[petsc-users] How to find the map between the high order coordinates of DMPlex and vertex numbering?
Zongze Yang
yangzongze at gmail.com
Mon May 15 08:54:55 CDT 2023
On Mon, 15 May 2023 at 17:24, Matthew Knepley <knepley at gmail.com> wrote:
> On Sun, May 14, 2023 at 7:23 PM Zongze Yang <yangzongze at gmail.com> wrote:
>
>> Could you try to project the coordinates into the continuity space by
>> enabling the option
>> `-dm_plex_gmsh_project_petscdualspace_lagrange_continuity true`?
>>
>
> There is a comment in the code about that:
>
> /* XXX FIXME Requires DMPlexSetClosurePermutationLexicographic() */
>
> So what is currently done is you project into the discontinuous space from
> the GMsh coordinates,
> and then we get the continuous coordinates from those later. This is why
> we get the right answer.
>
>
Sorry, I'm having difficulty understanding the comment and fully
understanding your intended meaning. Are you saying that we can only
project the space to a discontinuous space?
Additionally, should we always set
`dm_plex_gmsh_project_petscdualspace_lagrange_continuity` to false for
high-order gmsh files?
With the option set to `true`, I got the following error:
```
$ $PETSC_DIR/$PETSC_ARCH/tests/dm/impls/plex/tests/runex33_gmsh_3d_q2.sh -e
"-dm_plex_gmsh_project_petscdualspace_lagrange_continuity true"
not ok dm_impls_plex_tests-ex33_gmsh_3d_q2 # Error code: 77
# Volume: 0.46875
# [0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
# [0]PETSC ERROR: Petsc has generated inconsistent data
# [0]PETSC ERROR: Calculated volume 0.46875 != 1. actual volume
(error 0.53125 > 1e-06 tol)
# [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
shooting.
# [0]PETSC ERROR: Petsc Development GIT revision:
v3.19.1-294-g9cc24bc9b93 GIT Date: 2023-05-15 12:07:10 +0000
# [0]PETSC ERROR: ../ex33 on a arch-linux-c-debug named AMA-PC-RA18
by yzz Mon May 15 21:53:43 2023
# [0]PETSC ERROR: Configure options
--CFLAGS=-I/opt/intel/oneapi/mkl/latest/include
--CXXFLAGS=-I/opt/intel/oneapi/mkl/latest/include
--LDFLAGS="-Wl,-rpath,/opt/intel/oneapi/mkl/latest/lib/intel64
-L/opt/intel/oneapi/mkl/latest/lib/intel64" --download-bison
--download-chaco --download-cmake
--download-eigen="/home/yzz/firedrake/complex-int32-mkl-X-debug/src/eigen-3.3.3.tgz
" --download-fftw --download-hdf5 --download-hpddm --download-hwloc
--download-libpng --download-metis --download-mmg --download-mpich
--download-mumps --download-netcdf --download-p4est --download-parmmg
--download-pastix --download-pnetcdf --download-ptscotch
--download-scalapack --download-slepc --download-suitesparse
--download-superlu_dist --download-tetgen --download-triangle
--with-blaslapack-dir=/opt/intel/oneapi/mkl/latest --with-c2html=0
--with-debugging=1 --with-fortran-bindings=0
--with-mkl_cpardiso-dir=/opt/intel/oneapi/mkl/latest
--with-mkl_pardiso-dir=/opt/intel/oneapi/mkl/latest
--with-scalar-type=complex --with-shared-libraries=1 --with-x=1 --with-zlib
PETSC_ARCH=arch-linux-c-debug
# [0]PETSC ERROR: #1 CheckVolume() at
/home/yzz/opt/petsc/src/dm/impls/plex/tests/ex33.c:246
# [0]PETSC ERROR: #2 main() at
/home/yzz/opt/petsc/src/dm/impls/plex/tests/ex33.c:261
# [0]PETSC ERROR: PETSc Option Table entries:
# [0]PETSC ERROR: -coord_space 0 (source: command line)
# [0]PETSC ERROR: -dm_plex_filename
/home/yzz/opt/petsc/share/petsc/datafiles/meshes/cube_q2.msh (source:
command line)
