date:20171108

Re: [deal.II] deal.II on Mac OS Sierra

2017-11-08 Thread Pawan Takhar

Hi Uwe,

 

Thanks for providing such a detailed reply. The following suggestion solved my 
problem.

 

export 
DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/OCE-0.18/lib:/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/parmetis-4.0.3/lib

 

I included this line in my .bash_profile file by using appropriate paths for 
OCE and parmetis files. Now after compiling the deal-ii programs, when I run 
them in command line, they run fine. I appreciate your looking into my error 
messages and troubleshooting.

 

Regards,

Pawan

 

From: "'Uwe Köcher' via deal.II User Group" 
Reply-To: 
Date: Wednesday, November 8, 2017 at 10:20 AM
To: "deal.II User Group" 
Subject: Re: [deal.II] deal.II on Mac OS Sierra

 

export 
DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/OCE-0.18/lib:/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/parmetis-4.0.3/lib

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Re: [deal.II] A_inverse in step-57

2017-11-08 Thread Jie Cheng

Hi Timo and Wolfgang

It turns out the SparseILU needs to be tuned very carefully. I set the
AdditioalData to (0.03, 0) the solver now works fine. Although it is still
slower than UMFPACK. Maybe using just the right parameters in
AdditionalData can further improve it. I observed similar thing in step-57
too. Using ILU + GMRES for A inverse won't even converge in reasonable time
with default AdditionalData. Playing with the AdditionalData helps... In a
word, SparseILU seems to be sensitive to the AdditionalData and how to
choose the right parameter is unclear.

Wolfgang, would you like me to contribute this code to the code gallery? Is
there anything in this code that I should polish?

Thank you
Jie

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[deal.II] deal.II Newsletter #10

2017-11-08 Thread Rene Gassmoeller

Hello everyone!

This is deal.II newsletter #10.
It automatically reports recently merged features and discussions about the 
deal.II finite element library.


## Below you find a list of recently proposed or merged features:

#5425: Consistently use UNIX line endings. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/5425

#5424: Fix test. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/5424

#5423: Disambiguate parallel::GridTools and GridTools. (proposed by drwells) 
https://github.com/dealii/dealii/pull/5423

#5422: doxygen: fix deprecated function signatures (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/5422

#5421: Fix expansion for Adol-C numbers (proposed by jppelteret; merged) 
https://github.com/dealii/dealii/pull/5421

#5419: Allow outputting complex-valued data through DataOut. (proposed by 
bangerth) https://github.com/dealii/dealii/pull/5419

#5418: Minor updates to DoFRenumbering::Cuthill_McKee. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/5418

#5416: lower the tolerance for full_matrix_10 test with float numbers (proposed 
by davydden; merged) https://github.com/dealii/dealii/pull/5416

#5415: Replace std::fabs() by std::abs() for complex numbers. (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/5415

#5414: Adding distributed_compute_point_locations (WIP) (proposed by GivAlz) 
https://github.com/dealii/dealii/pull/5414

#5412: Fix erroneous assert and add a test (proposed by agrayver; merged) 
https://github.com/dealii/dealii/pull/5412

#5411: Make fe_field_function compute::point locations use the gridtools 
version (proposed by GivAlz) https://github.com/dealii/dealii/pull/5411

#5410: Performance improvement for transfinite interpolation manifold. 
(proposed by kronbichler) https://github.com/dealii/dealii/pull/5410

#5409: Make a few more tests more robust (proposed by kronbichler; merged) 
https://github.com/dealii/dealii/pull/5409

#5408: Speed up SphericalManifold::get_new_point (proposed by kronbichler) 
https://github.com/dealii/dealii/pull/5408

#5406: Add functionality to create sparsity pattern for MG interface matrices 
(proposed by tcclevenger; merged) https://github.com/dealii/dealii/pull/5406

#5405: Fix a bug in cmake when using CUDA. (proposed by Rombur; merged) 
https://github.com/dealii/dealii/pull/5405

#5404: Use PolarManifold in 2D SphericalManifold (proposed by masterleinad; 
merged) https://github.com/dealii/dealii/pull/5404

#5403: Make a number of tests more robust (proposed by kronbichler; merged) 
https://github.com/dealii/dealii/pull/5403

#5401: Fix missing norm_sqr in parallel vector. This is requied by SolverQMRS. 
(proposed by mwichro) https://github.com/dealii/dealii/pull/5401

