[deal.II] Re: confusing result when read, refine, output, and re-read a mesh in gmsh format

[曾元圆]

this phenomenon also happens if the line "if(cell->face(face)->boundary_id() 
== 3)" is replaced with "if(cell->at_boundary() == true)". 

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[deal.II] confusing result when read, refine, output, and re-read a mesh in gmsh format

[曾元圆]

hi all, I met a confusing problem when I try to create a mesh as follows:

1. I create a coarse mesh using gmsh. I used number 0, 1, 2  as 
boundary_indicators to denote three different boundary. The resulting 
square.msh looks good.



2. Then I read the square.msh into dealii, and refine those cells with 
boundary_indicator 0. Then output again (I used GridOutFlags::Msh() flags 
to keep the boundary indicators  in the output file). The resulting 
square_refined0.msh still looks good.



3.  I want to refine the mesh more, so I re-read the square_refined0.msh 
again, run the same code (still refine those with boundary_indicator 0), 
and output the mesh again.  But this time, the resulting 
square_refined1.msh is no longer the same as I expected.



Apparantly this final mesh is not what I wanted, because I only want those 
active cells at boundary be refined.

I know in dealii, the default boundary_indicator of boundary faces is 0. 
But from this resulting mesh, it seems that the interior faces are also 
bound with indicators 0. I don't know why this happened. 

I do further experienments: I changed the boundary_indicator of the left 
and right side from 0 to 3, repeat above steps, and this time the resulting 
mesh is good:



It seems that if I use 0 as boundary_indicator, then when dealii read in 
the .msh fille, it will lose some information  related to the bounday. So 
do I have to use non-zero boundary indicators? Or is this a bug? 

Someone explain it a little bit? 





My code is like:

void test_square(){

   Triangulation<2> triangulation;

   GridIn<2> gridin;

   gridin.attach_triangulation(triangulation);


   std::ifstream f("square_refined0.msh");

   gridin.read_msh(f);

   

   typename Triangulation<2>::active_cell_iterator 

cell = triangulation.begin_active(),

endc = triangulation.end();

   for(; cell!=endc; cell++){

  for(unsigned int face = 0; face::faces_per_cell; 
face++){

 if(cell->face(face)->boundary_id() == 3)

cell->set_refine_flag();

  }

   }

   triangulation.execute_coarsening_and_refinement();


   std::ofstream out("square_refined1.msh");

   GridOut grid_out;

  

   grid_out.set_flags(GridOutFlags::Msh(true,false)); //write out the 
boundary indicator explicitly

   grid_out.write_msh(triangulation, out);

}

 



 

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

#include
#include

#include

using namespace dealii;

void test_square(){
   Triangulation<2> triangulation;
   GridIn<2> gridin;
   gridin.attach_triangulation(triangulation);
   std::ifstream f("square.msh");
   gridin.read_msh(f);

   typename Triangulation<2>::active_cell_iterator
cell = triangulation.begin_active(),
endc = triangulation.end();
   for(; cell!=endc; cell++){
  for(unsigned int face = 0; face::faces_per_cell; face++){
 if(cell->face(face)->boundary_id() == 0)
cell->set_refine_flag();
  }
   }
   triangulation.execute_coarsening_and_refinement();

   std::ofstream out("square_refined0.msh");
   GridOut grid_out;

   grid_out.set_flags(GridOutFlags::Msh(true,false));
   grid_out.write_msh(triangulation, out);
}

int main(){
	try{
		   test_square();
	}
	catch(std::exception ){
		std::cerr<

Re: [deal.II] some problems concerning step-14

[曾元圆]

Thank you so much Bangerth!

Now I understand why we need to rewrite the error formula on a cell as 
residual times dual weight. But I'm still a little confused with the reason 
why we must introduce z_h. 
Just as you mentioned, if we introduce z_h, then z-z_h is a quantity that 
is only large where the dual solution is rough. But why do we need to care 
about the accuracy of z here? I think the only  thing we need to care about 
is the value of z on that cell, because z is a quantity that represents how 
important the residual on that cell is.
  
My understanding is: now the dual_weight z-z_h does not only represent how 
important the residual on a certain cell is, but also tells us some 
information about how good the dual solution on that cell is. But another 
problem is, does z-z_h still has the same tendency as z? If not, how z-z_h 
can represent the importance of a certan cell as z can?
 
I'm not sure if my understanding is correct. I tried to run the code using 
only z as dual_weights, and I found the result almost the same as that 
using z-z_h.

Finally, I am certainly glad to submit patches to deal.II and make my own 
contribution. But I didn't fork deal.ii on my github account yet, and this 
is relatively a small issue, so I will be glad if you can do it for the 
moment. 

