Re: [deal.II] Finite Element Software deal.II Version 9.2.0 released

2020-06-11 Thread Wolfgang Bangerth

On 6/10/20 9:19 PM, Matthias Maier wrote:

Version 9.2.0 of deal.II, the object-oriented finite element library
awarded the J. H. Wilkinson Prize for Numerical Software, has been
released. It is available for free under an Open Source license from the
deal.II homepage at [...]


All,
the link to it is somewhere further down in the announcement, but I'd like to
highlight as always the paper in which we summarize the major improvements in
this version:
  https://www.dealii.org/deal92-preprint.pdf
You may find it interesting.

As always, many many people have contributed to this release. In
addition to the 17 authors of the paper above, section 4 lists another 79
people, also listed below. I think that's an awesome number, and we owe all of 
them for all of their contributions -- thank you!


Best
 Wolfgang & the rest of the principal developers


Pasquale Africa,
Ashna Aggarwal,
Giovanni Alzetta,
Mathias Anselmann,
Kirana Bergstrom,
Manaswinee Bezbaruah,
Benjamin Brands,
Yong-Yong Cai,
Fabian Castelli,
Joshua Christopher,
Ester Comellas,
Katherine Cosburn,
Denis Davydov,
Elias Dejene,
Stefano Dominici,
Brett Dong,
Luel Emishaw,
Niklas Fehn,
Rebecca Fildes,
Menno Fraters,
Andres Galindo,
Daniel Garcia-Sanchez,
Rene Gassmoeller,
Melanie Gerault,
Nicola Giuliani,
Brandon Gleeson,
Anne Glerum,
Krishnakumar Gopalakrishnan,
Graham Harper,
Mohammed Hassan,
Nicole Hayes,
Bang He,
Johannes Heinz,
Jiuhua Hu,
Lise-Marie Imbert-Gerard,
Manu Jayadharan,
Daniel Jodlbauer,
Marie Kajan,
Guido Kanschat,
Alexander Knieps,
Uwe K{\"o}cher,
Paras Kumar,
Konstantin Ladutenko,
Charu Lata,
Adam Lee,
Wenyu Lei,
Katrin Mang,
Mae Markowski,
Franco Milicchio,
Adriana Morales Miranda,
Bob Myhill,
Emily Novak,
Omotayo Omosebi,
Alexey Ozeritskiy,
Rebecca Pereira,
Geneva Porter,
Laura Prieto Saavedra,
Roland Richter,
Jonathan Robey,
Irabiel Romero,
Matthew Russell,
Tonatiuh Sanchez-Vizuet,
Natasha S. Sharma,
Doug Shi-Dong,
Konrad Simon,
Stephanie Sparks,
Sebastian Stark,
Simon Sticko,
Jan Philipp Thiele,
Jihuan Tian,
Sara Tro,
Ferdinand Vanmaele,
Michal Wichrowski,
Julius Witte,
Winnifried Wollner,
Ming Yang,
Mario Zepeda Aguilar,
Wenjuan Zhang,
Victor Zheng.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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[deal.II] Xcode as an IDE for deal.II

2020-06-11 Thread Siva Nadarajah
Dear All, 
My group has been using deal.ii for the past two years. I just switched to 
using XCode. I have a problem where std::cout does write out to the console 
within Xcode, but I do see it when the code runs on command line. Any 
thoughts?
Best Regards,
Siva

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Re: [deal.II] Re: Is it possible to copy_triangulation for fullydistributed with periodic face?