# [0]PETSC ERROR: -dm_plex_gmsh_project (source: command line)
# [0]PETSC ERROR:
-dm_plex_gmsh_project_petscdualspace_lagrange_continuity true (source:
command line)
# [0]PETSC ERROR: -tol 1e-6 (source: command line)
# [0]PETSC ERROR: -volume 1.0 (source: command line)
# [0]PETSC ERROR: ----------------End of Error Message -------send
entire error message to petsc-maint at mcs.anl.gov----------
# application called MPI_Abort(MPI_COMM_SELF, 77) - process 0
ok dm_impls_plex_tests-ex33_gmsh_3d_q2 # SKIP Command failed so no diff
```
Best wishes,
Zongze
Thanks,
>
> Matt
>
>
>> Best wishes,
>> Zongze
>>
>>
>> On Mon, 15 May 2023 at 04:24, Matthew Knepley <knepley at gmail.com> wrote:
>>
>>> On Sun, May 14, 2023 at 12:27 PM Zongze Yang <yangzongze at gmail.com>
>>> wrote:
>>>
>>>>
>>>>
>>>>
>>>> On Sun, 14 May 2023 at 23:54, Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Sun, May 14, 2023 at 9:21 AM Zongze Yang <yangzongze at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi, Matt,
>>>>>>
>>>>>> The issue has been resolved while testing on the latest version of
>>>>>> PETSc. It seems that the problem has been fixed in the following merge
>>>>>> request: https://gitlab.com/petsc/petsc/-/merge_requests/5970
>>>>>>
>>>>>
>>>>> No problem. Glad it is working.
>>>>>
>>>>>
>>>>>> I sincerely apologize for any inconvenience caused by my previous
>>>>>> message. However, I would like to provide you with additional information
>>>>>> regarding the test files. Attached to this email, you will find two Gmsh
>>>>>> files: "square_2rd.msh" and "square_3rd.msh." These files contain
>>>>>> high-order triangulated mesh data for the unit square.
>>>>>>
>>>>>> ```
>>>>>> $ ./ex33 -coord_space 0 -dm_plex_filename square_2rd.msh
>>>>>> -dm_plex_gmsh_project
>>>>>> -dm_plex_gmsh_project_petscdualspace_lagrange_continuity true
>>>>>> -dm_plex_gmsh_project_fe_view -volume 1
>>>>>> PetscFE Object: P2 1 MPI process
>>>>>> type: basic
>>>>>> Basic Finite Element in 2 dimensions with 2 components
>>>>>> PetscSpace Object: P2 1 MPI process
>>>>>> type: sum
>>>>>> Space in 2 variables with 2 components, size 12
>>>>>> Sum space of 2 concatenated subspaces (all identical)
>>>>>> PetscSpace Object: sum component (sumcomp_) 1 MPI process
>>>>>> type: poly
>>>>>> Space in 2 variables with 1 components, size 6
>>>>>> Polynomial space of degree 2
>>>>>> PetscDualSpace Object: P2 1 MPI process
>>>>>> type: lagrange
>>>>>> Dual space with 2 components, size 12
>>>>>> Continuous Lagrange dual space
>>>>>> Quadrature on a triangle of order 5 on 9 points (dim 2)
>>>>>> Volume: 1.
>>>>>> $ ./ex33 -coord_space 0 -dm_plex_filename square_3rd.msh
>>>>>> -dm_plex_gmsh_project
>>>>>> -dm_plex_gmsh_project_petscdualspace_lagrange_continuity true
>>>>>> -dm_plex_gmsh_project_fe_view -volume 1
>>>>>> PetscFE Object: P3 1 MPI process
>>>>>> type: basic
>>>>>> Basic Finite Element in 2 dimensions with 2 components
>>>>>> PetscSpace Object: P3 1 MPI process
>>>>>> type: sum
>>>>>> Space in 2 variables with 2 components, size 20
>>>>>> Sum space of 2 concatenated subspaces (all identical)
>>>>>> PetscSpace Object: sum component (sumcomp_) 1 MPI process
>>>>>> type: poly
>>>>>> Space in 2 variables with 1 components, size 10
>>>>>> Polynomial space of degree 3
>>>>>> PetscDualSpace Object: P3 1 MPI process
>>>>>> type: lagrange
>>>>>> Dual space with 2 components, size 20
>>>>>> Continuous Lagrange dual space
>>>>>> Quadrature on a triangle of order 7 on 16 points (dim 2)
>>>>>> Volume: 1.