在 2018年3月4日星期日 UTC+8上午1:42:27，Wolfgang Bangerth写道：
>
> On 03/02/2018 03:36 AM, 曾元圆 wrote: 
> > Hi, nowadays I'm learning about the goal oriented error estimator and I 
> > read the tutorial of step-14 
> > (http://www.dealii.org/developer/doxygen/deal.II/step_14.html.) But I'm 
> > confused about some problems and hope you can help me with these: 1. 
> When 
> > deriving the error with respect to the functional, why must we change 
> > J(e)=a(e,z) to J(e)=a(e,z-z_h) ? I know the dual solution z must be 
> > approximated in a richer space than the primal solution, otherwise J(e) 
> > will be 0. But why not just solve the dual problem in a richer space 
> > without subtracting its interpolation to the primal space? I didn't see 
> the 
> > necessity to introduce z_h into the formula. 
>
> You are correct: the values you get from both of these formulas are 
> exactly 
> the same. So it is not *necessary* to introduce z_h if you are interested 
> in 
> computing the *error*. 
>
> We introduce the interpolant because z-z_h is a quantity that is only 
> large 
> where the dual solution is rough, where z may be large also in other 
> places. 
> Doing so ensures that the error estimator is *localized*: It is large 
> exactly 
> where the primal and dual solutions are rough, i.e., where we expect the 
> error 
> to be caused. As mentioned above, if you sum the contributions of all 
> cells, 
> you will get the same value whether you introduce z_h or not, but the 
> contribution of each cell is going to be different. If you want the 
> contributions of each cell to serve as a good mesh refinement criterion, 
> then 
> it turns out that you need to introduce z_h. 
>
>
> > 2. Why must we change J(e)=∑(f+△ uh,z-zh)-(∂uh,z-zh) to J(e)=∑(f+△ 
> > uh,z-zh)-(1/2[∂uh],z-zh)? Is it just an implementation consideration for 
> > saving computational effort? 
>
> For the same kind of reason. For a smooth (primal) solution, the term 
>(∂uh,z-zh) 
> may be large because the normal derivative of the primal solution may 
> simply 
> be what it is -- think of, for example, a linear exact solution u that can 
> be 
> perfectly approximated by u_h. So if you leave this term as is, this would 
> suggest that the error on this cell is large. But that's wrong -- the 
> error is 
> actually quite small because you can approximate linear functions well. 
>
> On the other hand, if you do the rewrite (which again leaves the *sum* 
> over 
> all cells the same, but change the contributions of each cell), then 
>(1/2[∂uh],z-zh) 
> is going to be small because while the normal derivative of u_h may be 
> large, 
> the *jump* of the normal derivative is small if the solution is linear or 
> nearly so. 
>
> Another way of seeing this is to think of both of the terms in J(e) as 
>residual times dual weight. 
> The residuals here are f+△ uh and 1/2[∂uh]. You want to define these 
> residuals 
> in such a way that they are zero for the exact solution. That is true for 
> these two residuals: f+△ u is zero because 'u' satisfies the equation, and 
> 1/2[∂u] is zero because the solutions of the Laplace equation have 
> continuous 
> gradients (if f is smooth enough). 
>
> On the other hand, the term ∂u is not zero, even for the exact solution. 
>
>
> > Can this kind of rewriting be generally adopted in other kind of 
> > problems(e.g in advection problem where the face integrals in J(e) 

[deal.II] Re: some problems concerning step-14

[曾元圆]

3. In the member function: WeightedResidual::refine_grid(), you 
firstly defined a Vector error_indicators whose dimension is n_active_cells 
of the triangulation, then you call the function 
"estimate_error(error_indicators)" to compute the error_indicators. But in 
the function "estimate_error(Vector& error_indicators)", I noticed 
that you reinitialize the error_indicators by calling 
"error_indicators.reinit(DualSolver::dof_handler.get_triangulation().n_active_cells());",
 
so why you do this?   Since the PrimalSolver and DualSolver are both 
derived from the base class and they share the same triangulation, then 
what is the purpose of using DualSolver::dof_handler.get_triangulation 
to reinit error_indicator?

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[deal.II] Re: what does it mean “the neighbor is coarser, but still has children which are finer than our current cell” in step 30？

[曾元圆]

Thank you for your reply, Bruno. 
Now I understand what you mean. But I'm still curious about how the cell # 
can figure out the correct "neighbor" of it. You mentioned that when you 
ask for the neighbor of cell #, you get a cell that has the same level of 
refinement or that is coarser. But in anisotropic refinement we don't 
identify a coarser cell though the "level" it belongs to, which is the case 
in isotropic refinement.
I suppose we have stored a "neighbor" of cell # correctly before ask for 
that. But how do we in fact set the link between cell# and it's neighbor, 
i.e. the right whole mother cell? I just want to know how these cells 
belonging to different "levels" are connected. I know perhaps it is not 
easy to explain in a few words, so it's preferable if there are some 
available thesis or documentation related to this. 
Thank you again anyway.

