date:20230711

Re: [deal.II] Compiling release 9.5.0

2023-07-11 Thread Matthias Maier

I can reproduce. Thanks a lot for the bug report!

We will track this issue here

  https://github.com/dealii/dealii/issues/15724

We will have a new point release very soon...

For background: we have a regression testsuite variant that should check
that we can indeed compile successfully with all bundled
dependencies. But it turns out that the testsuite is misconfigured :-(

In the meantime you can either disable tbb with "-DDEAL_II_WITH_TBB=off"
when configuring deal.II (which also means no thread/task support), or
install tbb with your distribution package manager
(apt install libtbb-dev on debian/ubuntu)
and use the external one.

Best,
Matthias



On Tue, Jul 11, 2023, at 21:25 CDT, Jack Urombo  wrote:

> Here is the detailed log.
>
> On Sat, 8 Jul 2023 at 17:37, Matthias Maier  wrote:
>
>> Hi,
>>
>> Would you mind to also send us the "detailed.log" file located in your
>> build directory?
>>
>> Best,
>> Matthias
>>
>>
>>
>> On Sat, Jul  8, 2023, at 03:16 CDT, jack urombo  wrote:
>>
>> > The new release has this error on compiling.
>> >
>> > [ 10%] Building CXX object
>> > bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/tbb/ar
>> > ena.cpp.o
>> > In file included from
>> > /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/s
>> > cheduler_common.h:43,
>> > from
>> > /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/s
>> > cheduler.h:24,
>> > from
>> > /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/a
>> > rena.cpp:23:
>> > /home/
>> ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:266:2
>> > 0: error: declaration of ‘tbb::task& tbb::internal::task_prefix::task()’
>> > changes meaning o
>> > f ‘task’ [-Wchanges-meaning]
>> >  266 | tbb::task& task() {return
>> > *reinterpret_cast(this+1);}
>> >  |^~~~
>> > /home/
>> ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:225:9
>> > : note: used here to mean ‘class tbb::task’
>> >  225 | task* next_offloaded;
>> >  | ^~~~
>> > /home/
>> ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:33:7
>> :
>> > note: declared here
>> >   33 | class task;
>> >  |   ^~~~
>> > make[2]: ***
>> > [bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/build.make:90:
>> > bund
>> > led/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/tbb/arena.cpp.o]
>> Error
>> > 1
>> > make[1]: *** [CMakeFiles/Makefile2:1782:
>> > bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_de
>> > bug.dir/all] Error 2
>> > make: *** [Makefile:136: all] Error 2
>> >
>> >
>> >
>> > --
>> >
>> >
>> >
>> >
>> > The information in this message is confidential and legally
>> > privileged.
>> > It is intended solely for the addressee(s). Access to this message
>> > by
>> > anyone else is unauthorized. If received in error, please accept our
>> > apologies
>> > and notify the sender immediately. You must also delete the
>> > original message
>> > from your machine. If you are not the intended recipient,
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>> > copying, distribution or action taken in reliance of
>> > it, is prohibited and may
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>>
>
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[deal.II] how to define periodic bc in delal.II

2023-07-11 Thread ztdep...@gmail.com

I waant to know how to define periodic bc in delal.II. 

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[deal.II] Computational Materials Scientist opening at the PRISMS Center (University of Michigan)

2023-07-11 Thread David Montiel Taboada

 

Hello everyone,

I would like to share that we have an opening for Computational Materials 
Scientist position at the PRISMS Center of the University of Michigan. 

The specific area is in the *development and application of our crystal 
plasticity and fracture simulations codes* that are housed in the finite 
element-based *PRISMS-Plasticity *code, which is *based upon the deal.II 
library*.

Please visit this page 

 for 
more details, requirements and information on how to apply. 

Best, 

David

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Re: [deal.II] Compiling release 9.5.0

2023-07-11 Thread Jack Urombo

Here is the detailed log.

