Re: [deal.II] install problems with clang@12.0.0 and Xcode12.0 from spack

2020-09-29 Thread Luca Heltai
Dear Alex,

what happens after loading dealii with `spack load dealii`, if you try to
build (from scratch) `step-40`?

Can you send us the output of  cmake and make?

Luca.

On Mon, Sep 28, 2020 at 4:46 PM 'Alexander Greiner' via deal.II User Group <
dealii@googlegroups.com> wrote:

> Hi Luca,
>
> I installed environment-modules and currently have the following lines in
> my .bash_profile:
>
> ### dealii 9.2 ###
> SPACK_ROOT=/Users/alexandergreiner/spack
> export PATH=$SPACK_ROOT/bin:$PATH
> MODULES_HOME=$(spack location -i environment-modules)
> source ${MODULES_HOME}/init/zsh
> . $SPACK_ROOT/share/spack/setup-env.sh
>
> After spack load dealii, spack find --loaded shows (attached).
>
> But, echo $DYLD_LIBRARY_PATH shows nothing. Do I have to pay attention to
> something due to its clumsiness? Is there any further helpful
> information/files that I can provide to you?
> I highly appreciate the help I am receiving from all of you!
>
> Regards
> Alex
> luca@gmail.com schrieb am Montag, 28. September 2020 um 14:23:46
> UTC+2:
>
>> My suggestion is to install also environment-modules, and then use
>>
>> spack load dealii
>>
>> This will popolate DYLD_LIBRARY_PATH with the correct values and allows
>> your cmake to find all libraries.
>>
>> Unfortunately, recent updates to spack have made its functionality a bit
>> clumsy in Mac OS...
>>
>> L.
>>
>> > On 28 Sep 2020, at 13:40, 'Alexander Greiner' via deal.II User Group <
>> dea...@googlegroups.com> wrote:
>> >
>> > Hi, thanks for your suggestions.
>> >
>> > Yes, Trilinos is installed by spack and
>> > ls `spack location -i trilinos`/lib/libmuelu*
>> > shows me the correct paths to the libmuelu libraries.
>> > I also enabled Full Disk Access for Terminal.app and restarted the App
>> as described.
>> > Still, the libraries are not linked properly.
>> >
>> > Best
>> > Alex
>> >
>> > Praveen C schrieb am Montag, 28. September 2020 um 13:08:14 UTC+2:
>> > No, you dont have to recompile deal.II for what I am suggesting.
>> >
>> > I suppose that lib is installed by spack, have you checked
>> >
>> > ls `spack location -i trilinos`/lib/libmuelu*
>> >
>> > Not sure if this will help, but
>> >
>> > Have you enabled Full Disk Access for Terminal.app
>> >
>> > If not, can you enable it and try. See this
>> >
>> >
>> https://macperformanceguide.com/blog/2020/20200208_2004macOS-Catalina-add-fullDiskAccess-Terminal.html
>> >
>> > best
>> > praveen
>> >
>> >
>> >> On 28-Sep-2020, at 3:53 PM, 'Alexander Greiner' via deal.II User Group
>>  wrote:
>> >>
>> >> Hi Praveen,
>> >>
>> >> "Stupid" question beforehand: Do I have to reinstall deal.II? If yes,
>> you can skip the remainder. If no, I did the following:
>> >>
>> >> I added that line to my ./bash_profile opened a new terminal window
>> and executed
>> >> source ./bash_profile
>> >> spack load dealii
>> >> cd spack/opt/.../deal.II/examples/step-1
>> >> cmake . (I removed all previously generated "make"-files to obtain the
>> initial directory content of step-1)
>> >> make run
>> >> Unfortunately, libmuelu is still not found. I attached a printout of
>> my environment variables, if this might help...
>> >
>> >
>> > --
>> > 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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>> Groups "deal.II User Group" group.
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>> https://groups.google.com/d/msgid/dealii/97294b8d-4815-4f96-a346-8d8d6037ff35n%40googlegroups.com.
>>
>>
>> --
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Re: [deal.II] step-1 Error

2020-09-19 Thread Luca Heltai
Are you running the terminal, or the deal.II application?

When you run the deal.II application, you are dropped into a terminal (with 
instructions) to run deal.II examples. Including how to set up your bashrc (or 
zshrc) to point to the deal.II 
Installation/the module command. 

Only after you instructed the terminal of the right paths, you’ll be able to 
run deal.II from the standard terminal. 

Luca

> Il giorno 18 set 2020, alle ore 23:37, Scott Ziegler 
>  ha scritto:
> 
> Thanks for the response! I might be misunderstanding, but in my directory 
> for step-1 I tried running the command exactly as "module load dealii" and I 
> just get "bash: module: command not found" in return. What am I doing wrong?
> 
>> On Wednesday, August 26, 2020 at 12:14:41 PM UTC-6 luca@gmail.com wrote:
>> The 9.0.0 image contains a spack installation. Can you run "module load 
>> dealii" before trying to run?
>> 
>> Luca. 
>> 
>> Il giorno mer 26 ago 2020 alle 19:51 Scott Ziegler 
>>  ha scritto:
>>> Hello,
>>> 
>>> I tried running the first tutorial on my machine and I am getting an error 
>>> message I don't understand. The "cmake step-1.cc ." and "make step-1.cc" 
>>> commands ran fine, but when I try "make run step-1.cc" I get the following 
>>> error:
>>> 
>>> Scanning dependencies of target step-1
>>> 
>>> [ 33%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o
>>> 
>>> [ 66%] Linking CXX executable step-1
>>> 
>>> [ 66%] Built target step-1
>>> 
>>> Scanning dependencies of target run
>>> 
>>> [100%] Run step-1 with Debug configuration
>>> 
>>> dyld: Library not loaded: libiomp5.dylib
>>> 
>>>   Referenced from: 
>>> /Applications/deal.II-9.0.0.app/Contents/Resources/spack/opt/spack/darwin-highsierra-x86_64/clang-6.0.0/assimp-4.0.1-pdlrx32676yct2pztierxgvynk5gx277/lib/libassimp.4.dylib
>>> 
>>>   Reason: image not found
>>> 
>>> make[3]: *** [CMakeFiles/run] Abort trap: 6
>>> 
>>> make[2]: *** [CMakeFiles/run.dir/all] Error 2
>>> 
>>> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
>>> 
>>> make: *** [run] Error 2
>>> 
>>> 
>>> 
>>> I am running an older version of deal.ii (deal.ii.9.0.0) because the latest 
>>> version wasn't compatible with my laptop. I have a 2012 MacBook Pro running 
>>> macOS 10.13.6. Any help would be greatly appreciated, thank you.
>>> 
>> 
>>> -- 
>>> 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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>>> https://groups.google.com/d/msgid/dealii/b46da6bf-895b-4cb2-b5aa-c60845f85c61n%40googlegroups.com.
> 
> -- 
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Re: [deal.II] step-1 Error

2020-08-26 Thread Luca Heltai
The 9.0.0 image contains a spack installation. Can you run "module load
dealii" before trying to run?

Luca.

Il giorno mer 26 ago 2020 alle 19:51 Scott Ziegler <
scott...@rams.colostate.edu> ha scritto:

> Hello,
>
> I tried running the first tutorial on my machine and I am getting an error
> message I don't understand. The "cmake step-1.cc ." and "make step-1.cc"
> commands ran fine, but when I try "make run step-1.cc" I get the following
> error:
>
> *Scanning dependencies of target step-1*
>
> [ 33%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o
>
> [ 66%] *Linking CXX executable step-1*
>
> [ 66%] Built target step-1
>
> *Scanning dependencies of target run*
>
> [100%] *Run step-1 with Debug configuration*
>
> dyld: Library not loaded: libiomp5.dylib
>
>   Referenced from:
> /Applications/deal.II-9.0.0.app/Contents/Resources/spack/opt/spack/darwin-highsierra-x86_64/clang-6.0.0/assimp-4.0.1-pdlrx32676yct2pztierxgvynk5gx277/lib/libassimp.4.dylib
>
>   Reason: image not found
>
> make[3]: *** [CMakeFiles/run] Abort trap: 6
>
> make[2]: *** [CMakeFiles/run.dir/all] Error 2
>
> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
>
> make: *** [run] Error 2
>
>
> I am running an older version of deal.ii (deal.ii.9.0.0) because the
> latest version wasn't compatible with my laptop. I have a 2012 MacBook Pro
> running macOS 10.13.6. Any help would be greatly appreciated, thank you.
>
> --
> 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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Re: [deal.II] Problem implementing Neumann boundary condition

2020-08-21 Thread Luca Heltai
You use it to compute the Neumann boundary condition in your program. You 
compute the gradient of the boundary function and dot it with the normal 
vector. 