在 2017年11月16日星期四 UTC+8下午10:07:53，Bruno Turcksin写道：
>
> Hi,
>
> Basically, what happen is that if you ask for the right neighbor of the 
> cell # you will get the coarse right cell. The reason is that when you ask 
> for the neighbor, you get a cell that has the same level of refinement or 
> that is coarser. Now, when you look at cell # you could think that the 
> neighbor is a coarse cell formed by the two cells + but this is not the 
> case because that potential coarse cell does not exist.  You either have 
> the whole coarse cell or the four refined cells. Does that make sense?
>
> Best,
>
> Bruno
>
> On Wednesday, November 15, 2017 at 10:37:43 PM UTC-5, 曾元圆 wrote:
>>
>> hi, I am reading the tutorial of step-30, it talks about anisotropic 
>> refinement.
>>
>>
>> <https://lh3.googleusercontent.com/-scDSvXNeGUc/Wg0FCUT7QzI/ACo/e61oKfNuIP8DdaXdgVsiQHKnMfTwVK_EQCLcBGAs/s1600/1510802654%25281%2529.png>
>> it says: "It might be, that the neighbor is coarser, but still has 
>> children which are finer than our current cell. This situation can occur if 
>> two equally coarse cells are refined, where one of the cells has two 
>> children at the face under consideration and the other one four. The cells 
>> in the next graphic are only separated from each other to show the 
>> individual refinement cases."
>> "The left cell marked with # has two finer neighbors marked with +, but 
>> the actual neighbor of the left cell is the complete right mother cell, as 
>> the two cells marked with + are finer and their direct mother is the one 
>> large cell."
>> what it mean by saying "the actual neighbor of the left cell is the 
>> complete right mother cell"?  Can somebody help to explain this in 
>> detail? By the way, where can I find a documentation simply explain the 
>> data structure and the hierarchy in anisotropic refinement?
>>
>

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[deal.II] what does it mean “the neighbor is coarser, but still has children which are finer than our current cell” in step 30？

[曾元圆]

hi, I am reading the tutorial of step-30, it talks about anisotropic 
refinement.


it says: "It might be, that the neighbor is coarser, but still has children 
which are finer than our current cell. This situation can occur if two 
equally coarse cells are refined, where one of the cells has two children 
at the face under consideration and the other one four. The cells in the 
next graphic are only separated from each other to show the individual 
refinement cases."
"The left cell marked with # has two finer neighbors marked with +, but the 
actual neighbor of the left cell is the complete right mother cell, as the 
two cells marked with + are finer and their direct mother is the one large 
cell."
what it mean by saying "the actual neighbor of the left cell is the 
complete right mother cell"?  Can somebody help to explain this in detail? 
By the way, where can I find a documentation simply explain the data 
structure and the hierarchy in anisotropic refinement?

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Re: [deal.II] NamedData is not supported, how to change NamedData to AnyData？

[曾元圆]

Wow, it's really surprising and exciting to see the original developer of 
the code I'm now runing answering this question! Thank you so much Prof. 
Praveen.This is greetings from remote China! I'm now a master student and 
am running and learning the DG code developed by you. So I really want to 
show my respect and gratitude to you. By the way, though I have leared 
deal.II for a few days, but still found it difficult to grasp this tool. I 
find it too difficult to handle that many classes/functions and assemble 
them to do something. When I try to use a class or a funtion I always try 
to understand what is going on underneath. But when I tried to go deep into 
the code, I found there are too many things to learn and too difficult to 
learn. Take the MeshWorker::DoFInfo/IntegrationInfoBox... as an example, 
it's always difficult for me to understand the designing philosophy and the 
logic behind it, though there are many tutorial examples and documentations 
already. Could you kindly introduce some experience and give advices on how 
to efficiently learn and master this tool and make it into use for a 
beginner like me. Best regards and many thanks!


在 2017年10月26日星期四 UTC+8下午9:07:56，Praveen C写道：
>
> step-39 should be of some help to you. 
>
> best 
> praveen 
>
> > On 26-Oct-2017, at 5:45 PM, 曾元圆 <2012...@gmail.com > 
> wrote: 
> > 
> > I am trying to run a open source code, but an error occurred. 
> > In the code it uses NamedData like this: 
> > NamedData< Vector  *> solution_data; 
> > Info_box.initialize(fe, mapping, solution_data); 
> > 
> > How should I use AnyData to replace it? 
> > Actually I am a new learner, I tried to read the documentation related 
> to AnyData class but didn't quite understand how to use it. 
> > 
> > -- 
> > 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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> an email to dealii+un...@googlegroups.com . 
> > For more options, visit https://groups.google.com/d/optout. 
>
>

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Re: [deal.II] NamedData is not supported, how to change NamedData to AnyData？

[曾元圆]

Sorry, I should have describe my problem more specificlly. The problem is, 
I'm running a code writen several years ago. In the code it used the class: 
NamedData< Vector  *>, but Deal.II has deleted this template class 
so I have no idea how it work and the way to use it. I searched in the 
mailing list and get to know that this class was replaced by a new class: 
AnyData. But AnyData is not a template class, so I don't know how to change 
from NameData to AnyData. I just looked up step 39 and solved the problem. 
It should be changed to like this:  

NamedData< Vector  *> solution_data;
solution_data.add (, "solution");
 -->
AnyData 
<http://www.dealii.org/developer/doxygen/deal.II/classAnyData.html> 
solution_data;
solution_data.add 
<http://www.dealii.org/developer/doxygen/deal.II/classAnyData.html#a5949f684f8ce7ccce9d45e65af32580c>
<Vector 
<http://www.dealii.org/developer/doxygen/deal.II/classVector.html>*>(, 
"solution");  

Is there a record on how the template/class/function names are changed, so 
I can find it quickly in case one day in the future I found the code I 
wrote today can't run?
Anyway, thank you so much for your reply Prof.Bangerth. Thank you! 

