Re: [petsc-users] Periodic BC in petsc DMPlex / firedrake

[Maximilian Hartig]

>> Ahh, thanks. I was missing the option " -dm_plex_gmsh_periodic “. But using 
>> this option I now generate a segmentation fault error when calling VecView() 
>> on the solution vector with vtk and hdf5 viewers. Any suggestions?
>>  

> Small example? VTK is deprecated. HDF5 should work, although it will require 
> you to have proper coordinates I think. We have to
> think about what you mean. If its for a checkpoint, there is no problem, but 
> for viz, those programs do not understand periodicity. Thus I embed it in a 
> higher dimensional space.
> 
>Matt

Building the small example I realised that hdf5 wasn’t working altogether. I’m 
trying to fix this and see if I can run VecView with the periodic DMPlex then.
I planned using this for visualisation. 


> On 25. Oct 2018, at 15:36, Stefano Zampini  wrote:
> 
> Maybe this is a fix
> 
> diff --git a/src/dm/impls/plex/plexvtu.c b/src/dm/impls/plex/plexvtu.c
> index acdea12c2f..1a8bbada6a 100644
> --- a/src/dm/impls/plex/plexvtu.c
> +++ b/src/dm/impls/plex/plexvtu.c
> @@ -465,10 +465,11 @@ PetscErrorCode DMPlexVTKWriteAll_VTU(DM dm,PetscViewer 
> viewer)
>  if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
>PetscScalar *xpoint;
>  
> -  ierr = DMPlexPointLocalRead(dm,v,x,);CHKERRQ(ierr);
> +  ierr = 
> DMPlexPointLocalRead(dm,closure[v],x,);CHKERRQ(ierr);
>y[cnt + off++] = xpoint[i];
>  }
>}
> +  cnt += off;
>ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, 
> , );CHKERRQ(ierr);
>  }
>}
> 
> Max, does this fix your problem? If you confirm, I'll fix this in the maint 
> branch

It did indeed fix the issue! Thank you. I’ve had problems with hdf5 before and 
switched to vtk. It’s good news I can continue to use it.
> 
> If I run the below command line with the patch and with snes tutorials ex12 I 
> get the nice picture attached
> $ ./ex12 -quiet -run_type test -interpolate 1 -bc_type dirichlet 
> -petscspace_degree 1 -vec_view vtk:test.vtu:vtk_vtu -f 
> ${PETSC_DIR}/share/petsc/datafiles/meshes/square_periodic.msh 
> -dm_plex_gmsh_periodic -x_periodicity periodic -y_periodicity periodic 
> -dm_refine 4
> 
> Il giorno gio 25 ott 2018 alle ore 15:11 Stefano Zampini 
> mailto:stefano.zamp...@gmail.com>> ha scritto:
> Matt,
> 
> you can reproduce it via
> 
> $ valgrind ./ex12 -quiet -run_type test -interpolate 1 -bc_type dirichlet 
> -petscspace_degree 1 -vec_view vtk:test.vtu:vtk_vtu -f 
> ${PETSC_DIR}/share/petsc/datafiles/meshes/square_periodic.msh 
> -dm_plex_gmsh_periodic
> 
> Long time ago I added support for viewing meshes with periodic vertices in 
> the VTK_VTU viewer, but I did not fix the part that writes fields
> 
> 
> Il giorno mer 24 ott 2018 alle ore 21:04 Matthew Knepley  > ha scritto:
> On Wed, Oct 24, 2018 at 11:36 AM Maximilian Hartig  > wrote:
> 
> 
>> On 24. Oct 2018, at 12:49, Matthew Knepley > > wrote:
>> 
>> On Wed, Oct 24, 2018 at 6:29 AM Lawrence Mitchell > > wrote:
>> Hi Max,
>> 
>> (I'm cc'ing in the petsc-users mailing list which may have more advice, if 
>> you are using PETSc you should definitely subscribe!
>> 
>> > On 24 Oct 2018, at 09:27, Maximilian Hartig > > > wrote:
>> > 
>> > Hello Lawrence,
>> > 
>> > sorry to message you out of the blue. My name is Max and I found your post 
>> > on GitHub (https://github.com/firedrakeproject/firedrake/issues/1246 
>> >  ) on DMPlex 
>> > being able to read periodic gmsh files. I am currently trying to do just 
>> > that (creating a periodic DMPlex mesh with gmsh) in the context of my PhD 
>> > work. So far I haven’ t found any documentation on the periodic BC’s with 
>> > DMPlex and gmsh in the official petsc documentation. 
>> > I was wondering whether you’d be so kind as to point me in a general 
>> > direction concerning how to achieve this. You seem experienced in using 
>> > petsc and I would greatly appreciate your help. 
>> 
>> 
>> I think the answer is "it depends". If you're just using DMPlex directly and 
>> all the of the functionality with PetscDS, then I /think/ that reading 
>> periodic meshes via gmsh (assuming you're using the appropriate gmsh mesh 
>> format [v2]) "just works".
>> 
>> There are two phases here: topological and geometric. DMPlex represents the 
>> periodic topological entity directly. For example,  a circle is just a 
>> segment with one end hooked to the other. Vertices are not duplicated, or 
>> mapped to each other. This makes topology simple and easy to implement. 
>> However, then geometry is more complicated. What Plex does is allow 
>> coordinates to be represented by a discontinuous field taking values on 
>> cells, in addition to vertices. In our circle example, each 

