[deal.II] Re: Some changes in arpack.h (Functionality to compute only eigenvalues)

[Animesh Rastogi IIT Gandhinagar]

Hi Bruno,

I would like to use this patch 

 
to compute the smallest eigenvalues in my case. Could you please let me 
know how should I update my source code in the arpack.h header file to 
accommodate these changes in the patch.  I understand that I would need to 
reinstall dealii after updating the source code, which I am fine with. 

When I am using the shift-inverse mode, I am not getting the results 
similar to what I would get using the eigenvalue solver in MATLAB or Python 
for the same matrix. There is a difference of about 15 to 20 in the 
eigenvalues (even when comparing it with the ARPACK solver in Python). This 
is the reason that I would want to try calculating the eigenvalues using 
the patch you created in regular mode.

Thanks!

Animesh
On Sunday, November 8, 2020 at 6:00:58 PM UTC+5:30 Animesh Rastogi IIT 
Gandhinagar wrote:

> Thank you Bruno, I was able to change the source code accordingly. I 
> reinstalled dealii and it worked fine!
>
> Thanks again!
>
> Animesh
>
> On Friday, November 6, 2020 at 3:55:29 AM UTC+5:30 bruno.t...@gmail.com 
> wrote:
>
>> Animesh,
>>
>> On Thursday, November 5, 2020 at 1:11:33 PM UTC-5 
>> animesh...@alumni.iitgn.ac.in wrote:
>>
>>> However, I have no way of passing it as a parameter to the solver 
>>> 
>>>  
>>> function. I was planning to edit the header file *arpack.h* 
>>> 
>>>  
>>> accordingly which is inside the */usr/local/include/deal.II/lac* to 
>>> have that functionality. I was actually thinking of passing the flag "rvec" 
>>> as an argument to the function solve 
>>> .
>>>  
>>> I was wondering if I change the permission of the file to write mode, edit 
>>> it and save it, would I be able to run my code inside the examples folder. 
>>> Or do I need to take care of something else while and after editing that 
>>> headerfile?
>>>
>> You should change the source code and reinstall deal.II. I would do what 
>> you propose only if you cannot compile deal.II on that machine. It might 
>> work in this particular case but I really advise you against it.
>>
>> Best,
>>
>> Bruno
>>  
>>
>

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[deal.II] Triangulation Merge Error

[pushkar...@gmail.com]

Dear deal.II community

As a beginner trying to understand this library I tried to merge two 
traingulations namely "cheese" and "hyper_cube" by modifying step-1 as -
void first_grid ()
{
  Triangulation<2> tria1,tria2,tria_merge;
  /*const double R = 13.0;
  const double r =7.0;*/
  const double  left = 0.0;
  const double right = 1.0;
  const std::vector holes={6,5};
  GridGenerator::cheese(tria1, holes);
  GridGenerator::hyper_cube(tria2, left, right);
  GridGenerator::merge_triangulations(tria1, tria2, tria_merge);
  unsigned int cells = tria_merge.n_cells(4);
  std::ofstream out ("grid-1.vtk");
  GridOut grid_out;
  grid_out.write_vtk (tria_merge, out);
  std::cout << "Grid written to grid-1.vtk" << std::endl;
  std::cout << "Number of cells:" << cells << std::endl;
}
int main ()
{
  first_grid ();
  //second_grid ();
}

After compiling I ran into an error that - 

terminate called after throwing an instance of 
'dealii::StandardExceptions::ExcInternalError'
  what():  

An error occurred in line <1999> of file 
 in function
static void 
dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
 
std::vector >&, const std::vector 
>&, const dealii::SubCellData&, dealii::Triangulation<2, spacedim>&) [with 
int spacedim = 2]
The violated condition was: 
(n_adj_cells >= 1) && (n_adj_cells <= 2)
Additional information: 
This exception -- which is used in many places in the library -- 
usually indicates that some condition which the author of the code thought 
must be satisfied at a certain point in an algorithm, is not fulfilled. An 
example would be that the first part of an algorithm sorts elements of an 
array in ascending order, and a second part of the algorithm later 
encounters an element that is not larger than the previous one.

There is usually not very much you can do if you encounter such an 
exception since it indicates an error in deal.II, not in your own program. 
Try to come up with the smallest possible program that still demonstrates 
the error and contact the deal.II mailing lists with it to obtain help.


So I am wondering that am I doing something wrong or is there any 
consistency check that needs to be performed while merging triangulations. 
Any direction in this regard will surely be beneficial.