在 2017年10月26日星期四 UTC+8下午8:51:24，Wolfgang Bangerth写道：
>
> On 10/26/2017 06:15 AM, 曾元圆 wrote: 
> > I am trying to run a open source code, but an error occurred. 
> > In the code it uses NamedData like this: 
> > NamedData< Vector  *> solution_data; 
> > Info_box.initialize(fe, mapping, solution_data); 
>
> What is the error you get? The first step in fixing an error is to 
> carefully 
> read the error message. 
>
> Best 
>   W. 
>
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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[deal.II] NamedData is not supported, how to change NamedData to AnyData？

[曾元圆]

I am trying to run a open source code, but an error occurred. 
In the code it uses NamedData like this:
NamedData< Vector  *> solution_data;
Info_box.initialize(fe, mapping, solution_data);

How should I use AnyData to replace it?
Actually I am a new learner, I tried to read the documentation related to 
AnyData class but didn't quite understand how to use it.

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[deal.II] error: wrong number of template arguments (1, should be 2) static MappingQ m(2);

[曾元圆]

I‘m compiling a source code written by others. And this error occurred.  I 
know it's because of the version of dealii. And I just want to know what 
this error really mean and how can I solve such kind of error. Because now 
I just want to be confirmed that the code work well so I don't want to go 
deep into the code (It's too time consuming to learn in detail how 
everything is going inside the code for me now)


/home/dyfluid/DG/dflo/src/claw.cc: In member function ‘const 
dealii::Mapping& ConservationLaw::mapping() const’:
/home/dyfluid/DG/dflo/src/claw.cc:175:26: error: wrong number of template 
arguments (1, should be 2)
   static MappingQ m(2);
  ^
In file included from 
/home/dyfluid/dealii_lib/deal.II-v8.5.1/include/deal.II/fe/mapping_q1.h:21:0,
 from /home/dyfluid/DG/dflo/src/claw.cc:26:
/home/dyfluid/dealii_lib/deal.II-v8.5.1/include/deal.II/fe/mapping_q_generic.h:34:26:
 
note: provided for ‘template, int  > class 
dealii::MappingQ’
 template  class MappingQ;
  ^
/home/dyfluid/DG/dflo/src/claw.cc: In instantiation of 
‘ConservationLaw::ConservationLaw(const char*, unsigned int, const 
dealii::FE_DGQArbitraryNodes&) [with int dim = 2]’:
/home/dyfluid/DG/dflo/src/claw.cc:1132:16:   required from here
/home/dyfluid/DG/dflo/src/claw.cc:72:59: warning: unused parameter ‘degree’ 
[-Wunused-parameter]
const unsigned int degree,
   ^
/home/dyfluid/DG/dflo/src/claw.cc: In instantiation of ‘void 
ConservationLaw::run() [with int dim = 2]’:
/home/dyfluid/DG/dflo/src/claw.cc:1132:16:   required from here
/home/dyfluid/DG/dflo/src/claw.cc:1043:20: warning: unused variable 
‘nonlin_iter’ [-Wunused-variable]
   unsigned int nonlin_iter = 0;
^
/home/dyfluid/DG/dflo/src/claw.cc: In instantiation of ‘void 
ConservationLaw::read_parameters(const char*) [with int dim = 2]’:
/home/dyfluid/DG/dflo/src/claw.cc:1132:16:   required from here
/home/dyfluid/DG/dflo/src/claw.cc:132:19: warning: ‘virtual bool 
dealii::ParameterHandler::read_input(const string&, bool, bool, const 
string&)’ is deprecated [-Wdeprecated-declarations]
prm.read_input (input_filename);
   ^
In file included from /home/dyfluid/DG/dflo/src/claw.cc:3:0:
/home/dyfluid/dealii_lib/deal.II-v8.5.1/include/deal.II/base/parameter_handler.h:1685:16:
 
note: declared here
   virtual bool read_input (const std::string ,
^
/home/dyfluid/DG/dflo/src/claw.cc: In instantiation of ‘const 
dealii::Mapping& ConservationLaw::mapping() const [with int dim = 
2]’:
/home/dyfluid/DG/dflo/src/claw.cc:1132:16:   required from here
/home/dyfluid/DG/dflo/src/claw.cc:176:14: error: invalid initialization of 
reference of type ‘const dealii::Mapping<2, 2>&’ from expression of type 
‘int’
   return m;
  ^
/home/dyfluid/DG/dflo/src/claw.cc: In instantiation of ‘void 
ConservationLaw::setup_system() [with int dim = 2]’:
/home/dyfluid/DG/dflo/src/claw.cc:1132:16:   required from here
/home/dyfluid/DG/dflo/src/claw.cc:344:17: warning: unused variable ‘EPS’ 
[-Wunused-variable]
const double EPS = 1.0e-10;
 ^
CMakeFiles/dflo.dir/build.make:206: recipe for target 
'CMakeFiles/dflo.dir/claw.cc.o' failed
make[2]: *** [CMakeFiles/dflo.dir/claw.cc.o] Error 1
CMakeFiles/Makefile2:195: recipe for target 'CMakeFiles/dflo.dir/all' failed
make[1]: *** [CMakeFiles/dflo.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2

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Re: [deal.II] Trouble getting UMFPACK to work

[曾元圆]

If I want to run all the 57 steps, should I install all the mentioned 
libraries? How can I know in advance which library I may need? Perhaps now 
I don't need PETSc, but maybe someday in the future I will need. 