You could get by if you knew beforehand the value of 

grad(g).n

But your  code uses grad(g) (which is not defined in Neumann.h), hence the 
error. 

Luca

> Il giorno 21 ago 2020, alle ore 10:07, Umair Hussain 
>  ha scritto:
> 
> 
> Thanx Luca. I got it. But I still don’t understand what is this “gradient” 
> used for?
> 
>> On Fri, 21 Aug 2020 at 12:22 PM, Luca Heltai  wrote:
>> Did you actually read the error message? :-)
>> 
>> It tells you exactly what you have to do. In particolar, you are using 
>> bc.gradient to evaluate the Neumann boundary value, but you did not 
>> implement the gradient in your Neumann.h file. This explained in detail in 
>> the error message you got. 
>> 
>> The default implementation of "gradient" for the class Function simply 
>> throws an exception. Id you implement it, everything should work. 
>> 
>> Best,
>> Luca
>> 
>>>> Il giorno 21 ago 2020, alle ore 04:59, husain.u...@gmail.com 
>>>>  ha scritto:
>>>> 
>>> 
>> 
>>> 
>>> Hello Deal II community,
>>> I have just started with deal ii, so I am trying to solve a basic laplace 
>>> equation on a square domain with dirichilet bc on two faces and neumann bc 
>>> on the remaining two. I have used steps from step-7 to implement neumann 
>>> bc, but i am running into the following error:
>>> 
>>> 
>>> 
>>> An error occurred in line <133> of file 
>>> 
>>>  in function
>>> dealii::Tensor<1, dim, Number> dealii::Function>> RangeNumberType>::gradient(const dealii::Point&, unsigned int) const 
>>> [with int dim = 2; RangeNumberType = double]
>>> The violated condition was: 
>>> false
>>> Additional information: 
>>> You (or a place in the library) are trying to call a function that is 
>>> declared as a virtual function in a base class but that has not been 
>>> overridden in your derived class.
>>> 
>>> This exception happens in cases where the base class cannot provide a 
>>> useful default implementation for the virtual function, but where we also 
>>> do not want to mark the function as abstract (i.e., with '=0' at the end) 
>>> because the function is not essential to the class in many contexts. In 
>>> cases like this, the base class provides a dummy implementation that makes 
>>> the compiler happy, but that then throws the current exception.
>>> 
>>> A concrete example would be the 'Function' class. It declares the existence 
>>> of 'value()' and 'gradient()' member functions, and both are marked as 
>>> 'virtual'. Derived classes have to override these functions for the values 
>>> and gradients of a particular function. On the other hand, not every 
>>> function has a gradient, and even for those that do, not every program 
>>> actually needs to evaluate it. Consequently, there is no *requirement* that 
>>> a derived class actually override the 'gradient()' function (as there would 
>>> be had it been marked as abstract). But, since the base class cannot know 
>>> how to compute the gradient, if a derived class does not override the 
>>> 'gradient()' function and it is called anyway, then the default 
>>> implementation in the base class will simply throw an exception.
>>> 
>>> The exception you see is what happens in cases such as the one just 
>>> illustrated. To fix the problem, you need to investigate whether the 
>>> function being called should indeed have been called; if the answer is 
>>> 'yes', then you need to implement the missing override in your class.
>>> 
>>> Stacktrace:
>>> ---
>>> #0  /usr/local/lib/libdeal_II.g.so.9.1.1: dealii::Function<2, 
>>> double>::gradient(dealii::Point<2, double> const&, unsigned int) const
>>> #1  /home/umair/CLionProjects/MyLaplace2/cmake-build-debug/MyLaplace2: 
>>> laplace_solver::assemble_system()
>>> #2  /home/umair/CLionProjects/MyLaplace2/cmake-build-debug/MyLaplace2: 
>>> laplace_solver::run()
>>> #3  /home/umair/CLionProjects/MyLaplace2/cmake-build-debug/MyLaplace2: main
>>> 
>>> 
>>> 
>>> I have attached my code for more help.
>>> Thank you in

Re: [deal.II] Problem implementing Neumann boundary condition

2020-08-21 Thread Luca Heltai
Did you actually read the error message? :-)

It tells you exactly what you have to do. In particolar, you are using 
bc.gradient to evaluate the Neumann boundary value, but you did not implement 
the gradient in your Neumann.h file. This explained in detail in the error 
message you got. 

The default implementation of "gradient" for the class Function simply throws 
an exception. Id you implement it, everything should work. 

Best,
Luca

> Il giorno 21 ago 2020, alle ore 04:59, husain.u...@gmail.com 
>  ha scritto:
> 
> 
> Hello Deal II community,
> I have just started with deal ii, so I am trying to solve a basic laplace 
> equation on a square domain with dirichilet bc on two faces and neumann bc on 
> the remaining two. I have used steps from step-7 to implement neumann bc, but 
> i am running into the following error:
> 
> 
> 
> An error occurred in line <133> of file 
> 
>  in function
> dealii::Tensor<1, dim, Number> dealii::Function RangeNumberType>::gradient(const dealii::Point&, unsigned int) const 
> [with int dim = 2; RangeNumberType = double]
> The violated condition was: 
> false
> Additional information: 
> You (or a place in the library) are trying to call a function that is 
> declared as a virtual function in a base class but that has not been 
> overridden in your derived class.
> 
> This exception happens in cases where the base class cannot provide a useful 
> default implementation for the virtual function, but where we also do not 
> want to mark the function as abstract (i.e., with '=0' at the end) because 
> the function is not essential to the class in many contexts. In cases like 
> this, the base class provides a dummy implementation that makes the compiler 
> happy, but that then throws the current exception.
> 
> A concrete example would be the 'Function' class. It declares the existence 
> of 'value()' and 'gradient()' member functions, and both are marked as 
> 'virtual'. Derived classes have to override these functions for the values 
> and gradients of a particular function. On the other hand, not every function 
> has a gradient, and even for those that do, not every program actually needs 
> to evaluate it. Consequently, there is no *requirement* that a derived class 
> actually override the 'gradient()' function (as there would be had it been 
> marked as abstract). But, since the base class cannot know how to compute the 
> gradient, if a derived class does not override the 'gradient()' function and 
> it is called anyway, then the default implementation in the base class will 
> simply throw an exception.
> 
> The exception you see is what happens in cases such as the one just 
> illustrated. To fix the problem, you need to investigate whether the function 
> being called should indeed have been called; if the answer is 'yes', then you 
> need to implement the missing override in your class.
> 
> Stacktrace:
> ---
> #0  /usr/local/lib/libdeal_II.g.so.9.1.1: dealii::Function<2, 
> double>::gradient(dealii::Point<2, double> const&, unsigned int) const
> #1  /home/umair/CLionProjects/MyLaplace2/cmake-build-debug/MyLaplace2: 
> laplace_solver::assemble_system()
> #2  /home/umair/CLionProjects/MyLaplace2/cmake-build-debug/MyLaplace2: 
> laplace_solver::run()
> #3  /home/umair/CLionProjects/MyLaplace2/cmake-build-debug/MyLaplace2: main
> 
> 
> 
> I have attached my code for more help.
> Thank you in advance,
> Umair.
> 
> -- 
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> 
> 
> 
> 
> 
> 

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Re: [deal.II] Reading a Tensor from parameter file

2020-08-05 Thread Luca Heltai

> Thank you. This really shortens the code. Is it also possible to set the 
> delimiter to a user desired value, say "|" instead of ",".

All functions of the Convert class take a unique pointer to a pattern. You can 
specify your own pattern, and use that in the conversion. The code is all in

deal.II/base/patterns_tools.h

After the Class declarations, you’ll find the implementations for the basic 
classes of deal.II, including vector, map, pairs and tuples of them. 

