On Fri, Jan 17, 2025 at 10:08 AM MIGUEL MOLINOS PEREZ <mmoli...@us.es>
wrote:
> Thank you Matt, this the piece of code I use to change the coordinates of
> the DM obtained using:
>
You do not need the call to DMSetCoordinates(). What happens when you
remove it?
Thanks,
Matt
>
> DMSwarmGetCellDM(Simulation.atomistic_data, &bounding_cell);
> DMGetApplicationContext(bounding_cell, &background_mesh);
>
> Thanks,
> Miguel
>
> /************************************************************************/
>
> PetscErrorCode Volumetric_Expansion(DM dm, const Eigen::Matrix3d& F) {
> PetscErrorCode ierr;
> Vec coordinates;
> PetscScalar* coordArray;
> PetscInt xs, ys, zs, xm, ym, zm, i, j, k;
> PetscInt dim, M, N, P;
>
> PetscFunctionBegin;
> // Get DMDA information
> ierr = DMDAGetInfo(dm, &dim, &M, &N, &P, NULL, NULL, NULL, NULL, NULL,
> NULL,
> NULL, NULL, NULL);
> CHKERRQ(ierr);
> ierr = DMDAGetCorners(dm, &xs, &ys, &zs, &xm, &ym, &zm);
> CHKERRQ(ierr);
>
> // Get the coordinates vector
> ierr = DMGetCoordinates(dm, &coordinates);
> CHKERRQ(ierr);
> ierr = VecGetArray(coordinates, &coordArray);
> CHKERRQ(ierr);
>
> // Update the coordinates based on the desired transformation
> for (k = zs; k < zs + zm; k++) {
> for (j = ys; j < ys + ym; j++) {
> for (i = xs; i < xs + xm; i++) {
> PetscInt idx =
> ((k * N + j) * M + i) * dim; // Index for the i, j, k point
> coordArray[idx] = coordArray[idx] * F(0,0); // Update x-coordinate
> coordArray[idx + 1] = coordArray[idx + 1] * F(1,1); // Update y-coordinate
> coordArray[idx + 2] = coordArray[idx + 2] * F(2,2); // Update z-coordinate
> }
> }
> }
>
> // Restore the coordinates vector
> ierr = VecRestoreArray(coordinates, &coordArray);
> CHKERRQ(ierr);
>
> // Set the updated coordinates back to the DMDA
> ierr = DMSetCoordinates(dm, coordinates);
> CHKERRQ(ierr);
>
> PetscFunctionReturn(0);
> }
>
> /************************************************************************/
>
> On 17 Jan 2025, at 16:00, Matthew Knepley <knep...@gmail.com> wrote:
>
> On Fri, Jan 17, 2025 at 9:45 AM MIGUEL MOLINOS PEREZ <mmoli...@us.es>
> wrote:
>
>> I tried what you suggested, but still I got this error message. Maybe I
>> should use main release?
>>
>
> No. I suspect something is wrong with the way you are setting coordinates.
> Can you share the code?
>
> Thanks,
>
> Matt
>
>
>> Miguel
>>
>> [4]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [4]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> [4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [4]PETSC ERROR: or see
>> https://urldefense.us/v3/__https://petsc.org/release/faq/*valgrind__;Iw!!G_uCfscf7eWS!dJKWPsc1_mVgyNyxpcFQO1Nl87DPYNbTLxZ9_kNPDWyv49krXGZa3Oba51VGWtFGBsHYWP6pM9S2njbVhFRk$
>> and
>> https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!dJKWPsc1_mVgyNyxpcFQO1Nl87DPYNbTLxZ9_kNPDWyv49krXGZa3Oba51VGWtFGBsHYWP6pM9S2nm1YDaq3$
>>
>> [4]PETSC ERROR: --------------------- Stack Frames
>> ------------------------------------
>> [4]PETSC ERROR: The line numbers in the error traceback are not always
>> exact.