On Sat, 8 Jul 2023 at 17:37, Matthias Maier  wrote:

> Hi,
>
> Would you mind to also send us the "detailed.log" file located in your
> build directory?
>
> Best,
> Matthias
>
>
>
> On Sat, Jul  8, 2023, at 03:16 CDT, jack urombo  wrote:
>
> > The new release has this error on compiling.
> >
> > [ 10%] Building CXX object
> > bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/tbb/ar
> > ena.cpp.o
> > In file included from
> > /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/s
> > cheduler_common.h:43,
> > from
> > /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/s
> > cheduler.h:24,
> > from
> > /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/a
> > rena.cpp:23:
> > /home/
> ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:266:2
> > 0: error: declaration of ‘tbb::task& tbb::internal::task_prefix::task()’
> > changes meaning o
> > f ‘task’ [-Wchanges-meaning]
> >  266 | tbb::task& task() {return
> > *reinterpret_cast(this+1);}
> >  |^~~~
> > /home/
> ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:225:9
> > : note: used here to mean ‘class tbb::task’
> >  225 | task* next_offloaded;
> >  | ^~~~
> > /home/
> ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:33:7
> :
> > note: declared here
> >   33 | class task;
> >  |   ^~~~
> > make[2]: ***
> > [bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/build.make:90:
> > bund
> > led/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/tbb/arena.cpp.o]
> Error
> > 1
> > make[1]: *** [CMakeFiles/Makefile2:1782:
> > bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_de
> > bug.dir/all] Error 2
> > make: *** [Makefile:136: all] Error 2
> >
> >
> >
> > --
> >
> >
> >
> >
> > The information in this message is confidential and legally
> > privileged.
> > It is intended solely for the addressee(s). Access to this message
> > by
> > anyone else is unauthorized. If received in error, please accept our
> > apologies
> > and notify the sender immediately. You must also delete the
> > original message
> > from your machine. If you are not the intended recipient,
> > any use, disclosure,
> > copying, distribution or action taken in reliance of
> > it, is prohibited and may
> > be unlawful. The information, attachments,
> > opinions or advice contained in this
> > email are not the views or opinions of
> > Harare Institute of Technology, its
> > subsidiaries or affiliates. Although
> > this email and any attachments are
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> > accepted by Harare Institute of
> > Technology and/or its subsidiaries for any loss
> > or damage arising in any
> > way from the receipt or use thereof.
>
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>


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The information in this message is confidential and legally
privileged. 
It is intended solely for the addressee(s). Access to this message
by 
anyone else is unauthorized. If received in error, please accept our 
apologies
and notify the sender immediately. You must also delete the 
original message
from your machine. If you are not the intended recipient, 
any use, disclosure,
copying, distribution or action taken in reliance of 
it, is prohibited and may
be unlawful. The information, attachments, 
opinions or advice contained in this
email are not the views or opinions of 
Harare Institute of Technology, its
subsidiaries or affiliates. Although 
this email and any attachments are
believed to be free of any virus or 
other defects which might affect any
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are received, no responsibility is
accepted by Harare Institute of 
Technology and/or its subsidiaries for any loss
or damage arising in any 
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[deal.II] Re: Matrix Free Multiple DoFHandlers

2023-07-11 Thread Sean Johnson

Okay the problem is the global vector that I use for the additional 
DoFHandler does not have a mg_transfer to help the vector have the right 
amount of indices on all levels of the multigrid.

I don't see a way to construct the preconditioner with multiple transfers 
though it does allow multiple DoFHandlers. Is there something I am missing 
or does Deal.II not allow for this yet?

