Re: [deal.II] Looking for clarification on a few places on Step-44

[Matthew Rich]

at exactly we were
>>> trying to identify with this comment. I'll think about it, as that seems to
>>> be a point that we could improve on in the documentation. That there is no
>>> K_{pp} contribution is significant, because it makes condensing out the p
>>> and J fields easier. Maybe we meant to refer to the lack of contribution to
>>> K_{pp} (as there is no second derivative involving a variation and
>>> linearisation of p.
>>>
>>> *I am also confused how K_pJ, K_Jp and K_JJ  form a block diagonal
>>> matrix. I could get there if I ignore the top row but then the equations
>>> below do not make sense I think. Some detail on this part of the process
>>> would be great. *
>>>
>>> So this is more easy to explain. We specifically choose discontinuous
>>> shape function to discretise these fields. As there are no interface/flux
>>> contributions, all local element contributions for these terms will remain
>>> local and you therefore end up with an assembled matrix for these
>>> contributions that has a block-like structure. The K_{JJ} matrix is
>>> evidently block-diagonal, as it is a field that couples with itself. As for
>>> the coupling matrices K_{pJ} and K_{Jp}, they are block-diagonal because we
>>> chose *exactly* the same discretisation for both fields (i.e. the shape
>>> functions and polynomial order match).
>>>
>>> Does that make sense?
>>>
>>> Best,
>>>
>>> Jean-Paul
>>> On 2022/09/30 19:16, Matthew Rich wrote:
>>>
>>> Hi,
>>>
>>> Step-44 has a lot going on and really sets you up to tackle a variety of
>>> real world problems. There is a significant jump in complexity between this
>>> tutorial and steps 8,17 & 18.
>>>
>>> I have been reading the references and I am about there but need few
>>> clarifications for why things are the way they are.
>>>
>>> Any assistance would be much appreciated...
>>>
>>> My first question deals with the statement "The Euler-Lagrange equations
>>> corresponding to the residual"
>>>
>>> Directly above this sentence is the residual, whose derivation I
>>> understand. Where I am lost is that s tact on to equations. I have only one
>>> residual equation. I cannot bridge that disconnect.
>>>
>>> My other question has to deal with the solving procedure for K (see
>>> snippet below)
>>> [image: Ksolve.png]
>>>
>>>
>>> I am completely lost here. What is the significance of p and J not
>>> having derivatives on them that makes it "easy" to solve for those terms in
>>> isolation? I am also confused how K_pJ, K_Jp and K_JJ  form a block
>>> diagonal matrix. I could get there if I ignore the top row but then the
>>> equations below do not make sense I think. Some detail on this part of the
>>> process would be great.
>>>
>>> Thanks in advance,
>>>
>>> Matt
>>> --
>>> The deal.II project is located at http://www.dealii.org/
>>> For mailing list/forum options, see
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>>> .
>>>
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>>>
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Re: [deal.II] Looking for clarification on a few places on Step-44

[Matthew Rich]

This was very helpful!

I am trying to understand the process so I could potentially extend this
formulation for biphasic materials. The way it handles incompressibility is
perfect for high water content tissues. My concern revolves around adding
another phase and explicitly solving for the fluid displacements in the
system. I was going to follow a similar strategy, but I am worried that
this approach is very specific.

IMHO the key feature for this approach is the ability to condense out the
pressure and volumetric ratio variables and recover the displacement only
formulation but with anti-locking properties baked in as opposed to
starting with a pure displacement formulation. I would like to preserve
that if possible. I am just worried I will wind up in a hole I cannot climb
out of...

These comments were very helpful. One quick question if you just
proceed without the condensation would that still work? In one of the
tutorials, If I abandoned the notion of using the CG solver and used
something like GMRES can I avoid some of the manipulation after I have the
linearized system?

Thanks for the prompt response and thoughtful answers! This stuff is hard
and fascinating at the same time.

Matt

On Tue, 4 Oct 2022 at 14:03, Jean-Paul Pelteret 
wrote:

> Hi Matthew,
>
> I'm glad that you find step-44 to be a useful tutorial! Let me try to
> answer your questions directly.
>
> *My first question deals with the statement "The Euler-Lagrange equations
> corresponding to the residual"*
>
> *Directly above this sentence is the residual, whose derivation I
> understand. Where I am lost is that s tact on to equations. I have** only
> one residual equation. I cannot bridge that disconnect. *
>
> This is just another way of saying that the three equations listed there
> (these E-L equations) are the strong form of the governing equations.
> Basically, if you take each of these equations (along the way, modifying
> the definition of the stress in the equilibrium equation), test them with
> the appropriate test function and sum up the three residual contributions
> then you recover the (total) residual, or stationary point of the residual,
> that is listed above. The point is that it not necessarily so straight
> forward to go from the strong form to the weak form for this mixed
> formulation, so identifying the conservation equations a-postori is a
> helpful sanity check here. They seem to align with what we're trying to do
> here.
>
>
> *I am completely lost here. What is the significance of p and J not having
> derivatives on them that makes it "easy" to solve for those terms in
> isolation? *
>
> Well, that's a valid point. I can't quite recall what exactly we were
> trying to identify with this comment. I'll think about it, as that seems to
> be a point that we could improve on in the documentation. That there is no
> K_{pp} contribution is significant, because it makes condensing out the p
> and J fields easier. Maybe we meant to refer to the lack of contribution to
> K_{pp} (as there is no second derivative involving a variation and
> linearisation of p.
>
> *I am also confused how K_pJ, K_Jp and K_JJ  form a block diagonal matrix.
> I could get there if I ignore the top row but then the equations below do
> not make sense I think. Some detail on this part of the process would be
> great. *
>
> So this is more easy to explain. We specifically choose discontinuous
> shape function to discretise these fields. As there are no interface/flux
> contributions, all local element contributions for these terms will remain
> local and you therefore end up with an assembled matrix for these
> contributions that has a block-like structure. The K_{JJ} matrix is
> evidently block-diagonal, as it is a field that couples with itself. As for
> the coupling matrices K_{pJ} and K_{Jp}, they are block-diagonal because we
> chose *exactly* the same discretisation for both fields (i.e. the shape
> functions and polynomial order match).
>
> Does that make sense?
>
> Best,
>
> Jean-Paul
> On 2022/09/30 19:16, Matthew Rich wrote:
>
> Hi,
>
> Step-44 has a lot going on and really sets you up to tackle a variety of
> real world problems. There is a significant jump in complexity between this
> tutorial and steps 8,17 & 18.
>
> I have been reading the references and I am about there but need few
> clarifications for why things are the way they are.
>
> Any assistance would be much appreciated...
>
> My first question deals with the statement "The Euler-Lagrange equations
> corresponding to the residual"
>
> Directly above this sentence is the residual, whose derivation I
> understand. Where I am lost is that s tact on to equations. I have only one
> residua

[deal.II] Looking for clarification on a few places on Step-44

[Matthew Rich]

Hi,

Step-44 has a lot going on and really sets you up to tackle a variety of 
real world problems. There is a significant jump in complexity between this 
tutorial and steps 8,17 & 18. 

I have been reading the references and I am about there but need few 
clarifications for why things are the way they are. 

Any assistance would be much appreciated...

My first question deals with the statement "The Euler-Lagrange equations 
corresponding to the residual"

Directly above this sentence is the residual, whose derivation I 
understand. Where I am lost is that s tact on to equations. I have only one 
residual equation. I cannot bridge that disconnect. 

My other question has to deal with the solving procedure for K (see snippet 
below) 
[image: Ksolve.png]


I am completely lost here. What is the significance of p and J not having 
derivatives on them that makes it "easy" to solve for those terms in 
isolation? I am also confused how K_pJ, K_Jp and K_JJ  form a block 
diagonal matrix. I could get there if I ignore the top row but then the 
equations below do not make sense I think. Some detail on this part of the 
process would be great. 

Thanks in advance, 

Matt

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Re: [deal.II] Issue linking GMSH when installing & building dealii 9.4

[Matthew Rich]

Thanks for the reply.  I tried building from source a couple times and no
luck. I see tetgen and netgen in the cmake output but not  blas

Anyone do this recently? I have LAPACK debian package but that does not
seem to do the job. I think this is my issue is BLAS is missing but not
sure how to rectify.


