[deal.II] Problem with Adaptive mesh refinement for NavierStokesProjection (Step-35)
Hi everyone, I am trying to implement an adaptive mesh refinement scheme for the Step-35 examle program. I implemented the mesh-refinement acording to the Step-26 tutorial. So I proceeded in the refine_mesh function as follows: 1. Create a Solution_Transfer object for each Vector; 2. prepare refinement_and_coarsing; (here I also made a hangiing node constraint) 3. execute_ref_and_coars; 4. create_triangulation_and_dofs; 5. Interpolate_solution for each Solution_transfer vector; 6. finally distribute_constraints; But the problem is, that after one mesh-refinement step the time-step solving of the Navierstokesprojection (in Step-35 it is in diffusion_step()) diverges. And I don't see why. Does anyone have an idea? First I thought that I used the Boundary conditions in a wrong way during te refinement step, but the problem also comes up when I apply zero Boundary values on the whole domain for the velocity u. Tanks for your help. Best regards Gabriel -- 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. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: Applying boundary values in parll::distr:triang setting for two dof_handler Sparsematrux
Am Dienstag, 2. April 2019 01:48:41 UTC+2 schrieb Daniel Arndt: > > Alex, > > Hey I just added my changes to a github branch ( >> https://github.com/gabpeters/dealii/tree/sparsity ) >> I changed the make_sparsity_pattern(dof_row,dor_col,sparsity) function >> and also changed the header in the >> dof_tools.h file and the signature in the dof_tools_sparsity.inst.in >> file. >> But still I get the following error, when I compile my code: >> >> undefined reference to `void >> dealii::DoFTools::make_sparsity_pattern, >> >> dealii::DynamicSparsityPattern>(dealii::DoFHandler<3, 3> const&, >> dealii::DoFHandler<3, 3> >> const&, >> dealii::DynamicSparsityPattern&, dealii::ConstraintMatrix const&, bool)' >> >> Did I still forget to change any reference? >> > > Looking at the GitHub branch it seems that you copied a lot of files from > an older deal.II version (you probably modified) to a recent developer > version. That is not going to work. > It's best if you make modifications on top off the master branch. > Otherwise, it is also fine to make the modifications to an older release. > We can certainly sort out how to convert such a patch to one to the recent > master. > > Best, > Daniel > Hey, you are right, that github branch doesnt look very serious. Now I cloned a more recent version, and added the Constraintsmatrix and changed the instantiations. https://github.com/gabpeters/dealii/tree/sparse But somehow it still doesn't work. I still get the error "undefined reference..." I hope I dont bother you too much with all these questions. Best Gabriel -- 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. For more options, visit https://groups.google.com/d/optout.
Aw: [deal.II] Re: Applying boundary values in parll::distr:triang setting for two dof_handler Sparsematrux
Hey, I just worked through the make_sparsity_pattern code. I think I know how to fix the mentioned problem. But I dont understand the how to use the "bool_dof_mask" in the correct way. It is used in he constraints.add_entries_local_to_global(...) function. In the make_sparsity_pattern function with a single dof_handler and a constraintmatrix, it is constructed by a fe_collection. But I don't see how to construct the bool_dof_mask with 2 dof_handlers and respectively 2 fe_collections. Do you have a clue? Best Gabriel Gesendet: Dienstag, 26. März 2019 um 13:32 Uhr Von: "Daniel Arndt" An: "deal.II User Group" Betreff: [deal.II] Re: Applying boundary values in parll::distr:triang setting for two dof_handler Sparsematrux Gabriel, I am trying to apply boundary conditions on a Sparsematrix with two Dof_handlers in a parallel::distributed::trinagulation setting for the Step-35 tutorial. ( Same context as in this thread https://groups.google.com/forum/#!topic/dealii/9ibgrQ0mFBs). At initializing the gradient_operator, I have an object with two Dof_Handlers, which I use for a sparsity pattern. DoFTools::make_sparsity_pattern (dof_handler_velocity,dof_handler_pressure,dsp); But when I apply boundary values to a PETSCWrapper::SparseMatrix using this sparsity pattern I get the following error at the function MatrixTools::apply_boundary_values" The violated condition was: !has_ghost_elements() This issue does not come unexpected if you don't tell DoFTools::make_sparsity_pattern about the constraints you wan't to use. :-) I tried another way to apply the boundary conditions with the use of a COnstraintMatrix as in the Step-40 tutorial. But in that case the make_sparsity_pattern function doesn't work, when I use the commandd: DoFTools::make_sparsity_pattern (dof_handler_velocity,dof_handler_pressure,dsp,constraints_velocity,false); (There I get the error "candidate expects 3 arguments, 5 provided). A function taking two DoFHandle objects and an AffineConstraints (resp. ConstraintMatrix) object is simply not yet implemented. It should not be terribly difficult to do that, though. You could essentially just give the overload of DoFTools::make_sparsity_pattern you are looking at (https://github.com/dealii/dealii/blob/master/source/dofs/dof_tools_sparsity.cc#L212-L350) some more (defaulted) parameters and replace sparsity.add_entries(...) with constraints.add_entries_local_to_global(...). Do you want to give it a shot? We would happily take such a contribution! Feel free to ask if you have any questions, but https://github.com/dealii/dealii/wiki/Contributing should give a good overview. Best, Daniel -- 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. For more options, visit https://groups.google.com/d/optout.
