Re: [deal.II] Dirichlet boundary condition (homogeneous) on selected dofs
Thanks, Prof. Bangerth for your response. I understood that the the Dirichlet boundary condition in this problem was being applied on only the top surface. But what I am trying to implement seems a little different to me. I will try to explain in a little more detail with an example in the following part. I have a a part of boundary with boundary indicator 2 which has two nodes. Each node has 3 degrees of freedom: displacements along x and y, and pressure. I am trying to implement x displacement to be 0 on both the nodes on this part of the boundary, and y displacement to be 0 on only one of these nodes. I felt that this is a little different from step-22 as in that case all the degrees of freedom corresponding to displacements on the part of the boundary (top surface) were constrained. I would be happy to learn about your thoughts on this. Thanks, Krishanu On Sunday, 26 January 2020 09:12:24 UTC-6, Wolfgang Bangerth wrote: > > On 1/25/20 4:10 PM, Krishanu Sen wrote: > > > > I am able to understand that step-22 has Dirichlet boundary condition on > all > > the degrees of freedom corresponding to displacement components. But I > am > > trying to have the Dirichlet boundary conditions on only some of the > degrees > > of freedom (e. g. all x dofs on the boundary and only one (this one is > to > > prevent rigid body motion) of the y dofs). To do that, I think some > > modifications are needed in the BoundaryValues() function and the > part > > where 'interpolate_boundary_values' is used in the 'setup_dofs'. But I > am not > > able to figure out what the modifications would actually be. > > step-22 actually only uses Dirichlet boundary conditions on the top > surface. > This is done by setting different boundary indicators for the different > parts > of the boundary, and interpolating Dirichlet boundary conditions for only > one > of these boundary indicators. > > Best > W. > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > > www: http://www.math.colostate.edu/~bangerth/ > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/7fec7938-57f5-4f09-984d-4673ff2e3351%40googlegroups.com.
[deal.II] ParameterHandler question
Greetings!
I currently work on the Lethe project,
(https://github.com/lethe-cfd/lethe), and we currently are facing a problem
with ParameterHandler.
We need a way to have a list of variable size in a .prm file (eg; set array
= [{set var = bool, set var2 = string, etc}, {...}, ...])
>From reading the official doc, I don't think we can do something like this.
Or else just having a way to know if a subsection already exists would
work, (which we can't do I seem to understand), so we can simply have a
variable number of subsections, and know the number of subsections.
Is there any workaround?
I was thinking maybe just using JSONs instead of a prm would work.
Thanks for your help! :)
Simon
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Re: [deal.II] Dirichlet boundary condition (homogeneous) on selected dofs
On 1/25/20 4:10 PM, Krishanu Sen wrote: > > I am able to understand that step-22 has Dirichlet boundary condition on all > the degrees of freedom corresponding to displacement components. But I am > trying to have the Dirichlet boundary conditions on only some of the degrees > of freedom (e. g. all x dofs on the boundary and only one (this one is to > prevent rigid body motion) of the y dofs). To do that, I think some > modifications are needed in the BoundaryValues() function and the part > where 'interpolate_boundary_values' is used in the 'setup_dofs'. But I am not > able to figure out what the modifications would actually be. step-22 actually only uses Dirichlet boundary conditions on the top surface. This is done by setting different boundary indicators for the different parts of the boundary, and interpolating Dirichlet boundary conditions for only one of these boundary indicators. Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/1630c99d-2ff4-46c8-aced-89165a2878fc%40colostate.edu.