Thanks
Pushkar




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[deal.II] Gmsh support on Deal.II Virtualbox image

[husain.u...@gmail.com]

Hello Deal.II community,
I am working on deal.II via the VM image (release 9.1.1). I am having 
trouble reading the .msh file. I even tried running running step 49 and 
received this error:


Exception on processing: 


An error occurred in line <1408> of file 
 in function
void dealii::GridIn::read_msh(std::istream&) [with int 
dim = 2; int spacedim = 2; std::istream = std::basic_istream]
The violated condition was: 
in
Additional information: 
An input/output error has occurred. There are a number of reasons why 
this may be happening, both for reading and writing operations.

If this happens during an operation that tries to read data: First, you may 
be trying to read from a file that doesn't exist or that is not readable 
given its file permissions. Second, deal.II uses this error at times if it 
tries to read information from a file but where the information in the file 
does not correspond to the expected format. An example would be a truncated 
file, or a mesh file that contains not only sections that describe the 
vertices and cells, but also sections for additional data that deal.II does 
not understand.

If this happens during an operation that tries to write data: you may be 
trying to write to a file to which file or directory permissions do not 
allow you to write. A typical example is where you specify an output file 
in a directory that does not exist.


Aborting!


I checked the detailed.log file and found DEAL_II_WITH_GMSH is OFF.  
I also tried to install the latest version of gmsh (4.7.1) and ran the 
cmake command for deal ii installation with -DGMSH_DIR=/path/to/gmsh added 
to it. But it gives me warning 

CMake Warning:
  Manually-specified variables were not used by the project:

GMSH_DIR

Can someone please suggest if I am missing anything here?

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[deal.II] Re: Gmsh support on Deal.II Virtualbox image

[Aaditya Lakshmanan]

Hi,
  You probably also need to supply the flag *-DDEAL_II_WITH_GMSH=ON* in the 
cmake line.

Best,
Aaditya

On Tuesday, December 15, 2020 at 1:21:00 PM UTC-5 husain.u...@gmail.com 
wrote:

>
> Hello Deal.II community,
> I am working on deal.II via the VM image (release 9.1.1). I am having 
> trouble reading the .msh file. I even tried running running step 49 and 
> received this error:
>
> 
> Exception on processing: 
>
> 
> An error occurred in line <1408> of file 
>  in function
> void dealii::GridIn::read_msh(std::istream&) [with int 
> dim = 2; int spacedim = 2; std::istream = std::basic_istream]
> The violated condition was: 
> in
> Additional information: 
> An input/output error has occurred. There are a number of reasons why 
> this may be happening, both for reading and writing operations.
>
> If this happens during an operation that tries to read data: First, you 
> may be trying to read from a file that doesn't exist or that is not 
> readable given its file permissions. Second, deal.II uses this error at 
> times if it tries to read information from a file but where the information 
> in the file does not correspond to the expected format. An example would be 
> a truncated file, or a mesh file that contains not only sections that 
> describe the vertices and cells, but also sections for additional data that 
> deal.II does not understand.
>
> If this happens during an operation that tries to write data: you may be 
> trying to write to a file to which file or directory permissions do not 
> allow you to write. A typical example is where you specify an output file 
> in a directory that does not exist.
> 
>
> Aborting!
> 
>
> I checked the detailed.log file and found DEAL_II_WITH_GMSH is OFF.  
> I also tried to install the latest version of gmsh (4.7.1) and ran the 
> cmake command for deal ii installation with -DGMSH_DIR=/path/to/gmsh added 
> to it. But it gives me warning 
>
> CMake Warning:
>   Manually-specified variables were not used by the project:
>
> GMSH_DIR
>
> Can someone please suggest if I am missing anything here?
>

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Re: [deal.II] Re: Gmsh support on Deal.II Virtualbox image

[Timo Heister]

This has nothing to do with DEAL_II_WITH_GMSH. That feature is only
required if you use functionality from the Gmsh namespace
(https://www.dealii.org/developer/doxygen/deal.II/namespaceGmsh.html).
The error message

The violated condition was:
in
Additional information:
An input/output error has occurred.

occurs when the .msh file is not found. Does the file exist in the
current folder?