[deal.II] Applying boundary values in parll::distr:triang setting for two dof_handler Sparsematrux
Hey everyone, I am trying to apply boundary conditions on a Sparsematrix with two Dof_handlers in a parallel::distributed::trinagulation setting for the Step-35 tutorial. ( Same context as in this thread https://groups.google.com/forum/#!topic/dealii/9ibgrQ0mFBs). At initializing the gradient_operator, I have an object with two Dof_Handlers, which I use for a sparsity pattern. DoFTools::make_sparsity_pattern (dof_handler_velocity,dof_handler_pressure,dsp); But when I apply boundary values to a PETSCWrapper::SparseMatrix using this sparsity pattern I get the following error at the function MatrixTools::apply_boundary_values" The violated condition was: !has_ghost_elements() I tried another way to apply the boundary conditions with the use of a COnstraintMatrix as in the Step-40 tutorial. But in that case the make_sparsity_pattern function doesn't work, when I use the commandd: DoFTools::make_sparsity_pattern (dof_handler_velocity,dof_handler_pressure,dsp,constraints_velocity,false); (There I get the error "candidate expects 3 arguments, 5 provided). Does somebody have an idea how I can apply the boundary values efficiently in that case? Thanks a lot and best regards Gabriel -- 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. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: Applying boundary values in parll::distr:triang setting for two dof_handler Sparsematrux
Hi. Thanks a lot for the advice. I will Try it tomorrow and send a response whether it works. Regards Gabriel Gabriel Peters Endenicher Str. 310 53121 Bonn 00491525/5478185 gabriel.pet...@koeln.de Am 26.03.19 um 13:32 schrieb Daniel Arndt > Gabriel, > > > > I am trying to apply boundary conditions on a Sparsematrix with two > > Dof_handlers in a parallel::distributed::trinagulation setting for the > > Step-35 tutorial. > > ( Same context as in this thread > > https://groups.google.com/forum/#!topic/dealii/9ibgrQ0mFBs). > > > > At initializing the gradient_operator, I have an object with two > > Dof_Handlers, which I use for a sparsity pattern. > > > > DoFTools::make_sparsity_pattern > > (dof_handler_velocity,dof_handler_pressure,dsp); > > > > But when I apply boundary values to a PETSCWrapper::SparseMatrix using > > this sparsity pattern I get the following error > > at the function MatrixTools::apply_boundary_values" > > > > The violated condition was: !has_ghost_elements() > > > > This issue does not come unexpected if you don't tell > DoFTools::make_sparsity_pattern about the constraints you wan't to use. :-) > > > > > > I tried another way to apply the boundary conditions with the use of a > > COnstraintMatrix as in the Step-40 tutorial. But in that case the > > make_sparsity_pattern function doesn't work, when I use the commandd: > > > > DoFTools::make_sparsity_pattern > > (dof_handler_velocity,dof_handler_pressure,dsp,constraints_velocity,false); > > > > (There I get the error "candidate expects 3 arguments, 5 provided). > > > > A function taking two DoFHandle objects and an AffineConstraints (resp. > ConstraintMatrix) object is simply not yet implemented. > It should not be terribly difficult to do that, though. You could > essentially just give the overload of DoFTools::make_sparsity_pattern > you are looking at > (https://github.com/dealii/dealii/blob/master/source/dofs/dof_tools_sparsity.cc#L212-L350) > > some more (defaulted) parameters and replace sparsity.add_entries(...) with > constraints.add_entries_local_to_global(...). > > Do you want to give it a shot? We would happily take such a contribution! > Feel free to ask if you have any questions, but > https://github.com/dealii/dealii/wiki/Contributing should give a good > overview. > > Best, > Daniel > > -- > 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. > For more options, visit https://groups.google.com/d/optout. -- 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. For more options, visit https://groups.google.com/d/optout.
Aw: Re: [deal.II] Re: Applying boundary values in parll::distr:triang setting for two dof_handler Sparsematrux
Hey Daniel, thanks for the pull, with this instantiation everything compiles fine and I can use it. But I think I did a mistake somewhere in the function. Using the definiion of the function from your pull request I call DoFTools::make_sparsity_pattern (dof_handler_velocity,dof_handler_pressure,dsp, constraints_vel,false); and afterwards I call SparsityTools::distribute_sparsity_pattern (dsp, dof_handler_velocity.n_locally_owned_dofs_per_processor(),mpi_communicator,locally_relevant_dofs_vel); When I run the program on more than 2 processors I get the following error during the distribute_sparsity... function: The violated condition was: local_lines.is_element(line_n) Additional information: The index set given to this constraints object indicates constraints for degree of freedom 16 should not be stored by this object, but a constraint is being added. Do you have an idea how I can fix this? (When I run the code on 1 or 2 processors, this error doesnt come up. But I get divergence in the Gmres mehod, which might imply that the boundaryconditions are not applied in the correct way yet, but I first want to focus on the upper error.) Thanks and best regards Gabriel Gesendet: Mittwoch, 03. April 2019 um 03:03 Uhr Von: "Daniel Arndt" An: "deal.II User Group" Betreff: Re: [deal.II] Re: Applying boundary values in parll::distr:triang setting for two dof_handler Sparsematrux Gabriel, Now I cloned a more recent version, and added the Constraintsmatrix and changed the instantiations. https://github.com/gabpeters/dealii/tree/sparse That looks much better! But somehow it still doesn't work. I still get the error "undefined reference..." Admittedly, getting the instantiations right in this case might not be straightforward. I created a pull request to your branch at https://github.com/gabpeters/dealii/pull/1 to fix some issues such that the branch at least compiles for me. If you are satisfied with everything, please create a pull request to the master branch. I hope I dont bother you too much with all these questions. Not at all! We are happily helping people to contribute. Best, Daniel -- 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. For more options, visit https://groups.google.com/d/optout. -- 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. For more options, visit https://groups.google.com/d/optout.