>> [4]PETSC ERROR: #1 Pack_PetscReal_1_0() at
>> /Users/migmolper/petsc/src/vec/is/sf/impls/basic/sfpack.c:373
>> [4]PETSC ERROR: #2 PetscSFLinkPackRootData_Private() at
>> /Users/migmolper/petsc/src/vec/is/sf/impls/basic/sfpack.c:932
>> [4]PETSC ERROR: #3 PetscSFLinkPackRootData() at
>> /Users/migmolper/petsc/src/vec/is/sf/impls/basic/sfpack.c:966
>> [4]PETSC ERROR: #4 PetscSFBcastBegin_Basic() at
>> /Users/migmolper/petsc/src/vec/is/sf/impls/basic/sfbasic.c:357
>> [4]PETSC ERROR: #5 PetscSFBcastWithMemTypeBegin() at
>> /Users/migmolper/petsc/src/vec/is/sf/interface/sf.c:1513
>> [4]PETSC ERROR: #6 VecScatterBegin_Internal() at
>> /Users/migmolper/petsc/src/vec/is/sf/interface/vscat.c:70
>> [4]PETSC ERROR: #7 VecScatterBegin() at
>> /Users/migmolper/petsc/src/vec/is/sf/interface/vscat.c:1316
>> [4]PETSC ERROR: #8 DMGlobalToLocalBegin_DA() at
>> /Users/migmolper/petsc/src/dm/impls/da/dagtol.c:15
>> [4]PETSC ERROR: #9 DMGlobalToLocalBegin() at
>> /Users/migmolper/petsc/src/dm/interface/dm.c:2844
>> [4]PETSC ERROR: #10 DMGetCoordinatesLocalSetUp() at
>> /Users/migmolper/petsc/src/dm/interface/dmcoordinates.c:565
>> [4]PETSC ERROR: #11 DMGetCoordinatesLocal() at
>> /Users/migmolper/petsc/src/dm/interface/dmcoordinates.c:599
>> [4]PETSC ERROR: #12 _DMLocatePoints_DMDARegular_IS() at
>> /Users/migmolper/DMD/SOLERA/Atoms/Atom.cpp:531
>> [4]PETSC ERROR: #13 DMLocatePoints_DMDARegular() at
>> /Users/migmolper/DMD/SOLERA/Atoms/Atom.cpp:586
>> [4]PETSC ERROR: #14 DMLocatePoints() at
>> /Users/migmolper/petsc/src/dm/interface/dmcoordinates.c:1194
>> [4]PETSC ERROR: #15 DMSwarmMigrate_CellDMScatter() at
>> /Users/migmolper/petsc/src/dm/impls/swarm/swarm_migrate.c:219
>> [4]PETSC ERROR: #16 DMSwarmMigrate() at
>> /Users/migmolper/petsc/src/dm/impls/swarm/swarm.c:1349
>> [4]PETSC ERROR: #17 main() at
>> /Users/migmolper/DMD/driver-tasting-SOLERA.cpp:41
>>
>>
>>
>> On Jan 15, 2025, at 4:56 PM, MIGUEL MOLINOS PEREZ <mmoli...@us.es> wrote:
>>
>> Thank you Matt for the useful info. I’ll try your idea.
>>
>> Miguel
>>
>> On 15 Jan 2025, at 16:48, Matthew Knepley <knep...@gmail.com> wrote:
>>
>> On Wed, Jan 15, 2025 at 10:41 AM MIGUEL MOLINOS PEREZ <mmoli...@us.es>
>> wrote:
>>
>>> Thank you Matt.
>>>
>>> Yes, I am getting the "CellDM" from the DMSwarm.
>>>
>>> 1. I have recently overhauled this functionality because it was not
>>> flexible enough for the plasma simulation we do. Thus main and release work
>>> differently.
>>>
>>>
>>> Nice to hear that. Should I move to main?
>>>
>>
>> The changes allow you to have several cell DMs. I want to bin particles
>> in space, but also in velocity, and then in the tensor product of space and
>> velocity. Moreover, sometimes I want to use different Swarm fields as the
>> DM field for the solver. You can do all that with main now. If you just
>> need a single DM with the same DM fields, release is fine.
>>
>>
>>> 2. I assume you are using release
>>>
>>>
>>> You are correct.
>>>
>>> 3. In both main and release, if you change the coordinates of your
>>> CellDM mesh, you need to rebin the particles. The easiest way to do this is
>>> to call DMSwarmMigrate(sw, PETSC_FALSE).
>>>
>>>
>>> What do you mean by rebin?
>>>
>>
>> When you provide the cell DM, Swrm makes a "sort context" that bins the
>> particles into DM cells. If you change the coordinates, this binning will
>> change, so you need it to "rebin" or recreate the sort context.
>>
>> Thanks,
>>
>> Matt
>>
>>
>>> Miguel
>>>
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> Best,
>>>> Miguel
>>>>
>>> --
>>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dJKWPsc1_mVgyNyxpcFQO1Nl87DPYNbTLxZ9_kNPDWyv49krXGZa3Oba51VGWtFGBsHYWP6pM9S2ns1RezIu$
>>>
>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dJKWPsc1_mVgyNyxpcFQO1Nl87DPYNbTLxZ9_kNPDWyv49krXGZa3Oba51VGWtFGBsHYWP6pM9S2nqKhIaVk$
>>> >
>>>
>>>
>>>
>>
>> --
>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dJKWPsc1_mVgyNyxpcFQO1Nl87DPYNbTLxZ9_kNPDWyv49krXGZa3Oba51VGWtFGBsHYWP6pM9S2ns1RezIu$
>>
>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dJKWPsc1_mVgyNyxpcFQO1Nl87DPYNbTLxZ9_kNPDWyv49krXGZa3Oba51VGWtFGBsHYWP6pM9S2nqKhIaVk$
>> >
>>
>>
>>
>>
>
> --
> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dJKWPsc1_mVgyNyxpcFQO1Nl87DPYNbTLxZ9_kNPDWyv49krXGZa3Oba51VGWtFGBsHYWP6pM9S2ns1RezIu$
>
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dJKWPsc1_mVgyNyxpcFQO1Nl87DPYNbTLxZ9_kNPDWyv49krXGZa3Oba51VGWtFGBsHYWP6pM9S2nqKhIaVk$
> >
>
>
>
--
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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dJKWPsc1_mVgyNyxpcFQO1Nl87DPYNbTLxZ9_kNPDWyv49krXGZa3Oba51VGWtFGBsHYWP6pM9S2ns1RezIu$
<https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dJKWPsc1_mVgyNyxpcFQO1Nl87DPYNbTLxZ9_kNPDWyv49krXGZa3Oba51VGWtFGBsHYWP6pM9S2nqKhIaVk$
>