Re: [petsc-users] Periodic BC in petsc DMPlex / firedrake

[Stephen Wornom]

Did you forget to attach "The nice picture attached" 
Stephen 

> From: "Stefano Zampini" 
> To: "petsc-maint" 
> Cc: "imilian hartig" , "PETSc users list"
> 
> Sent: Thursday, October 25, 2018 4:47:43 PM
> Subject: Re: [petsc-users] Periodic BC in petsc DMPlex / firedrake

> Opened the PR [
> https://bitbucket.org/petsc/petsc/pull-requests/1203/fix-dump-vtk-field-with-periodic-meshes/diff
> |
> https://bitbucket.org/petsc/petsc/pull-requests/1203/fix-dump-vtk-field-with-periodic-meshes/diff
> ]

> Il giorno gio 25 ott 2018 alle ore 17:44 Matthew Knepley < [
> mailto:knep...@gmail.com | knep...@gmail.com ] > ha scritto:

>> Good catch Stefano.
>> Matt

>> On Thu, Oct 25, 2018 at 9:36 AM Stefano Zampini < [
>> mailto:stefano.zamp...@gmail.com | stefano.zamp...@gmail.com ] > wrote:

>>> Maybe this is a fix
>>> diff --git a/src/dm/impls/plex/plexvtu.c b/src/dm/impls/plex/plexvtu.c
>>> index acdea12c2f..1a8bbada6a 100644
>>> --- a/src/dm/impls/plex/plexvtu.c
>>> +++ b/src/dm/impls/plex/plexvtu.c
>>> @@ -465,10 +465,11 @@ PetscErrorCode DMPlexVTKWriteAll_VTU(DM dm,PetscViewer
>>> viewer)
>>> if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
>>> PetscScalar *xpoint;
>>> - ierr = DMPlexPointLocalRead(dm,v,x,);CHKERRQ(ierr);
>>> + ierr = DMPlexPointLocalRead(dm,closure[v],x,);CHKERRQ(ierr);
>>> y[cnt + off++] = xpoint[i];
>>> }
>>> }
>>> + cnt += off;
>>> ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, ,
>>> );CHKERRQ(ierr);
>>> }
>>> }

>>> Max, does this fix your problem? If you confirm, I'll fix this in the maint
>>> branch

>>> If I run the below command line with the patch and with snes tutorials ex12 
>>> I
>>> get the nice picture attached
>>> $ ./ex12 -quiet -run_type test -interpolate 1 -bc_type dirichlet
>>> -petscspace_degree 1 -vec_view vtk:test.vtu:vtk_vtu -f
>>> ${PETSC_DIR}/share/petsc/datafiles/meshes/square_periodic.msh
>>> -dm_plex_gmsh_periodic -x_periodicity periodic -y_periodicity periodic
>>> -dm_refine 4

>>> Il giorno gio 25 ott 2018 alle ore 15:11 Stefano Zampini < [
>>> mailto:stefano.zamp...@gmail.com | stefano.zamp...@gmail.com ] > ha scritto:

>>>> Matt,

>>>> you can reproduce it via
>>>> $ valgrind ./ex12 -quiet -run_type test -interpolate 1 -bc_type dirichlet
>>>> -petscspace_degree 1 -vec_view vtk:test.vtu:vtk_vtu -f
>>>> ${PETSC_DIR}/share/petsc/datafiles/meshes/square_periodic.msh
>>>> -dm_plex_gmsh_periodic

>>>> Long time ago I added support for viewing meshes with periodic vertices in 
>>>> the
>>>> VTK_VTU viewer, but I did not fix the part that writes fields

>>>> Il giorno mer 24 ott 2018 alle ore 21:04 Matthew Knepley < [
>>>> mailto:knep...@gmail.com | knep...@gmail.com ] > ha scritto:

>>>>> On Wed, Oct 24, 2018 at 11:36 AM Maximilian Hartig < [
>>>>> mailto:imilian.har...@gmail.com | imilian.har...@gmail.com ] > wrote:

>>>>>>> On 24. Oct 2018, at 12:49, Matthew Knepley < [ mailto:knep...@gmail.com 
>>>>>>> |
>>>>>>> knep...@gmail.com ] > wrote:

>>>>>>> On Wed, Oct 24, 2018 at 6:29 AM Lawrence Mitchell < [ 
>>>>>>> mailto:we...@gmx.li |
>>>>>>> we...@gmx.li ] > wrote:

>>>>>>>> Hi Max,

>>>>>>>> (I'm cc'ing in the petsc-users mailing list which may have more 
>>>>>>>> advice, if you
>>>>>>>> are using PETSc you should definitely subscribe!