Best,
Luca 

> Also, where exactly is the procedure for conversion from string to 
> deali::Tensor or some other type say std::vector defined? I could not 
> find it in the source code.
> 
> Best regards,
> Paras
> 
>> On Tuesday, August 4, 2020 at 6:15:47 PM UTC+2, Paras Kumar wrote:
>> Hi,
>> 
>> Could you please provide an MWE to describe how the 
>> Patterns::Convert::to_value() function would work in this case.
>> 
>> Is it must to use prm.add_parameter()  to be able to do so? I usually use 
>> prm.declare_entry() and prm.get(). 
>> 
>> Best regards,
>> Paras
>> 
>>> On Wednesday, April 15, 2020 at 6:01:53 PM UTC+2, Luca Heltai wrote:
>>> Currently, this is also the simplest way:
>>> 
>>> Tensor tens;
>>> prm.add_parameter("Tensor", tens);
>>> 
>>> Take a look at the documentation of the add parameter method.
>>> 
>>> Patterns::Tools::to_string(tens);
>>> 
>>> And 
>>> 
>>> Patterns::Tools::to_value 
>>> 
>>> Are also available to simplify what you want to achieve. 
>>> 
>>> Alternatively: Patterns::Tools::Convert offers ways to construct default 
>>> Patterns for many types, including Tensors. 
>>> 
>>> Best,
>>> Luca
>>> 
>>  
> 
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Re: [deal.II] Installation didn't give any errors but when I tried make test, it failed all tests

2020-07-30 Thread Luca Heltai
Take a look at your parameter file. It is probably trying to write output file 
to a directory that does not exist. 

Luca

> Il giorno 30 lug 2020, alle ore 10:58, kaleem iqbal  
> ha scritto:
> 
> 
> Dear Prof. Wolfgang; 
> During running step-70. I found the following error  
> Exception on processing: 
> 
> 
> An error occurred in line <1360> of file 
> 
>  in function
> void dealii::ParameterHandler::print_parameters(const string&, 
> dealii::ParameterHandler::OutputStyle) const
> The violated condition was: 
> out
> 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!
> 
> CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run' failed
> make[3]: *** [CMakeFiles/run] Error 1
> CMakeFiles/Makefile2:131: recipe for target 'CMakeFiles/run.dir/all' failed
> make[2]: *** [CMakeFiles/run.dir/all] Error 2
> CMakeFiles/Makefile2:138: recipe for target 'CMakeFiles/run.dir/rule' failed
> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
> Makefile:144: recipe for target 'run' failed
> make: *** [run] Error 2
> Please guide me
> Regards
> Kaleem iqbal
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Re: [deal.II] Re: KDTree implementation error

2020-07-24 Thread Luca Heltai
If you are using version 9.3pre of deal.II, kdtree was removed. Use RTree 
instead, which is faster and more flexible. 

Luca

> Il giorno 24 lug 2020, alle ore 05:41, heena patel  ha 
> scritto:
> 
> 
> Dear Bruno,
>I had already added kdree.h header file, check 
> the question again. But it seems it does not read KDTree; something is not 
> compatible between class and header file.
> 
> Regards,
> Heena
> 
>> On Thu, Jul 23, 2020 at 9:03 PM Bruno Turcksin  
>> wrote:
>> Heena,
>> 
>> You are missing an include. Try adding #include 
>> 
>> Best,
>> 
>> Bruno
>> 
>>> On Thursday, July 23, 2020 at 2:55:53 PM UTC-4, heena patel wrote:
>>> 
>>> Dear all,
>>>   I had tried to implement KDTree in step_1 tutoria 
>>> and header file for kdtree is added to the codel. It is as follows:
>>> 
>>> void first_grid()
>>> {
>>> 
>>>   Triangulation<2> triangulation;
>>> 
>>>   GridGenerator::hyper_cube(triangulation);
>>>   triangulation.refine_global(4);
>>>   Point<2>  p;
>>>KDTree<2> tree(10,triangulation.get_vertices());
>>>auto w = tree.get_closest_points(p, 3);
>>>   std::ofstream out("grid-1.svg");
>>>   GridOut   grid_out;
>>>   grid_out.write_svg(triangulation, out);
>>>   std::cout << "Grid written to grid-1.svg" << std::endl;
>>> }
>>> 
>>> 
>>> 
>>> It gives me error as below 
>>> 
>>> /home/heena/Project/examples/step-1/step-1.cc:76:4: error: ‘KDTree’ was not 
>>> declared in this scope
>>> KDTree<2> tree(10,triangulation.get_vertices());
>>> ^~
>>> /home/heena/Project/examples/step-1/step-1.cc:76:4: note: suggested 
>>> alternative: ‘free’
>>> KDTree<2> tree(10,triangulation.get_vertices());
>>> ^~
>>> free
>>> /home/heena/Project/examples/step-1/step-1.cc:76:14: error: ‘tree’ was not 
>>> declared in this scope
>>> KDTree<2> tree(10,triangulation.get_vertices());
>>>   ^~~~
>>> /home/heena/Project/examples/step-1/step-1.cc:76:14: note: suggested 
>>> alternative: ‘free’
>>> KDTree<2> tree(10,triangulation.get_vertices());
>>>   ^~~~
>>>   free
>>> 
>>> 
>>> 
>>> Is there something missing?
>>> 
>>> 
>>> 
>>> Regards,
>>> Heena
>> 
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> 
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Re: [deal.II] Particles and field interpolation error

2020-07-15 Thread Luca Heltai
Franco,

The interpolated field says that the field value is zero (on the line above 
your arrow). This is how it is documented: if a particle is removed, its 
interpolated value is left unchanged in the target vector. Zero in your case. 

Luca

> Il giorno 15 lug 2020, alle ore 18:18, Franco Milicchio 
>  ha scritto:
> 
> 
> Dear all,
> 
> I am playing with 9.2 and particles, but I've encountered a weird problem. If 
> I remove a particle, the interpolated field on particle locations yields a 
> wrong answer.
> 
> My code does (now) everything by hand:
> 
>   // Here be drangons...
> 
>   Point<2> p_0(0.1,0.5);
>   auto ref_cell_0 = GridTools::find_active_cell_around_point(dof_handler, 
> p_0);
>   Point<2> ref_p_0 = 
> StaticMappingQ1<2>::mapping.transform_real_to_unit_cell(ref_cell_0, p_0);
> 
>   Point<2> p_1(0.5,0.5);
>   auto ref_cell_1 = GridTools::find_active_cell_around_point(dof_handler, 
> p_1);
>   Point<2> ref_p_1 = 
> StaticMappingQ1<2>::mapping.transform_real_to_unit_cell(ref_cell_1, p_1);
> 
>   Point<2> p_2(0.9,0.5);
>   auto ref_cell_2 = GridTools::find_active_cell_around_point(dof_handler, 
> p_2);
>   Point<2> ref_p_2 = 
> StaticMappingQ1<2>::mapping.transform_real_to_unit_cell(ref_cell_2, p_2);
> 
>   particle_handler.insert_particle(Particles::Particle<2>(p_0, ref_p_0, 0), 
> ref_cell_0);
>   particle_handler.insert_particle(Particles::Particle<2>(p_1, ref_p_1, 1), 
> ref_cell_1);
>   particle_handler.insert_particle(Particles::Particle<2>(p_2, ref_p_2, 2), 
> ref_cell_2);
> 
>   particle_handler.update_cached_numbers();
> 
>   std::cout << "Printing particle id, location and reference location" << 
> std::endl;
>   for(auto :particle_handler)
>   {
> std::cout << "id: " << p.get_id() << "  loc: " << p.get_location() << "  
> ref_loc: " << p.get_reference_location() << std::endl;
>   }
> 
>   field_on_particles.reinit(particle_handler.n_global_particles());
>   Particles::Utilities::interpolate_field_on_particles(dof_handler, 
> particle_handler, field, field_on_particles);
> 
>   std::cout << "Printing field value on particle location" << std::endl;
>   for(int pp = 0; pp< particle_handler.n_global_particles(); pp++)
>   {
>   std::cout << "fluid id: " << pp << " value: " << field_on_particles[pp] 
> << std::endl;
>   }
> 
>   // 
>   // NOW REMOVE A PARTICLE...
>   // 
> 
>   for(auto itr=particle_handler.begin(); itr != particle_handler.end(); itr++)
>   {
> if(itr->get_id()==1) particle_handler.remove_particle(itr);
>   }
> 
>   particle_handler.update_cached_numbers();
> 
> 
>   // ***
>   // ...AND VALUES ARE WRONG
>   // ***
> 
>   std::cout << "Printing particle id, location and reference location after 
> removing particle" << std::endl;
> 
>   for(auto itr_2=particle_handler.begin(); itr_2 != particle_handler.end(); 
> itr_2++)
>   {
> std::cout << "id: " << itr_2->get_id() << "  loc: " << 
> itr_2->get_location() << "  ref_loc: " << itr_2->get_reference_location() << 
> std::endl;
>   }
> 
>   field_on_particles.reinit(particle_handler.n_global_particles());
>   Particles::Utilities::interpolate_field_on_particles(dof_handler, 
> particle_handler, field, field_on_particles);
> 
> 
>   std::cout << "Printing field value on particles location after removing 
> particle" << std::endl;
> 
>   for(int ppp = 0; ppp < particle_handler.n_global_particles(); ppp++)
>   {
>   std::cout << "fluid id: " << ppp << " value: " << 
> field_on_particles[ppp] << std::endl;
>   }
> 
> The scalar field is generated with the X component, so its range is [0-1], 
> and as you can see before the removal the field is perfect. After, though, I 
> have weird numbers (forgive the ugly code and the useless reinit):
> 
> 
> Number of active cells: 1024
> Number of degrees of freedom: 1089
> Printing particle id, location and reference location
> id: 0  loc: 0.1 0.5  ref_loc: 0.2 1
> id: 1  loc: 0.5 0.5  ref_loc: 1 1
> id: 2  loc: 0.9 0.5  ref_loc: 0.8 1
> Printing field value on particles location
> fluid id: 0 value: 0.1   <--- OK!
> fluid id: 1 value: 0.5   <--- OK!
> fluid id: 2 value: 0.9   <--- OK!
> Printing particle id, location and reference location after removing particle
> id: 0  loc: 0.1 0.5  ref_loc: 0.2 1
> id: 2  loc: 0.9 0.5  ref_loc: 0.8 1
> Printing field value on particles location after removing particle
> fluid id: 0 value: 0.1   <-- STILL OK, I HOPE IT IS
> fluid id: 1 value: 0.<-- 
> 
> Am I using the particles the way they're not intended? Any hints are really 
> welcome!
> 
> Thanks!
>Franco
> 
> PS. I am attaching a ZIP file with a minimal working code adapting the step 3 
> of the tutorial.
> 
> 
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Re: [deal.II] parallel::distributed::SolutionTransfer for FE_FaceQ element

