Re: [petsc-users] Gmsh 8-noded quadrilateral
Sounds good. Note that if you use direct solvers, that extra node is basically
free because the vertex separators are unchanged. It's a marginal cost in the
storage of assembled matrices and the length of state vectors. And in 3D, even
less significant.
Susanne Claus writes:
> Dear Matthew and Jed,
>
> Brilliant. Thank you so much!
>
> Your changes work like a charm Matthew (I tested your branch on the gmsh
> file I sent) and thank you so much for your advice Jed. The loss of one
> order of convergence for an inf-sup stable pressure discretization seems
> indeed a very high price to pay for the moderate increase in efficiency
> by elimination of the interior modes. You have given me food for thought
> and I will probably personally not use 8-node quadrilaterals.
> Nevertheless, for our code it will be important to support 8-node
> quadrilaterals as it is still an element widely used in solid mechanics
> simulations. LibCEED looks very interesting.
>
> Thank you so much again.
>
> Best wishes from Paris,
> Susanne
>
> On 11.02.2022 20:27, Matthew Knepley wrote:
>
>> Jed is right about the numerics. However, this does not look hard. Here
>> is my try at it:
>>
>> https://gitlab.com/petsc/petsc/-/merge_requests/4838
>>
>> Please tell me if this works and I will make a test and merge.
>>
>> Thanks,
>>
>> Matt
>>
>> On Thu, Feb 10, 2022 at 6:47 PM Jed Brown wrote:
>>
>>> Susanne, do you want PetscFE to make the serendipity (8-node) finite
>>> element space or do you just want to read these meshes? I.e., would it
>>> be okay with you if the coordinates were placed in a Q_2 (9-node,
>>> biquadratic) finite element space?
>>>
>>> This won't matter if you're traversing the dofs per edge manually, but
>>> there are some efficiency benefits of using the Q_2 space (especially
>>> if your code can use the tensor product, perhaps via a library like
>>> libCEED). Note that Q_2 spaces have better stability properties. For
>>> example, the Q_2 space is inf-sup stable with P_1 discontinuous
>>> pressure (gives third order L^2 and second order H^1 convergence), but
>>> serendipity (8-node) is only stable with piecewise constant pressure
>>> (gives second order L^2 and first order H^1 convergence).
>>>
>>> Susanne Claus writes:
>>>
Dear Matthew,
Thank you so much.
I have a attached a small 8-noded quadrilateral mesh file (Version 4
ASCII) generated with gmsh 4.8.4.
Best wishes,
Susanne
On 10.02.2022 16:23, Matthew Knepley wrote:
> On Thu, Feb 10, 2022 at 10:12 AM Susanne Claus
>
> wrote:
>
>> Hello,
>>
>> I am using DMPlex for the mesh structure of a solid mechanics
>> finite
>> element code. I mainly use gmsh as input file format. When I try to
>> read in 8-noded Quadrilaterals (Element type 16 in gmsh) DMPlex
>> tells
>> me that this element type is unknown. However a 9-noded
>> Quadrilateral
>> can be read without problem. On inspecting the plexgmsh.c source
>> code
>> I can see that 8-noded quadrilaterals are deactivated:
>>
>> #if 0
>> 146: {20, GMSH_TRI, 2, 3, 3, 9, NULL},
>> 147: {16, GMSH_QUA, 2, 2, 4, 8, NULL},
>>
>> For our application these 8-noded quadrilateral are very important.
>>
>> Is there any reason why they have not been implemented/deactivated
>> in
>> the dmplex gmsh reader?
>
> No, we can handle them in the same way I think. Let me look at it.
> Hopefully it is easy.
>
> Thanks,
>
> Matt
>
>> Thank you for all the great work you are doing. PETSc is amazing.
>>
>> Best wishes,
>> Susanne Claus
>
> --
>
> 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/ [1]
--
Susanne Claus
Ingénieur Chercheur
Applied Mathematics and Scientific Computing Group
DTIS
ONERA - The French Aerospace Lab
6 Chemin de la Vauve aux Granges, 91120 Palaiseau
Links:
--
[1] http://www.cse.buffalo.edu/~knepley/
$MeshFormat
4.1 0 8
$EndMeshFormat
$PhysicalNames
2
1 2 "Neumann"
2 1 "Domain"
$EndPhysicalNames
$Entities
4 4 1 0
1 0 0 0 0
2 1 0 0 0
3 1 1 0 0
4 0 1 0 0
1 -9.4736442e-08 -1e-07 -1e-07 1.001 1e-07 1e-07 0 2 1 -2
2 0.9991 -9.4736442e-08 -1e-07 1.001
1.001 1e-07 1 2 2 2 -3
3 -9.4736442e-08 0.9991 -1e-07 1.001
1.001 1e-07 0 2 3 -4
4 -1e-07 -9.4736442e-08 -1e-07 1e-07 1.001 1e-07 0 2 4 -1
1 -9.4736442e-08 -9.4736442e-08 -1e-07 1.001
1.001 1e-07 1 1 4 1 2 3 4
Re: [petsc-users] Gmsh 8-noded quadrilateral
Dear Matthew and Jed,
Brilliant. Thank you so much!