2020-06-11 Thread heena patel
Dear Peter,
 Thanks for the reply. It gives the following error







*error: no matching function for call to
‘dealii::parallel::fullydistributed::Triangulation<2,
2>::Triangulation(ompi_communicator_t*&, dealii::Triangulation<2,
2>::MeshSmoothing)’is_periodic(is_periodic)
 ^In file included from
/home/heena/Project/MsFEM/advection-diffusion-equation/include/advectiondiffusion_multiscale.hpp:39:0,
   from
/home/heena/Project/MsFEM/advection-diffusion-equation/source/AdvectionDiffusionProblem.cc:13:/home/heena/lib/dealII/include/deal.II/distributed/fully_distributed_tria.h:134:16:
note: candidate: dealii::parallel::fullydistributed::Triangulation::Triangulation(MPI_Comm) [with int dim = 2; int spacedim = 2;
MPI_Comm = ompi_communicator_t*]   explicit Triangulation(MPI_Comm
mpi_communicator);*


It seems that the link you send me explains that I have to create serial
triangulation and then apply periodicity?

Regards,
Heena

On Thu, Jun 11, 2020 at 11:36 AM 'peterrum' via deal.II User Group <
dealii@googlegroups.com> wrote:

> Dear Heena,
>
> may I ask you to be more specific regarding to
> parallel::fullydistributed::Triangualation (p:f:t) error. In the case of
> p:f:t you can copy indeed refined meshes, however users need to deal with
> periodicity on their own by applying the periodicy once again. See the
> following test:
> https://github.com/dealii/dealii/blob/master/tests/fullydistributed_grids/copy_serial_tria_04.cc#L102
>
> This is kinda annoying, but I was not able to come up with a more
> transparent solution during the development of p:f:t.
>
> Hope that helps,
> Peter
>
> On Thursday, 11 June 2020 10:06:49 UTC+2, heena patel wrote:
>>
>> Dear all,
>>  I am trying to solve semilagrangian advection
>> problem?
>> I have traingulation with periodic face.
>> I wanted to copy_triangulation and trace back mesh. The thing is with 
>> *parallel
>> distributed triangulation* it refuse to copy for refine mesh, that is
>> written in documentation as well. When  I try to use fullydistributed
>> triangulation it gives me error with periodicity. Is there a way that I can
>> copy triangulation with periodicity or I am missing something? The code
>> works if I create new_triangulation with parallel distributed triangulation
>> and work on it. But it is expensive step. Kindly find code in attachment.
>>
>>
>> Regards,
>> Heena
>>
> --
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> 
> .
>

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[deal.II] Re: Is it possible to copy_triangulation for fullydistributed with periodic face?

2020-06-11 Thread 'peterrum' via deal.II User Group
Dear Heena,

may I ask you to be more specific regarding to 
parallel::fullydistributed::Triangualation (p:f:t) error. In the case of 
p:f:t you can copy indeed refined meshes, however users need to deal with 
periodicity on their own by applying the periodicy once again. See the 
following test: 
https://github.com/dealii/dealii/blob/master/tests/fullydistributed_grids/copy_serial_tria_04.cc#L102

This is kinda annoying, but I was not able to come up with a more 
transparent solution during the development of p:f:t.

Hope that helps,
Peter

On Thursday, 11 June 2020 10:06:49 UTC+2, heena patel wrote:
>
> Dear all,
>  I am trying to solve semilagrangian advection 
> problem?
> I have traingulation with periodic face.
> I wanted to copy_triangulation and trace back mesh. The thing is with 
> *parallel 
> distributed triangulation* it refuse to copy for refine mesh, that is 
> written in documentation as well. When  I try to use fullydistributed 
> triangulation it gives me error with periodicity. Is there a way that I can 
> copy triangulation with periodicity or I am missing something? The code 
> works if I create new_triangulation with parallel distributed triangulation 
> and work on it. But it is expensive step. Kindly find code in attachment.
>
>
> Regards,
> Heena
>

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[deal.II] Is it possible to copy_triangulation for fullydistributed with periodic face?