Thanks,
Sean Johnson

On Monday, July 10, 2023 at 1:57:49 PM UTC-6 Sean Johnson wrote:

> Hello it is me again,
>
> I am trying to something very similar to this discussion: 
> https://groups.google.com/g/dealii/c/Hh4iBsM21FI/m/cF-mzDP4GkwJ
>
> My question would be how could I pass the solution vector of the 
> pre-determined solution into the matrix free operator.
>
> I know this is a bad idea but currently I have the vector as a global 
> variable so I don't have to pass it into the local_apply function or 
> anything really. I do call initialize_dof_vector with the correct index but 
> in the conjugate gradient solve function the preconditioner throws the 
> error included at the bottom of this message.
>
> Also, attached is the just the setup_system() function similar to step-37 
> to try and keep code to a minimal. Nothing has been altered in the solve() 
> function from step-37 in the code.
>
> Thanks if anyone has the time to get to this beforehand,
> Sean Johnson
>
> 
> An error occurred in line <238> of file 
> 
>  
> in function
> void dealii::internal::check_vector_compatibility(const VectorType&, 
> const dealii::MatrixFree&, const 
> dealii::internal::MatrixFreeFunctions::DoFInfo&) [with int dim = 2; Number 
> = double; VectorizedArrayType = dealii::VectorizedArray; 
> VectorType = dealii::LinearAlgebra::distributed::Vector; typename 
> std::enable_if, 
> VectorType>::type*  = 0]
> The violated condition was: 
> false
> Additional information: 
> The parallel layout of the given vector is compatible neither with the
> Partitioner of the current FEEvaluation with dof_handler_index=1 nor
> with any Partitioner in MatrixFree. A potential reason is that you did
> not use MatrixFree::initialize_dof_vector() to get a compatible
> vector.
>
> Stacktrace:
> ---
> #0  ./step-37_minimal: void 
> dealii::internal::check_vector_compatibility<2, double, 
> dealii::VectorizedArray, 
> dealii::LinearAlgebra::distributed::Vector dealii::MemorySpace::Host>, 
> (dealii::LinearAlgebra::distributed::Vector dealii::MemorySpace::Host>*)0>(dealii::LinearAlgebra::distributed::Vector  
> dealii::MemorySpace::Host> const&, dealii::MatrixFree<2, double, 
> dealii::VectorizedArray > const&, 
> dealii::internal::MatrixFreeFunctions::DoFInfo const&)
> #1  ./step-37_minimal: void dealii::FEEvaluationBase<2, 1, double, false, 
> dealii::VectorizedArray 
> >::read_write_operation dealii::MemorySpace::Host> const, dealii::internal::VectorReader dealii::VectorizedArray > 
> >(dealii::internal::VectorReader 2ul> > const&, 
> std::array dealii::MemorySpace::Host> const*, 1ul> const&, 
> std::array  
> dealii::MemorySpace::Host>::value_type const, dealii::MemorySpace::Host>, 
> std::allocator  
> dealii::MemorySpace::Host>::value_type const, dealii::MemorySpace::Host> > 
> > const*, 1ul> const&, std::bitset<2ul> const&, bool) const
> #2  ./step-37_minimal: void dealii::FEEvaluationBase<2, 1, double, false, 
> dealii::VectorizedArray 
> >::read_dof_values dealii::MemorySpace::Host> 
> >(dealii::LinearAlgebra::distributed::Vector dealii::MemorySpace::Host> const&, unsigned int, std::bitset<2ul> const&)
> #3  ./step-37_minimal: Step37::LaplaceOperator<2, 3, 
> double>::local_apply(dealii::MatrixFree<2, double, 
> dealii::VectorizedArray > const&, 
> dealii::LinearAlgebra::distributed::Vector dealii::MemorySpace::Host>&, 
> dealii::LinearAlgebra::distributed::Vector dealii::MemorySpace::Host> const&, std::pair 
> const&) const
> #4  ./step-37_minimal: dealii::internal::MFWorker double, dealii::VectorizedArray >, 
> dealii::LinearAlgebra::distributed::Vector dealii::MemorySpace::Host>, 
> dealii::LinearAlgebra::distributed::Vector dealii::MemorySpace::Host>, Step37::LaplaceOperator<2, 3, double>, 
> true>::process_range(void (Step37::LaplaceOperator<2, 3, double>::* 
> const&)(dealii::MatrixFree<2, double, dealii::VectorizedArray 
> > const&, dealii::LinearAlgebra::distributed::Vector dealii::MemorySpace::Host>&, 
> dealii::LinearAlgebra::distributed::Vector dealii::MemorySpace::Host> const&, std::pair 
> const&) const, std::vector > 
> const&, std::vector > const&, 
> unsigned int)
> #5  ./step-37_minimal: dealii::internal::MFWorker double, dealii::VectorizedArray >, 
> dealii::LinearAlgebra::distributed::Vector dealii::MemorySpace::Host>, 
> dealii::LinearAlgebra::distributed::Vector dealii::MemorySpace::Host>, Step37::LaplaceOperator<2, 3, double>, 
> true>::cell(unsigned int)
> #6  /home/sjohnson/AE_beginnings/dealii/lib/libdeal_II.g.so.9.4.0: 
>