Your changes work like a charm Matthew (I tested your branch on the gmsh
file I sent) and thank you so much for your advice Jed. The loss of one
order of convergence for an inf-sup stable pressure discretization seems
indeed a very high price to pay for the moderate increase in efficiency
by elimination of the interior modes. You have given me food for thought
and I will probably personally not use 8-node quadrilaterals.
Nevertheless, for our code it will be important to support 8-node
quadrilaterals as it is still an element widely used in solid mechanics
simulations. LibCEED looks very interesting.
Thank you so much again.
Best wishes from Paris,
Susanne
On 11.02.2022 20:27, Matthew Knepley wrote:
Jed is right about the numerics. However, this does not look hard. Here
is my try at it:
https://gitlab.com/petsc/petsc/-/merge_requests/4838
Please tell me if this works and I will make a test and merge.
Thanks,
Matt
On Thu, Feb 10, 2022 at 6:47 PM Jed Brown wrote:
Susanne, do you want PetscFE to make the serendipity (8-node) finite
element space or do you just want to read these meshes? I.e., would it
be okay with you if the coordinates were placed in a Q_2 (9-node,
biquadratic) finite element space?
This won't matter if you're traversing the dofs per edge manually, but
there are some efficiency benefits of using the Q_2 space (especially
if your code can use the tensor product, perhaps via a library like
libCEED). Note that Q_2 spaces have better stability properties. For
example, the Q_2 space is inf-sup stable with P_1 discontinuous
pressure (gives third order L^2 and second order H^1 convergence), but
serendipity (8-node) is only stable with piecewise constant pressure
(gives second order L^2 and first order H^1 convergence).
Susanne Claus writes:
Dear Matthew,
Thank you so much.
I have a attached a small 8-noded quadrilateral mesh file (Version 4
ASCII) generated with gmsh 4.8.4.
Best wishes,
Susanne
On 10.02.2022 16:23, Matthew Knepley wrote:
On Thu, Feb 10, 2022 at 10:12 AM Susanne Claus
wrote:
Hello,
I am using DMPlex for the mesh structure of a solid mechanics
finite
element code. I mainly use gmsh as input file format. When I try to
read in 8-noded Quadrilaterals (Element type 16 in gmsh) DMPlex
tells
me that this element type is unknown. However a 9-noded
Quadrilateral
can be read without problem. On inspecting the plexgmsh.c source
code
I can see that 8-noded quadrilaterals are deactivated:
#if 0
146: {20, GMSH_TRI, 2, 3, 3, 9, NULL},
147: {16, GMSH_QUA, 2, 2, 4, 8, NULL},
For our application these 8-noded quadrilateral are very important.
Is there any reason why they have not been implemented/deactivated
in
the dmplex gmsh reader?
No, we can handle them in the same way I think. Let me look at it.
Hopefully it is easy.
Thanks,
Matt
Thank you for all the great work you are doing. PETSc is amazing.