2020-06-11 Thread heena patel
Dear all,
 I am trying to solve semilagrangian advection 
problem?
I have traingulation with periodic face.
I wanted to copy_triangulation and trace back mesh. The thing is with *parallel 
distributed triangulation* it refuse to copy for refine mesh, that is 
written in documentation as well. When  I try to use fullydistributed 
triangulation it gives me error with periodicity. Is there a way that I can 
copy triangulation with periodicity or I am missing something? The code 
works if I create new_triangulation with parallel distributed triangulation 
and work on it. But it is expensive step. Kindly find code in attachment.


Regards,
Heena

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/*
 * semilagrangian.hpp
 *
 *  Created on: Jun 10, 2020
 *  Author: heena
 */

#ifndef INCLUDE_SEMILAGRANGIAN_HPP_
#define INCLUDE_SEMILAGRANGIAN_HPP_

#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 

// Distributed triangulation
#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 

// STL
#include 
#include 
#include 
#include 

// My Headers
#include "advection_field.hpp"
#include "advectiondiffusion_basis.hpp"
#include "advectiondiffusion_basis_reconstruction.hpp"
#include "config.h"
#include "dirichlet_bc.hpp"
#include "initial_value.hpp"
#include "matrix_coeff.hpp"
#include "neumann_bc.hpp"
#include "right_hand_side.hpp"

namespace Timedependent_AdvectionDiffusionProblem {
using namespace dealii;

template 
class Semilagrangian : public ParameterAcceptor {
public:
  Semilagrangian() = delete;
  Semilagrangian(unsigned int n_refine, bool is_periodic);
  ~Semilagrangian();
  void run();

private:
  void make_grid();
  void copy_grid();

  MPI_Comm mpi_communicator;

parallel::distributed::Triangulation triangulation;
parallel::distributed::Triangulation test_triangulation;


  /*!
   * Time-dependent vector coefficient (velocity).
   */
  Coefficients::AdvectionField advection_field;

  /*!
   * Index Set
   */
  IndexSet locally_owned_dofs;
  IndexSet locally_relevant_dofs;

  ConditionalOStream pcout;
  TimerOutput computing_timer;
  double time;
  double time_step;
  unsigned int timestep_number;
  /*!
   * parameter to determine the "implicitness" of the method.
   * Zero is fully implicit and one is (almost explicit).
   */
  const double theta;

  /*!
   * Final simulation time.
   */
  double T_max;

  /*!
   * Number of global refinements.
   */
  const unsigned int n_refine;

  /*!
   * If this flag is true then periodic boundary conditions
   * are used.
   */
  bool is_periodic;
};

template 
Semilagrangian::Semilagrangian(
unsigned int n_refine, bool is_periodic)
: mpi_communicator(MPI_COMM_WORLD),
  triangulation(mpi_communicator,
typename Triangulation::MeshSmoothing(
Triangulation::smoothing_on_refinement |
Triangulation::smoothing_on_coarsening)),
  test_triangulation(mpi_communicator,
 typename Triangulation::MeshSmoothing(
 Triangulation::smoothing_on_refinement |
 Triangulation::smoothing_on_coarsening)),
  fe(1),
	  dof_handler(triangulation),
  pcout(std::cout,
(Utilities::MPI::this_mpi_process(mpi_communicator) == 0)),
  computing_timer(mpi_communicator,
	  pcout, TimerOutput::summary,
  TimerOutput::wall_times),
  time(0.0),
	  time_step(1. / 100),
	  timestep_number(0),
  /*
   * theta=1 is implicit Euler,
   * theta=0 is explicit Euler,
   * theta=0.5 is Crank-Nicolson
   */
  theta(0.0),
	  T_max(1.0),
	  n_refine(n_refine),
	  is_periodic(is_periodic)
	  {}


template  void Semilagrangian::make_grid()
{
  TimerOutput::Scope t(computing_timer, "coarse mesh generation");

  GridGenerator::hyper_cube(triangulation, 0, 1,
/* colorize */ true);

  if (is_periodic) {
std::vector::cell_iterator>>
periodicity_vector;

for (unsigned int d = 0; d < dim; ++d) {