>>>>>> ```
>>>>>>
>>>>>> Thank you for your attention and understanding. I apologize once
>>>>>> again for my previous oversight.
>>>>>>
>>>>>
>>>>> Great! If you make an MR for this, you will be included on the next
>>>>> list of PETSc contributors. Otherwise, I can do it.
>>>>>
>>>>>
>>>> I appreciate your offer to handle the MR. Please go ahead and take care
>>>> of it. Thank you!
>>>>
>>>
>>> I have created the MR with your tests. They are working for me:
>>>
>>> https://gitlab.com/petsc/petsc/-/merge_requests/6463
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> Best Wishes,
>>>> Zongze
>>>>
>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> Best wishes,
>>>>>> Zongze
>>>>>>
>>>>>>
>>>>>> On Sun, 14 May 2023 at 16:44, Matthew Knepley <knepley at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> On Sat, May 13, 2023 at 6:08 AM Zongze Yang <yangzongze at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi, Matt,
>>>>>>>>
>>>>>>>> There seem to be ongoing issues with projecting high-order
>>>>>>>> coordinates from a gmsh file to other spaces. I would like to inquire
>>>>>>>> whether there are any plans to resolve this problem.
>>>>>>>>
>>>>>>>> Thank you for your attention to this matter.
>>>>>>>>
>>>>>>>
>>>>>>> Yes, I will look at it. The important thing is to have a good test.
>>>>>>> Here are the higher order geometry tests
>>>>>>>
>>>>>>>
>>>>>>> https://gitlab.com/petsc/petsc/-/blob/main/src/dm/impls/plex/tests/ex33.c
>>>>>>>
>>>>>>> I take shapes with known volume, mesh them with higher order
>>>>>>> geometry, and look at the convergence to the true volume. Could you add a
>>>>>>> GMsh test, meaning the .msh file and known volume, and I will fix it?
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Matt
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>> Best wishes,
>>>>>>>> Zongze
>>>>>>>>
>>>>>>>>
>>>>>>>> On Sat, 18 Jun 2022 at 20:31, Zongze Yang <yangzongze at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Thank you for your reply. May I ask for some references on the
>>>>>>>>> order of the dofs on PETSc's FE Space (especially high order elements)?
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Zongze
>>>>>>>>>
>>>>>>>>> Matthew Knepley <knepley at gmail.com> 于2022年6月18日周六 20:02写道：
>>>>>>>>>
>>>>>>>>>> On Sat, Jun 18, 2022 at 2:16 AM Zongze Yang <yangzongze at gmail.com>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> In order to check if I made mistakes in the python code, I try
>>>>>>>>>>> to use c code to show the issue on DMProjectCoordinates. The code and mesh
>>>>>>>>>>> file is attached.
>>>>>>>>>>> If the code is correct, there must be something wrong with
>>>>>>>>>>> `DMProjectCoordinates` or `DMPlexCreateGmshFromFile` for high-order mesh.
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Something is definitely wrong with high order, periodic simplices
>>>>>>>>>> from Gmsh. We had not tested that case. I am at a conference and cannot
>>>>>>>>>> look at it for a week.
>>>>>>>>>> My suspicion is that the space we make when reading in the Gmsh
>>>>>>>>>> coordinates does not match the values (wrong order).
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Matt
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> The command and the output are listed below: (Obviously the
>>>>>>>>>>> bounding box is changed.)
>>>>>>>>>>> ```
>>>>>>>>>>> $ ./test_gmsh_load_2rd -filename cube-p2.msh -old_fe_view
>>>>>>>>>>> -new_fe_view
>>>>>>>>>>> Old Bounding Box:
>>>>>>>>>>> 0: lo = 0. hi = 1.
>>>>>>>>>>> 1: lo = 0. hi = 1.
>>>>>>>>>>> 2: lo = 0. hi = 1.