Best wishes,
Susanne Claus
--
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/ [1]
--
Susanne Claus
Ingénieur Chercheur
Applied Mathematics and Scientific Computing Group
DTIS
ONERA - The French Aerospace Lab
6 Chemin de la Vauve aux Granges, 91120 Palaiseau
Links:
--
[1] http://www.cse.buffalo.edu/~knepley/
$MeshFormat
4.1 0 8
$EndMeshFormat
$PhysicalNames
2
1 2 "Neumann"
2 1 "Domain"
$EndPhysicalNames
$Entities
4 4 1 0
1 0 0 0 0
2 1 0 0 0
3 1 1 0 0
4 0 1 0 0
1 -9.4736442e-08 -1e-07 -1e-07 1.001 1e-07 1e-07 0 2 1 -2
2 0.9991 -9.4736442e-08 -1e-07 1.001
1.001 1e-07 1 2 2 2 -3
3 -9.4736442e-08 0.9991 -1e-07 1.001
1.001 1e-07 0 2 3 -4
4 -1e-07 -9.4736442e-08 -1e-07 1e-07 1.001 1e-07 0 2 4 -1
1 -9.4736442e-08 -9.4736442e-08 -1e-07 1.001
1.001 1e-07 1 1 4 1 2 3 4
$EndEntities
$Nodes
9 21 1 46
0 1 0 1
1
0 0 0
0 2 0 1
2
1 0 0
0 3 0 1
3
1 1 0
0 4 0 1
4
0 1 0
1 1 0 3
5
35
36
0.5 0 0
0.25 0 0
0.75 0 0
1 2 0 3
6
37
38
1 0.5 0
1 0.25 0
1 0.75 0
1 3 0 3
7
39
40
0.5 1 0
0.75 1 0
0.25 1 0
1 4 0 3
8
41
42
0 0.5 0
0 0.75 0
0 0.25 0
2 1 0 5
9
43
44
45
46
0.5 0.5 0
0.75 0.5 0
0.5 0.25 0
0.25 0.5 0
0.5 0.75 0
$EndNodes
$Elements
2 6 197 206
1 2 8 2
197 2 6 37
198 6 3 38
2 1 16 4
203 2 6 9 5 37 43 44 36
204 1 5 9 8 35 44 45 42
205 4 8 9 7 41 45 46 40
206 3 7 9 6 39 46 43 38
$EndElements
--
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/ [1]
--
Susanne Claus
Ingénieur Chercheur
Applied Mathematics and Scientific Computing Group
DTIS
ONERA - The French Aerospace Lab
6 Chemin de la Vauve aux Granges, 91120 Palaiseau
Links:
--
[1]
Re: [petsc-users] Gmsh 8-noded quadrilateral
Jed is right about the numerics. However, this does not look hard. Here is
my try at it:
https://gitlab.com/petsc/petsc/-/merge_requests/4838
Please tell me if this works and I will make a test and merge.
Thanks,
Matt
On Thu, Feb 10, 2022 at 6:47 PM Jed Brown wrote:
> Susanne, do you want PetscFE to make the serendipity (8-node) finite
> element space or do you just want to read these meshes? I.e., would it be
> okay with you if the coordinates were placed in a Q_2 (9-node, biquadratic)
> finite element space?
>
> This won't matter if you're traversing the dofs per edge manually, but
> there are some efficiency benefits of using the Q_2 space (especially if
> your code can use the tensor product, perhaps via a library like libCEED).
> Note that Q_2 spaces have better stability properties. For example, the Q_2
> space is inf-sup stable with P_1 discontinuous pressure (gives third order
> L^2 and second order H^1 convergence), but serendipity (8-node) is only
> stable with piecewise constant pressure (gives second order L^2 and first
> order H^1 convergence).
>
> Susanne Claus writes:
>
> > Dear Matthew,
> >
> > Thank you so much.
> > I have a attached a small 8-noded quadrilateral mesh file (Version 4
> > ASCII) generated with gmsh 4.8.4.
> >
> > Best wishes,
> > Susanne
> >
> > On 10.02.2022 16:23, Matthew Knepley wrote:
> >
> >> On Thu, Feb 10, 2022 at 10:12 AM Susanne Claus
>
> >> wrote:
> >>
> >>> Hello,
> >>>
> >>> I am using DMPlex for the mesh structure of a solid mechanics finite
> >>> element code. I mainly use gmsh as input file format. When I try to
> >>> read in 8-noded Quadrilaterals (Element type 16 in gmsh) DMPlex tells
> >>> me that this element type is unknown. However a 9-noded Quadrilateral
> >>> can be read without problem. On inspecting the plexgmsh.c source code
> >>> I can see that 8-noded quadrilaterals are deactivated:
> >>>
> >>> #if 0
> >>> 146: {20, GMSH_TRI, 2, 3, 3, 9, NULL},
> >>> 147: {16, GMSH_QUA, 2, 2, 4, 8, NULL},
> >>>
> >>> For our application these 8-noded quadrilateral are very important.
> >>>
> >>> Is there any reason why they have not been implemented/deactivated in
> >>> the dmplex gmsh reader?
> >>
> >> No, we can handle them in the same way I think. Let me look at it.
> >> Hopefully it is easy.
> >>
> >> Thanks,
> >>
> >> Matt
> >>
> >>> Thank you for all the great work you are doing. PETSc is amazing.
