[petsc-users] How to find the map between the high order coordinates of DMPlex and vertex numbering?
Zongze Yang
yangzongze at gmail.com
Sat May 13 05:08:23 CDT 2023
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.
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/>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20230513/7f7bbe77/attachment-0001.html>
More information about the petsc-users
mailing list