>>>>>>>>> On 24 Oct 2018, at 09:27, Maximilian Hartig < [ 
>>>>>>>>> mailto:imilian.har...@gmail.com
>>>>>>>> > | imilian.har...@gmail.com ] > wrote:

>>>>>>>> > Hello Lawrence,

>>>>>>>>> sorry to message you out of the blue. My name is Max and I found your 
>>>>>>>>> post on
>>>>>>>>> GitHub ( [ https://github.com/firedrakeproject/firedrake/issues/1246 |
>>>>>>>>> https://github.com/firedrakeproject/firedrake/issues/1246 ] ) on 
>>>>>>>>> DMPlex being
>>>>>>>>> able to read periodic gmsh files. I am currently trying to do just 
>>>>>>>>> that
>>>>>>>>> (creating a periodic DMPle

Re: [petsc-users] Periodic BC in petsc DMPlex / firedrake

[Stefano Zampini]

Opened the PR
https://bitbucket.org/petsc/petsc/pull-requests/1203/fix-dump-vtk-field-with-periodic-meshes/diff

Il giorno gio 25 ott 2018 alle ore 17:44 Matthew Knepley 
ha scritto:

> Good catch Stefano.
>
>   Matt
>
> On Thu, Oct 25, 2018 at 9:36 AM Stefano Zampini 
> wrote:
>
>> Maybe this is a fix
>>
>> diff --git a/src/dm/impls/plex/plexvtu.c b/src/dm/impls/plex/plexvtu.c
>> index acdea12c2f..1a8bbada6a 100644
>> --- a/src/dm/impls/plex/plexvtu.c
>> +++ b/src/dm/impls/plex/plexvtu.c
>> @@ -465,10 +465,11 @@ PetscErrorCode DMPlexVTKWriteAll_VTU(DM
>> dm,PetscViewer viewer)
>>  if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
>>PetscScalar *xpoint;
>>
>> -  ierr =
>> DMPlexPointLocalRead(dm,v,x,);CHKERRQ(ierr);
>> +  ierr =
>> DMPlexPointLocalRead(dm,closure[v],x,);CHKERRQ(ierr);
>>y[cnt + off++] = xpoint[i];
>>  }
>>}
>> +  cnt += off;
>>ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE,
>> , );CHKERRQ(ierr);
>>  }
>>}
>>
>> Max, does this fix your problem? If you confirm, I'll fix this in the
>> maint branch
>>
>> If I run the below command line with the patch and with snes tutorials
>> ex12 I get the nice picture attached
>> $ ./ex12 -quiet -run_type test -interpolate 1 -bc_type dirichlet
>> -petscspace_degree 1 -vec_view vtk:test.vtu:vtk_vtu -f
>> ${PETSC_DIR}/share/petsc/datafiles/meshes/square_periodic.msh
>> -dm_plex_gmsh_periodic -x_periodicity periodic -y_periodicity periodic
>> -dm_refine 4
>>
>> Il giorno gio 25 ott 2018 alle ore 15:11 Stefano Zampini <
>> stefano.zamp...@gmail.com> ha scritto:
>>
>>> Matt,
>>>
>>> you can reproduce it via
>>>
>>> $ valgrind ./ex12 -quiet -run_type test -interpolate 1 -bc_type
>>> dirichlet -petscspace_degree 1 -vec_view vtk:test.vtu:vtk_vtu -f
>>> ${PETSC_DIR}/share/petsc/datafiles/meshes/square_periodic.msh
>>> -dm_plex_gmsh_periodic
>>>
>>> Long time ago I added support for viewing meshes with periodic vertices
>>> in the VTK_VTU viewer, but I did not fix the part that writes fields
>>>
>>>
>>> Il giorno mer 24 ott 2018 alle ore 21:04 Matthew Knepley <
>>> knep...@gmail.com> ha scritto:
>>>
 On Wed, Oct 24, 2018 at 11:36 AM Maximilian Hartig <
 imilian.har...@gmail.com> wrote:

>
>
> On 24. Oct 2018, at 12:49, Matthew Knepley  wrote:
>
> On Wed, Oct 24, 2018 at 6:29 AM Lawrence Mitchell 
> wrote:
>
>> Hi Max,
>>
>> (I'm cc'ing in the petsc-users mailing list which may have more
>> advice, if you are using PETSc you should definitely subscribe!
>>
>> > On 24 Oct 2018, at 09:27, Maximilian Hartig <
>> imilian.har...@gmail.com> wrote:
>> >
>> > Hello Lawrence,
>> >
>> > sorry to message you out of the blue. My name is Max and I found
>> your post on GitHub (
>> https://github.com/firedrakeproject/firedrake/issues/1246 ) on
>> DMPlex being able to read periodic gmsh files. I am currently trying to 
>> do
>> just that (creating a periodic DMPlex mesh with gmsh) in the context of 
>> my
>> PhD work. So far I haven’ t found any documentation on the periodic BC’s
>> with DMPlex and gmsh in the official petsc documentation.
>> > I was wondering whether you’d be so kind as to point me in a
>> general direction concerning how to achieve this. You seem experienced in
>> using petsc and I would greatly appreciate your help.
>>
>>
>> I think the answer is "it depends". If you're just using DMPlex
>> directly and all the of the functionality with PetscDS, then I /think/ 
>> that
>> reading periodic meshes via gmsh (assuming you're using the appropriate
>> gmsh mesh format [v2]) "just works".
>>
>
> There are two phases here: topological and geometric. DMPlex
> represents the periodic topological entity directly. For example,  a 
> circle
> is just a segment with one end hooked to the other. Vertices are not
> duplicated, or mapped to each other. This makes topology simple and easy 
> to
> implement. However, then geometry is more complicated. What Plex does is
> allow coordinates to be represented by a discontinuous field taking values
> on cells, in addition to vertices. In our circle example, each cells near
> the cut will have 2 coordinates, one for each vertex, but they will not
> agree across the cut. If you define a periodic domain, then Plex can
> construct this coordinate field automatically using DMPlexLocalize(). 
> These
> DG coordinates are then used by the integration routines.
>
>
> Ok, I think I understand the concept. DMPlex reads information about
> both topology and coordinates from the .msh file. Creating a periodic mesh
> in gmsh then should allow DMPlex to identify the periodic boundaries as 
> the
> “cut” and build the mesh 

Re: [petsc-users] Periodic BC in petsc DMPlex / firedrake

[Matthew Knepley]

Good catch Stefano.