On Tue, Dec 15, 2020 at 1:48 PM Aaditya Lakshmanan
 wrote:
>
> Hi,
>   You probably also need to supply the flag -DDEAL_II_WITH_GMSH=ON in the 
> cmake line.
>
> Best,
> Aaditya
>
> On Tuesday, December 15, 2020 at 1:21:00 PM UTC-5 husain.u...@gmail.com wrote:
>>
>>
>> Hello Deal.II community,
>> I am working on deal.II via the VM image (release 9.1.1). I am having 
>> trouble reading the .msh file. I even tried running running step 49 and 
>> received this error:
>>
>> 
>> Exception on processing:
>>
>> 
>> An error occurred in line <1408> of file 
>>  in function
>> void dealii::GridIn::read_msh(std::istream&) [with int 
>> dim = 2; int spacedim = 2; std::istream = std::basic_istream]
>> The violated condition was:
>> in
>> Additional information:
>> An input/output error has occurred. There are a number of reasons why 
>> this may be happening, both for reading and writing operations.
>>
>> If this happens during an operation that tries to read data: First, you may 
>> be trying to read from a file that doesn't exist or that is not readable 
>> given its file permissions. Second, deal.II uses this error at times if it 
>> tries to read information from a file but where the information in the file 
>> does not correspond to the expected format. An example would be a truncated 
>> file, or a mesh file that contains not only sections that describe the 
>> vertices and cells, but also sections for additional data that deal.II does 
>> not understand.
>>
>> If this happens during an operation that tries to write data: you may be 
>> trying to write to a file to which file or directory permissions do not 
>> allow you to write. A typical example is where you specify an output file in 
>> a directory that does not exist.
>> 
>>
>> Aborting!
>> 
>>
>> I checked the detailed.log file and found DEAL_II_WITH_GMSH is OFF.
>> I also tried to install the latest version of gmsh (4.7.1) and ran the cmake 
>> command for deal ii installation with -DGMSH_DIR=/path/to/gmsh added to it. 
>> But it gives me warning
>>
>> CMake Warning:
>>   Manually-specified variables were not used by the project:
>>
>> GMSH_DIR
>>
>> Can someone please suggest if I am missing anything here?
>
> --
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> https://groups.google.com/d/forum/dealii?hl=en
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-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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Re: [deal.II] Gmsh support on Deal.II Virtualbox image

[Wolfgang Bangerth]

I am working on deal.II via the VM image (release 9.1.1). I am having trouble 
reading the .msh file. I even tried running running step 49 and received this 
error:


I believe that's because we forgot to include two files in the release. Does 
this here help?

https://groups.google.com/g/dealii/c/ZtgMynOTx38/m/RsTGxUHqBgAJ

Best
 W.

--

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

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[deal.II] Making ParticlesHandler work with dealii::Triangulation and mesh refinement/coarsening

[lium...@gmail.com]

Hi deal.II Community,

I am new to the library and I'm trying to implement a prototype Stokes flow 
solver with tracer particles using shared memory computing. The overall 
procedure is something like:

1) Solve velocities and pressure analogous to Step-22.
2) Execute coarsening and refinement
3) Interpolate velocities to particles and move particles.

What I found is after grid coarsening, the particles which originally 
belong to the finer grid loses its host cell and an exception is thrown 
from ParticleAccessor::get_surrounding_cell().

I read through step-19 on Github. From my understanding the implementation 
there does not involve AMR and therefore such problems do not occur. I also 
consulted step-68 and 70. Those two implementations use 
parallel::distributed::Triangulation and attach pre- and post-refinement 
callback functions to save and reload particles. However in these functions 
the dynamic_cast from Triangulation to p::d::Triangulation is invalid and 
returns a nullptr.

My question is am I correct to assume that the library does not yet fully 
support particles on dealii::Triangulation with AMR? If yes can I ask for 
some guidance on how to implement it myself? One naive way out seems to be 
to store and reload procedure as is done in the library for 
p::d::Triangulation, but is it too costly?

I really appreciate your time and help.

Cheers,
Qihang.




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Re: [deal.II] Re: Some changes in arpack.h (Functionality to compute only eigenvalues)

[Bruno Turcksin]

Animesh,

You need to download the patch to the deal.II directory. If you cloned
deal.II, you can simply use git apply
0001-Enable-ARPACK-in-regular-mode.patch. If you didn't use git to get
deal.II, I think patch -i 0001-Enable-ARPACK-in-regular-mode.patch
should work. I have also noted that Arpack was not very accurate. I am
not sure why because according to the documentation, many other
packages are successfully using Arpack. At the end, we gave up on
Arpack and switched to lobpcg from anasazi. The results were more
accurate and more stable.

