Re: [deal.II] error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract type ‘dealii::parallel::distributed::Triangulation<3, 3>’

2020-08-07 Thread 孙翔
Hi, Wolfgang,

Oh, I see. Thank you very much.

Best,

Xiang

On Friday, 7 August 2020 11:12:18 UTC-7, Wolfgang Bangerth wrote:
>
> On 8/7/20 12:05 PM, 孙翔 wrote: 
> > Hi, Wolfgang, 
> > 
> > Thank you very much. Please see the following error message (red parts) 
> which 
> > is all I get from the Github version. 
> > 
> > 
> > Scanning dependencies of target thm 
> > [ 20%] Building CXX object CMakeFiles/thm.dir/src/main.cc.o 
> > In file included from /home/shyaan/thm/src/main.cc:8:0: 
> > /home/shyaan/thm/./include/geothermal.h: In instantiation of ‘class 
> CoupledTH<3>’: 
> > /home/shyaan/thm/src/main.cc:30:35:   required from here 
> > /home/shyaan/thm/./include/geothermal.h:112:45: error: cannot declare 
> field 
> > ‘CoupledTH<3>::triangulation’ to be of abstract type 
> > ‘dealii::parallel::distributed::Triangulation<3, 3>’ 
> > parallel::distributed::Triangulation triangulation;  // grid 
> >   ^ 
>
> Ah -- you are trying to use parallel::distributed::Triangulation but you 
> don't 
> have the p4est library available (or, at least, cmake has not detected 
> it). 
>
> In your build directory, run 'cmake .' and in the summary at the end, 
> check 
> that DEAL_II_WITH_P4EST says "set up with external dependencies". If it 
> isn't, 
> then you probably forgot to install p4est on that machine, or you forgot 
> to 
> tell cmake where it can be found. 
>
> There are a *lot* of warnings below. You should really try to address 
> those -- 
> otherwise, how will you know whether all of these things the compiler 
> tells 
> you about are harmless or not? 
>
> Best 
>   W. 
>
> > In file included from /home/shyaan/thm/src/main.cc:8:0: 
> > /home/shyaan/thm/./include/geothermal.h: In instantiation of 
> > ‘CoupledTH::CoupledTH(unsigned int) [with int dim = 3]’: 
> > /home/shyaan/thm/src/main.cc:30:37:   required from here 
> > /home/shyaan/thm/./include/geothermal.h:125:22: warning: 
> > ‘CoupledTH<3>::degree’ will be initialized after [-Wreorder] 
> > const unsigned int degree;  // element degree 
> >^~ 
> > /home/shyaan/thm/./include/geothermal.h:116:15: warning:  
>  ‘dealii::QGauss<3> 
> > CoupledTH<3>::quadrature_formula’ [-Wreorder] 
> > QGauss quadrature_formula; 
> > ^~ 
> > /home/shyaan/thm/./include/geothermal.h:161:1: warning:   when 
> initialized 
> > here [-Wreorder] 
> >   CoupledTH::CoupledTH(const unsigned int degree)  // 
> initialization 
> >   ^~ 
> > /home/shyaan/thm/./include/geothermal.h:150:16: warning: 
> > ‘CoupledTH<3>::T_iteration_namber’ will be initialized after [-Wreorder] 
> > unsigned int T_iteration_namber; 
> >  ^~ 
> > /home/shyaan/thm/./include/geothermal.h:109:22: warning:   
> >   ‘dealii::ConditionalOStream CoupledTH<3>::pcout’ [-Wreorder] 
> > ConditionalOStream pcout; 
> >^ 
> > /home/shyaan/thm/./include/geothermal.h:161:1: warning:   when 
> initialized 
> > here [-Wreorder] 
> >   CoupledTH::CoupledTH(const unsigned int degree)  // 
> initialization 
> >   ^~ 
>
> > /home/shyaan/thm/./include/geothermal.h:622:51: warning: comparison 
> between 
> > signed and unsigned integer expressions [-Wsign-compare] 
> >   if(cell->face(face_no)->boundary_id() == 
> > In file included from /home/shyaan/thm/src/main.cc:1:0: 
> > /home/shyaan/thm/./include/boundaryvalues.h: In instantiation of ‘double 
> > EquationData::TemperatureNeumanBoundaryValues::value(const 
> > dealii::Point&, unsigned int) const [with int dim = 3]’: 
> > /home/shyaan/thm/src/main.cc:84:1:   required from here 
> > /home/shyaan/thm/./include/boundaryvalues.h:165:16: warning: unused 
> variable 
> > ‘time’ [-Wunused-variable] 
> > const double time = this->get_time(); 
> >  ^~~~ 
> > /home/shyaan/thm/./include/boundaryvalues.h:159:23: warning: unused 
> parameter 
> > ‘p’ [-Wunused-paramete] 
> >   const Point& p, const unsigned int /*component*/) const { 
> > ^ 
> > In file included from /home/shyaan/thm/src/main.cc:6:0: 
> > /home/shyaan/thm/./include/sourceterm.h: In instantiation of ‘double 
> > EquationData::TemperatureSourceTerm::value(const 
> dealii::Point&, 
> > unsigned int) const [with int dim = 3]’: 
> > /home/shyaan/thm/src/main.cc:84:1:   required from here 
> > /home/shyaan/thm/./include/sourceterm.h:74:16: warning: unused variable 
> ‘time’ 
> > [-Wunused-variable] 
> > const double time = this->get_time();  // get time 
> >  ^~~~ 
> > /home/shyaan/thm/./include/sourceterm.h:69:60: warning: unused parameter 
> ‘p’ 
> > [-Wunused-parameter] 
> >   double TemperatureSourceTerm::value(const Point& p, 
> >  ^ 
> > In file included from /home/shyaan/thm/src/main.cc:1:0: 
> > /home/shyaan/thm/./include/boundaryvalues.h: In instantiation of 