>>>>>>>>>>> PetscFE Object: OldCoordinatesFE 1 MPI processes
>>>>>>>>>>> type: basic
>>>>>>>>>>> Basic Finite Element in 3 dimensions with 3 components
>>>>>>>>>>> PetscSpace Object: P2 1 MPI processes
>>>>>>>>>>> type: sum
>>>>>>>>>>> Space in 3 variables with 3 components, size 30
>>>>>>>>>>> Sum space of 3 concatenated subspaces (all identical)
>>>>>>>>>>> PetscSpace Object: sum component (sumcomp_) 1 MPI processes
>>>>>>>>>>> type: poly
>>>>>>>>>>> Space in 3 variables with 1 components, size 10
>>>>>>>>>>> Polynomial space of degree 2
>>>>>>>>>>> PetscDualSpace Object: P2 1 MPI processes
>>>>>>>>>>> type: lagrange
>>>>>>>>>>> Dual space with 3 components, size 30
>>>>>>>>>>> Discontinuous Lagrange dual space
>>>>>>>>>>> Quadrature of order 5 on 27 points (dim 3)
>>>>>>>>>>> PetscFE Object: NewCoordinatesFE 1 MPI processes
>>>>>>>>>>> type: basic
>>>>>>>>>>> Basic Finite Element in 3 dimensions with 3 components
>>>>>>>>>>> PetscSpace Object: P2 1 MPI processes
>>>>>>>>>>> type: sum
>>>>>>>>>>> Space in 3 variables with 3 components, size 30
>>>>>>>>>>> Sum space of 3 concatenated subspaces (all identical)
>>>>>>>>>>> PetscSpace Object: sum component (sumcomp_) 1 MPI processes
>>>>>>>>>>> type: poly
>>>>>>>>>>> Space in 3 variables with 1 components, size 10
>>>>>>>>>>> Polynomial space of degree 2
>>>>>>>>>>> PetscDualSpace Object: P2 1 MPI processes
>>>>>>>>>>> type: lagrange
>>>>>>>>>>> Dual space with 3 components, size 30
>>>>>>>>>>> Continuous Lagrange dual space
>>>>>>>>>>> Quadrature of order 5 on 27 points (dim 3)
>>>>>>>>>>> New Bounding Box:
>>>>>>>>>>> 0: lo = 2.5624e-17 hi = 8.
>>>>>>>>>>> 1: lo = -9.23372e-17 hi = 7.
>>>>>>>>>>> 2: lo = 2.72091e-17 hi = 8.5
>>>>>>>>>>> ```
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Zongze
>>>>>>>>>>>
>>>>>>>>>>> Zongze Yang <yangzongze at gmail.com> 于2022年6月17日周五 14:54写道：
>>>>>>>>>>>
>>>>>>>>>>>> I tried the projection operation. However, it seems that the
>>>>>>>>>>>> projection gives the wrong solution. After projection, the bounding box is
>>>>>>>>>>>> changed! See logs below.
>>>>>>>>>>>>
>>>>>>>>>>>> First, I patch the petsc4py by adding `DMProjectCoordinates`:
>>>>>>>>>>>> ```
>>>>>>>>>>>> diff --git a/src/binding/petsc4py/src/PETSc/DM.pyx
>>>>>>>>>>>> b/src/binding/petsc4py/src/PETSc/DM.pyx
>>>>>>>>>>>> index d8a58d183a..dbcdb280f1 100644
>>>>>>>>>>>> --- a/src/binding/petsc4py/src/PETSc/DM.pyx
>>>>>>>>>>>> +++ b/src/binding/petsc4py/src/PETSc/DM.pyx
>>>>>>>>>>>> @@ -307,6 +307,12 @@ cdef class DM(Object):
>>>>>>>>>>>> PetscINCREF(c.obj)
>>>>>>>>>>>> return c
>>>>>>>>>>>>
>>>>>>>>>>>> + def projectCoordinates(self, FE fe=None):
>>>>>>>>>>>> + if fe is None:
>>>>>>>>>>>> + CHKERR( DMProjectCoordinates(self.dm, NULL) )
>>>>>>>>>>>> + else:
>>>>>>>>>>>> + CHKERR( DMProjectCoordinates(self.dm, fe.fe) )
>>>>>>>>>>>> +
>>>>>>>>>>>> def getBoundingBox(self):
>>>>>>>>>>>> cdef PetscInt i,dim=0