  Matt

On Thu, Oct 25, 2018 at 9:36 AM Stefano Zampini 
wrote:

> Maybe this is a fix
>
> diff --git a/src/dm/impls/plex/plexvtu.c b/src/dm/impls/plex/plexvtu.c
> index acdea12c2f..1a8bbada6a 100644
> --- a/src/dm/impls/plex/plexvtu.c
> +++ b/src/dm/impls/plex/plexvtu.c
> @@ -465,10 +465,11 @@ PetscErrorCode DMPlexVTKWriteAll_VTU(DM
> dm,PetscViewer viewer)
>  if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
>PetscScalar *xpoint;
>
> -  ierr =
> DMPlexPointLocalRead(dm,v,x,);CHKERRQ(ierr);
> +  ierr =
> DMPlexPointLocalRead(dm,closure[v],x,);CHKERRQ(ierr);
>y[cnt + off++] = xpoint[i];
>  }
>}
> +  cnt += off;
>ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE,
> , );CHKERRQ(ierr);
>  }
>}
>
> Max, does this fix your problem? If you confirm, I'll fix this in the
> maint branch
>
> If I run the below command line with the patch and with snes tutorials
> ex12 I get the nice picture attached
> $ ./ex12 -quiet -run_type test -interpolate 1 -bc_type dirichlet
> -petscspace_degree 1 -vec_view vtk:test.vtu:vtk_vtu -f
> ${PETSC_DIR}/share/petsc/datafiles/meshes/square_periodic.msh
> -dm_plex_gmsh_periodic -x_periodicity periodic -y_periodicity periodic
> -dm_refine 4
>
> Il giorno gio 25 ott 2018 alle ore 15:11 Stefano Zampini <
> stefano.zamp...@gmail.com> ha scritto:
>
>> Matt,
>>
>> you can reproduce it via
>>
>> $ valgrind ./ex12 -quiet -run_type test -interpolate 1 -bc_type dirichlet
>> -petscspace_degree 1 -vec_view vtk:test.vtu:vtk_vtu -f
>> ${PETSC_DIR}/share/petsc/datafiles/meshes/square_periodic.msh
>> -dm_plex_gmsh_periodic
>>
>> Long time ago I added support for viewing meshes with periodic vertices
>> in the VTK_VTU viewer, but I did not fix the part that writes fields
>>
>>
>> Il giorno mer 24 ott 2018 alle ore 21:04 Matthew Knepley <
>> knep...@gmail.com> ha scritto:
>>
>>> On Wed, Oct 24, 2018 at 11:36 AM Maximilian Hartig <
>>> imilian.har...@gmail.com> wrote:
>>>


 On 24. Oct 2018, at 12:49, Matthew Knepley  wrote:

 On Wed, Oct 24, 2018 at 6:29 AM Lawrence Mitchell  wrote:

> Hi Max,
>
> (I'm cc'ing in the petsc-users mailing list which may have more
> advice, if you are using PETSc you should definitely subscribe!
>
> > On 24 Oct 2018, at 09:27, Maximilian Hartig <
> imilian.har...@gmail.com> wrote:
> >
> > Hello Lawrence,
> >
> > sorry to message you out of the blue. My name is Max and I found
> your post on GitHub (
> https://github.com/firedrakeproject/firedrake/issues/1246 ) on DMPlex
> being able to read periodic gmsh files. I am currently trying to do just
> that (creating a periodic DMPlex mesh with gmsh) in the context of my PhD
> work. So far I haven’ t found any documentation on the periodic BC’s with
> DMPlex and gmsh in the official petsc documentation.
> > I was wondering whether you’d be so kind as to point me in a general
> direction concerning how to achieve this. You seem experienced in using
> petsc and I would greatly appreciate your help.
>
>
> I think the answer is "it depends". If you're just using DMPlex
> directly and all the of the functionality with PetscDS, then I /think/ 
> that
> reading periodic meshes via gmsh (assuming you're using the appropriate
> gmsh mesh format [v2]) "just works".
>

 There are two phases here: topological and geometric. DMPlex represents
 the periodic topological entity directly. For example,  a circle is just a
 segment with one end hooked to the other. Vertices are not duplicated, or
 mapped to each other. This makes topology simple and easy to implement.
 However, then geometry is more complicated. What Plex does is allow
 coordinates to be represented by a discontinuous field taking values on
 cells, in addition to vertices. In our circle example, each cells near the
 cut will have 2 coordinates, one for each vertex, but they will not agree
 across the cut. If you define a periodic domain, then Plex can construct
 this coordinate field automatically using DMPlexLocalize(). These DG
 coordinates are then used by the integration routines.