Re: Re: [deal.II] Re: Applying boundary values in parll::distr:triang setting for two dof_handler Sparsematrux
Gabriel Peters Endenicher Str. 310 53121 Bonn 00491525/5478185 gabriel.pet...@koeln.de Am 05.04.19 um 15:55 schrieb Daniel Arndt > Gabriel, > > to extend on my last post. Finally, I think that your approach with the two > DoFHandler objects will give you some more problems. > What is likely happening here is that the AffineConstraints object here is > used both for rows and columns although row dofs and column dofs are > unrelated. > What you wanted here is to shift the pressure dofs such that they don't > overlap with the velocoty dofs. However, you can't just do this using a > renumbering since it is currently not allowed. That would habe Been my question to your First post, how to apply 2 constraints in the „constraints.add... function, but your described Problem seems Even Harder to solve. > Even if you get this to work here without shifting, you will have the same > problem when assembling your matrix and applying constraints. > I agree with David that the better approach here is to use a FESystem that > accounts both for velocity and pressure and follow step-32. > > Best, > Daniel > > -- This Sounds like but Problem. But thanks a lot again. I will try next week to implement the code using Blockmatrices as prescribed. I‘ll let you know if it works or if further questions come up. Best, Gabriel -- 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. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: Applying boundary values in parll::distr:triang setting for two dof_handler Sparsematrux
Am Mittwoch, 27. März 2019 13:58:47 UTC+1 schrieb Daniel Arndt: > > Gabriel, > > Am Mittwoch, 27. März 2019 06:16:18 UTC-4 schrieb Gabriel Peters: >> >> Hey, I just worked through the make_sparsity_pattern code. >> I think I know how to fix the mentioned problem. But I dont understand the >> how to use the "bool_dof_mask" in the correct way. It is used in he >> constraints.add_entries_local_to_global(...) >> function. >> In the make_sparsity_pattern function with a single dof_handler and a >> constraintmatrix, it is constructed by a fe_collection. >> But I don't see how to construct the bool_dof_mask with 2 dof_handlers >> and respectively 2 fe_collections. >> Do you have a clue? >> > > "bool_dof_mask" is only used in case the make_*_pattern has a `const > Table<2, Coupling> & couplings` parameter. That is currently not the case > for the function you are looking at. > For being backward-compatible we need to provide/keep the > > void DoFTools::make_sparsity_pattern ( const DoFHandlerType & dof_row, >const > DoFHandlerType & dof_col, > > SparsityPatternType & sparsity ) > > interface anyway, it is fine to add defaulted parameters at the end, but > adding `const Table<2, Coupling> & couplings` as third parameter would > not. > For now, I would simply assume that all components couple and ignore the > last argument for add_entries_local_to_global. We can always create another > overload later if specifying the coupling is desired/necessary. > > Best, > Daniel > Hey, its me again. Today I had various tries fixing the upper problem. At first I extended the make_sparsity_pattern function to void DoFTools::make_sparsity_pattern ( const DoFHandlerType & dof_row, const DoFHandlerType & dof_col, SparsityPatternType & sparsity, const ConstraintMatrix, const bool keep_constrained_dofs) and also changed the dof_tools.h file in deal.II\source\dofs and changed the adding function; but when I compiled this I got lots of errors of this kind: error:* template-id* ‘make_sparsity_pattern, dealii::BlockDynamicSparsityPattern>’ for ‘void dealii::DoFTools::make_sparsity_pattern(const dealii::hp::DoFHandler<1, 3>&, const dealii::hp::DoFHandler<1, 3>&, dealii::BlockDynamicSparsityPattern&)’ *does not match any template declaration* My second attempt was to make a new function, with a different name, which takes the same arguments as above and does exactly was the classical make_sp_pt(row_id,col_id,sparsity) function does, up to the constraints.add... function. I also added the header of these function to the dof_tools.h file. This compiled fine, but when I used this function in my program I got the error: undefined reference to: (function parameters). Could you maybe tel me what I did wrong, or did I do an fundamental error at editting the deal.ii code? Thanks a lot again and sorry for the long message Gabriel -- 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. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: Applying boundary values in parll::distr:triang setting for two dof_handler Sparsematrux
Okay Thanks a lot. If it works now, I will contribute it. Best Gabriel Gabriel Peters Endenicher Str. 310 53121 Bonn 00491525/5478185 gabriel.pet...@koeln.de Am 27.03.19 um 13:58 schrieb Daniel Arndt > Gabriel, > > Am Mittwoch, 27. März 2019 06:16:18 UTC-4 schrieb Gabriel Peters: > > > > Hey, I just worked through the make_sparsity_pattern code. > > I think I know how to fix the mentioned problem. But I dont understand the > > how to use the "bool_dof_mask" in the correct way. It is used in he > > constraints.add_entries_local_to_global(...) > > function. > > In the make_sparsity_pattern function with a single dof_handler and a > > constraintmatrix, it is constructed by a fe_collection. > > But I don't see how to construct the bool_dof_mask with 2 dof_handlers and > > respectively 2 fe_collections. > > Do you have a clue? > > > > "bool_dof_mask" is only used in case the make_*_pattern has a `const > Table<2, Coupling> & couplings` parameter. That is currently not the case > for the function you are looking at. > For being backward-compatible we need to provide/keep the > > void DoFTools::make_sparsity_pattern ( const DoFHandlerType & dof_row, >const > DoFHandlerType & dof_col, > > SparsityPatternType & sparsity ) > > interface anyway, it is fine to add defaulted parameters at the end, but > adding `const Table<2, Coupling> & couplings` as third parameter would not. > For now, I would simply assume that all components couple and ignore the > last argument for add_entries_local_to_global. We can always create another > overload later if specifying the coupling is desired/necessary. > > Best, > Daniel > > -- > 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. > For more options, visit https://groups.google.com/d/optout. -- 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. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: Applying boundary values in parll::distr:triang setting for two dof_handler Sparsematrux