>>>>>>>>>>>> CHKERR( DMGetCoordinateDim(self.dm, &dim) )
>>>>>>>>>>>> diff --git a/src/binding/petsc4py/src/PETSc/petscdm.pxi
>>>>>>>>>>>> b/src/binding/petsc4py/src/PETSc/petscdm.pxi
>>>>>>>>>>>> index 514b6fa472..c778e39884 100644
>>>>>>>>>>>> --- a/src/binding/petsc4py/src/PETSc/petscdm.pxi
>>>>>>>>>>>> +++ b/src/binding/petsc4py/src/PETSc/petscdm.pxi
>>>>>>>>>>>> @@ -90,6 +90,7 @@ cdef extern from * nogil:
>>>>>>>>>>>> int DMGetCoordinateDim(PetscDM,PetscInt*)
>>>>>>>>>>>> int DMSetCoordinateDim(PetscDM,PetscInt)
>>>>>>>>>>>> int DMLocalizeCoordinates(PetscDM)
>>>>>>>>>>>> + int DMProjectCoordinates(PetscDM, PetscFE)
>>>>>>>>>>>>
>>>>>>>>>>>> int
>>>>>>>>>>>> DMCreateInterpolation(PetscDM,PetscDM,PetscMat*,PetscVec*)
>>>>>>>>>>>> int DMCreateInjection(PetscDM,PetscDM,PetscMat*)
>>>>>>>>>>>> ```
>>>>>>>>>>>>
>>>>>>>>>>>> Then in python, I load a mesh and project the coordinates to P2:
>>>>>>>>>>>> ```
>>>>>>>>>>>> import firedrake as fd
>>>>>>>>>>>> from firedrake.petsc import PETSc
>>>>>>>>>>>>
>>>>>>>>>>>> # plex = fd.mesh._from_gmsh('test-fd-load-p2.msh')
>>>>>>>>>>>> plex = fd.mesh._from_gmsh('test-fd-load-p2-rect.msh')
>>>>>>>>>>>> print('old bbox:', plex.getBoundingBox())
>>>>>>>>>>>>
>>>>>>>>>>>> dim = plex.getDimension()
>>>>>>>>>>>> # (dim, nc, isSimplex, k,
>>>>>>>>>>>> qorder, comm=None)
>>>>>>>>>>>> fe_new = PETSc.FE().createLagrange(dim, dim, True, 2,
>>>>>>>>>>>> PETSc.DETERMINE)
>>>>>>>>>>>> plex.projectCoordinates(fe_new)
>>>>>>>>>>>> fe_new.view()
>>>>>>>>>>>>
>>>>>>>>>>>> print('new bbox:', plex.getBoundingBox())
>>>>>>>>>>>> ```
>>>>>>>>>>>>
>>>>>>>>>>>> The output is (The bounding box is changed!)
>>>>>>>>>>>> ```
>>>>>>>>>>>>
>>>>>>>>>>>> old bbox: ((0.0, 1.0), (0.0, 1.0), (0.0, 1.0))
>>>>>>>>>>>> PetscFE Object: P2 1 MPI processes
>>>>>>>>>>>> type: basic
>>>>>>>>>>>> Basic Finite Element in 3 dimensions with 3 components
>>>>>>>>>>>> PetscSpace Object: P2 1 MPI processes
>>>>>>>>>>>> type: sum
>>>>>>>>>>>> Space in 3 variables with 3 components, size 30
>>>>>>>>>>>> Sum space of 3 concatenated subspaces (all identical)
>>>>>>>>>>>> PetscSpace Object: sum component (sumcomp_) 1 MPI processes
>>>>>>>>>>>> type: poly
>>>>>>>>>>>> Space in 3 variables with 1 components, size 10
>>>>>>>>>>>> Polynomial space of degree 2
>>>>>>>>>>>> PetscDualSpace Object: P2 1 MPI processes
>>>>>>>>>>>> type: lagrange
>>>>>>>>>>>> Dual space with 3 components, size 30
>>>>>>>>>>>> Continuous Lagrange dual space
>>>>>>>>>>>> Quadrature of order 5 on 27 points (dim 3)
>>>>>>>>>>>> new bbox: ((-6.530133708576188e-17, 36.30670832662781), (-3.899962995254311e-17, 36.2406171632539), (-8.8036464152166e-17, 36.111577025012224))
>>>>>>>>>>>>
>>>>>>>>>>>> ```
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> By the way, for the original DG coordinates, where can I find the relation of the closure and the order of the dofs for the cell?