 Ok, I think I understand the concept. DMPlex reads information about
 both topology and coordinates from the .msh file. Creating a periodic mesh
 in gmsh then should allow DMPlex to identify the periodic boundaries as the
 “cut” and build the mesh topology accordingly. Coordinate information is
 handled separately.
 That means, as Lawrence suggested, building periodic meshes in gmsh and
 reading them in to petsc’s DMPlex should indeed “just work”.  (From the
 user perspective). The only extra step is to call DMLocalizeCoordinates()
 after DMPlexReadFromFile(). Sorry to 

Re: [petsc-users] Periodic BC in petsc DMPlex / firedrake

[Stefano Zampini]

Matt,

you can reproduce it via

$ valgrind ./ex12 -quiet -run_type test -interpolate 1 -bc_type dirichlet
-petscspace_degree 1 -vec_view vtk:test.vtu:vtk_vtu -f
${PETSC_DIR}/share/petsc/datafiles/meshes/square_periodic.msh
-dm_plex_gmsh_periodic

Long time ago I added support for viewing meshes with periodic vertices in
the VTK_VTU viewer, but I did not fix the part that writes fields


Il giorno mer 24 ott 2018 alle ore 21:04 Matthew Knepley 
ha scritto:

> On Wed, Oct 24, 2018 at 11:36 AM Maximilian Hartig <
> imilian.har...@gmail.com> wrote:
>
>>
>>
>> On 24. Oct 2018, at 12:49, Matthew Knepley  wrote:
>>
>> On Wed, Oct 24, 2018 at 6:29 AM Lawrence Mitchell  wrote:
>>
>>> Hi Max,
>>>
>>> (I'm cc'ing in the petsc-users mailing list which may have more advice,
>>> if you are using PETSc you should definitely subscribe!
>>>
>>> > On 24 Oct 2018, at 09:27, Maximilian Hartig 
>>> wrote:
>>> >
>>> > Hello Lawrence,
>>> >
>>> > sorry to message you out of the blue. My name is Max and I found your
>>> post on GitHub (
>>> https://github.com/firedrakeproject/firedrake/issues/1246 ) on DMPlex
>>> being able to read periodic gmsh files. I am currently trying to do just
>>> that (creating a periodic DMPlex mesh with gmsh) in the context of my PhD
>>> work. So far I haven’ t found any documentation on the periodic BC’s with
>>> DMPlex and gmsh in the official petsc documentation.
>>> > I was wondering whether you’d be so kind as to point me in a general
>>> direction concerning how to achieve this. You seem experienced in using
>>> petsc and I would greatly appreciate your help.
>>>
>>>
>>> I think the answer is "it depends". If you're just using DMPlex directly
>>> and all the of the functionality with PetscDS, then I /think/ that reading
>>> periodic meshes via gmsh (assuming you're using the appropriate gmsh mesh
>>> format [v2]) "just works".
>>>
>>
>> There are two phases here: topological and geometric. DMPlex represents
>> the periodic topological entity directly. For example,  a circle is just a
>> segment with one end hooked to the other. Vertices are not duplicated, or
>> mapped to each other. This makes topology simple and easy to implement.
>> However, then geometry is more complicated. What Plex does is allow
>> coordinates to be represented by a discontinuous field taking values on
>> cells, in addition to vertices. In our circle example, each cells near the
>> cut will have 2 coordinates, one for each vertex, but they will not agree
>> across the cut. If you define a periodic domain, then Plex can construct
>> this coordinate field automatically using DMPlexLocalize(). These DG
>> coordinates are then used by the integration routines.
>>
>>
>> Ok, I think I understand the concept. DMPlex reads information about both
>> topology and coordinates from the .msh file. Creating a periodic mesh in
>> gmsh then should allow DMPlex to identify the periodic boundaries as the
>> “cut” and build the mesh topology accordingly. Coordinate information is
>> handled separately.
>> That means, as Lawrence suggested, building periodic meshes in gmsh and
>> reading them in to petsc’s DMPlex should indeed “just work”.  (From the
>> user perspective). The only extra step is to call DMLocalizeCoordinates()
>> after DMPlexReadFromFile(). Sorry to reiterate, I am just trying to make
>> sense of this.
>>
>>
>>
>>> From my side, the issue is to do with mapping that coordinate field into
>>> one that I understand (within Firedrake). You may not have this problem.
>>>
>>
>> Firedrake uses its own coordinate mapping and integration routines, so
>> they must manage the second part independently. I hope to get change this
>> slightly soon by making the Firedrake representation a DMField, so that it
>> looks the same to Plex.
>>
>>   Thanks,
>>
>> Matt
>>
>>
>>> Thanks,
>>>
>>> Lawrence
>>
>>
>>
>> --
>> 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
>>
>> https://www.cse.buffalo.edu/~knepley/
>>
>>
>> To read periodic meshes from GMSH, you need to use the option
>> -dm_plex_gmsh_periodic and DMPlexCreateFromFile
>>
>>
>> Ahh, thanks. I was missing the option " -dm_plex_gmsh_periodic “. But
>> using this option I now generate a segmentation fault error when calling
>> VecView() on the solution vector with vtk and hdf5 viewers. Any suggestions?
>>
>
>  Small example? VTK is deprecated. HDF5 should work, although it will
> require you to have proper coordinates I think. We have to
> think about what you mean. If its for a checkpoint, there is no problem,
> but for viz, those programs do not understand periodicity. Thus I embed it
> in a higher dimensional space.
>
>Matt
>
>> See  src/dm/impls/plex/examples/tests/ex1.c. An example runs
>>
>> $ ./ex1 -filename
>> ${PETSC_DIR}/share/petsc/datafiles/meshes/cube_periodic_bin.msh
>> -dm_plex_gmsh_periodic -dm_view ::ascii_info_detail 