2020-07-13 Thread Luca Heltai
Dear Yu,

It is unclear what it means to transfer a solution for FE_FaceQ. On refined 
cells, the central part of the skeleton cannot be transferred from the outer 
skeleton (I.e., a refined grid is not a subspace Of the coarse grid), so 
technically we cannot transfer solutions for FE spaces defined only on faces. 
You should construct the solution transfer by hand, if you really need that. 

Luca

> Il giorno 13 lug 2020, alle ore 22:21, Yu Leng  ha 
> scritto:
> 
> 
> Wolfgang,
> 
> Thanks for your quick response. I added a function ( local_refine(),  line 
> 959 - 1010 ) to step-61, please see the example in the attachment.
> 
> I have this error in serial as well. The error comes from 
> SolutionTransfer.interpolate().
> 
> 
> Thanks,
> Yu 
> 
>> On Monday, July 13, 2020 at 3:08:41 PM UTC-4, Wolfgang Bangerth wrote:
>> On 7/12/20 5:06 PM, Yu Leng wrote: 
>> > 
>> > I am encountered with this error while using adaptive mesh refinement in 
>> > parallel. 
>> > 
>> > virtual const FullMatrix ::FiniteElement<2, 
>> > 2>::get_prolongation_matrix(const unsigned int, const RefinementCase 
>> > &) const 
>> > The violated condition was: 
>> >  prolongation[refinement_case - 1][child].n() == this->dofs_per_cell 
>> > Additional information: 
>> >You are trying to access the matrices that describe how to embed a 
>> > finite 
>> > element function on one cell into the finite element space on one of its 
>> > children (i.e., the 'embedding' or 'prolongation' matrices). However, the 
>> > current finite element can either not define this sort of operation, or it 
>> > has 
>> > not yet been implemented. 
>> 
>> Yu -- could you try to come up with a minimal example that demonstrates the 
>> error? It doesn't have to do anything useful -- just set up the FE, a 
>> DoFHandler, call SolutionTransfer. This way, it would be much simpler for us 
>> to reproduce the error. 
>> 
>> Best 
>>   W. 
>> 
>> -- 
>>  
>> Wolfgang Bangerth  email: bang...@colostate.edu 
>> www: http://www.math.colostate.edu/~bangerth/ 
>> 
> 
> -- 
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> 

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Re: [deal.II] Setting up dealii through Docker

2020-06-28 Thread Luca Heltai
If you want to develop using an ide, you could use visual studio code, with the 
remote development extension. This allows you to compile inside the docker as 
if it was a local compiler (including code completion, and debugging 
facilities):

https://code.visualstudio.com/docs/remote/containers

Best,
Luca

> Il giorno 28 giu 2020, alle ore 03:34, Bhavesh Shrimali 
>  ha scritto:
> 
> 
> Hi Luca, 
> 
> Thanks a lot for the reply! After a fresh pull of the container (with vim 
> installed) and changing CMakeLists.txt accordingly, everything works like 
> charm  
> 
> 
> Best,
> Bhavesh
> 
>> On Saturday, 27 June 2020 01:58:07 UTC-5, Luca Heltai wrote:
>> Are you using an example from deal.II master? If this is the case, the 
>> example looks for 9.3pre but the image we provide only has 9.1 installed.  
>> Try inspecting the CMakeList.txt to see which version is being looked for, 
>> and try changing to 9.1. 
>> 
>> Luca
>> 
>>>> Il giorno 27 giu 2020, alle ore 06:58, Bhavesh Shrimali 
>>>>  ha scritto:
>>>> 
>>> 
>>> Hi Daniel, 
>>> 
>>> Thanks for your reply. So the error above was pretty obvious 
>>> 
>>> So I was going to update this after today's try. I did see (after posting 
>>> this) yesterday that I could see
>>> 
>>> /usr/includ/deal.II
>>> 
>>> the directories therein. Also I sourced  `.bashrc` in /home/dealii, which I 
>>> thought would set the proper paths. I couldn't view the contents of .bashrc 
>>> (my bad that I didn't install a text editor inside the container). Now it 
>>> at least (perhaps) locates deal.II properly, but throws:
>>> 
>>> bshrima2@golubh1:/projects/meca/bshrima2/Deal2/examples/step-1$ cmake .
>>> -- The C compiler identification is GNU 7.5.0
>>> -- The CXX compiler identification is unknown
>>> -- Check for working C compiler: /usr/bin/gcc
>>> -- Check for working C compiler: /usr/bin/gcc -- works
>>> -- Detecting C compiler ABI info
>>> -- Detecting C compiler ABI info - done
>>> -- Detecting C compile features
>>> -- Detecting C compile features - done
>>> CMake Error at CMakeLists.txt:38 (PROJECT):
>>>   The CMAKE_CXX_COMPILER:
>>> 
>>> /usr/local/gcc/7.2.0/bin/c++
>>> 
>>>   is not a full path to an existing compiler tool.
>>> 
>>>   Tell CMake where to find the compiler by setting either the environment
>>>   variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full 
>>> path
>>>   to the compiler, or to the compiler name if it is in the PATH.
>>> 
>>> 
>>> I am using cmake/3.12 that is installed on our cluster. I would update the 
>>> container with a text editor and redo the entire process. 
>>> 
>>> As for building step-1, I copied step-1.cc and CMakeLists.txt in a new 
>>> folder and did `cmake .` following the instructions on the dealii website. 
>>> 
>>> Thanks
>>> Bhavesh
>>> 
>>>> On Friday, 26 June 2020 23:04:14 UTC-5, Daniel Arndt wrote:
>>>> Bhavesh,
>>>> 
>>>> It's hard to tell if there is something going wrong and if so what it is 
>>>> from just the information you provided.
>>>> If you inspect your container can you find the deal.II library, i.e. the 
>>>> include files and the shared library?
>>>> If so, how did you try to invoke CMake when trying to build step-1? Do you 
>>>> set any environment variables like DEAL_II_DIR?
>>>> 
>>>> Best,
>>>> Daniel
>>>> 
>>>>> Am Do., 25. Juni 2020 um 18:51 Uhr schrieb Bhavesh Shrimali 
>>>>> :
>>>>> Hi dealii users,
>>>>> 
>>>>> I wanted to get started with dealii (and in the long run hopefully use it 
>>>>> for my research). Naturally, I sought the easiest way forward through 
>>>>> docker. Since I use Singularity more often than docker (due to seamless 
>>>>> transition to running on our HPC cluster) I put together a container 
>>>>> here. It basically pulls the corresponding `tagged` image from DockerHub 
>>>>> and installs a bunch of other libraries that I use in my research.
>>>>> 
>>>>> However when I try to execute step-1 as listed in the tutorials section, 
>>>>> it seems that dealii isn't installed on the docker image (or maybe I am 
>>>>> missing something)
>>>>&g

Re: [deal.II] Setting up dealii through Docker

2020-06-27 Thread Luca Heltai
Are you using an example from deal.II master? If this is the case, the example 
looks for 9.3pre but the image we provide only has 9.1 installed.  Try 
inspecting the CMakeList.txt to see which version is being looked for, and try 
changing to 9.1. 