Am Donnerstag, 28. März 2019 21:37:19 UTC+1 schrieb Daniel Arndt: > > Gabriel, > > At first I extended the make_sparsity_pattern function to >> >> void DoFTools::make_sparsity_pattern ( const DoFHandlerType & dof_row, >>const >> DoFHandlerType & dof_col, >> >> SparsityPatternType & sparsity, >>const >> ConstraintMatrix, >>const >> bool keep_constrained_dofs) >> >> and also changed the dof_tools.h file in deal.II\source\dofs and changed >> the adding function; >> but when I compiled this I got lots of errors of this kind: >> error:* template-id* >> ‘make_sparsity_pattern, >> dealii::BlockDynamicSparsityPattern>’ for ‘void >> dealii::DoFTools::make_sparsity_pattern(const dealii::hp::DoFHandler<1, >> 3>&, const dealii::hp::DoFHandler<1, 3>&, >> dealii::BlockDynamicSparsityPattern&)’ *does not match any template >> declaration* >> >> > This looks like you were not adapting the signature in the function's > definition in source/dofs/dof_tools_constraints.h. It still only has three > instead of five parameters. > > >> My second attempt was to make a new function, with a different name, >> which takes the same arguments as above and does exactly was the classical >> make_sp_pt(row_id,col_id,sparsity) function does, up to the >> constraints.add... function. >> I also added the header of these function to the dof_tools.h file. >> This compiled fine, but when I used this function in my program I got the >> error: >> undefined reference to: (function parameters). >> > > This looks like you didn't provide a definition but only a declaration. > > Do you have your changes in a GitHub branch such that we can have a look > what you did precisely? > Hey I just added my changes to a github branch ( https://github.com/gabpeters/dealii/tree/sparsity ) I changed the make_sparsity_pattern(dof_row,dor_col,sparsity) function and also changed the header in the dof_tools.h file and the signature in the dof_tools_sparsity.inst.in file. But still I get the following error, when I compile my code: undefined reference to `void dealii::DoFTools::make_sparsity_pattern, dealii::DynamicSparsityPattern>(dealii::DoFHandler<3, 3> const&, dealii::DoFHandler<3, 3> const&, dealii::DynamicSparsityPattern&, dealii::ConstraintMatrix const&, bool)' Did I still forget to change any reference? Best Gabriel PS, you can ignore the make*s*_sparsity_pattern(...) function which I added to dof_tools_sparsity.cc > > Best, > Daniel > -- 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. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Sparsematrix initialization in P4est program
Am Montag, 18. Februar 2019 22:21:06 UTC+1 schrieb David Wells: > > Hi Gabriel, > > I believe that you are still using the standard deal.II SparseMatrix > class; is this correct? If so, this class won't work with fully distributed > calculations. You will need to use either the Trilinos or PETSc wrappers > since not all information is available on the local processor with the > default SparseMatrix class. > > Either way: I believe the error message you encountered is a result of a > bug in deal.II. I don't think that the routine > GridTools::get_finest_common_cells(), which is called by that particular > make_sparsity_pattern variant, works with distributed triangulations. If > you want to use distributed triangulations you will need to set up the > coupled sparsity pattern in a different way. > > If you want to parallelize step-35, it may be better to start by looking > at step-32, which shows how to implement the Stokes equations (coupled to a > Boussinesq equation) in a fully distributed setting. I believe they set up > the coupling of the matrix with velocity and pressure blocks in a different > way that should work for you. > > Does this make sense? > > Thanks, > David Wells > >> >> Hey, sorry for the late respons, I had some stuff to work at. Today I had a close look to the Step-32 and 31 tutorial and I think that this doen't help very much because in the Step-32 tutorial the pressure_fe_degree eguals the velocity_fe_degree, which, in my view, makes thi function "make_sparsity_pattern" applicable, because you only have to insert one Dof_Handler object. Thus one can use the same Dof_Handler for velocity and pressure, and everything is created as in the Step-32 In my case the velocity_fe_degree is one degree larger then the pressure_fe_degree. If I understood the construction right, I can't perform it in this case. Do you see my problem, or am I wrong? Best Regards Gabriel -- 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. For more options, visit https://groups.google.com/d/optout.
[deal.II] Sparsematrix initialization in P4est program
Hey everybody,
I have a problem with initializing a Sparsematrix in a parallel program.
am using a parallel::distributed::triangulaton (as in the Step40 tutorial)
on
the Navier Stokes Projection solver from the step35 tutorial.
The problem arises in the function
NavierStokesProjection::initialize_gradient_operator()
{
{
DynamicSparsityPattern
dsp(dof_handler_velocity.n_dofs(), dof_handler_pressure.n_dofs());
DoFTools::make_sparsity_pattern
(dof_handler_velocity, dof_handler_pressure, dsp);
sparsity_pattern_pres_vel.copy_from (dsp);
}
where I have to use two different FE-spaces, one for the pressure and one
for the velocity.
To perform this in parallel I used the following code (according to the
sparsematrices in step40)
{
DynamicSparsityPattern
dsp(locally_relevant_dofs_vel.size(),locally_relevant_dofs_pres.size());
DoFTools::make_sparsity_pattern (dof_handler_velocity,
dof_handler_pressure, dsp);
sparsity_pattern_pres_vel.copy_from (dsp);
}
This code compilates fine, but when Running it with MPI, it stops in the
"make_sparsity_pattern" line with the error code
"this->is_artificial() == false
Additional information:
Cant asks for Dofs on articial cells."
Does somebody know how I can fix this?
My last try was to use the Indexsets instead of their size, when declaring
dsp.
But unfortunately DynamicSparsityPattern can only take on IndexSet.
Thanks a lot
Gabriel
--
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.
For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Problem with Adaptive mesh refinement for NavierStokesProjection (Step-35)
Am Montag, 28. Januar 2019 15:19:36 UTC+1 schrieb Wolfgang Bangerth: > > On 1/28/19 6:38 AM, gabriel...@koeln.de wrote: > > > > But the problem is, that after one mesh-refinement step the time-step > solving > > of the Navierstokesprojection (in Step-35 it is in diffusion_step()) > > diverges. And I don't see why. Does anyone have an idea? > > > > First I thought that I used the Boundary conditions in a wrong way > during te > > refinement step, > > but the problem also comes up when I apply zero Boundary values on the > whole > > domain for > > the velocity u. > > How do you choose the timestep? Are you making sure that it satisfies a > CFL > condition? > > Best > W. > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > > www: http://www.math.colostate.edu/~bangerth/ > I already implemented a time-step-function to satisfy the CFL condition. The problem also comes up when I use global refinement in the refine_mesh step (for example in stead of KellyEstimator refinement). But when apply global refinement at the start of the program everything works fine, so I think there is a slight error somewhere, which I dont see. Regards Gabriel -- 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. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Problem with Adaptive mesh refinement for NavierStokesProjection (Step-35)
I tried some things, but also if I insert a safety factor of 0.1 or less
the GMRES-procedure in the diffusion-step diverges.
I implemented the time step function such that
dt <= max_{T} h_T/(u_max(T))
where the max is taken over all cells and u_max is the maximal value of u
on the cell T.