*cmake output  for GMSH*
cmake -DENABLE_BUILD_DYNAMIC=1 -DENABLE_BUILD_SHARED=1 -DENABLE_MUMPS=1
-ENABLE_NUMPY=1 -DENABLE_PETSC4PY=1 -DENABLE_OCC_TBB=1 -DENABLE_OPENACC=1
-DENABLE_PETSC=1 -DENABLE_REVOROPT=1 -VERBOSE=1 ../
-- Found 64Bit
-- Found OpenMP
-- Found OpenACC_C: -fopenacc
-- Found OpenACC_CXX: -fopenacc
-- Found OpenACC
-- Found Eigen[contrib]
-- Found Mesh
-- Found Solver
-- Found Post
-- Found Plugins
-- Found Parser
CMake Warning (dev) at /usr/share/cmake-3.18/Modules/FindOpenGL.cmake:305
(message):
  Policy CMP0072 is not set: FindOpenGL prefers GLVND by default when
  available.  Run "cmake --help-policy CMP0072" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  FindOpenGL found both a legacy GL library:

OPENGL_gl_LIBRARY: /usr/lib/x86_64-linux-gnu/libGL.so

  and GLVND libraries for OpenGL and GLX:

OPENGL_opengl_LIBRARY: /usr/lib/x86_64-linux-gnu/libOpenGL.so
OPENGL_glx_LIBRARY: /usr/lib/x86_64-linux-gnu/libGLX.so

  OpenGL_GL_PREFERENCE has not been set to "GLVND" or "LEGACY", so for
  compatibility with CMake 3.10 and below the legacy GL library will be
used.
Call Stack (most recent call first):
  /usr/share/cmake-3.18/Modules/FindFLTK.cmake:83 (find_package)
  CMakeLists.txt:633 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Could NOT find FLTK (missing: FLTK_LIBRARIES)
-- Found ONELAB
-- Found ONELABMetamodel
-- Found ANN[contrib]
-- Found ALGLIB[contrib]
-- Found DIntegration
-- Found Kbipack
-- GMP not found: Kbipack uses long int
-- Found MathEx[contrib]
-- Found Metis[contrib]
-- Found TetGen/BR
-- Found Voro++[contrib]
-- Found OptHom
-- Found DomHex
-- Found QuadTri
-- Found Blossom
-- Found Netgen
-- Found Bamg
-- Found Hxt
-- Found QuadMeshingTools
-- Found WinslowUntangler
-- Found Gmm[contrib]
-- Found PETSc
-- Found OpenCASCADE version 7.5.1 in /usr/include/opencascade
-- Found OpenCASCADE-CAF
-- Found OpenCASCADE
-- Found Dlopen
-- Found LinuxJoystick
-- Found Revoropt
--
-- Gmsh 4.10.5 has been configured for Linux64-sdk
--
--  * Build options: 64Bit ALGLIB[contrib] ANN[contrib] Bamg Blossom
DIntegration Dlopen DomHex Eigen[contrib] Gmm[contrib] Hxt Kbipack
LinuxJoystick MathEx[contrib] Mesh Metis[contrib] Netgen ONELAB
ONELABMetamodel OpenACC OpenCASCADE OpenCASCADE-CAF OpenMP OptHom PETSc
Parser Plugins Post QuadMeshingTools QuadTri Revoropt Solver TetGen/BR
Voro++[contrib] WinslowUntangler
--  * Build type: RelWithDebInfo
--  * C compiler: /usr/bin/cc
--  * C++ compiler: /usr/bin/c++
--  * Install prefix: /usr/local
--
-- Configuring done
-- Generating done
-- Build files have been written to: /home/mjrich/gmsh-4.10.5

On Thu, 8 Sept 2022 at 13:51, Daniel Arndt  wrote:

> Matthew,
>
> I don't know if the missing references are due to missing components in
> your gmsh installation (but I wouldn't be surprised).
> In any way, *"netgen, tetgen and blas support has to be enabled in Gmsh" *
> relates to CMake options when building gmsh from source, e.g.,
> https://gmsh.info/src/gmsh-4.10.5-source.tgz.
> I would try if building gmsh yourself with those dependencies/options
> resolves the issue.
>
> Best,
> Daniel
>
> On Thu, Sep 8, 2022 at 9:48 AM Matthew Rich  wrote:
>
>> Hi all,
>>
>> I was upgrading the 9.4 and I needed to include GMSH for a project I am
>> working on so I can use the API in my dealii code. I am getting the
>> following error despite getting the all clear from CMAKE. How can I fix
>> this , are there version limits on GMSH? I did notice this line*
>> "netgen, tetgen and blas support has to be enabled in Gmsh"  *How does
>> one ensure that? I do not see much in their github readme.
>>
>> *Some details- *
>> On a windows system running dealii in WSL2 under debian. I have built
>> gmsh from source and it is functional by itself, so I feel I did that part
>> right.  I have -DGMSH_DIR set to the root directory of my gmsh installation
>> so ~/gmsh-gmsh-4.10.5 cmake settings when I install dealii
>>
>> *make Error *
>> [ 75%] Linking CXX executable ../bin/step_3_mixed.debug
>> ../lib/libdeal_II.g.so.9.4.0: error: undefined reference to
>> 'gmsh::model::addPhysicalGroup(int, std::vector >
>> const&, int)'
>> ../lib/libdeal_II.g.so.9.4.0: error: undefined reference to
>> 'gmsh::model::mesh::removeDuplicateNodes()'
>> ../lib/libdeal_II.g.so.9.4.0: error: undefined reference to
>> 'gm

[deal.II] Issue linking GMSH when installing & building dealii 9.4

[Matthew Rich]

Hi all, 

I was upgrading the 9.4 and I needed to include GMSH for a project I am 
working on so I can use the API in my dealii code. I am getting the 
following error despite getting the all clear from CMAKE. How can I fix 
this , are there version limits on GMSH? I did notice this line* "netgen, 
tetgen and blas support has to be enabled in Gmsh"  *How does one ensure 
that? I do not see much in their github readme. 

*Some details- *
On a windows system running dealii in WSL2 under debian. I have built gmsh 
from source and it is functional by itself, so I feel I did that part 
right.  I have -DGMSH_DIR set to the root directory of my gmsh installation 
so ~/gmsh-gmsh-4.10.5 cmake settings when I install dealii  

*make Error *
[ 75%] Linking CXX executable ../bin/step_3_mixed.debug
../lib/libdeal_II.g.so.9.4.0: error: undefined reference to 
'gmsh::model::addPhysicalGroup(int, std::vector > 
const&, int)'
../lib/libdeal_II.g.so.9.4.0: error: undefined reference to 
'gmsh::model::mesh::removeDuplicateNodes()'
../lib/libdeal_II.g.so.9.4.0: error: undefined reference to 
'gmsh::initialize(int, char**, bool)'
collect2: error: ld returned 1 exit status
make[2]: *** [examples/CMakeFiles/step_3_mixed.debug.dir/build.make:292: 
bin/step_3_mixed.debug] Error 1
make[1]: *** [CMakeFiles/Makefile2:3926: 
examples/CMakeFiles/step_3_mixed.debug.dir/all] Error 2
make: *** [Makefile:149: all] Error 2