Luca

> Il giorno 27 giu 2020, alle ore 06:58, Bhavesh Shrimali 
>  ha scritto:
> 
> 
> Hi Daniel, 
> 
> Thanks for your reply. So the error above was pretty obvious 
> 
> So I was going to update this after today's try. I did see (after posting 
> this) yesterday that I could see
> 
> /usr/includ/deal.II
> 
> the directories therein. Also I sourced  `.bashrc` in /home/dealii, which I 
> thought would set the proper paths. I couldn't view the contents of .bashrc 
> (my bad that I didn't install a text editor inside the container). Now it at 
> least (perhaps) locates deal.II properly, but throws:
> 
> bshrima2@golubh1:/projects/meca/bshrima2/Deal2/examples/step-1$ cmake .
> -- The C compiler identification is GNU 7.5.0
> -- The CXX compiler identification is unknown
> -- Check for working C compiler: /usr/bin/gcc
> -- Check for working C compiler: /usr/bin/gcc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> CMake Error at CMakeLists.txt:38 (PROJECT):
>   The CMAKE_CXX_COMPILER:
> 
> /usr/local/gcc/7.2.0/bin/c++
> 
>   is not a full path to an existing compiler tool.
> 
>   Tell CMake where to find the compiler by setting either the environment
>   variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
>   to the compiler, or to the compiler name if it is in the PATH.
> 
> 
> I am using cmake/3.12 that is installed on our cluster. I would update the 
> container with a text editor and redo the entire process. 
> 
> As for building step-1, I copied step-1.cc and CMakeLists.txt in a new folder 
> and did `cmake .` following the instructions on the dealii website. 
> 
> Thanks
> Bhavesh
> 
>> On Friday, 26 June 2020 23:04:14 UTC-5, Daniel Arndt wrote:
>> Bhavesh,
>> 
>> It's hard to tell if there is something going wrong and if so what it is 
>> from just the information you provided.
>> If you inspect your container can you find the deal.II library, i.e. the 
>> include files and the shared library?
>> If so, how did you try to invoke CMake when trying to build step-1? Do you 
>> set any environment variables like DEAL_II_DIR?
>> 
>> Best,
>> Daniel
>> 
>>> Am Do., 25. Juni 2020 um 18:51 Uhr schrieb Bhavesh Shrimali 
>>> :
>>> Hi dealii users,
>>> 
>>> I wanted to get started with dealii (and in the long run hopefully use it 
>>> for my research). Naturally, I sought the easiest way forward through 
>>> docker. Since I use Singularity more often than docker (due to seamless 
>>> transition to running on our HPC cluster) I put together a container here. 
>>> It basically pulls the corresponding `tagged` image from DockerHub and 
>>> installs a bunch of other libraries that I use in my research.
>>> 
>>> However when I try to execute step-1 as listed in the tutorials section, it 
>>> seems that dealii isn't installed on the docker image (or maybe I am 
>>> missing something)
>>> 
>>> CMake Error at CMakeLists.txt:30 (MESSAGE):
>>> 
>>> 
>>>   *** Could not locate a (sufficiently recent) version of deal.II.  ***
>>> 
>>> 
>>> 
>>>   You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to cmake
>>> 
>>>   or set an environment variable "DEAL_II_DIR" that contains this path.
>>> 
>>> 
>>> -- Configuring incomplete, errors occurred!
>>> 
>>> 
>>> 
>>> 
>>> Does anyone know, what am I missing here ? 
>>> 
>>> Thanks in advance! 
>>> -- 
>>> 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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>>> "deal.II User Group" group.
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>>> email to dea...@googlegroups.com.
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>>> https://groups.google.com/d/msgid/dealii/d2840b63-7278-4519-a8dc-1282035dad2ao%40googlegroups.com.
> 
> -- 
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Re: [deal.II] Reading a Tensor from parameter file

2020-04-15 Thread Luca Heltai
Currently, this is also the simplest way:

Tensor tens;
prm.add_parameter("Tensor", tens);

Take a look at the documentation of the add parameter method.

Patterns::Tools::to_string(tens);

And 

Patterns::Tools::to_value 

Are also available to simplify what you want to achieve. 

Alternatively: Patterns::Tools::Convert offers ways to construct default 
Patterns for many types, including Tensors. 

Best,
Luca

> Il giorno 15 apr 2020, alle ore 14:57, Ahmad Shahba  ha 
> scritto:
> 
> 
> Ooops! The background was too dark :-)
> 
> #include 
> #include 
> #include 
> #include 
> #include 
> #include 
> 
> using namespace dealii;
> 
> int main() {
> 
> 
> // Let's read this tensor from an istringstream. You may read it from 
> istream in your
> // application
> std::istringstream is("set Tensor3x3 = 11, 12, 13, 21, 22, 23, 31, 32, 
> 33");
> 
> 
> // Now let's set up the ParameterHandler object. Since you are reading 
> 3x3 tensor, you are
> // dealing with 9 components and the default value should also have 9 
> components (here 9
> // zeros) in it
> ParameterHandler prm;
> 
> using Patterns::List;
> using Patterns::Double;
> prm.declare_entry("Tensor3x3",
>   "0,0,0,0,0,0,0,0,0",
>   List(Double(), 9, 9),
>   "Tensor components");
> 
> 
> // Let's read it in now
> prm.parse_input(is);
> const std::string tensorString = prm.get("Tensor3x3");
> 
> // Now let's split the string into individual components
> const std::vector tensorComponentsString =
> Utilities::split_string_list(tensorString);
> 
> // Now go over each component, convert it into double and put it in the 
> tensor
> Tensor<2, 3> tensor;
> unsigned int counter = 0;
> for (unsigned ii = 0; ii < tensor.dimension; ++ii) {
> for (unsigned jj = 0; jj < tensor.dimension; ++jj) {
> tensor[ii][jj] = 
> Utilities::string_to_double(tensorComponentsString[counter++]);
> }
> }
> 
> 
> // Let's check if we read the tensor correctly
> for (unsigned ii = 0; ii < tensor.dimension; ++ii) {
> for (unsigned jj = 0; jj < tensor.dimension; ++jj) {
> std::cout << "component [" << ii << ", " << jj << " ] = "
>   << tensor[ii][jj] << std::endl;
> }
> }
> 
> 
> }
> 
> 
> Enter code here...
> 
> 
> 
>> On Wednesday, April 15, 2020 at 8:53:55 AM UTC-4, Ahmad Shahba wrote:
>> Here is the code that does what I explained. I just switched up step 5 with 
>> a much simpler approach. Note that you can simply make this into a 
>> function/class template so that you could read general tensors, not just 3x3 
>> tensors. I leave that to you :-)
>> 
>> #include 
>> #include 
>> #include 
>> #include 
>> #include 
>> #include 
>> 
>> using namespace dealii;
>> 
>> int main() {
>> 
>> 
>> // Let's read this tensor from an istringstream. You may read it from 
>> istream in your
>> // application
>> std::istringstream is("set Tensor3x3 = 11, 12, 13, 21, 22, 23, 31, 32, 
>> 33");
>> 
>> 
>> // Now let's set up the ParameterHandler object. Since you are reading 
>> 3x3 tensor, you are
>> // dealing with 9 components and the default value should also have 9 
>> components (here 9 
>> // zeros) in it
>> ParameterHandler prm;
>> 
>> using Patterns::List;
>> using Patterns::Double;
>> prm.declare_entry("Tensor3x3",
>>   "0,0,0,0,0,0,0,0,0",
>>   List(Double(), 9, 9),
>>   "Tensor components");
>> 
>> 
>> // Let's read it in now
>> prm.parse_input(is);
>> const std::string tensorString = prm.get("Tensor3x3");
>> 
>> // Now let's split the string into individual components
>> const std::vector tensorComponentsString =
>> Utilities::split_string_list(tensorString);
>> 
>> // Now go over each component, convert it into double and put it in the 
>> tensor
>> Tensor<2, 3> tensor;
>> unsigned int counter = 0;
>> for (unsigned ii = 0; ii < tensor.dimension; ++ii) {
>> for (unsigned jj = 0; jj < tensor.dimension; ++jj) {
>> tensor[ii][jj] = 
>> Utilities::string_to_double(tensorComponentsString[counter++]);
>> }
>> }
>> 
>> 
>> // Let's check if we read the tensor correctly
>> for (unsigned ii = 0; ii < tensor.dimension; ++ii) {
>> for (unsigned jj = 0; jj < tensor.dimension; ++jj) {
>> std::cout << "component [" << ii << ", " << jj << " ] = "
>>   << tensor[ii][jj] << std::endl;
>> }
>> }
>> 
>> 
>> }
>> 
>> 
>> 
>> 
>> 
>> 
>>> On Wednesday, April 15, 2020 at 3:54:57 AM UTC-4, Paras Kumar wrote:
>>> Ahmad,
>>> 
 On Tuesday, April 14, 2020 at 5:39:06 PM UTC+2, Ahmad Shahba wrote:
 I don't know if it is the optimal way but I would use the following 
 approach
 Read tensor components as Patterns::List 
 Use  