#5400: Make line search for transfinite manifold more stable (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/5400

#5399: Minor doc update to GridRenumbering::Cuthill_McKee. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/5399

#5398: Instantiate everything also for complex-valued vectors. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/5398

#5397: Fix TransfiniteInterpolationManifold on complex geometry (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/5397

#5396: Make a few more things work with std::complex types. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/5396

#5395: Make LapackFullMatrix also work with std::complex data types. (proposed 
by bangerth; merged) https://github.com/dealii/dealii/pull/5395

#5394: Make a piece of code work for std::complex data types. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/5394

#5393: Fix algorithm in Manifold::normal_vector (proposed by gassmoeller; 
merged) https://github.com/dealii/dealii/pull/5393

#5392:  Implement type traits and helper classes for AD numbers (proposed by 
jppelteret) https://github.com/dealii/dealii/pull/5392

#5391: Implement more product types for AD numbers (proposed by jppelteret; 
merged) https://github.com/dealii/dealii/pull/5391

#5390: Document replacements for the Boundary objects (proposed by 
masterleinad; merged) https://github.com/dealii/dealii/pull/5390

#5389: Also describe complex types to MPI. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/5389

#5388: Make things work for std::complex data types. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/5388

#5387: Support sundials-3.0.0 (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/5387

#5386: [WIP] Replace broken mesh smoothing with Laplacian (proposed by 
kronbichler) https://github.com/dealii/dealii/pull/5386

#5385:  escape characters in LaTeX format of ParameterHandler (proposed by 
tjhei) https://github.com/dealii/dealii/pull/5385

#5384: move CellDataTransferBuffer out of internal namespace (proposed by 
davydden; merged)

[deal.II] query FE support point type and additional info?

2017-11-08 Thread Timo Heister

Hey all,

I am looking for ways to get more information about (generalized)
support points for a particular FE:
1. How can I translate between generalized_support_point j and
dof_per_cell index k? For example FE_DGRaviartThomas<2>(1) has 9
generalized_support_points but 12 dofs_per_cell.
2. 
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_developer_doxygen_deal.II_DEALGlossary.html-23GlossGeneralizedSupport=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=noUPzp6HQo5Ab1sMhXHEPDtKWiunYMqmACzbvcvljEk=xGxO7IMz8sGBENTwwyRKlCiJ7WNuI0hby0Co0ZQhaks=
 
says FE_Q_Hierarchical has no generalized support points but the
element actually returns 4 generalized support points in 2d with
degree 1. Who is right?
3. Elements like FE_QLegendre return 0 generalized support points. Is
there any information I can extract from the FE about the degrees of
freedom or support points in this case?

Thanks.

-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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Re: [deal.II] deal.II on Mac OS Sierra

2017-11-08 Thread 'Uwe Köcher' via deal . II User Group

ah, it seems that you have installed oce as well... I've checked my 
modulefile for macOS, an I set
all the lib-pathes...

depending on the packages you have installed, it should be 

export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/apps/candi/deal.II-toolchain/v8
.5.1/brew-openmpi/OCE-0.18/lib:/apps/candi/deal.II-toolchain/v8.5.1/brew-
openmpi/parmetis-4.0.3/lib


and so on... each lib path is divided by a colon (:).

Check for your lib-pathes in your installation destination.

You can include that in the "enable.sh" script.

For me, the current complete list (set in a modulefile) is:
prepend-pathDYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8
.5.1/brew-openmpi/parmetis-4.0.3/lib
prepend-pathDYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8
.5.1/brew-openmpi/superlu_dist_5.1.2/lib


#prepend-pathDYLD_LIBRARY_PATH   
/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/OCE-0.18/lib
prepend-pathDYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8
.5.1/brew-openmpi/deal.II-v8.5.1/lib
prepend-pathDYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8
.5.1/brew-openmpi/hdf5-1.10.1/lib
#prepend-pathDYLD_LIBRARY_PATH   
/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/p4est-2.0/FAST/lib
#prepend-pathDYLD_LIBRARY_PATH   
/apps/candi/deal.II-toolchain/v8.5.1/brew-openmpi/p4est-2.0/DEBUG/lib
prepend-pathDYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8
.5.1/brew-openmpi/petsc-3.7.6/lib
prepend-pathDYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8
.5.1/brew-openmpi/slepc-3.7.3/lib
prepend-pathDYLD_LIBRARY_PATH   /apps/candi/deal.II-toolchain/v8
.5.1/brew-openmpi/trilinos-release-12-10-1/lib