*CMAKE output *

#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, 
DEAL_II_ALLOW_AUTODETECTION = ON):
#  ( DEAL_II_WITH_64BIT_INDICES = OFF )
#  ( DEAL_II_WITH_ADOLC = OFF )
#  ( DEAL_II_WITH_ARBORX = OFF )
#DEAL_II_WITH_ARPACK set up with external dependencies
#DEAL_II_WITH_ASSIMP set up with external dependencies
#DEAL_II_WITH_BOOST set up with external dependencies
#  ( DEAL_II_WITH_CGAL = OFF )
#DEAL_II_WITH_COMPLEX_VALUES = ON
#  ( DEAL_II_WITH_CUDA = OFF )
#  ( DEAL_II_WITH_GINKGO = OFF )
#DEAL_II_WITH_GMSH set up with external dependencies
#DEAL_II_WITH_GSL set up with external dependencies
#DEAL_II_WITH_HDF5 set up with external dependencies
#DEAL_II_WITH_KOKKOS set up with external dependencies
#DEAL_II_WITH_LAPACK set up with external dependencies
#DEAL_II_WITH_METIS set up with external dependencies
#DEAL_II_WITH_MPI set up with external dependencies
#DEAL_II_WITH_MUPARSER set up with external dependencies
#DEAL_II_WITH_OPENCASCADE set up with external dependencies
#DEAL_II_WITH_P4EST set up with external dependencies
#DEAL_II_WITH_PETSC set up with external dependencies
#DEAL_II_WITH_SCALAPACK set up with external dependencies
#DEAL_II_WITH_SLEPC set up with external dependencies
#  ( DEAL_II_WITH_SUNDIALS = OFF )
#  ( DEAL_II_WITH_SYMENGINE = OFF )
#DEAL_II_WITH_TBB set up with external dependencies
#DEAL_II_WITH_TRILINOS set up with external dependencies
#DEAL_II_WITH_UMFPACK set up with external dependencies
#DEAL_II_WITH_ZLIB set up with external dependencies
#
#  Component configuration:
#  ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
#DEAL_II_COMPONENT_EXAMPLES
#  ( DEAL_II_COMPONENT_PACKAGE = OFF )
#  ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
#
#  Detailed information (compiler flags, feature configuration) can be 
found in detailed.log
#
#  Run  $ make info  to print a help message with a list of top level 
targets
#
###
-- Configuring done
-- Generating done
-- Build files have been written to: /home/mjrich/dealii-9.4.0/build


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[deal.II] Reference text for some of the theory with linear systems and block matricies

[Matthew Rich]

Hi all, 

I sort of crashed into a knowledge barrier in my learnings with the 
library, more specifically with Steps 20-22, which introduce block matrices 
and crafty manipulations to get the system ready for the CG solver. I am 
sort of lost with these tutorials and I think it is due to gaps in my 
understanding. 

I have been relying on Zienkiewicz texts to really get a solid 
understanding of FEM and work towards my aspirational use it for analyzing 
biological structures. However, those resources don't touch the numerical 
topics like Schur's compliment, preconditioners etc 

Is there a good textbook that consolidates these ideas or am I at the 
point, I just need to sift through journal articles? I am trying to apply 
some of the techniques utilized in the tutorials on different problems but 
the leap is too big at the moment.

Thanks in advance.  

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[deal.II] Proper use of fe_values.get_function_values to get values from a vector

[Matthew Rich]

Hi 

I am again tinkering with my favorite tutorial step 23 and I am have a 
question again on how to move forward. What I am attempting to do now is 
redo this setup but rather than using helper functions to create the system 
matrix and RHS, I am trying to build the system by looping over the cells. 

My question stems from how I get the appropriate local values from vectors 
to use in the loops. So in step 23 you would want to get values from 
old_solution_u and old_solution_v. Now I looked at other tutorials and I 
not 100% sure they had a similar need. In looking over the documentation my 
guess is that I would use the overloaded get_function_values 

void FEValuesBase 
< 
dim, spacedim >::get_function_values
(
const InputVector & fe_function,
const ArrayView 
< const 
types::global_dof_index 

 > 
& indices,
std::vector< typename InputVector::value_type > & values 
)

Is this correct? Also how would I deal with quadrature points in this 
instance in this context. Any help would be much appreciated?

Matt

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Re: [deal.II] Wave front not propagating through mesh modification on step 23, is Affine constraints wiping out my solution?

[Matthew Rich]

Just to close this out in case others run into the same problem. The
culprit was me declaring a local vector variable system_rhs in
WaveEquation::run
<https://www.dealii.org/current/doxygen/deal.II/namespaceWorkStream_1_1internal_1_1tbb__no__coloring.html#a8673698a405bf47aa24002aeb6d76d70>
().  A careless mistake, which had the net effect of having my RHS just be
zero since the global version of the variable, used in the solve function,
is never touched or updated with anything.  After that was addressed, I was
able to tweak some typos and now the solution matches the tutorial and the
case is closed.

I would like to ask about adding this approach to the tutorial of step 23
maybe at the bottom. For newcomers, it is not obvious how to deal with the
2nd order time derivative directly and there may be instances where my
approach is better suited. It is also a much shorter program.

Matt



On Sat, 30 Jul 2022 at 22:47, Wolfgang Bangerth 
wrote:

> On 7/30/22 15:45, Matthew Rich wrote:
> >
> > I am trying a different time integration approach using the generalized
> alpha
> > method rather then reposing with a velocity variable. I am also
> switching to
> > the BC handled by affine constraints.
> >
> > I am not sure why the wave wont move through the mesh. I just see the BC
> at
> > the edge which quickly fades out in the tutorial.
> >
> > Any hints or nudges would be appreciated code attached.
>
> Matthew -- I think you're asking too much of us as well of yourself. In
> essence, your question reads
>I started with code X which I know works. Then I made substantial
> changes
>A, B, and C and the code is no longer working. Any help?
> That's too many things at once one would have to check. Go back to the
> original code and make one change at a time, then test. Make another check
> and
> test. Go on like this. If you work along this strategy, you know which
> change
> broke the functionality, and you can focus on these changes in trying to
> figure out where the bug is.
>
> If, in addition, you use version control (via git or subversion or any
> other
> tool), you should commit every working version and you can always go back
> to
> that. You can also clearly identify what changes you have made and list
> the
> concrete lines where the newly introduced bug must be.
>
> 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
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> .
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Re: [deal.II] Wave front not propagating through mesh modification on step 23, is Affine constraints wiping out my solution?

[Matthew Rich]

OK,

One question regarding the statement about switching boundary conditions...
How so?

BoundaryValuesU is unchanged from the tutorial and directly
integrating eliminates the need for a BC on velocity so I should still
be aligned with the tutorial and the system described earlier in the
tutorial. Maybe this is my problem that my assumption is incorrect?


Anyways thanks for the correspondence.


Matt


On Sun, 31 Jul 2022 at 17:44, Wolfgang Bangerth 
wrote:

> On 7/30/22 21:15, Matthew Rich wrote:
> >
> > However, I am not sure how to slowly morph the Step 23 tutorial into
> what I
> > want to do. The different time integration approach is like swapping an
> engine
> > from a car.
>
> But you also switched the boundary conditions.
>
>
> > You have to commit and hope the car starts at the end. My car will
> > not turn over. I was hoping there was an obvious error in what I am
> doing
> > since the solution being just zero is pretty stark.
>
> Sorry, you'll have to debug this yourself I'm afraid :-( We don't have the
> resources to do this for all of our users.
>
> 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/
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> .
>

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Re: [deal.II] Wave front not propagating through mesh modification on step 23, is Affine constraints wiping out my solution?

[Matthew Rich]

Fair point and thanks for the reply.

However, I am not sure how to slowly morph the Step 23 tutorial into what I
want to do. The different time integration approach is like swapping an
engine from a car. You have to commit and hope the car starts at the end.
My car will not turn over. I was hoping there was an obvious error in what
I am doing since the solution being just zero is pretty stark.

I will keep on looking at this.



On Sat, 30 Jul 2022 at 22:47, Wolfgang Bangerth 
wrote:

> On 7/30/22 15:45, Matthew Rich wrote:
> >
> > I am trying a different time integration approach using the generalized
> alpha
> > method rather then reposing with a velocity variable. I am also
> switching to
> > the BC handled by affine constraints.
> >
> > I am not sure why the wave wont move through the mesh. I just see the BC
> at
> > the edge which quickly fades out in the tutorial.
> >
> > Any hints or nudges would be appreciated code attached.
>
> Matthew -- I think you're asking too much of us as well of yourself. In
> essence, your question reads
>I started with code X which I know works. Then I made substantial
> changes
>A, B, and C and the code is no longer working. Any help?
> That's too many things at once one would have to check. Go back to the
> original code and make one change at a time, then test. Make another check
> and
> test. Go on like this. If you work along this strategy, you know which
> change
> broke the functionality, and you can focus on these changes in trying to
> figure out where the bug is.
>
> If, in addition, you use version control (via git or subversion or any
> other
> tool), you should commit every working version and you can always go back
> to
> that. You can also clearly identify what changes you have made and list
> the
> concrete lines where the newly introduced bug must be.
>
> 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 a topic in the
> Google Groups "deal.II User Group" group.
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> .
>

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[deal.II] Wave front not propagating through mesh modification on step 23, is Affine constraints wiping out my solution?

[Matthew Rich]

Hi

I am trying a different time integration approach using the generalized 
alpha method rather then reposing with a velocity variable. I am also 
switching to the BC handled by affine constraints.  

