> separate file when you are doing AMR, you can't write multiple timesteps to
> the same file any more.
>
> --
> John
>
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Re: [Libmesh-users] DG and boundary conditions

[Renato P. <re...@gm...>]

Thanks Roy.

Well, I am working with fracture creation in between mesh elements. In
this case I believe it sort of makes sense to have 'strong' BCs and
internal discontinuous DOFs being tied together by interior
penalties... (not sure though)

I was considering to duplicate the DOFs myself during topology
creation: I would add triangles sharing vertices _coordinates_ but not
vertex _references_. Then I map the neighbors and tie them together
during assembly.

Would that be sound?

Rgds,
Renato

On Wed, May 2, 2018 at 2:00 PM, Roy Stogner <roy...@ic...> wrote:
>
> On Tue, 1 May 2018, Renato Poli wrote:
>
>> Are DirichletBoundary BCs expected to work in Discontinuous Galerkin
>> (L2_LAGRANGE)?
>
>
> Nope.  And you wouldn't want them to, would you?  I'm not a DG person
> myself, but I was under the impression that you always want the
> solution to be allowed to be discontinuous at *every* element
> boundary, even the ones on the domain boundary, with Dirichlet
> conditions instead enforced weakly via boundary penalties, to avoid
> overconstraining your solution.
>
> I'd love to let users be able to do "create a boundary condition
> object and then forget" about it with DG as well as CG, but I don't
> know if there's any simple way to make that happen; the boundary terms
> are inherently formulation-dependent, aren't they?
> ---
> Roy

Re: [Libmesh-users] ExodusII and AMR

[John P. <jwp...@gm...>]

On Wed, May 2, 2018 at 11:56 AM, Daniel Vasconcelos <dan...@ou...
> wrote:

> ​Dear libMesh users,
>
> I have been using Paraview to visualize outputs generated by my code. So
> far I have been using VTK to write the solutions however, recently, I have
> started testing Exodus II due to some issues with the available VTK
> installation. With a fixed mesh no problem at all, even with a time series.
> My problem starts when I add mesh adaptivity.
>
> Is there any available example on how to use Exodus II with a transient
> system and AMR and still be able to visualize the results with Paraview?
>

This is possible, the key is that each timestep must be written to a
separate file when you are doing AMR, you can't write multiple timesteps to
the same file any more.

-- 
John

[Libmesh-users] ExodusII and AMR

[Daniel V. <dan...@ou...>]

​Dear libMesh users,

I have been using Paraview to visualize outputs generated by my code. So far I have been using VTK to write the solutions however, recently, I have started testing Exodus II due to some issues with the available VTK installation. With a fixed mesh no problem at all, even with a time series. My problem starts when I add mesh adaptivity.

Is there any available example on how to use Exodus II with a transient system and AMR and still be able to visualize the results with Paraview?

Thanks in advance,

Daniel F. M. Vasconcelos.