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Zongze
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Matthew Knepley <knepley at gmail.com> 于2022年6月17日周五 01:11写道：
>>>>>>>>>>>>
>>>>>>>>>>>>> On Thu, Jun 16, 2022 at 12:06 PM Zongze Yang <
>>>>>>>>>>>>> yangzongze at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 在 2022年6月16日，23:22，Matthew Knepley <knepley at gmail.com> 写道：
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Thu, Jun 16, 2022 at 11:11 AM Zongze Yang <
>>>>>>>>>>>>>> yangzongze at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi, if I load a `gmsh` file with second-order elements, the
>>>>>>>>>>>>>>> coordinates will be stored in a DG-P2 space. After obtaining the
>>>>>>>>>>>>>>> coordinates of a cell, how can I map the coordinates to vertex and edge?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> By default, they are stored as P2, not DG.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I checked the coordinates vector, and found the dogs only
>>>>>>>>>>>>>> defined on cell other than vertex and edge, so I said they are stored as DG.
>>>>>>>>>>>>>> Then the function DMPlexVecGetClosure
>>>>>>>>>>>>>> <https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexVecGetClosure/> seems return
>>>>>>>>>>>>>> the coordinates in lex order.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Some code in reading gmsh file reads that
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 1756: if (isSimplex) continuity = PETSC_FALSE
>>>>>>>>>>>>>> <https://petsc.org/main/docs/manualpages/Sys/PETSC_FALSE/>;
>>>>>>>>>>>>>> /* XXX FIXME Requires DMPlexSetClosurePermutationLexicographic() */
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 1758: GmshCreateFE(comm, NULL, isSimplex, continuity,
>>>>>>>>>>>>>> nodeType, dim, coordDim, order, &fe)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The continuity is set to false for simplex.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Oh, yes. That needs to be fixed. For now, you can just project
>>>>>>>>>>>>> it to P2 if you want using
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> https://petsc.org/main/docs/manualpages/DM/DMProjectCoordinates/
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>> Zongze
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> You can ask for the coordinates of a vertex or an edge
>>>>>>>>>>>>>> directly using
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexPointLocalRead/
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> by giving the vertex or edge point. You can get all the
>>>>>>>>>>>>>> coordinates on a cell, in the closure order, using
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexVecGetClosure/
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Below is some code load the gmsh file, I want to know the
>>>>>>>>>>>>>>> relation between `cl` and `cell_coords`.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ```
>>>>>>>>>>>>>>> import firedrake as fd
>>>>>>>>>>>>>>> import numpy as np
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> # Load gmsh file (2rd)
>>>>>>>>>>>>>>> plex = fd.mesh._from_gmsh('test-fd-load-p2-rect.msh')
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> cs, ce = plex.getHeightStratum(0)
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> cdm = plex.getCoordinateDM()
>>>>>>>>>>>>>>> csec = dm.getCoordinateSection()
>>>>>>>>>>>>>>> coords_gvec = dm.getCoordinates()
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> for i in range(cs, ce):
>>>>>>>>>>>>>>> cell_coords = cdm.getVecClosure(csec, coords_gvec, i)
>>>>>>>>>>>>>>> print(f'coordinates for cell {i}
>>>>>>>>>>>>>>> :\n{cell_coords.reshape([-1, 3])}')
>>>>>>>>>>>>>>> cl = dm.getTransitiveClosure(i)
>>>>>>>>>>>>>>> print('closure:', cl)
>>>>>>>>>>>>>>> break
>>>>>>>>>>>>>>> ```
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Best wishes,
>>>>>>>>>>>>>>> Zongze
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> 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/
>>>>>>>>>>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> 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/
>>>>>>>>>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> 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/
>>>>>>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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/
>>>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> 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/
>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>
>>>>
>>>
>>> --
>>> 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/
>>> <http://www.cse.buffalo.edu/~knepley/>
>>>
>>
>
> --
> 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/
> <http://www.cse.buffalo.edu/~knepley/>
>
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