I am not sure why the wave wont move through the mesh. I just see the BC at 
the edge which quickly fades out in the tutorial. 

Any hints or nudges would be appreciated code attached. 

Matt

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#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 


namespace Final_Proj
{
using namespace dealii;


template 
class WaveEquation
{
public:
WaveEquation();
void run();

private:
void setup_system();
void solve();
void output_results() const;

Triangulation triangulation;
FE_Q  fe;
DoFHandlerdof_handler;

AffineConstraints constraints;

SparsityPattern  sparsity_pattern;
SparseMatrix mass_matrix;
SparseMatrix laplace_matrix;
SparseMatrix system_matrix;
SparseMatrix matrix_temp;

Vector solution_u, solution_udot, solution_udotdot;
Vector old_solution_u, old_solution_udot, 
old_solution_udotdot;
Vector system_rhs;

double   time_step;
double   time;
unsigned int timestep_number;
const double beta;
const double gamma;
const double alpha_f;
const double alpha_m;
const double wave_speed;
};

template 
class ExactSolution : public Function
{
public:
virtual double value(const Point &p, unsigned int component = 
0) const override
{
(void)component;
double t = this-> get_time();
double exact = -1*std::exp(-1*dim*std::pow(M_PI,2)*t);
for (auto i = 0; i < dim; i++)
exact *= std::sin(M_PI*p[i]); // fix me!!!
return exact;
}
};

template 
class InitialValuesU : public Function
{
public:
virtual double value(const Point & /*p*/, const unsigned int 
component = 0) const override
{
(void)component;
Assert(component == 0, ExcIndexRange(component, 0, 1));
return 0;
}
};

template 
class InitialValuesUdot : public Function
{
public:
virtual double value(const Point & /*p*/, const unsigned int 
component = 0) const override
{
(void)component;
Assert(component == 0, ExcIndexRange(component, 0, 1));
return 0;
}
};


template 
class RightHandSide : public Function
{
public:
virtual double value(const Point & /*p*/, const unsigned int 
component = 0) const override
{
(void)component;
Assert(component == 0, ExcIndexRange(component, 0, 1));
return 0;
}
};

template 
class BoundaryValuesU : public Function
{
public:
virtual double value(const Point & p, const unsigned int 
component = 0) const override
{
(void)component;
Assert(component == 0, ExcIndexRange(component, 0, 1));

if ((this->get_time() <= 0.5) && (p[0] < 0) && (p[1] < 1. / 3) 
&& (p[1] > -1. / 3))
return -std::sin(this->get_time() * 4 * numbers::PI);
else
return 0;
}
};

template 
WaveEquation::WaveEquation()
: fe(1)
, dof_handler(triangulation)
, time_step(1. / 64)
, time(time_step)
, timestep_number(1)
, beta(0.25) // unconditionally stable 
, gamma(0.5) // unconditionally stable 
, alpha_f(0.25)
, alpha_m(0.250)
, wave_speed(1)
{}

template 
void WaveEquation::setup_system()
{
GridGenerator::hyper_cube(triangulation, -1, 1);
triangulation.refine_global(7);

std::cout << "Number of active cells: " << 
triangulation.n_active_cells()
<< std::endl;

dof_handler.distribute_dofs(fe);

s

[deal.II] Not getting line numbers on stack trace

[Matthew Rich]

Hi all, 

I am not sure if this is a dealii issue or more a gcc issue but I am not 
getting line numbers on the stack traces, which makes debugging errors hard 
since I am a raw beginner. 

So for example I get the following 


An error occurred in line <182> of file 

 
in function
void dealii::VectorTools::internal::project_matrix_free(const 
dealii::Mapping&, const dealii::DoFHandler&, 
const dealii::AffineConstraints&, const dealii::Quadrature&, 
const dealii::Function::value_type>&, 
dealii::LinearAlgebra::distributed::Vector&, bool, const 
dealii::Quadrature<(dim - 1)>&, bool) [with int components = 2; int 
fe_degree = 3; int dim = 2; Number = double; int spacedim = 2; typename 
dealii::LinearAlgebra::distributed::Vector::value_type = double]
The violated condition was:
dof.get_fe(0).n_components() == function.n_components
Additional information:
Dimension 2 not equal to 1.

Stacktrace:
---
#0  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::internal::project_matrix_free<2, 3, 2, double, 
2>(dealii::Mapping<2, 2> const&, dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints const&, dealii::Quadrature<2> const&, 
dealii::Function<2, dealii::LinearAlgebra::distributed::Vector::value_type> const&, 
dealii::LinearAlgebra::distributed::Vector&, bool, dealii::Quadrature<(2)-(1)> const&, bool)
#1  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::internal::project_matrix_free_degree<2, 2, double, 
2>(dealii::Mapping<2, 2> const&, dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints const&, dealii::Quadrature<2> const&, 
dealii::Function<2, dealii::LinearAlgebra::distributed::Vector::value_type> const&, 
dealii::LinearAlgebra::distributed::Vector&, bool, dealii::Quadrature<(2)-(1)> const&, bool)
#2  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::internal::project_matrix_free_component<2, double, 
2>(dealii::Mapping<2, 2> const&, dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints const&, dealii::Quadrature<2> const&, 
dealii::Function<2, dealii::LinearAlgebra::distributed::Vector::value_type> const&, 
dealii::LinearAlgebra::distributed::Vector&, bool, dealii::Quadrature<(2)-(1)> const&, bool)
#3  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::internal::project_matrix_free_copy_vector<2, 
dealii::Vector, 2>(dealii::Mapping<2, 2> const&, 
dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints::value_type> const&, 
dealii::Quadrature<2> const&, dealii::Function<2, 
dealii::Vector::value_type> const&, dealii::Vector&, bool, 
dealii::Quadrature<(2)-(1)> const&, bool)
#4  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::internal::project, 
2>(dealii::Mapping<2, 2> const&, dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints::value_type> const&, 
dealii::Quadrature<2> const&, dealii::Function<2, 
dealii::Vector::value_type> const&, dealii::Vector&, bool, 
dealii::Quadrature<(2)-(1)> const&, bool)
#5  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::project<2, dealii::Vector, 
2>(dealii::Mapping<2, 2> const&, dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints::value_type> const&, 
dealii::Quadrature<2> const&, dealii::Function<2, 
dealii::Vector::value_type> const&, dealii::Vector&, bool, 
dealii::Quadrature<(2)-(1)> const&, bool)
#6  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::project<2, dealii::Vector, 
2>(dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints::value_type> const&, 
dealii::Quadrature<2> const&, dealii::Function<2, 
dealii::Vector::value_type> const&, dealii::Vector&, bool, 
dealii::Quadrature<(2)-(1)> const&, bool)
#7  ./final_proj: final_proj::WaveEquation<2>::run()
#8  ./final_proj: main


Aborted

So I would expect some line number show up on #7 which would help me find 
the offending line faster. Anyone else have this problem. 

I am using Win11 and have dealii installed under the debian app under WSL2 

Any help is appreciated. 

Matt 

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[deal.II] Step 23 - Theta method of time discretization when 2nd order time derivative

[Matthew Rich]

Hi 

My question is in relation to step 23. I am dipping my toes in the water 
with structural mechanics problems and I would like to avoid the 
quasistatic simplification. Now the example add velocity to reduce the 
order of the time derivative and proceeds  with the theta method. 

I wanted to know if that technique would be allowed if you replaced the 2nd 
order time derivative in the wave equation. The tutorial says it would be 
equivalent but I have not seen anything using the theta method that does 
not have just a 1st order time derivative. 

Is there a modification of the theta method that allows one to pretty much 
follow the steps of the tutorial but not reduce the order of the equation 
by variable substitution. 

Thanks in advance. 

Matt

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[deal.II] Re: Program compiles does not finish linking cannot resolve 'void dealii::SparseMatrix::vmult *snip*

[Matthew Rich]

ok disregard this message. I found the error. 