Re: [petsc-users] Periodic BC in petsc DMPlex / firedrake

[Matthew Knepley]

On Wed, Oct 24, 2018 at 11:36 AM Maximilian Hartig 
wrote:

>
>
> On 24. Oct 2018, at 12:49, Matthew Knepley  wrote:
>
> On Wed, Oct 24, 2018 at 6:29 AM Lawrence Mitchell  wrote:
>
>> Hi Max,
>>
>> (I'm cc'ing in the petsc-users mailing list which may have more advice,
>> if you are using PETSc you should definitely subscribe!
>>
>> > On 24 Oct 2018, at 09:27, Maximilian Hartig 
>> wrote:
>> >
>> > Hello Lawrence,
>> >
>> > sorry to message you out of the blue. My name is Max and I found your
>> post on GitHub (https://github.com/firedrakeproject/firedrake/issues/1246
>>  ) on DMPlex being able to read periodic gmsh files. I am currently
>> trying to do just that (creating a periodic DMPlex mesh with gmsh) in the
>> context of my PhD work. So far I haven’ t found any documentation on the
>> periodic BC’s with DMPlex and gmsh in the official petsc documentation.
>> > I was wondering whether you’d be so kind as to point me in a general
>> direction concerning how to achieve this. You seem experienced in using
>> petsc and I would greatly appreciate your help.
>>
>>
>> I think the answer is "it depends". If you're just using DMPlex directly
>> and all the of the functionality with PetscDS, then I /think/ that reading
>> periodic meshes via gmsh (assuming you're using the appropriate gmsh mesh
>> format [v2]) "just works".
>>
>
> There are two phases here: topological and geometric. DMPlex represents
> the periodic topological entity directly. For example,  a circle is just a
> segment with one end hooked to the other. Vertices are not duplicated, or
> mapped to each other. This makes topology simple and easy to implement.
> However, then geometry is more complicated. What Plex does is allow
> coordinates to be represented by a discontinuous field taking values on
> cells, in addition to vertices. In our circle example, each cells near the
> cut will have 2 coordinates, one for each vertex, but they will not agree
> across the cut. If you define a periodic domain, then Plex can construct
> this coordinate field automatically using DMPlexLocalize(). These DG
> coordinates are then used by the integration routines.
>
>
> Ok, I think I understand the concept. DMPlex reads information about both
> topology and coordinates from the .msh file. Creating a periodic mesh in
> gmsh then should allow DMPlex to identify the periodic boundaries as the
> “cut” and build the mesh topology accordingly. Coordinate information is
> handled separately.
> That means, as Lawrence suggested, building periodic meshes in gmsh and
> reading them in to petsc’s DMPlex should indeed “just work”.  (From the
> user perspective). The only extra step is to call DMLocalizeCoordinates()
> after DMPlexReadFromFile(). Sorry to reiterate, I am just trying to make
> sense of this.
>
>
>
>> From my side, the issue is to do with mapping that coordinate field into
>> one that I understand (within Firedrake). You may not have this problem.
>>
>
> Firedrake uses its own coordinate mapping and integration routines, so
> they must manage the second part independently. I hope to get change this
> slightly soon by making the Firedrake representation a DMField, so that it
> looks the same to Plex.
>
>   Thanks,
>
> Matt
>
>
>> Thanks,
>>
>> Lawrence
>
>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/
>
>
> To read periodic meshes from GMSH, you need to use the option
> -dm_plex_gmsh_periodic and DMPlexCreateFromFile
>
>
> Ahh, thanks. I was missing the option " -dm_plex_gmsh_periodic “. But
> using this option I now generate a segmentation fault error when calling
> VecView() on the solution vector with vtk and hdf5 viewers. Any suggestions?
>

 Small example? VTK is deprecated. HDF5 should work, although it will
require you to have proper coordinates I think. We have to
think about what you mean. If its for a checkpoint, there is no problem,
but for viz, those programs do not understand periodicity. Thus I embed it
in a higher dimensional space.

   Matt

> See  src/dm/impls/plex/examples/tests/ex1.c. An example runs
>
> $ ./ex1 -filename
> ${PETSC_DIR}/share/petsc/datafiles/meshes/cube_periodic_bin.msh
> -dm_plex_gmsh_periodic -dm_view ::ascii_info_detail -interpolate -test_shape
>
> generating periodic meshes in gmsh may be tricky, Lisandro for sure may
> advice.
>
>
> Thanks,
> Max
>
>

-- 
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

https://www.cse.buffalo.edu/~knepley/ 

Re: [petsc-users] Periodic BC in petsc DMPlex / firedrake

[Maximilian Hartig]