Re: [deal.II] Deformation gradient at face quadrature point for current traction

2023-07-11 Thread Abbas Ballout

Krish,

I could do this following step 18 and how history variables are constructed 
there.
It was straightforward in case you are interested.   



On Wednesday, June 28, 2023 at 7:55:19 PM UTC+2 Wolfgang Bangerth wrote:

> On 6/26/23 00:49, Krish wrote:
> > 
> > I am following step-44 to solve an elasticity problem. I am trying to 
> > implement current traction (as opposed to the dead load used in step-44) 
> > on a part of the boundary. For that I need to use the deformation 
> > gradient and its determinant at the f_q_point(s) (face quadrature 
> > points). I am interested to know what might be a suitable way to get 
> these.
>
> If you have the deformation field as a solution vector, then computing 
> its gradient at quadrature points on faces is easily done using 
> FEFaceValues. Take a look at the computation of "fluxes" here:
>
> https://dealii.org/developer/doxygen/deal.II/step_4.html#PostprocessingWhattodowiththesolution
> In your case, the gradients are going to be tensors, and you will 
> compute them using code such as
>
> std::vector> 
> solution_gradients(face_quadrature_formula.size());
>
> FEValuesExtractors::Vector deformation(...);
> ...
>
> fe_face_values[deformation].get_function_gradients(solution, 
> solution_gradients);
>
> There is a free function called 'determinant()' that can be used to 
> compute the determinant of a dim x dim tensor.
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>

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[deal.II] Applying non-homogeneous Neumann BC in step-18

2023-07-11 Thread Mohammad Amir Kiani Fordoei

Dear Deal.II group
I am trying to add boundary force (b) to step-18 as below

[image: Screenshot from 2023-07-11 14-01-30.png]
As I understood, I just need to specify a boundary_id on triangulation and 
apply traction force on that with code like this:
{ - loop over cells 
-loop over faces per cell && controlling being at_boundary
-loop over quadrature points of face
-loop over dof per cell && controlling intended boundary_id_NBC
-finally adding this term to rhs as
cell_rhs (i)+=
(fe_face_values.shape_value (i,q_point)

*traction_component 

*fe_face_values.JxW(q_point));}
But, I didn't see noticble variation of displacement or norm of stress in 
my solution, even for large traction force.
is it necessary to multiply traction_component to "* present_timestep * 
velocity " (like Dirichlet BC displacement)? (I tried this too, but similar 
to previous one no significant effect of load was observed.)

instead of procedure described in step-18, can I use functions " 
create_right_hand_side" and "create_boundary_right_hand_side" of 
VectorTools for applying body and traction force, respectively or they just 
belongs to Laplace equation?
Thanks for considering this!
Amir

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Re: [deal.II] Compiling release 9.5.0

[deal.II] how to define periodic bc in delal.II

[deal.II] Computational Materials Scientist opening at the PRISMS Center (University of Michigan)

Re: [deal.II] Compiling release 9.5.0

[deal.II] Re: Matrix Free Multiple DoFHandlers

Re: [deal.II] Deformation gradient at face quadrature point for current traction

[deal.II] Applying non-homogeneous Neumann BC in step-18

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