On Thursday, 14 April 2022 at 11:25:08 UTC-4 Matthew Rich wrote:

> Hi all,
>
> Trucking through a problem and hit a snag with linking 
>
> /home/mjrich/dealii/proj/proj.cc:294: error: undefined reference to 'void 
> dealii::SparseMatrix::vmult, 
> dealii::PackagedOperation > 
> >(dealii::Vector&, dealii::PackagedOperation 
> > const&) const'
> collect2: error: ld returned 1 exit status
> make[2]: *** [CMakeFiles/proj.dir/build.make:294: proj] Error 1
> make[1]: *** [CMakeFiles/Makefile2:291: CMakeFiles/proj.dir/all] Error 2
> make: *** [Makefile:103: all] Error 2
>
>
> the offending line 
>  mass_matrix.vmult(system_rhs, -1*old_old_solution_u);
>
> I am confused since I have it declared with 
>
> SparseMatrix mass_matrix;
>
> and 
> Vector old_old_solution_u;
> Vector system_rhs;
>
> my list of includes are below. Why am I getting this error at the linking 
> stage?
>
> #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 
>

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[deal.II] Program compiles does not finish linking cannot resolve 'void dealii::SparseMatrix::vmult *snip*

[Matthew Rich]

Hi all,

Trucking through a problem and hit a snag with linking 

/home/mjrich/dealii/proj/proj.cc:294: error: undefined reference to 'void 
dealii::SparseMatrix::vmult, 
dealii::PackagedOperation > 
>(dealii::Vector&, dealii::PackagedOperation 
> const&) const'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/proj.dir/build.make:294: proj] Error 1
make[1]: *** [CMakeFiles/Makefile2:291: CMakeFiles/proj.dir/all] Error 2
make: *** [Makefile:103: all] Error 2


the offending line 
 mass_matrix.vmult(system_rhs, -1*old_old_solution_u);

I am confused since I have it declared with 

SparseMatrix mass_matrix;

and 
Vector old_old_solution_u;
Vector system_rhs;

my list of includes are below. Why am I getting this error at the linking 
stage?

#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 

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[deal.II] How to use create_mass_matrix tools with FESystem

[Matthew Rich]

Hi all, 

I am trying to use the helper tools to assemble a system for a vector 
valued problem. 

I am looking to have 2 or 3 displacement DoFs. 

So I use 

FESystem fe;

and initialize with 

fe(FE_Q 
(1), 
dim)

So my code compiles, but when I try and run I get the following 


An error occurred in line <182> of file 

 
in function
void dealii::VectorTools::internal::project_matrix_free(const 
dealii::Mapping&, const dealii::DoFHandler&, 
const dealii::AffineConstraints&, const dealii::Quadrature&, 
const dealii::Function::value_type>&, 
dealii::LinearAlgebra::distributed::Vector&, bool, const 
dealii::Quadrature<(dim - 1)>&, bool) [with int components = 2; int 
fe_degree = 1; int dim = 2; Number = double; int spacedim = 2; typename 
dealii::LinearAlgebra::distributed::Vector::value_type = double]
The violated condition was:
dof.get_fe(0).n_components() == function.n_components
Additional information:
Dimension 2 not equal to 1.

Stacktrace:
---
#0  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::internal::project_matrix_free<2, 1, 2, double, 
2>(dealii::Mapping<2, 2> const&, dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints const&, dealii::Quadrature<2> const&, 
dealii::Function<2, dealii::LinearAlgebra::distributed::Vector::value_type> const&, 
dealii::LinearAlgebra::distributed::Vector&, bool, dealii::Quadrature<(2)-(1)> const&, bool)
#1  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::internal::project_matrix_free_degree<2, 2, double, 
2>(dealii::Mapping<2, 2> const&, dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints const&, dealii::Quadrature<2> const&, 
dealii::Function<2, dealii::LinearAlgebra::distributed::Vector::value_type> const&, 
dealii::LinearAlgebra::distributed::Vector&, bool, dealii::Quadrature<(2)-(1)> const&, bool)
#2  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::internal::project_matrix_free_component<2, double, 
2>(dealii::Mapping<2, 2> const&, dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints const&, dealii::Quadrature<2> const&, 
dealii::Function<2, dealii::LinearAlgebra::distributed::Vector::value_type> const&, 
dealii::LinearAlgebra::distributed::Vector&, bool, dealii::Quadrature<(2)-(1)> const&, bool)
#3  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::internal::project_matrix_free_copy_vector<2, 
dealii::Vector, 2>(dealii::Mapping<2, 2> const&, 
dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints::value_type> const&, 
dealii::Quadrature<2> const&, dealii::Function<2, 
dealii::Vector::value_type> const&, dealii::Vector&, bool, 
dealii::Quadrature<(2)-(1)> const&, bool)
#4  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::internal::project, 
2>(dealii::Mapping<2, 2> const&, dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints::value_type> const&, 
dealii::Quadrature<2> const&, dealii::Function<2, 
dealii::Vector::value_type> const&, dealii::Vector&, bool, 
dealii::Quadrature<(2)-(1)> const&, bool)
#5  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::project<2, dealii::Vector, 
2>(dealii::Mapping<2, 2> const&, dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints::value_type> const&, 
dealii::Quadrature<2> const&, dealii::Function<2, 
dealii::Vector::value_type> const&, dealii::Vector&, bool, 
dealii::Quadrature<(2)-(1)> const&, bool)
#6  /usr/lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: void 
dealii::VectorTools::project<2, dealii::Vector, 
2>(dealii::DoFHandler<2, 2> const&, 
dealii::AffineConstraints::value_type> const&, 
dealii::Quadrature<2> const&, dealii::Function<2, 
dealii::Vector::value_type> const&, dealii::Vector&, bool, 
dealii::Quadrature<(2)-(1)> const&, bool)
#7  ./final_proj: final_proj::WaveEquation<2>::run()
#8  ./final_proj: main


Using some crude debugging it is complaining about the create_mass_matrix 
call. Now I know there are two variants. I was trying to create the matrix 
without passing a mapping but that is generating this error. My issue is I 
am not sure how to create a mapping that works. 

How does one make a mapping for a system? I looked at some of the tutorials 
but I could not find what I am looking for


Thanks in advance. 




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[deal.II] Implementing a fiber reinforcement in a biphasic model

[Matthew Rich]

Hi all, 

I am trying to add some anisotropy to my model via fibers. These fibers 
would only be active in tension and have different orientations depending 
on spatial location in the model. My plan of attack was to simply store and 
extra value at the quadrature points that had a direction representing the 
fiber and update directions after each time step. (is this a good way to go 
about doing that). I see a lot of papers doing fiber models in ABAQUS or 
COMSOL, but I never see any details on how to do it so I am guessing it is 
trivial. 

Then I stumbled upon https://doi.org/10.1016/j.compstruc.2020.106334 which 
uses dealii to implement a fiber model that has two grids and some sort of 
junction between the grid representing the bulk material and one presenting 
the fiber. The formulation seemed way more involved than what I was going 
to try. 

Am I making a gross simplification in my proposed approach. 

Matt



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Re: [deal.II] Re: Compile Error: no type named ‘active_cell_iterator’

[Matthew Rich]

If some one would guide me on how to submit the patch, I am willing to give 
it a go! 

On Monday, 12 July 2021 at 09:54:32 UTC-4 Wolfgang Bangerth wrote:

> On 7/12/21 7:28 AM, Matthew Rich wrote:
> > 
> > At one time did dataout have an active_cell_iterator property. The code 
> > gallery stuff may not get the same upkeep as the tutorials and maybe the 
> > library updated and broke this piece of the code.
>
> Yes, that seems to be the case. Would you be interested in submitting a 
> patch? 
> The right approach is to simply use the corresponding DoFHandler iterator 
> type.
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

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[deal.II] Re: Compile Error: no type named ‘active_cell_iterator’

[Matthew Rich]

OK,

At one time did dataout have an active_cell_iterator property. The code 
gallery stuff may not get the same upkeep as the tutorials and maybe the 
library updated and broke this piece of the code. I see both 
  typename DoFHandler::active_cell_iterator

and 

DataOut::active_cell_iterator, which is with the outputting 
portion of the code. Is using the DoFHandler truly equivalent? 