> >>>
> >>> Best wishes,
> >>> Susanne Claus
> >>
> >> --
> >>
> >> 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/ [1]
> >
> > --
> >
> > Susanne Claus
> > Ingénieur Chercheur
> > Applied Mathematics and Scientific Computing Group
> > DTIS
> >
> > ONERA - The French Aerospace Lab
> > 6 Chemin de la Vauve aux Granges, 91120 Palaiseau
> >
> > Links:
> > --
> > [1] http://www.cse.buffalo.edu/~knepley/
> > $MeshFormat
> > 4.1 0 8
> > $EndMeshFormat
> > $PhysicalNames
> > 2
> > 1 2 "Neumann"
> > 2 1 "Domain"
> > $EndPhysicalNames
> > $Entities
> > 4 4 1 0
> > 1 0 0 0 0
> > 2 1 0 0 0
> > 3 1 1 0 0
> > 4 0 1 0 0
> > 1 -9.4736442e-08 -1e-07 -1e-07 1.001 1e-07 1e-07 0 2 1 -2
> > 2 0.9991 -9.4736442e-08 -1e-07 1.001 1.001
> 1e-07 1 2 2 2 -3
> > 3 -9.4736442e-08 0.9991 -1e-07 1.001 1.001
> 1e-07 0 2 3 -4
> > 4 -1e-07 -9.4736442e-08 -1e-07 1e-07 1.001 1e-07 0 2 4 -1
> > 1 -9.4736442e-08 -9.4736442e-08 -1e-07 1.001
> 1.001 1e-07 1 1 4 1 2 3 4
> > $EndEntities
> > $Nodes
> > 9 21 1 46
> > 0 1 0 1
> > 1
> > 0 0 0
> > 0 2 0 1
> > 2
> > 1 0 0
> > 0 3 0 1
> > 3
> > 1 1 0
> > 0 4 0 1
> > 4
> > 0 1 0
> > 1 1 0 3
> > 5
> > 35
> > 36
> > 0.5 0 0
> > 0.25 0 0
> > 0.75 0 0
> > 1 2 0 3
> > 6
> > 37
> > 38
> > 1 0.5 0
> > 1 0.25 0
> > 1 0.75 0
> > 1 3 0 3
> > 7
> > 39
> > 40
> > 0.5 1 0
> > 0.75 1 0
> > 0.25 1 0
> > 1 4 0 3
> > 8
> > 41
> > 42
> > 0 0.5 0
> > 0 0.75 0
> > 0 0.25 0
> > 2 1 0 5
> > 9
> > 43
> > 44
> > 45
> > 46
> > 0.5 0.5 0
> > 0.75 0.5 0
> > 0.5 0.25 0
> > 0.25 0.5 0
> > 0.5 0.75 0
> > $EndNodes
> > $Elements
> > 2 6 197 206
> > 1 2 8 2
> > 197 2 6 37
> > 198 6 3 38
> > 2 1 16 4
> > 203 2 6 9 5 37 43 44 36
> > 204 1 5 9 8 35 44 45 42
> > 205 4 8 9 7 41 45 46 40
> > 206 3 7 9 6 39 46 43 38
> > $EndElements
>
--
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] Gmsh 8-noded quadrilateral
Susanne, do you want PetscFE to make the serendipity (8-node) finite element
space or do you just want to read these meshes? I.e., would it be okay with you
if the coordinates were placed in a Q_2 (9-node, biquadratic) finite element
space?
This won't matter if you're traversing the dofs per edge manually, but there
are some efficiency benefits of using the Q_2 space (especially if your code
can use the tensor product, perhaps via a library like libCEED). Note that Q_2
spaces have better stability properties. For example, the Q_2 space is inf-sup
stable with P_1 discontinuous pressure (gives third order L^2 and second order
H^1 convergence), but serendipity (8-node) is only stable with piecewise
constant pressure (gives second order L^2 and first order H^1 convergence).
Susanne Claus writes:
> Dear Matthew,
>
> Thank you so much.
> I have a attached a small 8-noded quadrilateral mesh file (Version 4
> ASCII) generated with gmsh 4.8.4.
>
> Best wishes,
> Susanne
>
> On 10.02.2022 16:23, Matthew Knepley wrote:
>
>> On Thu, Feb 10, 2022 at 10:12 AM Susanne Claus
>> wrote:
>>
>>> Hello,
>>>
>>> I am using DMPlex for the mesh structure of a solid mechanics finite
>>> element code. I mainly use gmsh as input file format. When I try to
>>> read in 8-noded Quadrilaterals (Element type 16 in gmsh) DMPlex tells
>>> me that this element type is unknown. However a 9-noded Quadrilateral
>>> can be read without problem. On inspecting the plexgmsh.c source code
>>> I can see that 8-noded quadrilaterals are deactivated:
>>>
>>> #if 0
>>> 146: {20, GMSH_TRI, 2, 3, 3, 9, NULL},
>>> 147: {16, GMSH_QUA, 2, 2, 4, 8, NULL},
>>>
>>> For our application these 8-noded quadrilateral are very important.