Re: [deal.II] error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract type ‘dealii::parallel::distributed::Triangulation<3, 3>’

2020-08-07 Thread Wolfgang Bangerth

On 8/7/20 12:05 PM, 孙翔 wrote:

Hi, Wolfgang,

Thank you very much. Please see the following error message (red parts) which 
is all I get from the Github version.



Scanning dependencies of target thm
[ 20%] Building CXX object CMakeFiles/thm.dir/src/main.cc.o
In file included from /home/shyaan/thm/src/main.cc:8:0:
/home/shyaan/thm/./include/geothermal.h: In instantiation of ‘class 
CoupledTH<3>’:
/home/shyaan/thm/src/main.cc:30:35:   required from here
/home/shyaan/thm/./include/geothermal.h:112:45: error: cannot declare field 
‘CoupledTH<3>::triangulation’ to be of abstract type 
‘dealii::parallel::distributed::Triangulation<3, 3>’

    parallel::distributed::Triangulation triangulation;  // grid
                                              ^


Ah -- you are trying to use parallel::distributed::Triangulation but you don't 
have the p4est library available (or, at least, cmake has not detected it).


In your build directory, run 'cmake .' and in the summary at the end, check 
that DEAL_II_WITH_P4EST says "set up with external dependencies". If it isn't, 
then you probably forgot to install p4est on that machine, or you forgot to 
tell cmake where it can be found.


There are a *lot* of warnings below. You should really try to address those -- 
otherwise, how will you know whether all of these things the compiler tells 
you about are harmless or not?


Best
 W.


In file included from /home/shyaan/thm/src/main.cc:8:0:
/home/shyaan/thm/./include/geothermal.h: In instantiation of 
‘CoupledTH::CoupledTH(unsigned int) [with int dim = 3]’:

/home/shyaan/thm/src/main.cc:30:37:   required from here
/home/shyaan/thm/./include/geothermal.h:125:22: warning: 
‘CoupledTH<3>::degree’ will be initialized after [-Wreorder]

    const unsigned int degree;  // element degree
                       ^~
/home/shyaan/thm/./include/geothermal.h:116:15: warning:   ‘dealii::QGauss<3> 
CoupledTH<3>::quadrature_formula’ [-Wreorder]

    QGauss quadrature_formula;
                ^~
/home/shyaan/thm/./include/geothermal.h:161:1: warning:   when initialized 
here [-Wreorder]

  CoupledTH::CoupledTH(const unsigned int degree)  // initialization
  ^~
/home/shyaan/thm/./include/geothermal.h:150:16: warning: 
‘CoupledTH<3>::T_iteration_namber’ will be initialized after [-Wreorder]

    unsigned int T_iteration_namber;
                 ^~
/home/shyaan/thm/./include/geothermal.h:109:22: warning:  
  ‘dealii::ConditionalOStream CoupledTH<3>::pcout’ [-Wreorder]

    ConditionalOStream pcout;
                       ^
/home/shyaan/thm/./include/geothermal.h:161:1: warning:   when initialized 
here [-Wreorder]