On Monday, 12 July 2021 at 08:01:37 UTC-4 bruno.t...@gmail.com wrote:

> Hi,
>
> On Monday, July 12, 2021 at 5:40:40 AM UTC-4 mjri...@gmail.com wrote:
>
>>
>> Should I just change active_cell_iterator to cell_iterator? I am worried 
>> that they wont work the same creating problems downstream. 
>>
> Only cell_iterator is accessible not active_cell_iterator. So yes, 
> active_cell_iterator won't work but cell_iterator will. Like you expect, 
> active_cell_iterator and cell_iterator do different things. You probably 
> want to access the active_cell_iterator through the DoFHandler or the 
> Triangulation.
>
> Best,
>
> Bruno
>

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[deal.II] Compile Error: no type named ‘active_cell_iterator’

[Matthew Rich]

Hi all, 

Once again perplexed by the c++ compiler. I am getting the following error 
when trying to compile a program from the code gallery.

prog1.cc:In instantiation of ‘typename dealii::DataOut::cell_iterator Prog1::FilteredDataOut::first_cell() [with int dim = 3; DH = dealii::DoFHandler<3, 3>; 
typename dealii::DataOut::cell_iterator = 
dealii::TriaIterator >]’:
prog1.cc:2668:5:   required from here
prog1.cc:2670:54: error: no type named ‘active_cell_iterator’ in ‘class 
dealii::DataOut<3, dealii::DoFHandler<3, 3> >’
  typename DataOut::active_cell_iterator cell = 
this->dofs->begin_active();
  ^~~~
prog1.cc:2670:54: error: no type named ‘active_cell_iterator’ in ‘class 
dealii::DataOut<3, dealii::DoFHandler<3, 3> >’
prog1.cc: In instantiation of ‘typename dealii::DataOut::cell_iterator Cartilage::FilteredDataOut::next_cell(const typename dealii::DataOut::cell_iterator&) [with int dim = 3; DH = 
dealii::DoFHandler<3, 3>; typename dealii::DataOut::cell_iterator = 
dealii::TriaIterator >]’:
prog1.cc:2678:5:   required from here
prog1.cc:2684:10: error: no type named ‘active_cell_iterator’ in ‘class 
dealii::DataOut<3, dealii::DoFHandler<3, 3> >’
   ++(FilteredIterator::active_cell_iterator>
 ~^
(predicate,old_cell));


Looking in the manual I see the following which makes me think the code 
should work 

using DataOut 
< dim, 
DoFHandlerType >::cell_iterator 

 
= typename DataOut_DoFData 
::cell_iterator 


Should I just change active_cell_iterator to cell_iterator? I am worried 
that they wont work the same creating problems downstream. 

Thanks in advance.

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Re: [deal.II] New location for sacado.hpp

[Matthew Rich]

OK now I am finally all set. 

For other people who had this issue I needed to run CMAKE with the 
following flags

cmake -/"install dir" /"location of deal.ii source",  -DDEAL_II_WITH_MPI=ON 
-DDEAL_II_TRILINOS_WITH_SACADO=ON, -DTRILINOS_DIR=/usr/

without the sacado flag it does not work 


On Thursday, 8 July 2021 at 13:40:52 UTC-4 Matthew Rich wrote:

> So I thought I was in good shape. I had cmake run with the proper flags 
> and everything and built deal.ii
>
> But.
>
> I tried to build step-33 and got the following 
>
> -- Using the deal.II-9.3.1 installation found at /usr/local/deal.II
> -- Include macro 
> /usr/local/deal.II/share/deal.II/macros/macro_deal_ii_add_test.cmake
> -- Include macro 
> /usr/local/deal.II/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
> -- Include macro 
> /usr/local/deal.II/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
> -- Include macro 
> /usr/local/deal.II/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
> -- Include macro 
> /usr/local/deal.II/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
> -- Include macro 
> /usr/local/deal.II/share/deal.II/macros/macro_deal_ii_setup_target.cmake
> CMake Error at CMakeLists.txt:44 (MESSAGE):
>   
>
>   Error! This tutorial requires a deal.II library that was configured with
>   the following options:
>
>   DEAL_II_WITH_MUPARSER = ON
>   DEAL_II_TRILINOS_WITH_SACADO = ON
>
>   However, the deal.II library found at /usr/local/deal.II was configured
>   with these options:
>
>   DEAL_II_WITH_MUPARSER = ON
>   DEAL_II_TRILINOS_WITH_SACADO = 
>
>   This conflicts with the requirements.
>
>
> -- Configuring incomplete, errors occurred!
> I tried to redo cmake with this DEAL_II_TRILINOS_WITH_SACADO but it 
> doesn't exist. I can run with -DDEAL_II_WITH_TRILINOS=ON but that does not 
> appear to be sufficent. In the log cmake finds Sacado. I am not sure what 
> to do...
>
>
> On Wednesday, 7 July 2021 at 15:16:38 UTC-4 Jean-Paul Pelteret wrote:
>
>> Hi Matthew,
>>
>> Great, I’m glad to hear that! 
>>
>> So my last question is what is the difference between a flag being ON vs 
>> set up with external dependencies ( which is what trilinos is set at now) 
>>
>>
>> When you set one of these flags to “ON”, you are demanding from CMake 
>> that this option be enabled and expect that the associated package must be 
>> set up correctly. Similarly, when the flag is set to “OFF” then the 
>> auto-detection for that package will be skipped (and, even if you tell 
>> deal.II where that library is by providing its path, it will ignore it 
>> anyway). When you leave flag this out altogether  you rely on the 
>> auto-detection mechanism to find the package and if it cannot be found (or 
>> there’s some detected compatibility issue) then you give CMake the leeway 
>> to disable and ignore this package. So, in summary, it just gives the 
>> granularity to say “Yes, I definitely want this dependency enabled” or “No, 
>> under all circumstances ignore this optional dependency” or “if you find it 
>> and it works, then I want this enabled".
>>
>> When the package is said to be an "external dependency”, then it just 
>> means that the user or OS has provided said package. We bundle a few 
>> mandatory packages ourselves (e.g. the boost libraries), so that if the 
>> user hasn’t got them installed then we can fall back to these packages that 
>> are maintained within deal.II itself. 
>>
>> Will I be able to run those tutorials now? or is there still more work to 
>> be done. 
>>
>>
>> For step-72 and step-33, I’d say yes
>>
>> https://github.com/dealii/dealii/blob/master/examples/step-72/CMakeLists.txt#L40-L51
>>
>> https://github.com/dealii/dealii/blob/master/examples/step-33/CMakeLists.txt#L43-L53
>>
>> But to run step-71 you’ll also need to install SymEngine
>>
>> https://github.com/dealii/dealii/blob/master/examples/step-71/CMakeLists.txt#L40-L54
>>
>> I don’t think that there’s an Ubuntu package for that yet, but it’s not 
>> too hard to install by hand. You can take a look at their GitHub page for 
>> build instructions. At the bottom of the page there is their "Recommended 
>> options to build”, which you might want to take note of.
>> https://github.com/symengine/symengine
>>
>> Best,
>> Jean-Paul
>>
>> On 7. Jul 2021, at 20:49, Matthew Rich  wrote:
>>
>> Thanks that worked! 
>>
>> I needed to install the full trilinos-all-dev to get all the packages. I 
>> also 

Re: [deal.II] New location for sacado.hpp

[Matthew Rich]

So I thought I was in good shape. I had cmake run with the proper flags and 
everything and built deal.ii

But.

I tried to build step-33 and got the following 

-- Using the deal.II-9.3.1 installation found at /usr/local/deal.II
-- Include macro 
/usr/local/deal.II/share/deal.II/macros/macro_deal_ii_add_test.cmake
-- Include macro 
/usr/local/deal.II/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include macro 
/usr/local/deal.II/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include macro 
/usr/local/deal.II/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
-- Include macro 
/usr/local/deal.II/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
-- Include macro 
/usr/local/deal.II/share/deal.II/macros/macro_deal_ii_setup_target.cmake
CMake Error at CMakeLists.txt:44 (MESSAGE):
  

  Error! This tutorial requires a deal.II library that was configured with
  the following options:

  DEAL_II_WITH_MUPARSER = ON
  DEAL_II_TRILINOS_WITH_SACADO = ON

  However, the deal.II library found at /usr/local/deal.II was configured
  with these options:

  DEAL_II_WITH_MUPARSER = ON
  DEAL_II_TRILINOS_WITH_SACADO = 

  This conflicts with the requirements.


-- Configuring incomplete, errors occurred!
I tried to redo cmake with this DEAL_II_TRILINOS_WITH_SACADO but it doesn't 
exist. I can run with -DDEAL_II_WITH_TRILINOS=ON but that does not appear 
to be sufficent. In the log cmake finds Sacado. I am not sure what to do...