Re: [deal.II] "PETSc installation does not include a copy of the hypre package" while running the step-40 program
Not yet, I have a running version via docker images though. I'll try the bundle also, thank you, before I was thinking that it shouldn't support parallel programming, but now I see it is configured with "DEAL_II_WITH_MPI set up with external dependencies" and "DEAL_II_WITH_PETSC set up with external dependencies" and has all packages installed. But I'm still interested in solving the issue with "Your PETSc installation does not include a copy of the hypre package necessary for this preconditioner" when I do have the hypre package installed via the option "--download-hypre=1" while configuring PETSc. On Sunday, January 26, 2020 at 11:48:21 AM UTC+2, luca.heltai wrote: > > Did you try the pre-compiled deal.II package? > > Both > > dealii-9.1.1-clang-9.0.0.dmg > > and > > dealii-9.1.1-catalina-haswell-ro.dmg.zip > > > from https://github.com/dealii/dealii/releases/tag/v9.1.1 > > should work. > > Luca. > > > On 25 Jan 2020, at 21:29, Ihar Suvorau > > wrote: > > > > > > Software: > > • macOS Catalina 10.15.2 > > • deal.ii 9.1.1 > > • PETSc 3.12 > > Question: > > > > Hey, does somebody know a potential reason for this message while > running a well-compiled step-40 program: > > > > ihar@husky build3 % ./step-40 > > > > > > Running with PETSc on 1 MPI rank(s)... > > > > Cycle 0: > > > > Number of active cells: 1024 > > > > Number of degrees of freedom: 4225 > > > > > > > > --- > > > > > > An error occurred in line <543> of file > in function > > > >void dealii::PETScWrappers::PreconditionBoomerAMG::initialize(const > dealii::PETScWrappers::MatrixBase &, const > dealii::PETScWrappers::PreconditionBoomerAMG::AdditionalData &) > > > > The violated condition was: > > > >false > > > > Additional information: > > > >Your PETSc installation does not include a copy of the hypre package > necessary for this preconditioner. > > > > > > > > Stacktrace: > > > > --- > > > > #0 2 libdeal_II.g.9.1.1.dylib0x00011188b86f > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE > > + 95: 2 libdeal_II.g.9.1.1.dylib0x00011188b86f > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE > > > > > > #1 3 step-40 0x00010643881a > _ZN6Step4014LaplaceProblemILi2EE5solveEv + 266: 3 step-40 > 0x00010643881a _ZN6Step4014LaplaceProblemILi2EE5solveEv > > > > #2 4 step-40 0x00010642e633 > _ZN6Step4014LaplaceProblemILi2EE3runEv + 451: 4 step-40 > 0x00010642e633 _ZN6Step4014LaplaceProblemILi2EE3runEv > > > > #3 5 step-40 0x00010642e23a main + > 106: 5 step-40 0x00010642e23a main > > > > #4 6 libdyld.dylib 0x7fff6350f7fd start + > 1: 6 libdyld.dylib 0x7fff6350f7fd start > > > > > > > > > > > > [husky:92536] *** Process received signal *** > > > > [husky:92536] Signal: Abort trap: 6 (6) > > > > [husky:92536] Signal code: (0) > > > > [husky:92536] [ 0] 0 libsystem_platform.dylib > 0x7fff6370842d _sigtramp + 29 > > > > [husky:92536] [ 1] 0 ??? > 0x7ffee97d8838 0x0 + 140732815738936 > > > > [husky:92536] [ 2] 0 libsystem_c.dylib > 0x7fff635dda1c abort + 120 > > > > [husky:92536] [ 3] 0 libdeal_II.g.9.1.1.dylib > 0x0001119ec74d > _ZN6dealii18deal_II_exceptions9internals5abortERKNS_13ExceptionBaseE + 205 > > > > [husky:92536] [ 4] 0 libdeal_II.g.9.1.1.dylib > 0x00010de0f63f > _ZN6dealii18deal_II_exceptions9internals20issue_error_noreturnINS_18StandardExceptions10ExcMessageEEEvNS1_17ExceptionHandlingEPKciS7_S7_S7_T_ > > + 223 > > > > [husky:92536] [ 5] 0 libdeal_II.g.9.1.1.dylib > 0x00011188b86f > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE > > + 95 > > > > [husky:92536] [ 6] 0 step-40 > 0x00010643881a _ZN6Step4014LaplaceProblemILi2EE5solveEv + 266 > > > > [husky:92536] [ 7] 0 step-40 > 0x00010642e633 _ZN6Step4014LaplaceProblemILi2EE3runEv + 451 > > > > [husky:92536] [ 8] 0 step-40 > 0x00010642e23a main + 106 > > > > [husky:92536] [ 9] 0 libdyld.dylib > 0x7fff6350f7fd start + 1 > > > > [husky:92536] *** End of error message *** > > > > > > > > The thing is that I've compiled PETSC with the "--download-hypre=1" > option and there is a compiled
