Re: [deal.II] Re: Subdivided cylinder and boundary ids

2021-08-23 Thread blais...@gmail.com 
This issue is now fixed by a PR merged yesterday.
Best
Bruno


On Monday, June 28, 2021 at 6:40:04 a.m. UTC-4 alexanderc...@gmail.com 
wrote:

> Hi Bruno,
>
> Sure, I can try making a PR this week.
>
> Best,
> Alex
>
> On Sunday, June 27, 2021 at 9:36:50 p.m. UTC+2 blais...@gmail.com wrote:
>
>> I most likely copied this mistake from the regular Cylinder and did not 
>> think of it when I coded the subdivided cylinder.
>> Alex, if you feel comfortable, you could go ahead and make a PR following 
>> Wolfgang's suggestion. Otherwise, I'll gladly look into it this week :)
>> Best
>> BRuno
>>
>>
>> On Friday, June 25, 2021 at 11:52:51 p.m. UTC-4 Wolfgang Bangerth wrote:
>>
>>> On 6/25/21 12:37 PM, Marc Fehling wrote: 
>>> > # Instead of an absolute threshold, you can introduce a relative one, 
>>> for 
>>> > example, `epsilon * cell->diameter()` or something similar. 
>>>
>>> FWIW, in most places, this is what we do. 
>>> Best 
>>> W. 
>>>
>>>
>>> -- 
>>>  
>>> Wolfgang Bangerth email: bang...@colostate.edu 
>>> www: http://www.math.colostate.edu/~bangerth/ 
>>>
>>>

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Re: [deal.II] Re: Subdivided cylinder and boundary ids

2021-06-28 Thread Alex Cumberworth 
Hi Bruno,

Sure, I can try making a PR this week.

Best,
Alex

On Sunday, June 27, 2021 at 9:36:50 p.m. UTC+2 blais...@gmail.com wrote:

> I most likely copied this mistake from the regular Cylinder and did not 
> think of it when I coded the subdivided cylinder.
> Alex, if you feel comfortable, you could go ahead and make a PR following 
> Wolfgang's suggestion. Otherwise, I'll gladly look into it this week :)
> Best
> BRuno
>
>
> On Friday, June 25, 2021 at 11:52:51 p.m. UTC-4 Wolfgang Bangerth wrote:
>
>> On 6/25/21 12:37 PM, Marc Fehling wrote:
>> > # Instead of an absolute threshold, you can introduce a relative one, 
>> for 
>> > example, `epsilon * cell->diameter()` or something similar.
>>
>> FWIW, in most places, this is what we do.
>> Best
>> W.
>>
>>
>> -- 
>> 
>> Wolfgang Bangerth email: bang...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>>

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Re: [deal.II] Re: Subdivided cylinder and boundary ids

2021-06-27 Thread blais...@gmail.com 
I most likely copied this mistake from the regular Cylinder and did not 
think of it when I coded the subdivided cylinder.
Alex, if you feel comfortable, you could go ahead and make a PR following 
Wolfgang's suggestion. Otherwise, I'll gladly look into it this week :)
Best
BRuno


On Friday, June 25, 2021 at 11:52:51 p.m. UTC-4 Wolfgang Bangerth wrote:

> On 6/25/21 12:37 PM, Marc Fehling wrote:
> > # Instead of an absolute threshold, you can introduce a relative one, 
> for 
> > example, `epsilon * cell->diameter()` or something similar.
>
> FWIW, in most places, this is what we do.
> Best
> W.
>
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

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Re: [deal.II] Re: Subdivided cylinder and boundary ids

2021-06-25 Thread Wolfgang Bangerth 

On 6/25/21 12:37 PM, Marc Fehling wrote:
# Instead of an absolute threshold, you can introduce a relative one, for 
example, `epsilon * cell->diameter()` or something similar.


FWIW, in most places, this is what we do.
Best
 W.


--

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

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[deal.II] Re: Subdivided cylinder and boundary ids

2021-06-25 Thread Marc Fehling 
By the way, this function has just been introduced in April with #12003 
. Suggestions for improvement 
on this new feature are welcome!

Best,
Marc

On Friday, June 25, 2021 at 12:37:31 PM UTC-6 Marc Fehling wrote:

