date:20180409

[deal.II] Use of 'VectorTools::interpolate_boundary_values' using numerical solution.

2018-04-09 Thread Jaekwang Kim



Hi, all 


I am always thank you for all guys here in this community. 


I have a question on the use of  VectorTools::interpolate_boundary_values 
functions


Typically we use this function in when we set-up system as in the form 



VectorTools::interpolate_boundary_values (dof_handler,

1,

   *Original**_VelBndValues(),*

   constraints,

   fe.component_mask(velocities));



The red lined functions are usually declared out side of main class. 


One problem I am interested in now is to (Part A) solve stokes flow with no 
slip boundary condition on every boundary one time (as step-22), -


and then to (Part B) solve same system again with slightly different 
boundary condition comes from the straight problem


If I finish Part A, i have numerical solution of (u,p) linked with dot 
handler. 


In (Part B), I post process solutions part A, e.g. I calculated stress 
value and I calculated tangential velocity of a boundary using Navier slip 
condition, 


So, I need to use 



VectorTools::interpolate_boundary_values (dof_handler,

1,

   *New_VelBndValues(),*

   constraints,

   fe.component_mask(velocities));


such that 



 template

 double

 New_VelBndValues::value (constPoint  &p,

 constunsignedintcomponent) const

 {

 Assert (component < this->n_components,

 ExcIndexRange (component, 0, this->n_components));

 

 if(component == 0)

 *return calc_tangential_velocity (); (Error Here!!)*

 else

 return0;

 }




where '*calc_tangential_velocity ();' *is declared in main class, since I 
should have information of dot_handler and solution vectors.


  template

  classStokesProblem

  {

  public:

StokesProblem (constunsignedintdegree);

voidrun ();

  private:



  ……

 

*double calc_tangential_velocity ();*

 

BlockVector solution;

 

};



  

Obviously, this method does not work, I mean I cannot compile the code and 
it shows  'use of undeclared identifier 'calc_tangential_velocity' on the 
line  *(Error Here!!)*

I would appreciate any one who comment it. It seems that complier has to 
know what is that before. 


Will this be possible in a certain way? How can I  go around this problem ? 


Thanks, 


Jaekwang 



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[deal.II] deal.II Newsletter #27

2018-04-09 Thread Rene Gassmoeller

Hello everyone!

This is deal.II newsletter #27.
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:

#6209: Fix documentation of SparsityPattern (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/6209

#6206: Improve assertions (proposed by drwells) 
https://github.com/dealii/dealii/pull/6206

#6205: doc: mention Kelly estimator in step-37 extensions (proposed by 
davydden; merged) https://github.com/dealii/dealii/pull/6205

#6204: Allow setup_astyle.sh to be used on macOS as well (proposed by 
masterleinad; merged) https://github.com/dealii/dealii/pull/6204

#6203: Guard blank line by HTML comment (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/6203

#6202: Convert data structures in MF::MappingInfo to a face-compatible variant 
(proposed by kronbichler) https://github.com/dealii/dealii/pull/6202

#6201: Separate a note from 'The commented program' (proposed by masterleinad; 
merged) https://github.com/dealii/dealii/pull/6201

#6199: fix changelog date format (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/6199

#6198: make zero_out_ghosts() const (proposed by davydden; merged) 
https://github.com/dealii/dealii/pull/6198

#6196: Make a multigrid test more robust: Filter out small floats (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/6196

#6195: Use DEAL_II_ALWAYS_INLINE in SymmetricTensor (proposed by kronbichler; 
merged) https://github.com/dealii/dealii/pull/6195

#6193: Avoid using an alias variable. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/6193

#6192: Add a necessary include file. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/6192

#6191: Clarify a comment in FiniteElement. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/6191

#6190: Extend documentation of contrib/utilities/setup_astyle.sh. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/6190

#6189: Mark a couple of functions as '[[noreturn]]'. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/6189

#6188: Add replicate_triangulation to GridGenerator #6159 (proposed by 
weixiong-zheng-berkeley) https://github.com/dealii/dealii/pull/6188

#6187: Fix name in static_assert. (proposed by luca-heltai; merged) 
https://github.com/dealii/dealii/pull/6187

#6186: Add realpath for those OS that do not implement it (proposed by 
luca-heltai) https://github.com/dealii/dealii/pull/6186

#6185: Remove more boundary references (proposed by drwells) 
https://github.com/dealii/dealii/pull/6185

#6182: Clone manifolds + std::unique_ptr in Tria (proposed by luca-heltai) 
https://github.com/dealii/dealii/pull/6182

#6181: Check the result of a dynamic_cast. (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/6181

#6180: Move dynamic_unique_cast to Utilities (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/6180

#6178: Added to_string and to_value (proposed by luca-heltai) 
https://github.com/dealii/dealii/pull/6178

#6177: New function for Jacobi polynomial evaluation and its roots (proposed by 
kronbichler) https://github.com/dealii/dealii/pull/6177

#6176: Use dynamic_unique_cast in more places (proposed by masterleinad; 
merged) https://github.com/dealii/dealii/pull/6176

#6175: Add glossary entry on dimensions. (proposed by bangerth) 
https://github.com/dealii/dealii/pull/6175

#6174: Use dynamic_unique_cast() where appropriate. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/6174

#6173: Fix a couple minor issues with #6161. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/6173

#6171: Fix bug in patterns.h (proposed by luca-heltai; merged) 
https://github.com/dealii/dealii/pull/6171

#6170: Allow more digits for output in a few tests (proposed by masterleinad; 
merged) https://github.com/dealii/dealii/pull/6170

#6169: CMake: set policy in subdirectory (proposed by tamiko; merged) 
https://github.com/dealii/dealii/pull/6169