--
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.
For more options, visit https://groups.google.com/d/optout.
[deal.II] p4est balance_mesh
Hey everyone,
I am wondering, whether there is a deal.ii function, which balances a
parallel::distributed::triangulation neighbouring elements by 2:1,
like the p8est_balance_ext function
(see
http://p4est.github.io/api/p8est__extended_8h.html#ad3a61dc2b4b5cc69b03c995f188bfd8d
)
Such a function might be useful after calling
triagulation.execute_refinement_and_coarsening();
I think it mgiht be possible to proceed as in the p4est test programs and
called
* p4est_balance** (triangulation, P4EST_CONNECT_FULL, NULL);*
but I got the error message
cannot convert ‘dealii::parallel::distributed::Triangulation<3, 3>’ to
‘p4est_t* {aka p4est*}’ for argument ‘1’ to ‘void p4est_balance(p4est_t*,
p4est_connect_type_t, p4est_init_t)’
p4est_balance (triangulation, P4EST_CONNECT_FULL, NULL);
which is obvious because the p::d::triangulation is not a p4est*
Does someone have an idea how to fix this or how to balance the
triangulation?
Best regards
Gabriel
--
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/60d8aaf5-5b6a-44b8-8dae-d4b937fef516%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
Aw: Re: [deal.II] p4est balance_mesh
Hi
I am setting refinement_flags on cells, based on the geometry I use, and I want to ensure, that the mesh is still balanced. But if p4est does this automatically when I call execute_refine...() it might be enough.
Best
Gabriel
Gesendet: Dienstag, 04. Juni 2019 um 17:52 Uhr
Von: "Wolfgang Bangerth"
An: "dealii@googlegroups.com"
Betreff: Re: [deal.II] p4est balance_mesh
On 6/4/19 6:41 AM, Gabriel Peters wrote:
>
> I am wondering, whether there is a deal.ii function, which balances a
> parallel::distributed::triangulation neighbouring elements by 2:1,
> like the p8est_balance_ext function
> (see
> http://p4est.github.io/api/p8est__extended_8h.html#ad3a61dc2b4b5cc69b03c995f188bfd8d
> )
>
> Such a function might be useful after calling
> triagulation.execute_refinement_and_coarsening();
>
>
>
>
> I think it mgiht be possible to proceed as in the p4est test programs and called
> /p4est_balance//(triangulation, P4EST_CONNECT_FULL, NULL);/
> /
> /
> but I got the error message
> cannot convert ‘dealii::parallel::distributed::Triangulation<3, 3>’ to
> ‘p4est_t* {aka p4est*}’ for argument ‘1’ to ‘void p4est_balance(p4est_t*,
> p4est_connect_type_t, p4est_init_t)’
> p4est_balance (triangulation, P4EST_CONNECT_FULL, NULL);
>
> which is obvious because the p::d::triangulation is not a p4est*
>
>
>
> Does someone have an idea how to fix this or how to balance the triangulation?
What are you trying to achieve? The p::d::Triangulation class calls that
function internally anyway to ensure the 2:1 balance. There is nothing you
need to do yourself.
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/4595f80e-7d83-72d6-71e2-6c1fffe5bb32%40colostate.edu.
For more options, visit https://groups.google.com/d/optout.
--
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/trinity-414d3395-75ce-4e49-bf83-970d262dc820-1559727401019%403c-app-webde-bap55.
For more options, visit https://groups.google.com/d/optout.
Re: Aw: Re: [deal.II] p4est balance_mesh
Ok thanks a lot. Best Gabriel Gabriel Peters Endenicher Str. 310 53121 Bonn 00491525/5478185 gabriel.pet...@koeln.de Am 05.06.19 um 14:55 schrieb Wolfgang Bangerth > On 6/5/19 3:36 AM, Gabriel Peters wrote: > > I am setting refinement_flags on cells, based on the geometry I use, and I > > want to ensure, that the mesh is still balanced. But if p4est does this > > automatically when I call execute_refine...() it might be enough. > > p4est doesn't, but deal.II does when it refines the mesh. It automatically > calls p4est_balance after p4est_refine. > > 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/13f21b39-b827-79a6-cbfc-882d21acba07%40colostate.edu. > For more options, visit https://groups.google.com/d/optout. -- 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/trinity-6bd1cbf9-bab9-4c27-b0eb-d0880cd0664c-1559739808619%40msvc-mesg-web104. For more options, visit https://groups.google.com/d/optout.