On Wednesday, 8 November 2017 16:52:48 UTC+1, Pawan Takhar wrote:
>
> Hi Uwe,
>
>  
>
> When I type ./step-1 in the folder where step-1 was compiled, I get the 
> following error:
>
>  
>
> dyld: Library not loaded: libTKBO.11.dylib
>
>   Referenced from: /Users/username/Documents/deal2/examples/step1/./step-1
>
>   Reason: image not found
>
> Abort trap: 6
>
>  
>
> I tried searching for libTKBO.11.dylib, but could not find the package 
> that would contain this.
>
>  
>
> Regards,
>
> Pawan
>
>  
>

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Re: [deal.II] deal.II on Mac OS Sierra

2017-11-08 Thread Pawan Takhar

Hi Uwe,

 

When I type ./step-1 in the folder where step-1 was compiled, I get the 
following error:

 

dyld: Library not loaded: libTKBO.11.dylib

  Referenced from: /Users/username/Documents/deal2/examples/step1/./step-1

  Reason: image not found

Abort trap: 6

 

I tried searching for libTKBO.11.dylib, but could not find the package that 
would contain this.

 

Regards,

Pawan

 

From: "'Uwe Köcher' via deal.II User Group" 
Reply-To: 
Date: Wednesday, November 8, 2017 at 3:42 AM
To: "deal.II User Group" 
Subject: Re: [deal.II] deal.II on Mac OS Sierra

 

Hi Pawan,

 

what do you mean by

 

.3) /step-1 (does not run).

 

?

 

I only can see warnings and 100% Built & Linking, no errors.

Those warnings relates to the apple-clang compiler.

 

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Re: [deal.II] A few questions

2017-11-08 Thread Manav Bhatia

Thanks! 

> On Nov 8, 2017, at 3:14 AM, luca.heltai  wrote:
> 
> 
>>> — Are there any applications with immersed FEM (cut-cell, etc.) with 
>>> deal.II?
> 
> Yes. There are at least two open source codes, published on “Archive of 
> Numerical Software”:
> 
> http://journals.ub.uni-heidelberg.de/index.php/ans/issue/view/2930
> 
> "Carraro, Wetterauer: On the implementation of the eXtended Finite Element 
> Method (XFEM) for interface problems”
> 
> and 
> 
> http://journals.ub.uni-heidelberg.de/index.php/ans/issue/view/1724
> 
> "Heltai, Roy, Costanzo: A Fully Coupled Immersed Finite Element Method for 
> Fluid Structure Interaction via the deal.II Library”
> 
> Best,
> Luca.
> 
> -- 
> 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
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Re: [deal.II] deal.II on Mac OS Sierra

2017-11-08 Thread 'Uwe Köcher' via deal . II User Group

Hi Pawan,

what do you mean by

.3) /step-1 (does not run).
>

?

I only can see warnings and 100% Built & Linking, no errors.
Those warnings relates to the apple-clang compiler.

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Re: [deal.II] A few questions

2017-11-08 Thread luca.heltai


>> — Are there any applications with immersed FEM (cut-cell, etc.) with deal.II?

Yes. There are at least two open source codes, published on “Archive of 
Numerical Software”:

http://journals.ub.uni-heidelberg.de/index.php/ans/issue/view/2930

"Carraro, Wetterauer: On the implementation of the eXtended Finite Element 
Method (XFEM) for interface problems”

and 

http://journals.ub.uni-heidelberg.de/index.php/ans/issue/view/1724

"Heltai, Roy, Costanzo: A Fully Coupled Immersed Finite Element Method for 
Fluid Structure Interaction via the deal.II Library”

Best,
Luca.

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Re: [deal.II] deal.II on Mac OS Sierra

Re: [deal.II] A_inverse in step-57

[deal.II] deal.II Newsletter #10

[deal.II] query FE support point type and additional info?

Re: [deal.II] deal.II on Mac OS Sierra

Re: [deal.II] deal.II on Mac OS Sierra

Re: [deal.II] A few questions

Re: [deal.II] deal.II on Mac OS Sierra

Re: [deal.II] A few questions

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