> On 24. Oct 2018, at 12:49, Matthew Knepley  wrote:
> 
> On Wed, Oct 24, 2018 at 6:29 AM Lawrence Mitchell  > wrote:
> Hi Max,
> 
> (I'm cc'ing in the petsc-users mailing list which may have more advice, if 
> you are using PETSc you should definitely subscribe!
> 
> > On 24 Oct 2018, at 09:27, Maximilian Hartig  > > wrote:
> > 
> > Hello Lawrence,
> > 
> > sorry to message you out of the blue. My name is Max and I found your post 
> > on GitHub (https://github.com/firedrakeproject/firedrake/issues/1246 
> >  ) on DMPlex 
> > being able to read periodic gmsh files. I am currently trying to do just 
> > that (creating a periodic DMPlex mesh with gmsh) in the context of my PhD 
> > work. So far I haven’ t found any documentation on the periodic BC’s with 
> > DMPlex and gmsh in the official petsc documentation. 
> > I was wondering whether you’d be so kind as to point me in a general 
> > direction concerning how to achieve this. You seem experienced in using 
> > petsc and I would greatly appreciate your help. 
> 
> 
> I think the answer is "it depends". If you're just using DMPlex directly and 
> all the of the functionality with PetscDS, then I /think/ that reading 
> periodic meshes via gmsh (assuming you're using the appropriate gmsh mesh 
> format [v2]) "just works".
> 
> There are two phases here: topological and geometric. DMPlex represents the 
> periodic topological entity directly. For example,  a circle is just a 
> segment with one end hooked to the other. Vertices are not duplicated, or 
> mapped to each other. This makes topology simple and easy to implement. 
> However, then geometry is more complicated. What Plex does is allow 
> coordinates to be represented by a discontinuous field taking values on 
> cells, in addition to vertices. In our circle example, each cells near the 
> cut will have 2 coordinates, one for each vertex, but they will not agree 
> across the cut. If you define a periodic domain, then Plex can construct this 
> coordinate field automatically using DMPlexLocalize(). These DG coordinates 
> are then used by the integration routines.

Ok, I think I understand the concept. DMPlex reads information about both 
topology and coordinates from the .msh file. Creating a periodic mesh in gmsh 
then should allow DMPlex to identify the periodic boundaries as the “cut” and 
build the mesh topology accordingly. Coordinate information is handled 
separately.
That means, as Lawrence suggested, building periodic meshes in gmsh and reading 
them in to petsc’s DMPlex should indeed “just work”.  (From the user 
perspective). The only extra step is to call DMLocalizeCoordinates() after 
DMPlexReadFromFile(). Sorry to reiterate, I am just trying to make sense of 
this. 
>  
> From my side, the issue is to do with mapping that coordinate field into one 
> that I understand (within Firedrake). You may not have this problem.
> 
> Firedrake uses its own coordinate mapping and integration routines, so they 
> must manage the second part independently. I hope to get change this slightly 
> soon by making the Firedrake representation a DMField, so that it looks the 
> same to Plex.
> 
>   Thanks,
> 
> Matt
>  
> Thanks,
> 
> Lawrence
> 
> 
> -- 
> 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
> 
> https://www.cse.buffalo.edu/~knepley/ 
> To read periodic meshes from GMSH, you need to use the option 
> -dm_plex_gmsh_periodic and DMPlexCreateFromFile

Ahh, thanks. I was missing the option " -dm_plex_gmsh_periodic “. But using 
this option I now generate a segmentation fault error when calling VecView() on 
the solution vector with vtk and hdf5 viewers. Any suggestions?

 
> 
> See  src/dm/impls/plex/examples/tests/ex1.c. An example runs
> 
> $ ./ex1 -filename 
> ${PETSC_DIR}/share/petsc/datafiles/meshes/cube_periodic_bin.msh 
> -dm_plex_gmsh_periodic -dm_view ::ascii_info_detail -interpolate -test_shape
> 
> generating periodic meshes in gmsh may be tricky, Lisandro for sure may 
> advice.

Thanks,
Max

Re: [petsc-users] Periodic BC in petsc DMPlex / firedrake

[Stefano Zampini]

To read periodic meshes from GMSH, you need to use the option
-dm_plex_gmsh_periodic and DMPlexCreateFromFile
See  src/dm/impls/plex/examples/tests/ex1.c. An example runs

$ ./ex1 -filename
${PETSC_DIR}/share/petsc/datafiles/meshes/cube_periodic_bin.msh
-dm_plex_gmsh_periodic -dm_view ::ascii_info_detail -interpolate -test_shape

generating periodic meshes in gmsh may be tricky, Lisandro for sure may
advice.

Il giorno mer 24 ott 2018 alle ore 13:51 Matthew Knepley 
ha scritto:

> On Wed, Oct 24, 2018 at 6:29 AM Lawrence Mitchell  wrote:
>
>> Hi Max,
>>
>> (I'm cc'ing in the petsc-users mailing list which may have more advice,
>> if you are using PETSc you should definitely subscribe!
>>
>> > On 24 Oct 2018, at 09:27, Maximilian Hartig 
>> wrote:
>> >
>> > Hello Lawrence,
>> >
>> > sorry to message you out of the blue. My name is Max and I found your
>> post on GitHub (https://github.com/firedrakeproject/firedrake/issues/1246
>> ) on DMPlex being able to read periodic gmsh files. I am currently trying
>> to do just that (creating a periodic DMPlex mesh with gmsh) in the context
>> of my PhD work. So far I haven’ t found any documentation on the periodic
>> BC’s with DMPlex and gmsh in the official petsc documentation.
>> > I was wondering whether you’d be so kind as to point me in a general
>> direction concerning how to achieve this. You seem experienced in using
>> petsc and I would greatly appreciate your help.
>>
>>
>> I think the answer is "it depends". If you're just using DMPlex directly
>> and all the of the functionality with PetscDS, then I /think/ that reading
>> periodic meshes via gmsh (assuming you're using the appropriate gmsh mesh
>> format [v2]) "just works".
>>
>
> There are two phases here: topological and geometric. DMPlex represents
> the periodic topological entity directly. For example,  a circle is just a
> segment with one end hooked to the other. Vertices are not duplicated, or
> mapped to each other. This makes topology simple and easy to implement.
> However, then geometry is more complicated. What Plex does is allow
> coordinates to be represented by a discontinuous field taking values on
> cells, in addition to vertices. In our circle example, each cells near the
> cut will have 2 coordinates, one for each vertex, but they will not agree
> across the cut. If you define a periodic domain, then Plex can construct
> this coordinate field automatically using DMPlexLocalize(). These DG
> coordinates are then used by the integration routines.
>
>
>> From my side, the issue is to do with mapping that coordinate field into
>> one that I understand (within Firedrake). You may not have this problem.
>>
>
> Firedrake uses its own coordinate mapping and integration routines, so
> they must manage the second part independently. I hope to get change this
> slightly soon by making the Firedrake representation a DMField, so that it
> looks the same to Plex.
>
>   Thanks,
>
> Matt
>
>
>> Thanks,
>>
>> Lawrence
>
>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/
> 
>


-- 
Stefano

Re: [petsc-users] Periodic BC in petsc DMPlex / firedrake

[Matthew Knepley]

On Wed, Oct 24, 2018 at 6:29 AM Lawrence Mitchell  wrote:

> Hi Max,
>
> (I'm cc'ing in the petsc-users mailing list which may have more advice, if
> you are using PETSc you should definitely subscribe!
>
> > On 24 Oct 2018, at 09:27, Maximilian Hartig 
> wrote:
> >
> > Hello Lawrence,
> >
> > sorry to message you out of the blue. My name is Max and I found your
> post on GitHub (https://github.com/firedrakeproject/firedrake/issues/1246
> ) on DMPlex being able to read periodic gmsh files. I am currently trying
> to do just that (creating a periodic DMPlex mesh with gmsh) in the context
> of my PhD work. So far I haven’ t found any documentation on the periodic
> BC’s with DMPlex and gmsh in the official petsc documentation.
> > I was wondering whether you’d be so kind as to point me in a general
> direction concerning how to achieve this. You seem experienced in using
> petsc and I would greatly appreciate your help.
>
>
> I think the answer is "it depends". If you're just using DMPlex directly
> and all the of the functionality with PetscDS, then I /think/ that reading
> periodic meshes via gmsh (assuming you're using the appropriate gmsh mesh
> format [v2]) "just works".
>

There are two phases here: topological and geometric. DMPlex represents the
periodic topological entity directly. For example,  a circle is just a
segment with one end hooked to the other. Vertices are not duplicated, or
mapped to each other. This makes topology simple and easy to implement.
However, then geometry is more complicated. What Plex does is allow
coordinates to be represented by a discontinuous field taking values on
cells, in addition to vertices. In our circle example, each cells near the
cut will have 2 coordinates, one for each vertex, but they will not agree
across the cut. If you define a periodic domain, then Plex can construct
this coordinate field automatically using DMPlexLocalize(). These DG
coordinates are then used by the integration routines.


> From my side, the issue is to do with mapping that coordinate field into
> one that I understand (within Firedrake). You may not have this problem.
>

Firedrake uses its own coordinate mapping and integration routines, so they
must manage the second part independently. I hope to get change this
slightly soon by making the Firedrake representation a DMField, so that it
looks the same to Plex.

  Thanks,

Matt


> Thanks,
>
> Lawrence



-- 
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

https://www.cse.buffalo.edu/~knepley/ 

Re: [petsc-users] Periodic BC in petsc DMPlex / firedrake

[Lawrence Mitchell]

Hi Max,

(I'm cc'ing in the petsc-users mailing list which may have more advice, if you 
are using PETSc you should definitely subscribe!

> On 24 Oct 2018, at 09:27, Maximilian Hartig  wrote:
> 
> Hello Lawrence,
> 
> sorry to message you out of the blue. My name is Max and I found your post on 
> GitHub (https://github.com/firedrakeproject/firedrake/issues/1246 ) on DMPlex 
> being able to read periodic gmsh files. I am currently trying to do just that 
> (creating a periodic DMPlex mesh with gmsh) in the context of my PhD work. So 
> far I haven’ t found any documentation on the periodic BC’s with DMPlex and 
> gmsh in the official petsc documentation. 
> I was wondering whether you’d be so kind as to point me in a general 
> direction concerning how to achieve this. You seem experienced in using petsc 
> and I would greatly appreciate your help. 


I think the answer is "it depends". If you're just using DMPlex directly and 
all the of the functionality with PetscDS, then I /think/ that reading periodic 
meshes via gmsh (assuming you're using the appropriate gmsh mesh format [v2]) 
"just works".

From my side, the issue is to do with mapping that coordinate field into one 
that I understand (within Firedrake). You may not have this problem.

Thanks,

Lawrence