在 2017年9月12日星期二 UTC+8下午8:08:14，Bruno Turcksin写道：
>
> 2017-09-11 23:45 GMT-04:00 曾元圆 <2012...@gmail.com >:
> >  Thank you very much! So you mean every time I want to use another 
> library,
> > I have to recompile and reinstall dealii again?
> Every time you add a new library you need to *reconfigure* and recompile 
> deal. Now if you want to use PETSc and Trilinos you can turn on both of 
> them at the same time. You don't need to recompile deal twice. Ideally, the 
> first time you configure deal, you would turn on the support for the all 
> libraries that you will need. This way you only have to compile deal.II 
> once.
>
> Best,
>
> Bruno
>

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Re: [deal.II] Trouble getting UMFPACK to work

[曾元圆]

 Thank you very much! So you mean every time I want to use another library, 
I have to recompile and reinstall dealii again?

在 2017年9月12日星期二 UTC+8上午1:25:25，Bruno Turcksin写道：
>
> 2017-09-11 13:11 GMT-04:00 曾元圆 <2012...@gmail.com >: 
> > Because I have already installed dealii, I don't quite understand what 
> you 
> > mean by saying "configuring". Do you mean I need to recompile the whole 
> > dealii then it can know where to find lapack?  LAPACK is a third party 
> > library right? so all I need to do is to tell the compiler where is the 
> > header and library. I suppose perhaps I don't need to configure dealii 
> > again?  sorry I really don't know much about cmake. Forgive me if I 
> asked 
> > you some silly questions. 
> To install deal.II, you have basically two steps: 1) the configuration 
> (that's when you use cmake and give all the options that you want for 
> example -DDEAL_II_WITH_UMFPACK=ON) 2) the compilation itself. 
> In step 1, all the compiler commands are generated and they are 
> executed during step 2. Like you correctly said, you need to tell the 
> compiler where the header and the library are, this is done during 
> step 1. However, this is slightly more complicated that just giving a 
> path, because some part of deal.II are only activated if some 
> libraries are present. For example, if you are using UMFPACK some 
> files will need to be compiled but if you are not using UMFPACK they 
> won't be compiled. So having deal.II compiled without UMFPACK support 
> and then, adding the flags to the library won't work because the files 
> that allow to use UMFPACK from deal.II won't be compiled. Basically 
> deal.II would not be aware that UMDPACK is installed. So what you need 
> to do is to reinstall deal.II from the very beginning in a new 
> directory. 
> Does it make sense? 
>
> Best, 
>
> Bruno 
>

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Re: [deal.II] Trouble getting UMFPACK to work

[曾元圆]

Because I have already installed dealii, I don't quite understand what you 
mean by saying "configuring". Do you mean I need to recompile the whole 
dealii then it can know where to find lapack?  LAPACK is a third party 
library right? so all I need to do is to tell the compiler where is the 
header and library. I suppose perhaps I don't need to configure dealii 
again?  sorry I really don't know much about cmake. Forgive me if I asked 
you some silly questions. 

best regards.

在 2017年9月11日星期一 UTC+8下午8:22:11，Bruno Turcksin写道：
>
> 2017-09-11 0:30 GMT-04:00 曾元圆 <2012...@gmail.com >: 
> > So UMFPACK is not installed, right? But what to do next?  How can I know 
> > whether my Ubuntu OS already installed the lapack and blas package? 
> No UMFPACK has not been installed and lapack has not been found. You 
> need to install the dev version of lapack otherwise the headers are 
> not installed. Without the headers, lapack cannot be used by deal. So 
> make sure you get ( DEAL_II_WITH_LAPACK = ON ) You can also add 
> -DDEAL_II_WITH_LAPACK=ON when configuring deal.II and cmake will let 
> you know if there is a problem. 
>
> > I can intall lapack and blas myself, but I don't know how to compile and 
> > install UMFPACK. 
> You don't need to install UMFPACK yourself. It will be installed by 
> deal.II. 
>
> Best, 
>
> Bruno 
>

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Re: [deal.II] Trouble getting UMFPACK to work

[曾元圆]

Now suppose I have installed blas and lapack by execute command in 
terminal. Then the remaining part is UMPACK. Since "DEAL_II_WITH_UMFPACK = 
OFF" is apparently not expected. What I want to know is what I should do to 
change it to  " DEAL_II_WITH_UMFPACK set up with bundled packages", which 
is what we want.


