On Fri, Jan 24, 2025 at 10:56 AM MIGUEL MOLINOS PEREZ <mmoli...@us.es> wrote:
> Sorry I wasn’t clear enough. By “the box is updated” I mean: I run > DMGetBoundingBox and the resulting coordinates are updated according to the > deformation gradient “F". > Oh, if you change the periodic extent, which you are, you have to recall DMSetPeriodicity(), which is what DMGetBoundaingBox() consults for the periodic extent (because the coordinates cannot be trusted). Thanks, Matt > Thanks, > Miguel > > On 24 Jan 2025, at 16:50, Matthew Knepley <knep...@gmail.com> wrote: > > On Fri, Jan 24, 2025 at 10:36 AM MIGUEL MOLINOS PEREZ <mmoli...@us.es> > wrote: > >> Thanks Matt, I tried that too, and the problem remains. The box is >> updated only if I set no periodic bcc. >> > > What do you mean by "The box is updated"? I am trying to understand how > you test things. Clearly the coordinates are updated, > even in the periodic case. Thus, I need to understand the test. Once we do > that, we can work backwards to the first broken thing. > > Thanks, > > Matt > > >> Miguel >> >> On 24 Jan 2025, at 14:20, Matthew Knepley <knep...@gmail.com> wrote: >> >> On Fri, Jan 24, 2025 at 4:41 AM MIGUEL MOLINOS PEREZ <mmoli...@us.es> >> wrote: >> >>> Dear Matt, the error was in the implementation of the volume expansion >>> function. I updated it, and it works finte under finite domains. However, >>> if I include periodic boundary conditions the volume of the cell does not >>> accommodate the volume expansion of the particles. The deformation gradient >>> is not the identity… I guess I am missing the fine detail on how periodic >>> bcc are implemented in DMDA mesh, I’m right? >>> >> >> DMDA identifies vertices using a VecScatter to implement periodic BC. >> This should be insensitive to coordinates. However, I don't think the >> algorithm below is correct for local coordinates. You use GlobalToLocal(), >> which means that some global coordinate "wins" for each local cell, so >> cells on the periodic boundary can be wrong. I would set the local >> coordinates by hand as well. >> >> Thanks, >> >> Matt >> >> >>> Thanks, >>> Miguel >>> >>> static PetscErrorCode Volumetric_Expansion_DMDA(DM * da, >>> const Eigen::Matrix3d& F) { >>> >>> PetscInt i, j, mstart, m, nstart, n, pstart, p, k; >>> Vec local, global; >>> DMDACoor3d ***coors, ***coorslocal; >>> DM cda; >>> >>> PetscFunctionBeginUser; >>> PetscCall(DMGetCoordinateDM(*da, &cda)); >>> PetscCall(DMGetCoordinates(*da, &global)); >>> PetscCall(DMGetCoordinatesLocal(*da, &local)); >>> PetscCall(DMDAVecGetArray(cda, global, &coors)); >>> PetscCall(DMDAVecGetArrayRead(cda, local, &coorslocal)); >>> PetscCall(DMDAGetCorners(cda, &mstart, &nstart, &pstart, &m, &n, &p)); >>> for (i = mstart; i < mstart + m; i++) { >>> for (j = nstart; j < nstart + n; j++) { >>> for (k = pstart; k < pstart + p; k++) { >>> coors[k][j][i].x = coorslocal[k][j][i].x * F(0, 0); >>> coors[k][j][i].y = coorslocal[k][j][i].y * F(1, 1); >>> coors[k][j][i].z = coorslocal[k][j][i].z * F(2, 2); >>> } >>> } >>> } >>> PetscCall(DMDAVecRestoreArray(cda, global, &coors)); >>> PetscCall(DMDAVecRestoreArrayRead(cda, local, &coorslocal)); >>> >>> PetscCall(DMGlobalToLocalBegin(cda, global, INSERT_VALUES, local)); >>> PetscCall(DMGlobalToLocalEnd(cda, global, INSERT_VALUES, local)); >>> >>> PetscFunctionReturn(PETSC_SUCCESS); >>> } >>> >>> On 17 Jan 2025, at 18:01, MIGUEL MOLINOS PEREZ <mmoli...@us.es> wrote: >>> >>> You are right!! Thank you again! >>> >>> Miguel >>> >>> On Jan 17, 2025, at 5:18 PM, Matthew Knepley <knep...@gmail.com> wrote: >>> >>> On Fri, Jan 17, 2025 at 10:49 AM MIGUEL MOLINOS PEREZ <mmoli...@us.es> >>> wrote: >>> >>>> Now the error is in the call to DMSwarmMigrate >>>> >>> >>> You have almost certainly overwritten memory somewhere. Can you use >>> vlagrind or Address Sanitizer? >>> >>> Thanks, >>> >>> Matt >>> >>> >>>> Miguel >>>> >>>> [0]PETSC ERROR: >>>> ------------------------------------------------------------------------ >>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >>>> probably memory access out of range >>>> [0]PETSC ERROR: Try option -start_in_debugger or >>>> -on_error_attach_debugger >>>> [0]PETSC ERROR: or see >>>> https://urldefense.us/v3/__https://petsc.org/release/faq/*valgrind__;Iw!!G_uCfscf7eWS!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8NYc1XCM$ >>>> and >>>> https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8MiTOrk_$ >>>> >>>> [0]PETSC ERROR: --------------------- Stack Frames >>>> ------------------------------------ >>>> [0]PETSC ERROR: The line numbers in the error traceback are not always >>>> exact. >>>> [0]PETSC ERROR: #1 DMSwarmDataBucketGetSizes() at >>>> /Users/migmolper/petsc/src/dm/impls/swarm/data_bucket.c:297 >>>> [0]PETSC ERROR: #2 DMSwarmMigrate_CellDMScatter() at >>>> /Users/migmolper/petsc/src/dm/impls/swarm/swarm_migrate.c:201 >>>> [0]PETSC ERROR: #3 DMSwarmMigrate() at >>>> /Users/migmolper/petsc/src/dm/impls/swarm/swarm.c:1349 >>>> [0]PETSC ERROR: #4 main() at >>>> /Users/migmolper/DMD/driver-tasting-SOLERA.cpp:41 >>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 >>>> >>>> On Jan 17, 2025, at 4:22 PM, Matthew Knepley <knep...@gmail.com> wrote: >>>> >>>> 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!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8NYc1XCM$ >>>>>> and >>>>>> https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8MiTOrk_$ >>>>>> >>>>>> [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!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8Eq7h-km$ >>>>>>> >>>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8DmSHMyQ$ >>>>>>> > >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> 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!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8Eq7h-km$ >>>>>> >>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8DmSHMyQ$ >>>>>> > >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> 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!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8Eq7h-km$ >>>>> >>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8DmSHMyQ$ >>>>> > >>>>> >>>>> >>>>> >>>> >>>> -- >>>> 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!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8Eq7h-km$ >>>> >>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8DmSHMyQ$ >>>> > >>>> >>>> >>>> >>> >>> -- >>> 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!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8Eq7h-km$ >>> >>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8DmSHMyQ$ >>> > >>> >>> >>> >>> >> >> -- >> 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!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8Eq7h-km$ >> >> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8DmSHMyQ$ >> > >> >> >> > > -- > 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!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8Eq7h-km$ > > <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8DmSHMyQ$ > > > > > -- 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!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8Eq7h-km$ <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fc8y_gbukKK4Ojqu74S_BEOm3W_FECUM5GpjTcm238J5eF-f3HAR5zO4lim3dgv93gMsf77ZnfXC8DmSHMyQ$ >