[deal.II] p4est tree initilization
Hey everyone, I am working with a parallel::distributed::triangulation. In my program I load a coarse grid from a file. Is there a function to manually initialize trees in my triangulation, according to some regions of my domain (just as p4est does) or is this automatically done by calling p::d::tria, in some way? If this is the case, how many trees are initialized then? Thaks a lot and best regards Gabriel -- 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/4ac1c3d5-df2c-4a4c-bd35-4f0952580453%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Problem Solving BlockSparsematrix system blockwise
Hey everyone, I have a problem at solving a blocksystem. I have a matrix called "system_matrix" in Blockform M = [[A,0],[B,C]] and I want to solve classical Mx = F. (F = [f,0], x = [x1,x2]) I proceed according to the LinearSolvers class in the step-32 tutorial. so by blockwise solving the system I want to solve A*x1 = f for x1 and later on I want to solve C*x2 = 0 - B*x1 for x2. In the code I use: *std::shared_ptr Mp_preconditioner;* and compute *TrilinosWrappers::SolverGMRES solver_gmres(solver_control_gmres); solver_gmres.solve(system_matrix.block(0,0),distributed_solution.block(0), rhs.block(0),Mp_preconditioner);* But when I compile this I get the error error: no matching function for call to ‘dealii::TrilinosWrappers::SolverGMRES::solve(dealii::BlockMatrixBase::BlockType&, dealii::BlockVectorBase::BlockType&, dealii::BlockVectorBase::BlockType&, std::shared_ptr&)’ rhs.block(0),Mp_preconditioner); This error also comes up at solving the lower right block *TrilinosWrappers::SolverCG solver_cg(solver_control_cg); solver_cg.solve(system_matrix.block(1,1), distributed_solution.block(1),u_tmp_p, Amg_preconditioner);* Can somebody tell me what actually went wrong? I think I did everything quite similar to the LinearSolvers class which works finely. Thanks a lot and best regards Gabriel -- 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/a89681fc-950b-473b-a18b-666feaf89207%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Problem Solving BlockSparsematrix system blockwise
Hey Jean-Paul Thanks a lot, Now it works finely. Best regards Gabriel Gabriel Peters Endenicher Str. 310 53121 Bonn 00491525/5478185 gabriel.pet...@koeln.de Am 20.05.19 um 15:01 schrieb Jean-Paul Pelteret > Dear Gabriel, > > It looks to me like you forgot to dereference the shared pointer for the > preconditioner. So, > > solver_gmres.solve( > system_matrix.block(0,0), > distributed_solution.block(0), > rhs.block(0), > *Mp_preconditioner); // <— here > > You probably have the same problem for the other call. > > I hope this was the correct observation to help sole the issue! > > Best, > Jean-Paul > > > > On 20 May 2019, at 13:56, Gabriel Peters wrote: > > > > Hey everyone, > > I have a problem at solving a blocksystem. > > > > I have a matrix called "system_matrix" in Blockform M = [[A,0],[B,C]] > > and I want to solve classical Mx = F. (F = [f,0], x = [x1,x2]) > > > > I proceed according to the LinearSolvers class in the step-32 tutorial. > > so by blockwise solving the system I want to solve A*x1 = f for x1 > > and later on I want to solve > > C*x2 = 0 - B*x1 for x2. > > > > In the code I use: > > std::shared_ptr Mp_preconditioner; > > > > and compute > > > > TrilinosWrappers::SolverGMRES solver_gmres(solver_control_gmres); > > > > > > solver_gmres.solve(system_matrix.block(0,0),distributed_solution.block(0), > > rhs.block(0),Mp_preconditioner); > > > > > > But when I compile this I get the error > > > > error: no matching function for call to > > ‘dealii::TrilinosWrappers::SolverGMRES::solve(dealii::BlockMatrixBase::BlockType&, > > > > dealii::BlockVectorBase::BlockType&, > > dealii::BlockVectorBase::BlockType&, > > std::shared_ptr&)’ > > rhs.block(0),Mp_preconditioner); > > > > > > > > This error also comes up at solving the lower right block > > TrilinosWrappers::SolverCG solver_cg(solver_control_cg); > > solver_cg.solve(system_matrix.block(1,1), > > distributed_solution.block(1), > > u_tmp_p, > > Amg_preconditioner); > > > > > > Can somebody tell me what actually went wrong? I think I did everything > > quite similar to the LinearSolvers class which works finely. > > Thanks a lot and best regards > > > > Gabriel > > > > > > > > > > > > > > > > > > -- > > The deal.II project is located at http://www.dealii.org/ > > <http://www.dealii.org/> > > For mailing list/forum options, see > > https://groups.google.com/d/forum/dealii?hl=en > > <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 > > <mailto:dealii+unsubscr...@googlegroups.com>. > > To view this discussion on the web visit > > https://groups.google.com/d/msgid/dealii/a89681fc-950b-473b-a18b-666feaf89207%40googlegroups.com > > > > <https://groups.google.com/d/msgid/dealii/a89681fc-950b-473b-a18b-666feaf89207%40googlegroups.com?utm_medium=email_source=footer>. > > For more options, visit https://groups.google.com/d/optout > > <https://groups.google.com/d/optout>. > > -- > 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/62B07170-EA44-4276-8813-4E8C9E25A1BF%40gmail.com. > For more options, visit https://groups.google.com/d/optout. -- 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/trinity-394d81e1-d8a2-4b6a-bc1d-d49182149cd8-1558358138435%40msvc-mesg-web003. For more options, visit https://groups.google.com/d/optout.
[deal.II] Problem Adding Trilinos::MPI::BlockVector
Hey everyone, I have a problem with adding Vectors in a Multiparallel program. Here I use TrilinosWrappers::MPI::BlockVector vector_1, vector_2; which are initialized ion the same fashion, as in the step-32 tutorial vector_1.reinit(stokes_relevant_partitioning, MPI_COMM_WORLD); vector_2.reinit(stokes_relevant_partitioning, MPI_COMM_WORLD); Now I want to call vector_1.block(0).add(1.0, vector_2.block(0)); This compiles fine, but when I run the executbale on >=2 processors I get the following error: *An error occurred in line <2015> of file in functionvoid dealii::TrilinosWrappers::MPI::Vector::add(dealii::TrilinosScalar, const dealii::TrilinosWrappers::MPI::Vector&, dealii::TrilinosScalar, const dealii::TrilinosWrappers::MPI::Vector&)The violated condition was: !has_ghost_elements()Additional information: You are trying an operation on a vector that is only allowed if the vector has no ghost elements, but the vector you are operating on does have ghost elements. Specifically, vectors with ghost elements are read-only and cannot appear in operations that write into these vectors.* I tried to avoid the ghost cells, so I had another try, intializing the Vectors in another fashion: vector_1.reinit(stokes_partitioning, stokes_relevant_partitioning, MPI_COMM_WORLD, true); In this case the adding of the vectors worked out fineliy, but later on in the program I want to use Extractors to get the function_values at quadrature_points. So I call if(cell->is_locally_owned) [...] fe_values,reinit(cell); std::vector > vector_1_values(n_q_points); fe_values[velocities].get_function_values(vector_1,vector_1_values); But with the new initialization of vector_1 now the "get_function_values" function fails with the error: *dealii::TrilinosScalar dealii::TrilinosWrappers::MPI::Vector::operator()(dealii::TrilinosWrappers::MPI::Vector::size_type) constThe violated condition was: falseAdditional information: You tried to access element 225 of a distributed vector, but this element is not stored on the current processor. Note: There are 972 elements stored on the current processor from within the range 1215 through 2186 but Trilinos vectors need not store contiguous ranges on each processor, and not every element in this range may in fact be stored locally.* Does somebody have an idea how either add the vectors in the right way or fix the get_function_value function call? Thanks a lot and best regards Gabriel -- 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/af7d94f3-c906-4730-9a1c-6f593c01d98f%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Adding TrilinosWrapper::BlockSparseMatrix
Hey everyone, I got a problem regarding TrilnosWrappers::BlockSparseMatrix. In my program I have a TrilnosWrappers::BlockSparseMatrix system_matrix which consists of two parts, one permanent part, which is computed at the beginning at the programm, not every iteration, to save time (called system_matrix_permanent) and one iterative part, which is computed in every iteration (called system_matrix_iterative). Hence system_matrix = system_matrix_permanent + system_matrix_iterative Thus, after assembling those matrices, I want to call something like system_matrix.add(system_matrix_permanent,system_matrix_permanent); But I always get the error message error: no matching function for call to ‘dealii::TrilinosWrappers::BlockSparseMatrix::add(dealii::TrilinosWrappers::BlockSparseMatrix&)’ system_matrix.add(system_matrix_iterative); Is there any function which adds up TrilinosWrappers::BlockSparseMatrix objects? Thanks a lot and best regards Gabriel -- 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. For more options, visit https://groups.google.com/d/optout.