>>>
>>> Is there any reason why they have not been implemented/deactivated in
>>> the dmplex gmsh reader?
>>
>> No, we can handle them in the same way I think. Let me look at it.
>> Hopefully it is easy.
>>
>> Thanks,
>>
>> Matt
>>
>>> Thank you for all the great work you are doing. PETSc is amazing.
>>>
>>> Best wishes,
>>> Susanne Claus
>>
>> --
>>
>> 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/ [1]
>
> --
>
> Susanne Claus
> Ingénieur Chercheur
> Applied Mathematics and Scientific Computing Group
> DTIS
>
> ONERA - The French Aerospace Lab
> 6 Chemin de la Vauve aux Granges, 91120 Palaiseau
>
> Links:
> --
> [1] http://www.cse.buffalo.edu/~knepley/
> $MeshFormat
> 4.1 0 8
> $EndMeshFormat
> $PhysicalNames
> 2
> 1 2 "Neumann"
> 2 1 "Domain"
> $EndPhysicalNames
> $Entities
> 4 4 1 0
> 1 0 0 0 0
> 2 1 0 0 0
> 3 1 1 0 0
> 4 0 1 0 0
> 1 -9.4736442e-08 -1e-07 -1e-07 1.001 1e-07 1e-07 0 2 1 -2
> 2 0.9991 -9.4736442e-08 -1e-07 1.001 1.001 1e-07
> 1 2 2 2 -3
> 3 -9.4736442e-08 0.9991 -1e-07 1.001 1.001 1e-07
> 0 2 3 -4
> 4 -1e-07 -9.4736442e-08 -1e-07 1e-07 1.001 1e-07 0 2 4 -1
> 1 -9.4736442e-08 -9.4736442e-08 -1e-07 1.001 1.001
> 1e-07 1 1 4 1 2 3 4
> $EndEntities
> $Nodes
> 9 21 1 46
> 0 1 0 1
> 1
> 0 0 0
> 0 2 0 1
> 2
> 1 0 0
> 0 3 0 1
> 3
> 1 1 0
> 0 4 0 1
> 4
> 0 1 0
> 1 1 0 3
> 5
> 35
> 36
> 0.5 0 0
> 0.25 0 0
> 0.75 0 0
> 1 2 0 3
> 6
> 37
> 38
> 1 0.5 0
> 1 0.25 0
> 1 0.75 0
> 1 3 0 3
> 7
> 39
> 40
> 0.5 1 0
> 0.75 1 0
> 0.25 1 0
> 1 4 0 3
> 8
> 41
> 42
> 0 0.5 0
> 0 0.75 0
> 0 0.25 0
> 2 1 0 5
> 9
> 43
> 44
> 45
> 46
> 0.5 0.5 0
> 0.75 0.5 0
> 0.5 0.25 0
> 0.25 0.5 0
> 0.5 0.75 0
> $EndNodes
> $Elements
> 2 6 197 206
> 1 2 8 2
> 197 2 6 37
> 198 6 3 38
> 2 1 16 4
> 203 2 6 9 5 37 43 44 36
> 204 1 5 9 8 35 44 45 42
> 205 4 8 9 7 41 45 46 40
> 206 3 7 9 6 39 46 43 38
> $EndElements
Re: [petsc-users] Gmsh 8-noded quadrilateral
On Thu, Feb 10, 2022 at 10:12 AM Susanne Claus
wrote:
> Hello,
>
> I am using DMPlex for the mesh structure of a solid mechanics finite
> element code. I mainly use gmsh as input file format. When I try to read in
> 8-noded Quadrilaterals (Element type 16 in gmsh) DMPlex tells me that this
> element type is unknown. However a 9-noded Quadrilateral can be read
> without problem. On inspecting the plexgmsh.c source code I can see that
> 8-noded quadrilaterals are deactivated:
>
> #if 0146: {20, GMSH_TRI, 2, 3, 3, 9, NULL},147: {16, GMSH_QUA, 2, 2, 4,
> 8, NULL},
>
> For our application these 8-noded quadrilateral are very important.
>
> Is there any reason why they have not been implemented/deactivated in the
> dmplex gmsh reader?
>
> No, we can handle them in the same way I think. Let me look at it.
Hopefully it is easy.
Thanks,
Matt
> Thank you for all the great work you are doing. PETSc is amazing.
>
> Best wishes,
> Susanne Claus
>
>
--
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/