Re: [deal.II] Deal.II on Docker

2020-03-13 Thread Luca Heltai
The examples you are using are likely looking for deal.II 9.2.pre. Try changing 
the makefile, and see if that works. :-)

Luca

> Il giorno 13 mar 2020, alle ore 02:47, Robert Kopp  
> ha scritto:
> 
> 
> After some false starts, I was able to use deal.II on Ubuntu 18.04 by 
> installing it from the backport PPA. It occurred to me that I might want to 
> use it during a Windows session, and since Windows does not support it 
> natively, the use of a pre-built Docker container came to mind.
> 
> The most likely candidate was dealii/dealii:latest. I was disappointed to 
> note the the "examples" weren't there (or, at least, I can't find them) so I 
> downloaded these from Github. As in the case of my abortive attempts on bare 
> metal, I received such messages as the following:
> 
> dealii@5ee4b768bb50:~/dealii/examples/step-5$ cmake .
> CMake Error at CMakeLists.txt:30 (MESSAGE):  
> 
>   *** Could not locate a (sufficiently recent) version of deal.II.  ***  
> 
>   You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to cmake
> 
>   or set an environment variable "DEAL_II_DIR" that contains this path.
> 
> I was hoping that it would be a complete kit, but upbeat_albattani had let me 
> down. Can anyone suggest a good way (reference, etc.) to get up to speed on 
> this container? I can do everything I need to do on Linux, but there would be 
> some advantage to being able to use it on Windows as well. 
> 
> -- 
> 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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[deal.II] Intensive course on Finite Element Methods using deal.II @ SISSA

2020-01-17 Thread Luca Heltai
Dear All, 

the Master in High Performance Computing (www.mhpc.it) is organising an 
intensive 5 days course dedicated to MHPC and PhD students. The course will 
take place @ SISSA (www.sisssa.it), in Trieste, Italy:

Course title: “The Finite Element Method using deal.II”
Course lecturers: Wolfgang Bangerth and Luca Heltai

More information on the course schedule is available here:

http://tiny.cc/xqttiz

A limited number of seats is available for external PhD students, postdocs, and 
researcher. No fee is required, but registration is mandatory.

To reserve a seat, please complete this form: 

https://forms.gle/TwupiUvcXdUDTQ2F8

Best,
Luca.

--
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Phone:  +39 040 3787 449, Office: 608
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Re: [deal.II] Particle contact detection

2019-10-14 Thread Luca Heltai
Take a look at the Particles namespace, and at the rtree boost documentation 
(we wrap rtree from boost into the RTree alias, which is compatible with 
Point, BoundingBox and Segment).

The tests/boost directory contains some examples that may be useful. 

Luca

> Il giorno 14 ott 2019, alle ore 06:55, Shahab Golshan 
>  ha scritto:
> 
> Dear all,
> I am writing a code for handling collisions between large numbers of 
> particles.
> I need to find all the available classes in dealII, which might be useful.
> These classes may include methods to find neighbor particles in the system or 
> calculation of particles' overlap during a collision.
> Any information would be appreciated.
> Best
> Shahab
> -- 
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> For mailing list/forum options, see 
> https://groups.google.com/d/forum/dealii?hl=en
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Re: [deal.II] Reading mesh from vtk file

2019-08-05 Thread Luca Heltai
Dear Andreas,

You are trying to read a vtk file that was generated by DataOut. 

Try to write the file with GridOut::write_vtk. 

DataOut produces files that are split cell wise (to allow for some flexibility 
in discontinuos fields. 

Luca

> Il giorno 5 ago 2019, alle ore 03:05, Andreas Rupp  ha 
> scritto:
> 
> Dear all,
> 
> I am trying to read a grid from a vtk file created by Paraview. 
> Unfortunately, this does not work.
> Moreover, reading a vtk file that has been created using deal.ii also does 
> not work for me. It seems to me that deal.ii reads the file but does not 
> connect the faces to form a mesh. This is underlined by the attached minimal 
> toy example which creates a two dimensional cross, prints the cross' interior 
> and boundary faces, writes it to a vtk file, reads the mesh from the file, 
> and again prints the interior and boundary faces. Execution of the program 
> gives the following output:
> 
> Self Interface  1  0 -0.5
> Self Interface  2  -0.5 0
> Self Interface  3  0.5 0
> Self Boundaryface  1  1 -0.5
> Self Interface  4  0 0.5
> Self Boundaryface  2  -0.5 1
> Self Boundaryface  3  1 0.5
> Self Boundaryface  4  0.5 1
> Self Boundaryface  5  -1 -0.5
> Self Boundaryface  6  -1.5 0
> Self Boundaryface  7  -1 0.5
> Self Boundaryface  8  1.5 0
> Self Boundaryface  9  -0.5 -1
> Self Boundaryface  10  0 -1.5
> Self Boundaryface  11  0.5 -1
> Self Boundaryface  12  0 1.5
> 
> Read Boundaryface  1  0 -0.5
> Read Boundaryface  2  -0.5 0
> Read Boundaryface  3  0.5 0
> Read Boundaryface  4  0 0.5
> Read Boundaryface  5  -1 -0.5
> Read Boundaryface  6  -1.5 0
> Read Boundaryface  7  -0.5 0
> Read Boundaryface  8  -1 0.5
> Read Boundaryface  9  1 -0.5
> Read Boundaryface  10  0.5 0
> Read Boundaryface  11  1.5 0
> Read Boundaryface  12  1 0.5
> Read Boundaryface  13  0 -1.5
> Read Boundaryface  14  -0.5 -1
> Read Boundaryface  15  0.5 -1
> Read Boundaryface  16  0 -0.5
> Read Boundaryface  17  0 0.5
> Read Boundaryface  18  -0.5 1
> Read Boundaryface  19  0.5 1
> Read Boundaryface  20  0 1.5
> 
> Is there any quick fix to this issue (except for not using vtk)? I failed 
> with merging the mesh with itself to eliminate the double boundary faces 
> (e.g. 1 and 16).
> Thank you very much!
> 
> Best regards,
> Andreas
> -- 
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> 

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[deal.II] Old Mac Users wanted.

2018-05-19 Thread Luca Heltai
Dear All, 

I just uploaded a version of deal.II 9.1.0pre (master version of yesterday) 
here:

https://github.com/luca-heltai/dealii/releases/tag/v9.1.0-pre-1 
<https://github.com/luca-heltai/dealii/releases/tag/v9.1.0-pre-1>

This was compiled with clang 6.0.0, downloaded from the official llvm website. 
The compiler is included in the package, making this a good candidate for users 
of older Macs that did not (or do not want to) update Xcode to get Apple clang 
9.1.0.

This package should work for you too. If there is anyone that has not updated 
yet to Apple clang 9.1.0, can you try to see if this package works for you?

Thanks!
Luca.