在 2017年9月11日星期一 UTC+8下午8:22:11，Bruno Turcksin写道：
>
> 2017-09-11 0:30 GMT-04:00 曾元圆 <2012...@gmail.com >: 
> > So UMFPACK is not installed, right? But what to do next?  How can I know 
> > whether my Ubuntu OS already installed the lapack and blas package? 
> No UMFPACK has not been installed and lapack has not been found. You 
> need to install the dev version of lapack otherwise the headers are 
> not installed. Without the headers, lapack cannot be used by deal. So 
> make sure you get ( DEAL_II_WITH_LAPACK = ON ) You can also add 
> -DDEAL_II_WITH_LAPACK=ON when configuring deal.II and cmake will let 
> you know if there is a problem. 
>
> > I can intall lapack and blas myself, but I don't know how to compile and 
> > install UMFPACK. 
> You don't need to install UMFPACK yourself. It will be installed by 
> deal.II. 
>
> Best, 
>
> Bruno 
>

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Re: [deal.II] Trouble getting UMFPACK to work

[曾元圆]

more specifically？

在 2017年9月11日星期一 UTC+8下午8:22:11，Bruno Turcksin写道：
>
> 2017-09-11 0:30 GMT-04:00 曾元圆 <2012...@gmail.com >: 
> > So UMFPACK is not installed, right? But what to do next?  How can I know 
> > whether my Ubuntu OS already installed the lapack and blas package? 
> No UMFPACK has not been installed and lapack has not been found. You 
> need to install the dev version of lapack otherwise the headers are 
> not installed. Without the headers, lapack cannot be used by deal. So 
> make sure you get ( DEAL_II_WITH_LAPACK = ON ) You can also add 
> -DDEAL_II_WITH_LAPACK=ON when configuring deal.II and cmake will let 
> you know if there is a problem. 
>
> > I can intall lapack and blas myself, but I don't know how to compile and 
> > install UMFPACK. 
> You don't need to install UMFPACK yourself. It will be installed by 
> deal.II. 
>
> Best, 
>
> Bruno 
>

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Re: [deal.II] Trouble getting UMFPACK to work

[曾元圆]

hi John,
have you solve this problem? I encountered the same problem as you. 
Actually I'm following an FEM open course on coursera and I'm trying to 
compile the source code in the homework. I have installed the dealii just a 
few days ago so I don't think it has something to do with the version of 
dealii.

在 2017年9月1日星期五 UTC+8上午3:52:44，John写道：
>
>  Timo, 
>
> I do eventually plan on updating the code to the latest release.
> I was doing the commands inside a folder in deal.II (similar to if I was 
> in deal.II/examples/step-1). I already have deal.II installed and compiled. 
> I have been going through a few of the examples perfectly fine. Should I be 
> trying to run the commands elsewhere? Everything else in the code has been 
> running just fine until it reaches the point it needs UMFPACK. Thank you 
> for responding.
>

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Re: [deal.II] Can someone send me an offline documentation of dealii？

[曾元圆]

Thank you so much！

在 2017年8月18日星期五 UTC+8下午11:58:12，Matthias Maier写道：
>
>
> On Fri, Aug 18, 2017, at 10:11 CDT, 曾元圆 <2012...@gmail.com > 
> wrote: 
>
> > I don’t know why I can't download it from the website, the download 
> speed 
> > is too slow. Can someone send it to me？My email address: 
> > 1213...@buaa.edu.cn . Thanks! 
>
> 150MB is a bit too much to send via e-mail. Please try one of the 
> following URLS: 
>
>   
> http://www-users.math.umn.edu/~msmaier/dealii-8.5.1-offline_documentation.tar.gz
>  
>   
> https://tamiko.kyomu.43-1.org/tmp/dealii-8.5.1-offline_documentation.tar.gz 
>
> Best, 
> Matthias 
>

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[deal.II] Can someone send me an offline documentation of dealii？

[曾元圆]

I don’t know why I can't download it from the website, the download speed 
is too slow. Can someone send it to me？My email address: 
12131...@buaa.edu.cn. Thanks!

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Re: [deal.II] Re: errors when installing dealii-8.5.1 after successful cmake configuation

[曾元圆]

I tried to install it in a sub-directory of /home and it really worked! 
Thank you so much, but I'm still confused why I can't install it in the 
shared directory. Probably there are some conflicts between Windows 
environment and Linux?