  CoupledTH::CoupledTH(const unsigned int degree)  // initialization
  ^~


/home/shyaan/thm/./include/geothermal.h:622:51: warning: comparison between 
signed and unsigned integer expressions [-Wsign-compare]

              if(cell->face(face_no)->boundary_id() ==
In file included from /home/shyaan/thm/src/main.cc:1:0:
/home/shyaan/thm/./include/boundaryvalues.h: In instantiation of ‘double 
EquationData::TemperatureNeumanBoundaryValues::value(const 
dealii::Point&, unsigned int) const [with int dim = 3]’:

/home/shyaan/thm/src/main.cc:84:1:   required from here
/home/shyaan/thm/./include/boundaryvalues.h:165:16: warning: unused variable 
‘time’ [-Wunused-variable]

    const double time = this->get_time();
                 ^~~~
/home/shyaan/thm/./include/boundaryvalues.h:159:23: warning: unused parameter 
‘p’ [-Wunused-paramete]

      const Point& p, const unsigned int /*component*/) const {
                        ^
In file included from /home/shyaan/thm/src/main.cc:6:0:
/home/shyaan/thm/./include/sourceterm.h: In instantiation of ‘double 
EquationData::TemperatureSourceTerm::value(const dealii::Point&, 
unsigned int) const [with int dim = 3]’:

/home/shyaan/thm/src/main.cc:84:1:   required from here
/home/shyaan/thm/./include/sourceterm.h:74:16: warning: unused variable ‘time’ 
[-Wunused-variable]

    const double time = this->get_time();  // get time
                 ^~~~
/home/shyaan/thm/./include/sourceterm.h:69:60: warning: unused parameter ‘p’ 
[-Wunused-parameter]

  double TemperatureSourceTerm::value(const Point& p,
                                                             ^
In file included from /home/shyaan/thm/src/main.cc:1:0:
/home/shyaan/thm/./include/boundaryvalues.h: In instantiation of ‘double 
EquationData::PressureNeumanBoundaryValues::value(const 
dealii::Point&, unsigned int) const [with int dim = 3]’:

/home/shyaan/thm/src/main.cc:84:1:   required from here
/home/shyaan/thm/./include/boundaryvalues.h:133:10: warning: unused variable 
‘time’ [-Wunused-variable]

    double time = this->get_time();  // get time
           ^~~~
/home/shyaan/thm/./include/boundaryvalues.h:128:23: warning: unused parameter 
‘p’ [-Wunused-paramete]

      const Point& p, const unsigned int /*component*/) const {
                        ^
In file 

Re: [deal.II] error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract type ‘dealii::parallel::distributed::Triangulation<3, 3>’

2020-08-07 Thread 孙翔
Hi, Wolfgang,

Thank you very much. Please see the following error message (red parts) 
which is all I get from the Github version.


