Modifying Entries Tied to Specific Points in Finite Element Stiffness Matrix using DMPlex
Hello! I'm trying to adapt a serial Finite Element code using PETSc. In this code it reads in special stiffness terms between the boundary DoFs from an input file, and add them to corresponding locations in the global Jacobian matrix. I currently use a DM Plex object to store the mesh information. My understanding is that once the DM is distributed its points are renumbered across different ranks. I wonder if there is a good way to find the corresponding entries that needs to be modified in the global Jacobian matrix? For Vectors I'm currently creating a Natural Vector and simply do DMPlexNaturalToGlobal. Is there a way to create a "Natural Mat" just like "Natural Vector" and then do some sort of NaturalToGlobal for this Mat? Any help would be highly appreciated! Kevin
On Thu, Dec 8, 2022 at 6:06 PM Hongrui Yu <[email protected]> wrote:
Hello! I’m trying to adapt a serial Finite Element code using PETSc. In this code it reads in special stiffness terms between the boundary DoFs from an input file, and add them to corresponding locations in the global Jacobian matrix.
Hmm, so in completely general locations, or on the diagonal?
I currently use a DM Plex object to store the mesh information. My understanding is that once the DM is distributed its points are renumbered across different ranks.
That is true.
I wonder if there is a good way to find the corresponding entries that needs to be modified in the global Jacobian matrix?
For Vectors I’m currently creating a Natural Vector and simply do DMPlexNaturalToGlobal. Is there a way to create a “Natural Mat” just like “Natural Vector” and then do some sort of NaturalToGlobal for this Mat?
Any help would be highly appreciated!
If it is completely general, this will take some coding. Thanks, Matt
Kevin
-- 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/>
Thank you for your reply! Unfortunately yes.. I’ll need to modify stiffness between nodes on the boundary so most of them are going to be in completely general location. I can create an IS after distribution using DMPlexCreatePointNumbering() but they are Global numbering. Is there a way to get a map from Natural numbering to Global numbering? I assume this is used somewhere in DMPlexNaturalToGlobal()? This way I can find the correct entry to modify. Thanks, Kevin
On Dec 9, 2022, at 09:10, Matthew Knepley <[email protected]> wrote:
On Thu, Dec 8, 2022 at 6:06 PM Hongrui Yu <[email protected]> wrote:
Hello! I’m trying to adapt a serial Finite Element code using PETSc. In this code it reads in special stiffness terms between the boundary DoFs from an input file, and add them to corresponding locations in the global Jacobian matrix.
Hmm, so in completely general locations, or on the diagonal?
I currently use a DM Plex object to store the mesh information. My understanding is that once the DM is distributed its points are renumbered across different ranks.
That is true.
I wonder if there is a good way to find the corresponding entries that needs to be modified in the global Jacobian matrix?
For Vectors I’m currently creating a Natural Vector and simply do DMPlexNaturalToGlobal. Is there a way to create a “Natural Mat” just like “Natural Vector” and then do some sort of NaturalToGlobal for this Mat?
Any help would be highly appreciated!
If it is completely general, this will take some coding.
Thanks,
Matt
Kevin
-- 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
On Fri, Dec 9, 2022 at 10:51 AM Hongrui Yu <[email protected]> wrote:
Thank you for your reply! Unfortunately yes.. I’ll need to modify stiffness between nodes on the boundary so most of them are going to be in completely general location.
Hmm, there is usually a better way to do this. This is a mesh and discretization dependent way to impose boundary conditions. However, it is possible.
I can create an IS after distribution using DMPlexCreatePointNumbering() but they are Global numbering. Is there a way to get a map from Natural numbering to Global numbering? I assume this is used somewhere in DMPlexNaturalToGlobal()? This way I can find the correct entry to modify.
You can get the SF that maps global vectors to natural vectors: https://petsc.org/main/docs/manualpages/DM/DMGetNaturalSF/ and pull out the information https://petsc.org/main/docs/manualpages/PetscSF/PetscSFGetGraph/ The roots should be global dofs and the leaves should be natural dofs. So you look through the ilocal leaves for your natural dof and the corresponding remote will be your global dof (but the local number, so you would have to add the rStart to make it a true global dof). Thanks, MAtt
Thanks, Kevin
On Dec 9, 2022, at 09:10, Matthew Knepley <[email protected]> wrote:
On Thu, Dec 8, 2022 at 6:06 PM Hongrui Yu <[email protected]> wrote:
Hello! I’m trying to adapt a serial Finite Element code using PETSc. In this code it reads in special stiffness terms between the boundary DoFs from an input file, and add them to corresponding locations in the global Jacobian matrix.
Hmm, so in completely general locations, or on the diagonal?
I currently use a DM Plex object to store the mesh information. My understanding is that once the DM is distributed its points are renumbered across different ranks.
That is true.
I wonder if there is a good way to find the corresponding entries that needs to be modified in the global Jacobian matrix?
For Vectors I’m currently creating a Natural Vector and simply do DMPlexNaturalToGlobal. Is there a way to create a “Natural Mat” just like “Natural Vector” and then do some sort of NaturalToGlobal for this Mat?
Any help would be highly appreciated!
If it is completely general, this will take some coding.
Thanks,
Matt
Kevin
-- 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/>
participants (2)
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Hongrui Yu -
Matthew Knepley