在 2017年8月17日星期四 UTC+8下午8:23:48，Bruno Turcksin写道：
>
> Do you have the same problem if you try to install deal.II in a 
> directory that is not shared with windows? 
>
> Best, 
>
> Bruno 
>
> 2017-08-17 8:18 GMT-04:00 曾元圆 <2012...@gmail.com >: 
> > Yes, I have deleted the previous dealii and restart from unpack the 
> > compressed package, so I think the name of the parent directory is not 
> the 
> > problem. 
> > 
> > I have googled the reason for "Scanning dependencies of target 
> > expand_instantiations_exe 
> > cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/depend.make:4: 
> *** 
> > missing separator.  Stop." 
> > and it is probably caused by the default editor on my Linux system(some 
> > error occurs if confuse Tab with space) so I have changed the default 
> editor 
> > to vim but still doesn't work. 
> > 
> > Then I checked the file under the directory of the error message 
> > (build/cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/) 
> > open the file "depend.make", and find the following file content: 
> > 
> > # CMAKE generated file: DO NOT EDIT! 
> > # Generated by "Unix Makefiles" Generator, CMake Version 3.5 
> > 
> > 
> cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/expand_instantiations.cc.o:
>  
>
> > ../cmake/scripts/expand_instantiations.cc 
> > 
> > I'm not sure if this is where the error lies and don't know how to solve 
> > this. Sincerely hope someone can help me with this. 
>

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[deal.II] Re: errors when installing dealii-8.5.1 after successful cmake configuation

[曾元圆]

Yes, I have deleted the previous dealii and restart from unpack the 
compressed package, so I think the name of the parent directory is not the 
problem. 

I have googled the reason for "Scanning dependencies of target 
expand_instantiations_exe
cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/depend.make:4: *** 
missing separator.  Stop." 
and it is probably caused by the default editor on my Linux system(some 
error occurs if confuse Tab with space) so I have changed the default 
editor to vim but still doesn't work. 

Then I checked the file under the directory of the error message (build
/cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/) 
open the file "depend.make", and find the following file content:

# CMAKE generated file: DO NOT EDIT!
# Generated by "Unix Makefiles" Generator, CMake Version 3.5

cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/expand_instantiations.cc.o:
 
../cmake/scripts/expand_instantiations.cc

I'm not sure if this is where the error lies and don't know how to solve 
this. Sincerely hope someone can help me with this.

在 2017年8月17日星期四 UTC+8下午7:35:59，Jean-Paul Pelteret写道：
>
> Hi,
>
> Did you delete your build directory after renaming the parent directory? 
> If not, then you might want to do so and try to configure and build deal.II 
> again. Sometimes CMake caches some data that remains stale even after a 
> project is reconfigured. 
>
> I hope that this helps,
> Jean-Paul
>  
>
>> -- Build files have been written to: /mnt/hgfs/My_code/dealii/build
>> dyfluid@dyfluid:/mnt/hgfs/My_code/dealii/build$ make
>> Scanning dependencies of target expand_instantiations_exe
>> cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/depend.make:4: *** 
>> missing separator.  Stop.
>> CMakeFiles/Makefile2:381: recipe for target 
>> 'cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all' failed
>> make[1]: *** [cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all] 
>> Error 2
>> Makefile:127: recipe for target 'all' failed
>> make: *** [all] Error 2
>>
>

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[deal.II] Re: errors when installing dealii-8.5.1 after successful cmake configuation

[曾元圆]

ncies not satisfied
--   step-56 - dependencies not satisfied
--   step-57 - dependencies not satisfied
-- Setting up examples - Done
-- Setting up quick_tests in DEBUG mode
-- Setting up quick_tests in DEBUG mode - Done
-- Setting up testsuite
-- Setting up testsuite - Done
###
#
#  deal.II configuration:
#CMAKE_BUILD_TYPE:   DebugRelease
#BUILD_SHARED_LIBS:  ON
#CMAKE_INSTALL_PREFIX:   /mnt/hgfs/My_code/dealii/lib
#CMAKE_SOURCE_DIR:   /mnt/hgfs/My_code/dealii
#(version 9.0.0-pre)
#CMAKE_BINARY_DIR:   /mnt/hgfs/My_code/dealii/build
#CMAKE_CXX_COMPILER: GNU 5.4.0 on platform Linux x86_64
#/usr/bin/c++
#
#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, 
DEAL_II_ALLOW_AUTODETECTION = ON):
#  ( DEAL_II_WITH_64BIT_INDICES = OFF )
#  ( DEAL_II_WITH_ADOLC = OFF )
#  ( DEAL_II_WITH_ARPACK = OFF )
#DEAL_II_WITH_BOOST set up with bundled packages
#  ( DEAL_II_WITH_BZIP2 = OFF )
#  ( DEAL_II_WITH_CUDA = OFF )
#DEAL_II_WITH_CXX14 = ON
#  ( DEAL_II_WITH_CXX17 = OFF )
#  ( DEAL_II_WITH_GSL = OFF )
#  ( DEAL_II_WITH_HDF5 = OFF )
#  ( DEAL_II_WITH_LAPACK = OFF )
#  ( DEAL_II_WITH_METIS = OFF )
#  ( DEAL_II_WITH_MPI = OFF )
#DEAL_II_WITH_MUPARSER set up with bundled packages
#  ( DEAL_II_WITH_NANOFLANN = OFF )
#  ( DEAL_II_WITH_NETCDF = OFF )
#  ( DEAL_II_WITH_OPENCASCADE = OFF )
#  ( DEAL_II_WITH_P4EST = OFF )
#  ( DEAL_II_WITH_PETSC = OFF )
#  ( DEAL_II_WITH_SLEPC = OFF )
#  ( DEAL_II_WITH_SUNDIALS = OFF )
#DEAL_II_WITH_THREADS set up with bundled packages
#  ( DEAL_II_WITH_TRILINOS = OFF )
#  ( DEAL_II_WITH_UMFPACK = OFF )
#DEAL_II_WITH_ZLIB set up with external dependencies
#
#  Component configuration:
#  ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
#DEAL_II_COMPONENT_EXAMPLES
#  ( DEAL_II_COMPONENT_PACKAGE = OFF )
#  ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
#
#  Detailed information (compiler flags, feature configuration) can be 
found in detailed.log
#
#  Run  $ make info  to print a help message with a list of top level 
targets
#
###
-- Configuring done
-- Generating done
-- Build files have been written to: /mnt/hgfs/My_code/dealii/build
dyfluid@dyfluid:/mnt/hgfs/My_code/dealii/build$ make
Scanning dependencies of target expand_instantiations_exe
cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/depend.make:4: *** 
missing separator.  Stop.
CMakeFiles/Makefile2:381: recipe for target 
'cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all' failed
make[1]: *** [cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all] 
Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2