On Wednesday, 7 July 2021 at 15:16:38 UTC-4 Jean-Paul Pelteret wrote:

> Hi Matthew,
>
> Great, I’m glad to hear that! 
>
> So my last question is what is the difference between a flag being ON vs 
> set up with external dependencies ( which is what trilinos is set at now) 
>
>
> When you set one of these flags to “ON”, you are demanding from CMake that 
> this option be enabled and expect that the associated package must be set 
> up correctly. Similarly, when the flag is set to “OFF” then the 
> auto-detection for that package will be skipped (and, even if you tell 
> deal.II where that library is by providing its path, it will ignore it 
> anyway). When you leave flag this out altogether  you rely on the 
> auto-detection mechanism to find the package and if it cannot be found (or 
> there’s some detected compatibility issue) then you give CMake the leeway 
> to disable and ignore this package. So, in summary, it just gives the 
> granularity to say “Yes, I definitely want this dependency enabled” or “No, 
> under all circumstances ignore this optional dependency” or “if you find it 
> and it works, then I want this enabled".
>
> When the package is said to be an "external dependency”, then it just 
> means that the user or OS has provided said package. We bundle a few 
> mandatory packages ourselves (e.g. the boost libraries), so that if the 
> user hasn’t got them installed then we can fall back to these packages that 
> are maintained within deal.II itself. 
>
> Will I be able to run those tutorials now? or is there still more work to 
> be done. 
>
>
> For step-72 and step-33, I’d say yes
>
> https://github.com/dealii/dealii/blob/master/examples/step-72/CMakeLists.txt#L40-L51
>
> https://github.com/dealii/dealii/blob/master/examples/step-33/CMakeLists.txt#L43-L53
>
> But to run step-71 you’ll also need to install SymEngine
>
> https://github.com/dealii/dealii/blob/master/examples/step-71/CMakeLists.txt#L40-L54
>
> I don’t think that there’s an Ubuntu package for that yet, but it’s not 
> too hard to install by hand. You can take a look at their GitHub page for 
> build instructions. At the bottom of the page there is their "Recommended 
> options to build”, which you might want to take note of.
> https://github.com/symengine/symengine
>
> Best,
> Jean-Paul
>
> On 7. Jul 2021, at 20:49, Matthew Rich  wrote:
>
> Thanks that worked! 
>
> I needed to install the full trilinos-all-dev to get all the packages. I 
> also needed to install libptscotch-dev. 
>
> So my last question is what is the difference between a flag being ON vs 
> set up with external dependencies ( which is what trilinos is set at now) 
>
> Will I be able to run those tutorials now? or is there still more work to 
> be done. 
>
> Thank you for all your help resolving this issue. 
>
>
>
> On Wednesday, 7 July 2021 at 14:36:36 UTC-4 Jean-Paul Pelteret wrote:
>
>> Hi again Matthew,
>>
>> I’ve also found this build log for the Debian deal.II apt package
>>
>> https://buildd.debian.org/status/fetch.php?pkg=deal.ii&arch=all&ver=9.2.0-3&stamp=1606990185&raw=0
>> and you can see that in amongst all of the dependencies are listed the 
>> "trilinos-all-dev” and " trilino

Re: [deal.II] New location for sacado.hpp

[Matthew Rich]

Thanks that worked! 

I needed to install the full trilinos-all-dev to get all the packages. I 
also needed to install libptscotch-dev. 

So my last question is what is the difference between a flag being ON vs 
set up with external dependencies ( which is what trilinos is set at now) 

Will I be able to run those tutorials now? or is there still more work to 
be done. 

Thank you for all your help resolving this issue. 



On Wednesday, 7 July 2021 at 14:36:36 UTC-4 Jean-Paul Pelteret wrote:

> Hi again Matthew,
>
> I’ve also found this build log for the Debian deal.II apt package
>
> https://buildd.debian.org/status/fetch.php?pkg=deal.ii&arch=all&ver=9.2.0-3&stamp=1606990185&raw=0
> and you can see that in amongst all of the dependencies are listed the 
> "trilinos-all-dev” and " trilinos-dev” packages. They are meta-packages for 
> all 
> of the development files for Trilinos 
> <https://packages.ubuntu.com/groovy/trilinos-all-dev>. I reckon that you 
> should install these packages, and then give it another try. 
>
> Best,
> Jean-Paul
>
>
> On 7. Jul 2021, at 20:15, Jean-Paul Pelteret  wrote:
>
> Hi Matthew,
>
> If you look at either log file, then you’ll see that Trilinos was in fact 
> not detected for some reason.
>
> DEAL_II_WITH_TRILINOS = OFF
>
>
> I’m no longer experienced in building deal.II using apt packages, but it 
> might be that you have to install the entire trilinos-dev to get all of the 
> headers. Some of the modules that Trilinos provides are mandatory, and some 
> like Sacado are optional. It could be that some of the other necessary 
> headers aren’t there for the mandatory modules, and so the configure-time 
> checks for core Trilinos packages cannot pass.
>
> Try that, and if it fails then you can also add this
> -DDEAL_II_WITH_TRILINOS=ON -DTRILINOS_DIR=“/usr"
>  to the cmake command to explicitly state that you want Trilinos enabled. 
> Then if it doesn’t detect it CMake should emit an error and you’ll know for 
> sure that there’s still something wrong. From these lines
>
> https://github.com/dealii/dealii/blob/master/cmake/configure/configure_2_trilinos.cmake#L58-L68
> there should also be some messages that indicate exactly which modules it 
> could not find.
>
> I hope that this helps.
>
> Best,
> Jean-Paul
>
>
> On 7. Jul 2021, at 19:43, Matthew Rich  wrote:
>
> Hi 
>
> Thanks for the prompt reply.
>
> Yes I built deal.II from source but libtrilinos-sacado-dev was installed 
> via the debian package and apt (log files attached). I have all the headers 
> in my /usr/include/trilinos directory. Just skimming the summary file it 
> appears that deal.II did not detect sacado. Not sure why not though. 
>
> Thanks for the tip on the new tutorials. I will check them out once I get 
> this working. 
>
> Matt
>
> On Wednesday, 7 July 2021 at 12:51:26 UTC-4 Jean-Paul Pelteret wrote:
>
>> Hi Matthew,
>>
>> I don’t quite understand exactly how you installed deal.II and Trilinos. 
>> Perhaps you can provide some more explicit details so that we can help you 
>> out.
>>
>> * Is Trilinos installed using the apt package, and deal.II installed from 
>> source? If you built deal.II from source, may you please attach the build 
>> logs (summary.log and detailed.log) for us to look at.
>>
>> * Did you install the Trilinos development packages (e.g. trilinos-dev or 
>> libtrilinos-sacado-dev), which should install the headers into a central 
>> location?
>>
>> * When you built deal.II, and it detects Trilinos and Sacado, the 
>> following two variable is defined in config.h (this is also output to the 
>> console during configuration):
>> $ cat include/deal.II/base/config.h | grep SACADO
>>   #define DEAL_II_TRILINOS_WITH_SACADO
>> Do you see it there? If not, then deal.II did not successfully detect 
>> Sacado during configuration, and does not support it. If you try to 
>> configure step-33, an error should be emitted that expresses this.
>>
>> When you #include  then the compiler first looks for this 
>> header in the default location for the system, which I think is  
>> /usr/include. 
>> If it doesn’t find it there then it looks in some other specific locations 
>> that deal.II (through the configured packages) suggests that it goes 
>> looking in.
>>
>> As a side note, there are two new tutorials (step-71 
>> <https://www.dealii.org/current/doxygen/deal.II/step_71.html> and step-72 
>> <https://www.dealii.org/current/doxygen/deal.II/step_72.html>) that 
>> cover the topic of auto-differentiation as well. You might want to consider 
>&

Re: [deal.II] New location for sacado.hpp

[Matthew Rich]

So I tried running cmake again to get trilinos picked up. It does not seem 
to be detected. I even try supplying the directory 
with 

 cmake -/usr/local ./  -DTRILINOS_DIR=/usr/include/trilinos

But it still does not get detected. 

Should I build trilinos from source as well?  I attached another log where 
I pipe all cmake output to a file 

Matt




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.