Scanning dependencies of target thm
[ 20%] Building CXX object CMakeFiles/thm.dir/src/main.cc.o
In file included from /home/shyaan/thm/src/main.cc:8:0:
/home/shyaan/thm/./include/geothermal.h: In instantiation of ‘class 
CoupledTH<3>’:
/home/shyaan/thm/src/main.cc:30:35:   required from here
/home/shyaan/thm/./include/geothermal.h:112:45: error: cannot declare field 
‘CoupledTH<3>::triangulation’ to be of abstract type 
‘dealii::parallel::distributed::Triangulation<3, 3>’
   parallel::distributed::Triangulation triangulation;  // grid
 ^
In file included from /home/shyaan/thm/./include/geothermal.h:32:0,
 from /home/shyaan/thm/src/main.cc:8:
/home/shyaan/dealii/include/deal.II/distributed/tria.h:1402:11: note:  
 because the following virtual functions are pure within 
‘dealii::parallel::distributed::Triangulation<3, 3>’:
 class Triangulation
   ^
In file included from 
/home/shyaan/dealii/include/deal.II/dofs/dof_handler.h:29:0,
 from 
/home/shyaan/dealii/include/deal.II/numerics/vector_tools_boundary.h:22,
 from 
/home/shyaan/dealii/include/deal.II/numerics/vector_tools.h:22,
 from /home/shyaan/thm/./include/boundaryvalues.h:8,
 from /home/shyaan/thm/src/main.cc:1:
/home/shyaan/dealii/include/deal.II/distributed/tria_base.h:105:5: note:
bool dealii::parallel::TriangulationBase::is_multilevel_hierarchy_constructed() const [with int dim = 3; 
int spacedim = 3]
 is_multilevel_hierarchy_constructed() const = 0;
 ^~~
In file included from /home/shyaan/thm/src/main.cc:8:0:
/home/shyaan/thm/./include/geothermal.h: In instantiation of 
‘CoupledTH::CoupledTH(unsigned int) [with int dim = 3]’:
/home/shyaan/thm/src/main.cc:30:37:   required from here
/home/shyaan/thm/./include/geothermal.h:125:22: warning: 
‘CoupledTH<3>::degree’ will be initialized after [-Wreorder]
   const unsigned int degree;  // element degree
  ^~
/home/shyaan/thm/./include/geothermal.h:116:15: warning:  
 ‘dealii::QGauss<3> CoupledTH<3>::quadrature_formula’ [-Wreorder]
   QGauss quadrature_formula;
   ^~
/home/shyaan/thm/./include/geothermal.h:161:1: warning:   when initialized 
here [-Wreorder]
 CoupledTH::CoupledTH(const unsigned int degree)  // initialization
 ^~
/home/shyaan/thm/./include/geothermal.h:150:16: warning: 
‘CoupledTH<3>::T_iteration_namber’ will be initialized after [-Wreorder]
   unsigned int T_iteration_namber;
^~
/home/shyaan/thm/./include/geothermal.h:109:22: warning:  
 ‘dealii::ConditionalOStream CoupledTH<3>::pcout’ [-Wreorder]
   ConditionalOStream pcout;
  ^
/home/shyaan/thm/./include/geothermal.h:161:1: warning:   when initialized 
here [-Wreorder]
 CoupledTH::CoupledTH(const unsigned int degree)  // initialization
 ^~
/home/shyaan/thm/./include/geothermal.h:183:63: error: no matching function 
for call to ‘dealii::parallel::distributed::Triangulation<3, 
3>::Triangulation(ompi_communicator_t*&)’
  EquationData::file_name_interpolation) {
   ^
In file included from /home/shyaan/thm/./include/geothermal.h:32:0,
 from /home/shyaan/thm/src/main.cc:8:
/home/shyaan/dealii/include/deal.II/distributed/tria.h:1410:7: note: 
candidate: dealii::parallel::distributed::Triangulation::Triangulation() [with int dim = 3; int spacedim = 3] 
   Triangulation() = delete;
   ^
/home/shyaan/dealii/include/deal.II/distributed/tria.h:1410:7: note:  
 candidate expects 0 arguments, 1 provided
/home/shyaan/dealii/include/deal.II/distributed/tria.h:1402:11: note: 
candidate: dealii::parallel::distributed::Triangulation<3, 
3>::Triangulation(const dealii::parallel::distributed::Triangulation<3, 
3>&) 
 class Triangulation
   ^
/home/shyaan/dealii/include/deal.II/distributed/tria.h:1402:11: note:   no 
known conversion for argument 1 from ‘MPI_Comm {aka ompi_communicator_t*}’ 
to ‘const dealii::parallel::distributed::Triangulation<3, 3>&’
/home/shyaan/dealii/include/deal.II/distributed/tria.h:1402:11: note: 
candidate: dealii::parallel::distributed::Triangulation<3, 
3>::Triangulation(dealii::parallel::distributed::Triangulation<3, 3>&&) 

/home/shyaan/dealii/include/deal.II/distributed/tria.h:1402:11: note:   no 
known conversion for argument 1 from ‘MPI_Comm {aka ompi_communicator_t*}’ 
to ‘dealii::parallel::distributed::Triangulation<3, 3>&&’
In file included from /home/shyaan/thm/src/main.cc:8:0:
/home/shyaan/thm/./include/geothermal.h: In instantiation of ‘void 
CoupledTH::assemble_P_system() [with int dim = 3]’:

Re: [deal.II] error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract type ‘dealii::parallel::distributed::Triangulation<3, 3>’

2020-08-07 Thread Wolfgang Bangerth



Thank you for your reply. The complete code can be found on GitHub and we also 
have the instruction for compiling the code on TACC in UTA. This code is in 
the branch thm_seg_distributed. You may like to download it and build it.


https://github.com/cb-geo/thm/tree/thm_seg_distributed 



Xiang,
this compiles fine for me. Can you show me the exact and complete error 
message you get with the version on github?


Best
 W.