在 2017年8月16日星期三 UTC+8下午8:31:17，Bruno Turcksin写道：
>
> Hello,
>
> On Wednesday, August 16, 2017 at 7:45:25 AM UTC-4, 曾元圆 wrote:
>
>> ###
>> -- Configuring done
>> -- Generating done
>> -- Build files have been written to: /mnt/hgfs/My code/dealii/build
>>
> On linux it is a bad idea to have a blank space in the name of a 
> directory. Instead of  /mnt/hgfs/My code/dealii/ use 
> /mnt/hgfs/My_code/dealii/ If it doesn't work send the detailed.log file 
> that should have been created by cmake.
>
> Best,
>
> Bruno
>

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[deal.II] Re: errors when installing dealii-8.5.1 after successful cmake configuation

[曾元圆]

By the way, I'm installing it on the virtual machine on my windows.

在 2017年8月16日星期三 UTC+8下午7:45:25，曾元圆写道：
>
> hello,
> I follow following installation instructions to install dealii,
>
> $ mkdir build
> $ cd build
> $ cmake -DCMAKE_INSTALL_PREFIX=/path/where/dealii/should/be/installed/to 
> /path/to/dealii/sources
> $ make install(alternatively $ make -j install)
> $ make test
>
> and configured cmake successfully.
> ###
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /mnt/hgfs/My code/dealii/build
>
> However, when I input "make install", an error occurs:
>
> Scanning dependencies of target expand_instantiations_exe
> cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/depend.make:4: *** 
> missing separator.  Stop.
> CMakeFiles/Makefile2:381: recipe for target 
> 'cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all' failed
> make[1]: *** [cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all] 
> Error 2
> Makefile:127: recipe for target 'all' failed
> make: *** [all] Error 2
>
> I really don't have much experience on linux and cmake, Could please 
> someone help me on this? Thanks.
>
>

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[deal.II] Re: errors when installing dealii-8.5.1 after successful cmake configuation

[曾元圆]

在 2017年8月16日星期三 UTC+8下午7:45:25，曾元圆写道：
>
> hello,
> I follow following installation instructions to install dealii,
>
> $ mkdir build
> $ cd build
> $ cmake -DCMAKE_INSTALL_PREFIX=/path/where/dealii/should/be/installed/to 
> /path/to/dealii/sources
> $ make install(alternatively $ make -j install)
> $ make test
>
> and configured cmake successfully.
> ###
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /mnt/hgfs/My code/dealii/build
>
> However, when I input "make install", an error occurs:
>
> Scanning dependencies of target expand_instantiations_exe
> cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/depend.make:4: *** 
> missing separator.  Stop.
> CMakeFiles/Makefile2:381: recipe for target 
> 'cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all' failed
> make[1]: *** [cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all] 
> Error 2
> Makefile:127: recipe for target 'all' failed
> make: *** [all] Error 2
>
>   

> I really don't have much experience on linux and cmake, Could please 
> someone help me on this? Thanks.
>
> if I just ignore this and keep on inputting "make", the process will 
continue but a similar error will occur later, I don't know if this is OK.  

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[deal.II] errors when installing dealii-8.5.1 after successful cmake configuation

[曾元圆]

hello,
I follow following installation instructions to install dealii,

$ mkdir build
$ cd build
$ cmake -DCMAKE_INSTALL_PREFIX=/path/where/dealii/should/be/installed/to 
/path/to/dealii/sources
$ make install(alternatively $ make -j install)
$ make test

and configured cmake successfully.
###
-- Configuring done
-- Generating done
-- Build files have been written to: /mnt/hgfs/My code/dealii/build

However, when I input "make install", an error occurs:

Scanning dependencies of target expand_instantiations_exe
cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/depend.make:4: *** 
missing separator.  Stop.
CMakeFiles/Makefile2:381: recipe for target 
'cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all' failed
make[1]: *** [cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all] 
Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2

I really don't have much experience on linux and cmake, Could please 
someone help me on this? Thanks.

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