Best,

Bruno

Le mar. 15 déc. 2020 à 07:52, Animesh Rastogi IIT Gandhinagar
 a écrit :
>
> Hi Bruno,
>
> I would like to use this patch to compute the smallest eigenvalues in my 
> case. Could you please let me know how should I update my source code in the 
> arpack.h header file to accommodate these changes in the patch.  I understand 
> that I would need to reinstall dealii after updating the source code, which I 
> am fine with.
>
> When I am using the shift-inverse mode, I am not getting the results similar 
> to what I would get using the eigenvalue solver in MATLAB or Python for the 
> same matrix. There is a difference of about 15 to 20 in the eigenvalues (even 
> when comparing it with the ARPACK solver in Python). This is the reason that 
> I would want to try calculating the eigenvalues using the patch you created 
> in regular mode.
>
> Thanks!
>
> Animesh
> On Sunday, November 8, 2020 at 6:00:58 PM UTC+5:30 Animesh Rastogi IIT 
> Gandhinagar wrote:
>>
>> Thank you Bruno, I was able to change the source code accordingly. I 
>> reinstalled dealii and it worked fine!
>>
>> Thanks again!
>>
>> Animesh
>>
>> On Friday, November 6, 2020 at 3:55:29 AM UTC+5:30 bruno.t...@gmail.com 
>> wrote:
>>>
>>> Animesh,
>>>
>>> On Thursday, November 5, 2020 at 1:11:33 PM UTC-5 
>>> animesh...@alumni.iitgn.ac.in wrote:

 However, I have no way of passing it as a parameter to the solver 
 function. I was planning to edit the header file arpack.h accordingly 
 which is inside the /usr/local/include/deal.II/lac to have that 
 functionality. I was actually thinking of passing the flag "rvec" as an 
 argument to the function solve. I was wondering if I change the permission 
 of the file to write mode, edit it and save it, would I be able to run my 
 code inside the examples folder. Or do I need to take care of something 
 else while and after editing that headerfile?
>>>
>>> You should change the source code and reinstall deal.II. I would do what 
>>> you propose only if you cannot compile deal.II on that machine. It might 
>>> work in this particular case but I really advise you against it.
>>>
>>> Best,
>>>
>>> Bruno
>>>
>
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Re: [deal.II] Making ParticlesHandler work with dealii::Triangulation and mesh refinement/coarsening

[Wolfgang Bangerth]

On 12/15/20 2:49 PM, lium...@gmail.com wrote:


1) Solve velocities and pressure analogous to Step-22.
2) Execute coarsening and refinement
3) Interpolate velocities to particles and move particles.

What I found is after grid coarsening, the particles which originally belong 
to the finer grid loses its host cell and an exception is thrown from 
ParticleAccessor::get_surrounding_cell().


Qihang,
Interesting. Do you think you could put together a short testcase that 
illustrates this issue?


Best
 W.

--

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   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Triangulation Merge Error

[Wolfgang Bangerth]

On 12/15/20 9:19 AM, pushkar...@gmail.com wrote:


So I am wondering that am I doing something wrong or is there any consistency 
check that needs to be performed while merging triangulations. Any direction 
in this regard will surely be beneficial.


Pushkar,
I suspect (knowing where the error message is coming from) that the two 
triangulations overlap each other and that the algorithm is matching an 
internal edge of one triangulation with a boundary edge of the other 
triangulation. That doesn't work, but you can at least try that out by 
outputting the two triangulations and plotting them at the same time.


Best
 W.

--

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   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Gmsh support on Deal.II Virtualbox image

[husain.u...@gmail.com]

Dear all, thanx for the immediate support. Turns out Professor Heister was 
right. I am using an IDE CLion, and I still dont understand everything in 
it. I moved my .msh file to the cmake-build-debug folder (created when I 
run my project using that IDE) and was able to read it.
Regards
Umair

On Wednesday, December 16, 2020 at 2:29:44 AM UTC+5:30 Wolfgang Bangerth 
wrote:

>
> > I am working on deal.II via the VM image (release 9.1.1). I am having 
> trouble 
> > reading the .msh file. I even tried running running step 49 and received 
> this 
> > error:
>
> I believe that's because we forgot to include two files in the release. 
> Does 
> this here help?
> https://groups.google.com/g/dealii/c/ZtgMynOTx38/m/RsTGxUHqBgAJ
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

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