Aw: Re: [deal.II] Adding TrilinosWrapper::BlockSparseMatrix
Hey Jean-Paul Thanks a lot, that's what I was looking for, and now it works finely. Best Gabriel Gesendet: Montag, 06. Mai 2019 um 14:27 Uhr Von: "Jean-Paul Pelteret" An: dealii@googlegroups.com Betreff: Re: [deal.II] Adding TrilinosWrapper::BlockSparseMatrix Dear Gabriel, There is a function to do this operation https://dealii.org/9.0.0/doxygen/deal.II/classBlockMatrixBase.html#a9ee9987ece33a052d2b7a44034a8a01a So you should write this as system_matrix.add(1.0, system_matrix_iterative); I hope this helps. Best, Jean-Paul On 06 May 2019, at 13:55, gabriel.pet...@koeln.de wrote: Hey everyone, I got a problem regarding TrilnosWrappers::BlockSparseMatrix. In my program I have a TrilnosWrappers::BlockSparseMatrix system_matrix which consists of two parts, one permanent part, which is computed at the beginning at the programm, not every iteration, to save time (called system_matrix_permanent) and one iterative part, which is computed in every iteration (called system_matrix_iterative). Hence system_matrix = system_matrix_permanent + system_matrix_iterative Thus, after assembling those matrices, I want to call something like system_matrix.add(system_matrix_permanent,system_matrix_permanent); But I always get the error message error: no matching function for call to ‘dealii::TrilinosWrappers::BlockSparseMatrix::add(dealii::TrilinosWrappers::BlockSparseMatrix&)’ system_matrix.add(system_matrix_iterative); Is there any function which adds up TrilinosWrappers::BlockSparseMatrix objects? Thanks a lot and best regards Gabriel -- 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. For more options, visit https://groups.google.com/d/optout. -- 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. For more options, visit https://groups.google.com/d/optout. -- 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. For more options, visit https://groups.google.com/d/optout.
[deal.II] Setting up system matrix fails
Hey everyone, I am setting up a system matrix in Trilinos::Blocksparsematrix with a DOfHandler, which has 3 velocity components and 1 pressure component (analogously to step-32). Somehow everything worked fine a long time, but now I get an error I dont understand. I call: *std::vector div_sol_u (dofs_per_cell); std::vector sol_p (dofs_per_cell);* *[...]* * for (unsigned int k=0; khttp://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/2f4887c3-4853-4515-85b2-9280832b8d5a%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Error at Trilinos installation
Hey everyone, I have an error at compiling deal_ii_with_Trilinos=ON, which I dont understand. First I installed,then I called cmake -DCMAKE_INSTALL_PREFIIX=/home/peters/Documents/installs -DDEAL_II_WITH_TRILINOS=ON -DTRILINOS_DIR=/home/peters/Documents/build_trilinos This all worked finely, but when I called make install I get the following error: [ 55%] Linking CXX shared library ../lib/libdeal_II.so /usr/bin/ld: /home/peters/Documents/build_trilinos/lib/libmuelu-adapters.a(MueLu_CreateEpetraPreconditioner.cpp.o): relocation R_X86_64_PC32 against symbol `_ZTVN7Teuchos17SerialTriDiMatrixIidEE' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: Bad value collect2: error: ld returned 1 exit status source/CMakeFiles/deal_II.dir/build.make:964: recipe for target 'lib/libdeal_II.so.9.1.0-pre' failed make[2]: *** [lib/libdeal_II.so.9.1.0-pre] Error 1 CMakeFiles/Makefile2:941: recipe for target 'source/CMakeFiles/deal_II.dir/all' failed make[1]: *** [source/CMakeFiles/deal_II.dir/all] Error 2 Makefile:129: recipe for target 'all' failed make: *** [all] Error 2 peters@stud-04:~/programs/dealii$ m Can somebody tell me, what went wrong? And where do I have to add the order "recompile with -fPIC". Thanks a lot and best regards Gabriel -- 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. For more options, visit https://groups.google.com/d/optout.
[deal.II] Error at Trilinos installation
Hey everyone, I have an error at compiling deal_ii_with_Trilinos=ON, which I dont understand. First I installed Trilinos,then I called cmake -DCMAKE_INSTALL_PREFIIX=/home/peters/Documents/installs -DDEAL_II_WITH_TRILINOS=ON -DTRILINOS_DIR=/home/peters/Documents/build_trilinos This all worked finely, but when I called make install I get the following error: [ 55%] Linking CXX shared library ../lib/libdeal_II.so /usr/bin/ld: /home/peters/Documents/build_trilinos/lib/libmuelu-adapters.a(MueLu_CreateEpetraPreconditioner.cpp.o): relocation R_X86_64_PC32 against symbol `_ZTVN7Teuchos17SerialTriDiMatrixIidEE' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: Bad value collect2: error: ld returned 1 exit status source/CMakeFiles/deal_II.dir/build.make:964: recipe for target 'lib/libdeal_II.so.9.1.0-pre' failed make[2]: *** [lib/libdeal_II.so.9.1.0-pre] Error 1 CMakeFiles/Makefile2:941: recipe for target 'source/CMakeFiles/deal_II.dir/all' failed make[1]: *** [source/CMakeFiles/deal_II.dir/all] Error 2 Makefile:129: recipe for target 'all' failed make: *** [all] Error 2 peters@stud-04:~/programs/dealii$ m Can somebody tell me, what went wrong? And where do I have to add the order "recompile with -fPIC". Thanks a lot and best regards Gabriel -- 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. For more options, visit https://groups.google.com/d/optout.