> Hi Alex,
>
> > I scrolled through grid_generator.cc and found that subdivided_cylinder 
> has a hardcoded epsilon of 1e-5 for determining whether a face is at the 
> boundary. Of course, with a system of my size, all faces will end up being 
> considered to be at the boundary.
> >
> > Because it not only sets the boundary ids, but the manifold ids, it 
> seems I will have to modify the subdivided_cylinder to make the epsilon 
> value much smaller or somehow relative to the system size, which is simple 
> enough.
>
> That sounds like a good idea to me. Would you willing to write a patch and 
> open a pull request for the library? I'm sure others will benefit of your 
> changes as well!
>
> There are several options you can consider.
>
>1. You could provide epsilon as a parameter to the function and 
>default it to `1e-5`.
>2. Instead of an absolute threshold, you can introduce a relative one, 
>for example, `epsilon * cell->diameter()` or something similar.
>3. You can also try to use the machine precision 
>std::numeric_limits::epsilon 
> as a 
>substitute for `1e-5`.
>4. Why do we need these epsilons in the first place? Maybe it will 
>work if you just replace the greater/lesser checks with their equal 
>variants `>=` and `<=`.
>
> Best,
> Marc
>
> On Friday, June 25, 2021 at 6:45:12 AM UTC-6 alexanderc...@gmail.com 
> wrote:
>
>> I have been trying to construct a system that is small (a total length of 
>> 1e-5 m) with the subdivided cylinder grid generator. However, I have been 
>> having trouble with the boundary indicators. I wanted to set my own 
>> boundaries, and because there is no colorize option (it defaults to setting 
>> the left end face of the cylinder to 1, and the right end to 2), I tried to 
>> first set all boundary ids to 0. However, this leads to the following 
>> exception:
>>
>> terminate called after throwing an instance of 
>> 'dealii::TriaAccessorExceptions::ExcNoPeriodicNeighbor'
>>   what():  
>> 
>> An error occurred in line <2597> of file 
>>  
>> in function
>> dealii::TriaIterator > 
>> dealii::CellAccessor::neighbor_or_periodic_neighbor(unsigned 
>> int) const [with int dim = 3; int spacedim = 3]
>> The violated condition was: 
>> false
>> Additional information: 
>> (none)
>>
>> Since in my test system, I was setting the boundary ids to be the same as 
>> the default, I tried to rely on this instead. However, I was having strange 
>> behaviour where it seemed that the entire system was having the boundary 
>> conditions applied to it. I scrolled through grid_generator.cc and found 
>> that subdivided_cylinder has a hardcoded epsilon of 1e-5 for determining 
>> whether a face is at the boundary. Of course, with a system of my size, all 
>> faces will end up being considered to be at the boundary.
>>
>> Because it not only sets the boundary ids, but the manifold ids, it seems 
>> I will have to modify the subdivided_cylinder to make the epsilon value 
>> much smaller or somehow relative to the system size, which is simple enough.
>>
>> It would probably also be good to have the colorize option. However, I am 
>> not sure what to make of the exception when I try to set all the boundary 
>> ids to 0.
>>
>> Best,
>> Alex
>>
>

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[deal.II] Re: Subdivided cylinder and boundary ids

2021-06-25 Thread Marc Fehling 
Hi Alex,

> I scrolled through grid_generator.cc and found that subdivided_cylinder 
has a hardcoded epsilon of 1e-5 for determining whether a face is at the 
boundary. Of course, with a system of my size, all faces will end up being 
considered to be at the boundary.
>
> Because it not only sets the boundary ids, but the manifold ids, it seems 
I will have to modify the subdivided_cylinder to make the epsilon value 
much smaller or somehow relative to the system size, which is simple enough.

That sounds like a good idea to me. Would you willing to write a patch and 
open a pull request for the library? I'm sure others will benefit of your 
changes as well!

There are several options you can consider.

   1. You could provide epsilon as a parameter to the function and default 
   it to `1e-5`.
   2. Instead of an absolute threshold, you can introduce a relative one, 
   for example, `epsilon * cell->diameter()` or something similar.
   3. You can also try to use the machine precision std::numeric_limits::
   epsilon  
   as a substitute for `1e-5`.
   4. Why do we need these epsilons in the first place? Maybe it will work 
   if you just replace the greater/lesser checks with their equal variants 
   `>=` and `<=`.
   
Best,
Marc

On Friday, June 25, 2021 at 6:45:12 AM UTC-6 alexanderc...@gmail.com wrote:

> I have been trying to construct a system that is small (a total length of 
> 1e-5 m) with the subdivided cylinder grid generator. However, I have been 
> having trouble with the boundary indicators. I wanted to set my own 
> boundaries, and because there is no colorize option (it defaults to setting 
> the left end face of the cylinder to 1, and the right end to 2), I tried to 
> first set all boundary ids to 0. However, this leads to the following 
> exception:
>
> terminate called after throwing an instance of 
> 'dealii::TriaAccessorExceptions::ExcNoPeriodicNeighbor'
>   what():  
> 
> An error occurred in line <2597> of file 
>  
> in function
> dealii::TriaIterator > 
> dealii::CellAccessor::neighbor_or_periodic_neighbor(unsigned 
> int) const [with int dim = 3; int spacedim = 3]
> The violated condition was: 
> false
> Additional information: 
> (none)
>
> Since in my test system, I was setting the boundary ids to be the same as 
> the default, I tried to rely on this instead. However, I was having strange 
> behaviour where it seemed that the entire system was having the boundary 
> conditions applied to it. I scrolled through grid_generator.cc and found 
> that subdivided_cylinder has a hardcoded epsilon of 1e-5 for determining 
> whether a face is at the boundary. Of course, with a system of my size, all 
> faces will end up being considered to be at the boundary.
>
> Because it not only sets the boundary ids, but the manifold ids, it seems 
> I will have to modify the subdivided_cylinder to make the epsilon value 
> much smaller or somehow relative to the system size, which is simple enough.
>
> It would probably also be good to have the colorize option. However, I am 
> not sure what to make of the exception when I try to set all the boundary 
> ids to 0.
>
> Best,
> Alex
>

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