#6168: Improve changelog entry for #6129 (proposed by tjhei) 
https://github.com/dealii/dealii/pull/6168

#6167: Add double word script (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/6167

#6166: contrib/makeofflinedoc.sh: Use https instead of http (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/6166

#6165: Remove some unnecessary ';'s. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/6165

#6164: Remove double word typos. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/6164

#6163: Make using astyle for indenting a bit easier (proposed by masterleinad; 
merged) https://github.com/dealii/dealii/pull/6163

#6161: GridGenerator::extrude_triangulation overload (proposed by 
weixiong-zheng-berkeley; merged) https://github.com/dealii/dealii/p

[deal.II] Re: Error in writing and reading cell based data for restart

2018-04-09 Thread Sambit Das


>
>
> *An error occurred in line <3236> of file 
> 
>  
> in function*
> *void dealii::parallel::distributed::Triangulation spacedim>::notify_ready_to_unpack(unsigned int, const std::function (const dealii::Triangulation::cell_iterator &, 
> dealii::Triangulation::CellStatus, const void *)> &) [with 
> int dim = 3, int spacedim = 3]*
> *The violated condition was: *
> *offset < sizeof(CellStatus)+attached_data_size*
> *Additional information: *
> *invalid offset in notify_ready_to_unpack()*
>

I tried to debug this using ddt debugger- the reason the above condition is 
violated is due to attached_data_size=0, which is strange as the 
*triangulationChk*.*info *file mentions one object to be attached:

* triangulationChk.info *
*version nproc attached_bytes n_attached_objs n_coarse_cells*
*2 1 12 1 1* 

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[deal.II] Error in writing and reading cell based data for restart

2018-04-09 Thread Sambit Das

Hi all,

I have written the following failing minimal example (also attached) where 
I create a single element parallel distributed triangulation and try to 
write and read a double. 

*using namespace dealii;*
*int main (int argc, char *argv[])*
*{*
*  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv);*

*  const double L=20;*
*  parallel::distributed::Triangulation<3> triangulation(MPI_COMM_WORLD);*
*  GridGenerator::hyper_cube (triangulation, -L, L);*

*  unsigned int offset = triangulation.register_data_attach*
*   (sizeof(double),*
*[&](const typename 
dealii::parallel::distributed::Triangulation<3>::cell_iterator &cell,*
*const typename 
dealii::parallel::distributed::Triangulation<3>::CellStatus status,*
*void * data) -> void*
*{*

*  double* dataStore = reinterpret_cast(data);*
*  *dataStore=0.0;*
*}*
*);*

*  std::cout<< "offset=" << offset << std::endl;*
*  std::string filename="triangulationChk";*
*  triangulation.save(filename.c_str());*

*  triangulation.load(filename.c_str());*
*  triangulation.notify_ready_to_unpack*
*   (offset,[&](const typename 
dealii::parallel::distributed::Triangulation<3>::cell_iterator &cell,*
* const typename 
dealii::parallel::distributed::Triangulation<3>::CellStatus status,*
* const void * data) -> void*
* {*
* }*
*);*
*}*


I get the following error:

*An error occurred in line <3236> of file 

 
in function*
*void dealii::parallel::distributed::Triangulation::notify_ready_to_unpack(unsigned int, const std::function::cell_iterator &, 
dealii::Triangulation::CellStatus, const void *)> &) [with 
int dim = 3, int spacedim = 3]*
*The violated condition was: *
*offset < sizeof(CellStatus)+attached_data_size*
*Additional information: *
*invalid offset in notify_ready_to_unpack()*

I am wondering if I am missing something in my implementation.

Thanks,
Sambit

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//Include all deal.II header file
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
//Include generic C++ headers
#include 
#include 


using namespace dealii;
int main (int argc, char *argv[])
{
  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv);

  const double L=20;
  parallel::distributed::Triangulation<3> triangulation(MPI_COMM_WORLD);
  GridGenerator::hyper_cube (triangulation, -L, L);

  unsigned int offset = triangulation.register_data_attach
	  (sizeof(double),
		   [&](const typename dealii::parallel::distributed::Triangulation<3>::cell_iterator &cell,
		   const typename dealii::parallel::distributed::Triangulation<3>::CellStatus status,
		   void * data) -> void
		   {

			 double* dataStore = reinterpret_cast(data);
			 *dataStore=0.0;
		   }
		   );

  std::cout<< "offset=" << offset << std::endl;
  std::string filename="triangulationChk";
  triangulation.save(filename.c_str());

  triangulation.load(filename.c_str());
  triangulation.notify_ready_to_unpack
	  (offset,[&](const typename dealii::parallel::distributed::Triangulation<3>::cell_iterator &cell,
	const typename dealii::parallel::distributed::Triangulation<3>::CellStatus status,
	const void * data) -> void
	{
	}
	   );
}

[deal.II] Re: deal.II cannot found HDF5

2018-04-09 Thread Bruno Turcksin

Peng,

On Saturday, April 7, 2018 at 7:29:31 AM UTC-4, Peng Ding wrote:
>
> Dear group:
>   I have compiled the HDF5 with "--enable-parallel". but deal.II still 
> cannot recognize it. 
> How to resolve this problem.
> Regards
>
Like Daniel said you need to give us more information. One possibility is 
that another library is using a different HDF5. For example, Trilinos could 
pick up a different version of hdf5 and then, deal.II will use the same 
version of hdf5.

Best,

Bruno

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[deal.II] Use of 'VectorTools::interpolate_boundary_values' using numerical solution.

[deal.II] deal.II Newsletter #27

[deal.II] Re: Error in writing and reading cell based data for restart

[deal.II] Error in writing and reading cell based data for restart

[deal.II] Re: deal.II cannot found HDF5

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