[deal.II] Inserting FESolution into systemmatrix
Hey everyone, I want to set up a BlockMatrix, with entries, which are enforced by a velocity components of aBlockVector "solution_old". The Vector contains velocity entries in the first dim terms and pressure entries in the last component. Similar to the 'assemble_system' function of Step-21 tutorial, I use std::vector > solution_old_values(n_q_points); While assembling the system over all cells I call fe_values.get_function_values (solution_old, solution_old_values); In the Step-21 tutorial, they call const double old_s = old_solution_values[q](dim+1); to get the dim+2 component of the vector. Up to here, everything compiles fine, but I dont know how to apply the values correctly Therefore I have the following two questions: Do I simply have to call: const double solution_o = solution_old_values[q](0); to get the velocity component? In fact they are vector-valued, so a double doesn't make sense that much. And thus my second question is: Do I apply the value correctly to the local matrix by calling: local_matrix(i,j) += solution_o * fe_values[velocities].shape_value(i,q) * fe_values[velocities].shape_value(j,q); As always, thanks a lot anf best regards Gabriel -- 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. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Inserting FESolution into systemmatrix
Gabriel Peters Endenicher Str. 310 53121 Bonn 00491525/5478185 gabriel.pet...@koeln.de Am 25.04.19 um 15:28 schrieb Wolfgang Bangerth > On 4/25/19 4:51 AM, gabriel.pet...@koeln.de wrote: > > > > std::vector > solution_old_values(n_q_points); > > > > While assembling the system over all cells I call > > > > fe_values.get_function_values (solution_old, solution_old_values); > > > > In the Step-21 tutorial, they call > > > > const double old_s = old_solution_values[q](dim+1); > > > > to get the dim+2 component of the vector. > > > > Up to here, everything compiles fine, but I dont know how to apply the > > values > > correctly > > Therefore I have the following two questions: > > > > Do I simply have to call: const double solution_o = > > solution_old_values[q](0); > > to get the velocity component? In fact they are vector-valued, so a double > > doesn't make sense that much. > > Correct. The vector should be a `Tensor<1,dim>` and you would have to copy > the > first `dim` components of `solution_old_values[q]` into the tensor. That's > burdensome, so I would suggest that instead you use extractors: >std::vector> old_velocity_values(n_q_points); >fe_values[velocities].get_function_values (...); > and then you already have (only) the velocities and in their right data type. > > > > And thus my second question is: Do I apply the value correctly to the local > > matrix > > by calling: > > local_matrix(i,j) += solution_o * fe_values[velocities].shape_value(i,q) * > > fe_values[velocities].shape_value(j,q); > > This looks funny. You are multiplying a scalar 'solution_o' and phi_i*phi_j > where the latter two are vectors. This works, of course, but didn't you want > solution_o to be a vector as well? Oh thanks I Wrote bullshit. I wanted solution_o to be vector-valued. And I want to multiply it with a gradient function. So I want local_matrix(i,j) += solution_o * fe_values[velocities].shape_gradient(i,q) * fe_values[velocities].shape_gradient(j,q); Does this look any better? > > You are also missing the JxW. I left it out to here to keep Notation as Short as possible Best regards Gabriel > > 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. > For more options, visit https://groups.google.com/d/optout. -- 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. For more options, visit https://groups.google.com/d/optout.
[deal.II] getting components of Blockvector
Hey everyone,
I have the following problem
I have a classical velocity - pressure Blockvector "soluion" and a FEsystem
(initialized via
* fe(FE_Q(degree + 1), dim, FE_Q(degree), 1)*
For some testing I want to get the velocity compontents of solution in
seperate vectors,
i.e. a vector u_x which contains the velocity values of solution in
x-direction.
I am not really sure yet how to get these values.
My attempt is to use FEValues and quadrature points
u_x.reinit(n_dofs_in_one_direction);
*FEValues fe_values(fe,
quadrature_formula, update_values);*
*std::vector> velocity_values(n_q_points);*
*const FEValuesExtractors::Vector velocities(0);*
*for (const auto : dof_handler.active_cell_iterators())*
* {*
* fe_values.reinit(cell);*
* fe_values[velocities].get_function_values(solution,
velocity_values);*
*[...]*
*}*
With this procedure I get the vector of Tensors velocity_values, which
contains the velocity-values of "solution" in every direction at the
quadratue points. So now I an easily get the values of velocity_values in
the x-direction at the quadrature points. But how do I get the values of
u_x at the dofs?
Does somebody have an idea how to fix this, or a better way to do handle
this?
Best regards
Gabriel
--
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/ab0a6346-2529-4909-9d3e-b8da278e40fe%40googlegroups.com.
Re: [deal.II] Setting up system matrix fails
Am Donnerstag, 18. Juli 2019 10:52:46 UTC+2 schrieb Wolfgang Bangerth: > > On 7/9/19 9:01 AM, Gabriel Peters wrote: > > > > After some debugging I found out that the term /(-1)* > sol_p[i]*div_sol_u[j]/ > > makes this trouble. Can somebody tell me why? > > My suspicion would be that you are writing into an element of the matrix > for > which you have not allocated space in the sparsity pattern. Could that be > the > case? > > Thanks a lot for the hint, now I found an error in my coupling for the make_sparsity_pattern function. So indeed the space was not allocated. Thanks a lot Gabriel 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/1b940cdf-8252-49c8-8b0a-f59faa2b73dd%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.