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[deal.II] Re: Mac testers wanted

2018-05-06 Thread Luca Heltai
Sorry. The address is the following:

https://github.com/dealii/dealii/releases/v9.0.0-rc2

Luca

> Il giorno 06 mag 2018, alle ore 11:30, luca.heltai  ha 
> scritto:
> 
> Dear all, 
> 
> I have just uploaded a new package for deal.II-9.0.0-rc2 here:
> 
> https://github.com/dealii/dealii/releases/edit/v9.0.0-rc2
> 
> This was compiled with Apple clang 9.1.0, and gfortran from gcc 7.3.
> 
> Please test, and let me know if everything is ok.
> 
> Best,
> Luca.

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Re: [deal.II] New Mac OSX brew package

2017-11-09 Thread Luca Heltai
I'm using clang+gfortran. I have not tried using gcc for everything, but I 
could give it a shot if you think it would be worth it. 

Luca

> On 9 Nov 2017, at 17:59, Timo Heister  wrote:
> 
> thanks, Luca!
> 
> Are you using the system clang with the fortran compiler from gcc? Are
> the spack packages compiled with gcc or with clang?
> 
>> On Thu, Nov 9, 2017 at 3:40 AM, luca.heltai  wrote:
>> Dear All,
>> 
>> I just finished uploading a new brew based package for deal.II with a 
>> 9.0pre.1 version:
>> 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_luca-2Dheltai_dealii_releases_tag_v9.0.pre.1=DwIFaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=B4_I7m9Fb7UJr3fQ0YmopMCt2BsnKOY2uoFIQ28VKXs=UQTroVQ4XmKFbV4qTi4pGa6KPdjCdxglDVCGB7IPIo4=
>>  
>> 
>> It was compiled on a Mac OS X High Sierra: 10.13 (17A405), with Xcode 9.0.1 
>> (9A1004).
>> 
>> The application contains a full `spack` installation at
>> 
>> `/Applications/deal.II-9.0-spack/Contents/Resources/spack`
>> 
>> You’ll have access to all spack facilities (including modules) by adding
>> 
>> . 
>> /Applications/deal.II-9.0-spack.app/Contents/Resources/share/deal.II/dealii.conf
>> 
>> to your ~/.profile file.
>> 
>> Summary.log:
>> 
>> ###
>> #
>> #  deal.II configuration:
>> #CMAKE_BUILD_TYPE:   DebugRelease
>> #BUILD_SHARED_LIBS:  ON
>> #CMAKE_INSTALL_PREFIX:   
>> /Applications/deal.II-9.0-spack.app/Contents/Resources
>> #CMAKE_SOURCE_DIR:   /Users/heltai/dealii/dealii
>> #(version 9.0.0-pre, shortrev 88babf1a4d)
>> #CMAKE_BINARY_DIR:   /Users/heltai/dealii/dealii/build-9.0-spack
>> #CMAKE_CXX_COMPILER: AppleClang 9.0.0.938 on platform Darwin 
>> x86_64
>> #
>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/bin/mpic++
>> #
>> #  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, 
>> DEAL_II_ALLOW_AUTODETECTION = ON):
>> #  ( DEAL_II_WITH_64BIT_INDICES = OFF )
>> #DEAL_II_WITH_ADOLC set up with external dependencies
>> #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_CUDA = OFF )
>> #DEAL_II_WITH_CXX14 = ON
>> #DEAL_II_WITH_CXX17 = ON
>> #DEAL_II_WITH_GSL set up with external dependencies
>> #DEAL_II_WITH_HDF5 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_NANOFLANN set up with external dependencies
>> #DEAL_II_WITH_NETCDF 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_SLEPC set up with external dependencies
>> #DEAL_II_WITH_SUNDIALS set up with external dependencies
>> #DEAL_II_WITH_THREADS 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 = OFF )
>> #DEAL_II_COMPONENT_PACKAGE
>> #  ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
>> #
>> #  Detailed information (compiler flags, feature configuration) can be found 
>> in detailed.log
>> #
>> #  Run  $ ninja info  to print a help message with a list of top level 
>> targets
>> #
>> ###
>> 
>> And this is the output of spack find:
>> 
>> ==> 74 installed packages.
>> -- darwin-highsierra-x86_64 / clang@9.0.0-apple -
>> adol-c@develop  freetype@2.7.1lcms@2.8 
>> nasm@2.11.06pkg-config@0.29.2
>> arpack-ng@3.5.0 gcc@7.2.0 libjpeg-turbo@1.5.0  
>> ncurses@6.0 python@2.7.14
>> assimp@4.0.1gdbm@1.13 libpng@1.6.29
>> netcdf@4.4.1.1  readline@7.0
>> astyle@2.04 gettext@0.19.8.1  libsigsegv@2.11  
>> netcdf-cxx@4.2  slepc@3.8.0
>> autoconf@2.69   ghostscript@9.21  libtiff@4.0.8
>> netlib-scalapack@2.0.2  sqlite@3.20.0
>> automake@1.15.1 glm@0.9.7.1   libtool@2.4.6
>> ninja@1.8.2 suite-sparse@4.5.5
>> bison@3.0.4 gmp@6.1.2 libxml2@2.9.4
>> numdiff@5.9.0   sundials@3.0.0
>> boost@1.63.0   

[deal.II] New Mac OSX brew package

2017-11-09 Thread luca . heltai
Dear All, 

I just finished uploading a new brew based package for deal.II with a 9.0pre.1 
version:

https://github.com/luca-heltai/dealii/releases/tag/v9.0.pre.1

It was compiled on a Mac OS X High Sierra: 10.13 (17A405), with Xcode 9.0.1 
(9A1004).

The application contains a full `spack` installation at 

`/Applications/deal.II-9.0-spack/Contents/Resources/spack`

You’ll have access to all spack facilities (including modules) by adding

. 
/Applications/deal.II-9.0-spack.app/Contents/Resources/share/deal.II/dealii.conf
 

to your ~/.profile file.

Summary.log:

###
#
#  deal.II configuration:
#CMAKE_BUILD_TYPE:   DebugRelease
#BUILD_SHARED_LIBS:  ON
#CMAKE_INSTALL_PREFIX:   
/Applications/deal.II-9.0-spack.app/Contents/Resources
#CMAKE_SOURCE_DIR:   /Users/heltai/dealii/dealii
#(version 9.0.0-pre, shortrev 88babf1a4d)
#CMAKE_BINARY_DIR:   /Users/heltai/dealii/dealii/build-9.0-spack
#CMAKE_CXX_COMPILER: AppleClang 9.0.0.938 on platform Darwin 
x86_64
#
/Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/bin/mpic++
#
#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION 
= ON):
#  ( DEAL_II_WITH_64BIT_INDICES = OFF )
#DEAL_II_WITH_ADOLC set up with external dependencies
#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_CUDA = OFF )
#DEAL_II_WITH_CXX14 = ON
#DEAL_II_WITH_CXX17 = ON
#DEAL_II_WITH_GSL set up with external dependencies
#DEAL_II_WITH_HDF5 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_NANOFLANN set up with external dependencies
#DEAL_II_WITH_NETCDF 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_SLEPC set up with external dependencies
#DEAL_II_WITH_SUNDIALS set up with external dependencies
#DEAL_II_WITH_THREADS 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 = OFF )
#DEAL_II_COMPONENT_PACKAGE
#  ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
#
#  Detailed information (compiler flags, feature configuration) can be found in 
detailed.log
#
#  Run  $ ninja info  to print a help message with a list of top level targets
#
###

And this is the output of spack find:

==> 74 installed packages.
-- darwin-highsierra-x86_64 / clang@9.0.0-apple -
adol-c@develop  freetype@2.7.1lcms@2.8 nasm@2.11.06 
   pkg-config@0.29.2
arpack-ng@3.5.0 gcc@7.2.0 libjpeg-turbo@1.5.0  ncurses@6.0  
   python@2.7.14
assimp@4.0.1gdbm@1.13 libpng@1.6.29
netcdf@4.4.1.1  readline@7.0
astyle@2.04 gettext@0.19.8.1  libsigsegv@2.11  
netcdf-cxx@4.2  slepc@3.8.0
autoconf@2.69   ghostscript@9.21  libtiff@4.0.8
netlib-scalapack@2.0.2  sqlite@3.20.0
automake@1.15.1 glm@0.9.7.1   libtool@2.4.6ninja@1.8.2  
   suite-sparse@4.5.5
bison@3.0.4 gmp@6.1.2 libxml2@2.9.4
numdiff@5.9.0   sundials@3.0.0
boost@1.63.0graphviz@2.38.0   m4@1.4.18oce@0.18.2   
   superlu-dist@5.2.2
bzip2@1.0.6 gsl@2.4   matio@1.5.9  
openblas@0.2.20 tar@1.29
cmake@3.9.4 hdf5@1.10.1   metis@5.1.0  
openmpi@3.0.0   tcl@8.6.6
dealii@develop  help2man@1.47.4   mpc@1.0.3
openssl@1.0.2k  trilinos@12.12.1
doxygen@1.8.12  hwloc@1.11.8  mpfr@3.1.5   p4est@2.0
   xz@5.2.3
environment-modules@3.2.10  hypre@2.12.1  mumps@5.1.1  
parmetis@4.0.3  zip@3.0
expat@2.2.2 intel-tbb@2018.1  muparser@2.2.5   perl@5.24.1  
   zlib@1.2.11
flex@2.6.4  isl@0.18  nanoflann@1.2.3  petsc@3.8.1

You can also load individual module files.

module avail:
bash-3.2$ module avail

- 
/Applications/deal.II-9.0-spack.app/Contents/Resources/spack/share/spack/modules/dar

Re: [deal.II] Re: Deal for Mac OS 10.13

2017-10-11 Thread Luca Heltai
No need to revert OS. Xcode comes with developers toolkits. Newer versions of 
xcode allow users to develop codes for older macs. In order to do that, you 
have to install the corresponding developers toolkit. Namely 10.12. 

I never tried this, but it should work. The other way around is more difficult, 
I.e., it's difficult to make the package work on an older Mac with 10.y, y<12. 

Luca

> On 11 Oct 2017, at 12:25, Deepak Kukrety <deepak.kukr...@gmail.com> wrote:
> 
> Alberto
> 
> I am having similar problem as posted by Alberto. 
> 
> Luca
> 
> Thanks for the suggestion. I am new to both Mac OS and Deal. Can you possibly 
> advise how may I install 10.12 SDK. Would it mean reverting to an older 
> version of the OS for iMac as well? 
> 
> Regards 
> Deepak
> 
>> On Wednesday, 11 October 2017 15:21:15 UTC+8, Luca Heltai wrote:
>> Yes. It is trying to use the accelerate framework, but since it was 
>> installed using 10.12, it links to that one. 
>> 
>> If you install the 10.12 SDK you should have what you need. 
>> 
>> L. 
>> 
>> > On 11 Oct 2017, at 8:58, Alberto Salvadori <alberto@unibs.it> wrote: 
>> > 
>> > Sure, I will. Am I understanding properly that deal.ii is trying to use 
>> > the accelerate framework (I guess because of some lapack calls) when 
>> > compiled for MacOS? 
>> > 
>> > Alberto Salvadori 
>> >  Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambiente e 
>> > di Matematica (DICATAM) 
>> >  Universita` di Brescia, via Branze 43, 25123 Brescia 
>> >  Italy 
>> >  tel 030 3711239 
>> >  fax 030 3711312 
>> > 
>> > e-mail: 
>> >  alberto@unibs.it 
>> > web-pages: 
>> >  http://m4lab.unibs.it/faculty.html 
>> >  http://dicata.ing.unibs.it/salvadori 
>> > 
>> > On Wed, Oct 11, 2017 at 8:44 AM, Luca Heltai <luca@gmail.com> wrote: 
>> > Alberto, 
>> > 
>> > In the options of xcode, you should be able to install also the 10.12 sdk. 
>> > Can you try that? 
>> > 
>> > Luca 
>> > 
>> > On 11 Oct 2017, at 08:30, Alberto Salvadori <alberto@unibs.it> wrote: 
>> > 
>> >> Hi Daniel. 
>> >> 
>> >> After installation of High Sierra, Xcode9, upgrading cmake and using 
>> >> deal.ii/8.5.1 provided by Timo, I run usual regression tests that worked 
>> >> well under Xcode8.x. 
>> >> It turned out that they could not be linked anymore with this error 
>> >> (sorry for the code name): 
>> >> 
>> >> make[2]: *** No rule to make target 
>> >> `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/System/Library/Frameworks/Accelerate.framework',
>> >>  needed by `crap_code'.  Stop. 
>> >> 
>> >> make[1]: *** [CMakeFiles/crap_code.dir/all] Error 2 
>> >> 
>> >> make: *** [all] Error 2 
>> >> 
>> >> 
>> >> The simplest code that I attempted to run was the hello world, which run 
>> >> fine without being linked to deal.ii libraries but that provided the very 
>> >> same error with deal.ii. 
>> >> Hope it helps 
>> >> 
>> >> Alberto 
>> >> 
>> >> 
>> >> Il giorno martedì 10 ottobre 2017 14:53:37 UTC+2, Daniel Arndt ha 
>> >> scritto: 
>> >> Alberto and Deepak, 
>> >> 
>> >> what exactly are the problems you are facing? 
>> >> What kind of errors do you get? 
>> >> 
>> >> Best, 
>> >> Daniel 
>> >> 
>> >> 
>> >> Informativa sulla Privacy: http://www.unibs.it/node/8155 
>> >> 
>> >> -- 
>> >> 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 the Google Groups 
>> >> "deal.II User Group" group. 
>> >> To unsubscribe from this group and stop receiving emails from it, send an 
>> >> email to dealii+un...@googlegroups.com. 
>> >> For more options, visit https://groups.google.com/d/optout. 
>> > 
>> > -- 
>> > 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 
>&

Re: [deal.II] Re: Deal for Mac OS 10.13

2017-10-11 Thread Luca Heltai
Alberto,

In the options of xcode, you should be able to install also the 10.12 sdk. Can 
you try that?

Luca

> On 11 Oct 2017, at 08:30, Alberto Salvadori  
> wrote:
> 
> Hi Daniel.
> 
> After installation of High Sierra, Xcode9, upgrading cmake and using 
> deal.ii/8.5.1 provided by Timo, I run usual regression tests that worked well 
> under Xcode8.x.
> It turned out that they could not be linked anymore with this error (sorry 
> for the code name):
> 
> make[2]: *** No rule to make target 
> `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/System/Library/Frameworks/Accelerate.framework',
>  needed by `crap_code'.  Stop.
> 
> make[1]: *** [CMakeFiles/crap_code.dir/all] Error 2
> 
> make: *** [all] Error 2
> 
> 
> The simplest code that I attempted to run was the hello world, which run fine 
> without being linked to deal.ii libraries but that provided the very same 
> error with deal.ii. 
> Hope it helps
> 
> Alberto
> 
> 
> Il giorno martedì 10 ottobre 2017 14:53:37 UTC+2, Daniel Arndt ha scritto:
>> 
>> Alberto and Deepak,
>> 
>> what exactly are the problems you are facing?
>> What kind of errors do you get?
>> 
>> Best,
>> Daniel
> 
> 
> Informativa sulla Privacy: http://www.unibs.it/node/8155
> -- 
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Re: [deal.II] does the latest dealii prepackaged image file for Mac OSX come with 'other software packages' such as p4est, PETSc, Trilinos, etc?

2016-08-12 Thread Luca Heltai
Yes it does. 

Luca

> On 11 ago 2016, at 20:36, thomas stephens  wrote:
> 
> It's not clear to me from the github dealii wiki for MacOSX whether or not 
> the prepackaged image file for OSX comes with all of the optional third party 
> libraries that are listed as optional software in the dealii README file.  
> 
> Tom
> -- 
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Re: [deal.II] opencascade shape id

2016-08-05 Thread Luca Heltai
Hi Chang,

If you use salome to open your iges files, then it should tell you what is 
what. 

Best,

Luca

> On 05 ago 2016, at 09:19, Chang-Pao Chang  wrote:
> 
> Hello,
> 
> I am trying to follow step-54 to register shapes in occ and cells in tria 
> through projector.
> 
> However, in complex structure, the order and the type of shapes might be hard 
> to identify.
> 
> For example, in step-54, they use wire[0] and bow_surface, since there are 
> only 1 wire and 1 face involved.
> 
> If I create a complex structure, I wouldn't know which part of structure do 
> wire[i] or compounds refer to.
> 
> Is there any good method to visualize these information in my iges file?
> 
> 
> -- 
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