>>

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-- This is CMake 3.13.4
-- 
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/setup_external_macros.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_add_flags.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_check_compiler_setup.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_check_cxx_compiler_bug.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_check_mpi_interface.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_clear_cmake_required.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_clear_feature.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_configure_feature.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_add_definitions.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_add_library.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_add_test.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_find_file.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_find_library.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_find_path.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_find_program.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_insource_setup_target.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_package_handle.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_pickup_tests.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_query_git_information.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_deal_ii_setup_target.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_decorate_with_stars.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_enable_if_links.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_enable_if_supported.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_enable_language_optional.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_evaluate_expression.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_expand_instantiations.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_filter_system_libraries.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_find_package.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_find_system_library.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_item_matches.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_purge_feature.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_register_feature.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_remove_duplicates.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_replace_flag.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_reset_cmake_required.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_set_if_empty.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_setup_source_list.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_setup_unity_target.cmake
-- Include /home/mastermind/dealII/dealii-9.3.1/cmake/macros/macro_strip_flag.cmake
-- Includ

Re: [deal.II] New location for sacado.hpp

[Matthew Rich]

Hi 

Thanks for the prompt reply.

Yes I built deal.II from source but libtrilinos-sacado-dev was installed 
via the debian package and apt (log files attached). I have all the headers 
in my /usr/include/trilinos directory. Just skimming the summary file it 
appears that deal.II did not detect sacado. Not sure why not though. 

Thanks for the tip on the new tutorials. I will check them out once I get 
this working. 

Matt

On Wednesday, 7 July 2021 at 12:51:26 UTC-4 Jean-Paul Pelteret wrote:

> Hi Matthew,
>
> I don’t quite understand exactly how you installed deal.II and Trilinos. 
> Perhaps you can provide some more explicit details so that we can help you 
> out.
>
> * Is Trilinos installed using the apt package, and deal.II installed from 
> source? If you built deal.II from source, may you please attach the build 
> logs (summary.log and detailed.log) for us to look at.
>
> * Did you install the Trilinos development packages (e.g. trilinos-dev or 
> libtrilinos-sacado-dev), which should install the headers into a central 
> location?
>
> * When you built deal.II, and it detects Trilinos and Sacado, the 
> following two variable is defined in config.h (this is also output to the 
> console during configuration):
> $ cat include/deal.II/base/config.h | grep SACADO
>   #define DEAL_II_TRILINOS_WITH_SACADO
> Do you see it there? If not, then deal.II did not successfully detect 
> Sacado during configuration, and does not support it. If you try to 
> configure step-33, an error should be emitted that expresses this.
>
> When you #include  then the compiler first looks for this 
> header in the default location for the system, which I think is  
> /usr/include. 
> If it doesn’t find it there then it looks in some other specific locations 
> that deal.II (through the configured packages) suggests that it goes 
> looking in.
>
> As a side note, there are two new tutorials (step-71 
> <https://www.dealii.org/current/doxygen/deal.II/step_71.html> and step-72 
> <https://www.dealii.org/current/doxygen/deal.II/step_72.html>) that cover 
> the topic of auto-differentiation as well. You might want to consider 
> looking at those before step-33. Step-33 uses Sacado at a low-level, and 
> these two new tutorials introduce some wrappers that we’ve implemented 
> inside the library that make using Sacado a bit more tractable.
>
> Best,
> Jean-Paul
>
>
> On 7. Jul 2021, at 17:41, Matthew Rich  wrote:
>
> Hi all,
>
>  I am a bit confused on step-33 which uses the differentiation of sacado. 
> I installed the latest version. 9.3 which has trilinios in it, and 
> therefore sacado. Browsing that directory I see other header files for the 
> package but not sacado.hpp
>
> The tutorial has the line
> #include 
>
> Was this file renamed or something? I am on Debian and I have installed 
> the trilinios through their package, which does have the header file. 
> However I cannot get the program to work properly.
>
> I am looking for guidance on this issue of getting the right headers in 
> the program so I can run this tutorial and others leveraging the sacado 
> package.
>
> Thanks in advance,
>
> Maty
>
>
>
>
> -- 
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> For mailing list/forum options, see 
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>  
> <https://groups.google.com/d/msgid/dealii/CAN3OR9oH-Za8weU3xHrMs5H86VeJffqtnrNxo_xh%3DddjMhc88g%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>
>
>

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###
#
#  deal.II configuration:
#CMAKE_BUILD_TYPE:   DebugRelease
#BUILD_SHARED_LIBS:  ON
#CMAKE_INSTALL_PREFIX:   /usr/local/deal.II
#CMAKE_SOURCE_DIR:   /home/mastermind/dealII/dealii-9.3.1
#(version 9.3.1)
#

[deal.II] New location for sacado.hpp

[Matthew Rich]

Hi all,

 I am a bit confused on step-33 which uses the differentiation of sacado. I
installed the latest version. 9.3 which has trilinios in it, and therefore
sacado. Browsing that directory I see other header files for the package
but not sacado.hpp

The tutorial has the line
#include 

Was this file renamed or something? I am on Debian and I have installed the
trilinios through their package, which does have the header file. However I
cannot get the program to work properly.

I am looking for guidance on this issue of getting the right headers in the
program so I can run this tutorial and others leveraging the sacado package.

Thanks in advance,

Maty

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Re: [deal.II] Install and running deal.II with latest debian package

[Matthew Rich]

Thank you for the instructions. Only tweak would be you need to explicitly
specify the CMakechecklist file so

instead of just cmake

I had to type cmake CMakeLists.txt

Thanks again!

On Thu, Jan 14, 2021, 1:58 AM Matthias Maier  wrote:

> All,
>
> I have created an issue on github to track some much needed updates to
> our documentation :-)
>
> https://github.com/dealii/dealii/issues/11529
>
> Best,
> Matthias
>
>
>
> On Thu, Jan 14, 2021, at 00:47 CST, Matthias Maier 
> wrote:
>
> > Dear Matt,
> >
> > You need to compile and link your source code with all include
> > directives ( -I  ) and external libraries. It is easiest to simply
> > use the CMake configuration that we ship with the examples.
> >
> > I guess you installed the deal.II package via apt? If so, simply install
> > the doc package and required dependencies and toolchain:
> >
> >   sudo apt install libdeal.ii-dev libdeal.ii-doc cmake make
> >
> > and (as user) copy the first example step to a convenient location:
> >
> >   cp -r /usr/share/doc/libdeal.ii-doc/examples/step-1 .
> >   cd step-1
> >   cmake .
> >   make
> >   make run
> >
> > Best,
> > Matthias
> >
> >
> >
> > On Wed, Jan 13, 2021, at 23:22 CST, Matthew Rich 
> wrote:
> >
> >> Hi,
> >>
> >> I am new to deal.II and I wanted to mess with the tutorials. I am
> running
> >> the mint LDE distro of linux and just installed the package. per the
> >> website. On step one when you are just creating a mesh, I am getting an
> >> error regrading Sacado.h which appears to be a solver package external
> to
> >> deal.II. I was expecting the package management to cover all
> dependencies,
> >> so I am not sure how to proceed. I searched this group and no one else
> >> seems to have this error.
> >>
> >> to get this error I simply touched a file called example1.cpp  and cut
> and
> >> pasted all the code from the tutorial in there.
> >>
> >> initially tried compiling with g++ but that failed looking for mpi.h. I
> >> then switched mpiCC where I get *fatal error: Sacado.hpp: No such file
> or
> >> directory*.
> >>
> >> I am not sure if I need to install something else to get off the
> ground.
> >>
> >> Any help would be much appreciated.
> >>
> >> Matt
>
> --
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[deal.II] Install and running deal.II with latest debian package

[Matthew Rich]

Hi, 

I am new to deal.II and I wanted to mess with the tutorials. I am running 
the mint LDE distro of linux and just installed the package. per the 
website. On step one when you are just creating a mesh, I am getting an 
error regrading Sacado.h which appears to be a solver package external to 
deal.II. I was expecting the package management to cover all dependencies, 
so I am not sure how to proceed. I searched this group and no one else 
seems to have this error. 

to get this error I simply touched a file called example1.cpp  and cut and 
pasted all the code from the tutorial in there. 

initially tried compiling with g++ but that failed looking for mpi.h. I 
then switched mpiCC where I get *fatal error: Sacado.hpp: No such file or 
directory*. 

I am not sure if I need to install something else to get off the ground. 

Any help would be much appreciated. 

Matt

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