Re: [deal.II] "PETSc installation does not include a copy of the hypre package" while running the step-40 program
Did you try the pre-compiled deal.II package? Both dealii-9.1.1-clang-9.0.0.dmg and dealii-9.1.1-catalina-haswell-ro.dmg.zip from https://github.com/dealii/dealii/releases/tag/v9.1.1 should work. Luca. > On 25 Jan 2020, at 21:29, Ihar Suvorau wrote: > > > Software: > • macOS Catalina 10.15.2 > • deal.ii 9.1.1 > • PETSc 3.12 > Question: > > Hey, does somebody know a potential reason for this message while running a > well-compiled step-40 program: > > ihar@husky build3 % ./step-40 > > > Running with PETSc on 1 MPI rank(s)... > > Cycle 0: > > Number of active cells: 1024 > > Number of degrees of freedom: 4225 > > > > --- > > > An error occurred in line <543> of file > in function > >void dealii::PETScWrappers::PreconditionBoomerAMG::initialize(const > dealii::PETScWrappers::MatrixBase &, const > dealii::PETScWrappers::PreconditionBoomerAMG::AdditionalData &) > > The violated condition was: > >false > > Additional information: > >Your PETSc installation does not include a copy of the hypre package > necessary for this preconditioner. > > > > Stacktrace: > > --- > > #0 2 libdeal_II.g.9.1.1.dylib0x00011188b86f > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE > + 95: 2 libdeal_II.g.9.1.1.dylib0x00011188b86f > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE > > #1 3 step-40 0x00010643881a > _ZN6Step4014LaplaceProblemILi2EE5solveEv + 266: 3 step-40 > 0x00010643881a _ZN6Step4014LaplaceProblemILi2EE5solveEv > > #2 4 step-40 0x00010642e633 > _ZN6Step4014LaplaceProblemILi2EE3runEv + 451: 4 step-40 > 0x00010642e633 _ZN6Step4014LaplaceProblemILi2EE3runEv > > #3 5 step-40 0x00010642e23a main + 106: 5 > step-40 0x00010642e23a main > > #4 6 libdyld.dylib 0x7fff6350f7fd start + 1: 6 > libdyld.dylib 0x7fff6350f7fd start > > > > > > [husky:92536] *** Process received signal *** > > [husky:92536] Signal: Abort trap: 6 (6) > > [husky:92536] Signal code: (0) > > [husky:92536] [ 0] 0 libsystem_platform.dylib0x7fff6370842d > _sigtramp + 29 > > [husky:92536] [ 1] 0 ??? 0x7ffee97d8838 > 0x0 + 140732815738936 > > [husky:92536] [ 2] 0 libsystem_c.dylib 0x7fff635dda1c > abort + 120 > > [husky:92536] [ 3] 0 libdeal_II.g.9.1.1.dylib0x0001119ec74d > _ZN6dealii18deal_II_exceptions9internals5abortERKNS_13ExceptionBaseE + 205 > > [husky:92536] [ 4] 0 libdeal_II.g.9.1.1.dylib0x00010de0f63f > _ZN6dealii18deal_II_exceptions9internals20issue_error_noreturnINS_18StandardExceptions10ExcMessageEEEvNS1_17ExceptionHandlingEPKciS7_S7_S7_T_ > + 223 > > [husky:92536] [ 5] 0 libdeal_II.g.9.1.1.dylib0x00011188b86f > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE > + 95 > > [husky:92536] [ 6] 0 step-40 0x00010643881a > _ZN6Step4014LaplaceProblemILi2EE5solveEv + 266 > > [husky:92536] [ 7] 0 step-40 0x00010642e633 > _ZN6Step4014LaplaceProblemILi2EE3runEv + 451 > > [husky:92536] [ 8] 0 step-40 0x00010642e23a > main + 106 > > [husky:92536] [ 9] 0 libdyld.dylib 0x7fff6350f7fd > start + 1 > > [husky:92536] *** End of error message *** > > > > The thing is that I've compiled PETSC with the "--download-hypre=1" option > and there is a compiled library with the name "libHYPRE-2.18.2.dylib" > alongside "libpetsc.3.12.3.dylib" and others in the folder for my > architecture "arch-darwin-c-debug". Environment variables "PETSC_DIR" and > "PETSC_ARCH" all point to the correct folder like in the instruction at > https://www.dealii.org/developer/external-libs/petsc.html. > > Did I miss something? > > I'm trying to install all the packages with "dealii/candi", but PETSc > compilation fails there also, but for a different reason though > (https://github.com/dealii/candi/issues/133). > > -- > The deal.II project is located at http://www.dealii.org/ > For mailing list/forum options, see > https://groups.google.com/d/forum/dealii?hl=en > --- > You received this message because you are subscribed to the Google Groups > "deal.II User Group" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to dealii+unsubscr...@googlegroups.com. > To view this discussion on the