--

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

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Re: [deal.II] error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract type ‘dealii::parallel::distributed::Triangulation<3, 3>’

2020-08-05 Thread 孙翔
Hi, Wolfgang,

Thank you for your reply. The complete code can be found on GitHub and we 
also have the instruction for compiling the code on TACC in UTA. This code 
is in the branch thm_seg_distributed. You may like to download it and build 
it. 

https://github.com/cb-geo/thm/tree/thm_seg_distributed

Best,

Xiang


On Wednesday, 5 August 2020 16:23:07 UTC-7, Wolfgang Bangerth wrote:
>
> On 8/5/20 10:42 AM, 孙翔 wrote: 
> > 
> > Please see the attached file, which is the head file that used the 
> library. 
> > Thank you very much. 
>
> That's not enough -- you're using a file "interpolation.h" that I don't 
> have, 
> and parts of the rest of that file depend on this. You need to give me 
> something that's sufficiently complete for me to try and compile this to 
> obtain the error you see. 
>
> Best 
>   W. 
>
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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Re: [deal.II] error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract type ‘dealii::parallel::distributed::Triangulation<3, 3>’

2020-08-05 Thread Wolfgang Bangerth

On 8/5/20 10:42 AM, 孙翔 wrote:


Please see the attached file, which is the head file that used the library. 
Thank you very much.


That's not enough -- you're using a file "interpolation.h" that I don't have, 
and parts of the rest of that file depend on this. You need to give me 
something that's sufficiently complete for me to try and compile this to 
obtain the error you see.


Best
 W.


--

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

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Re: [deal.II] error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract type ‘dealii::parallel::distributed::Triangulation<3, 3>’

2020-08-05 Thread 孙翔
Hi, Wolfgang,

Please see the attached file, which is the head file that used the library. 
Thank you very much.

Best,

Xiang

On Wednesday, 5 August 2020 09:14:51 UTC-7, Wolfgang Bangerth wrote:
>
> On 8/5/20 10:13 AM, 孙翔 wrote: 
> > 
> > I have included it actually, and also the distributed/grid_refinement.h 
> was 
> > also included. Because I want to import the outside mesh to build up the 
> > triangulation, I also used Gridin to work on the triangulation, which is 
> like 
> > as the following: 
>
> Then I have no other idea -- send us the file that produces the error, I 
> think 
> that's the only way we can help :-) 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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sample
Description: Binary data


Re: [deal.II] error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract type ‘dealii::parallel::distributed::Triangulation<3, 3>’

2020-08-05 Thread Wolfgang Bangerth

On 8/5/20 10:13 AM, 孙翔 wrote:


I have included it actually, and also the distributed/grid_refinement.h was 
also included. Because I want to import the outside mesh to build up the 
triangulation, I also used Gridin to work on the triangulation, which is like 
as the following:


Then I have no other idea -- send us the file that produces the error, I think 
that's the only way we can help :-)


Best
 W.

--

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

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Re: [deal.II] error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract type ‘dealii::parallel::distributed::Triangulation<3, 3>’

2020-08-05 Thread 孙翔
Hi, Wolfgang,

I have included it actually, and also the distributed/grid_refinement.h was 
also included. Because I want to import the outside mesh to build up the 
triangulation, I also used Gridin to work on the triangulation, which is 
like as the following:

void CoupledTH::make_grid_and_dofs() {

  GridIn gridin;  // instantiate a gridinput
  gridin.attach_triangulation(triangulation);
  std::ifstream f("inputfiles/mesh.msh");
  gridin.read_msh(f);
...

I am not sure if this impacts the declaration. 

Thank you very much.

Best,

Xiang


On Wednesday, 5 August 2020 08:23:00 UTC-7, Wolfgang Bangerth wrote:
>
> On 8/5/20 3:01 AM, 孙翔 wrote: 
> > 
> > error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of 
> abstract 
> > type ‘dealii::parallel::distributed::Triangulation<3, 3>’ 
>
> I suspect that you forgot in 
>#include  
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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Re: [deal.II] error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract type ‘dealii::parallel::distributed::Triangulation<3, 3>’

2020-08-05 Thread Wolfgang Bangerth

On 8/5/20 3:01 AM, 孙翔 wrote:


error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract 
type ‘dealii::parallel::distributed::Triangulation<3, 3>’


I suspect that you forgot in
  #include 

Best
 W.

--

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

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[deal.II] error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract type ‘dealii::parallel::distributed::Triangulation<3, 3>’

2020-08-05 Thread 孙翔
Hi, I want to declare a variable triangulation as the 
type dealii::parallel::distributed::Triangulation<3, 3>.  The code is :

in main function, 

using namespace dealii;

Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);

CoupledTH<3> coupled_TH_solver(1);
coupled_TH_solver.run();

in class CoupledTH,

parallel::distributed::Triangulation triangulation;

I also included the .h files which are shown in Step-40. 

When I compile the code, I got the error:  

error: cannot declare field ‘CoupledTH<3>::triangulation’ to be of abstract 
type ‘dealii::parallel::distributed::Triangulation<3, 3>’

Thank you very much.

Best,

Xiang


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