dolfin team mailing list archive

["Thomas Gazzola" <thomas.gazzola@xxxxxxxxx>]

Hello everyone!

Since I post for the first time on the M-list, I thank you all for the
fenics suite.

I am developing some code in C++, and I use dolfin in order to solve
some BVP problem. I did include dolfin.h and two forms compiled with
ffc in each file. I had a trouble when linking my stuff.
I am no C++ expert, so I don't know wether it is because of me or not.

I did use the recent revision number 5349 (result of `hg id -n`).

When compiling my stuff, I did have some _linking_ problems like:

(...snip...)
Output.o: in function «
boost::numeric::ublas::compressed_matrix<double,
boost::numeric::ublas::basic_row_major<unsigned long, long>, 0ul,
boost::numeric::ublas::unbounded_array<unsigned long,
std::allocator<unsigned long> >,
boost::numeric::ublas::unbounded_array<double, std::allocator<double>
> >::size1() const»:
$PREFIX/local/include/dolfin/fem/assemble.h:89: multiple definitions
of « dolfin::assemble_system(dolfin::GenericMatrix&,
dolfin::GenericVector&, dolfin::Form const&, dolfin::Form const&,
std::vector<dolfin::DirichletBC const*,
std::allocator<dolfin::DirichletBC const*> >&,
dolfin::MeshFunction<unsigned int> const*,
dolfin::MeshFunction<unsigned int> const*,
dolfin::MeshFunction<unsigned int> const*, dolfin::GenericVector
const*, bool)»
main.o:/homes/tgax/local/include/dolfin/fem/assemble.h:89: first definition here
(...snip...)

In other words, I have troubles with function assemble_system in file
dolfin/fem/assemble.h .

I had a look at the assemble.h file. It is a file with code calling
methods from the Assembler class (defined in files
dolfin/fem/Assembler.*).

A `nm` on my *.o did show undefined symbols for function
assemble_system, in several object files. Assembler::assemble_system
were OK.

The code from assemble.h seems to be compiled in several of my object
files, so the linker just cannot link.

In order to solve this, I did split dolfin/fem/assemble.h into a .cpp
and a real header file. The SConstruct process automatically compiles
assemble.cpp, and the link could be done to my program.

I don't know if it is a real problem of dolfin, or if I did something
wrong, but I wanted to let you known. What do you think?

With the best regards,

Thomas G.

13,15d12
< #ifndef __ASSEMBLE_H
< #define __ASSEMBLE_H
< 
27c24,27
<                 bool reset_tensor);
---
>                 bool reset_tensor=true)
>   {
>     Assembler::assemble(A, a, reset_tensor);
>   }
33c33,36
<                 bool reset_tensor);
---
>                 bool reset_tensor=true)
>   {
>     Assembler::assemble(A, a, sub_domain, reset_tensor);
>   }
41c44,47
<                 bool reset_tensor);
---
>                 bool reset_tensor=true)
>   {
>     Assembler::assemble(A, a, cell_domains, exterior_facet_domains, interior_facet_domains);
>   }
49c55,58
<                        bool reset_tensors);
---
>                        bool reset_tensors=true)
>   {
>     Assembler::assemble_system(A, b, a, L, bc, reset_tensors);
>   }
57c66,69
<                        bool reset_tensors);
---
>                        bool reset_tensors=true)
>   {
>     Assembler::assemble_system(A, b, a, L, bcs, reset_tensors);
>   }
69c81,86
<                        bool reset_tensors);
---
>                        bool reset_tensors=true)
>   {
>     Assembler::assemble_system(A, b, a, L, bcs, 
>                                cell_domains, exterior_facet_domains, interior_facet_domains,
>                                x0, reset_tensors);
>   }
75c92,98
<                   bool reset_tensor);
---
>                   bool reset_tensor=true)
>   {
>     if (a.rank() != 0) error("Unable to assemble, form is not scalar.");
>     Scalar s;
>     Assembler::assemble(s, a, reset_tensor);
>     return s;
>   }
80c103,109
<                   bool reset_tensor);
---
>                   bool reset_tensor=true)
>   {
>     if (a.rank() != 0) error("Unable to assemble, form is not scalar.");
>     Scalar s;
>     Assembler::assemble(s, a, sub_domain, reset_tensor);
>     return s;
>   }
87,88c116,122
<                   bool reset_tensor);
< }
---
>                   bool reset_tensor=true)
>   {
>     if (a.rank() != 0) error("Unable to assemble, form is not scalar.");
>     Scalar s;
>     Assembler::assemble(s, a, cell_domains, exterior_facet_domains, interior_facet_domains, reset_tensor);
>     return s;
>   }
90c124
< #endif
---
> }

// Copyright (C) 2007-2008 Anders Logg.
// Licensed under the GNU LGPL Version 2.1.
//
// Modified by Garth N. Wells, 2008.
//
// First added:  2007-01-17
// Last changed: 2008-11-16
//
// This file duplicates the Assembler::assemble* functions in
// namespace dolfin, and adds special versions returning the value
// directly for scalars. For documentation, refer to Assemble.h.

#include <dolfin/log/log.h>
#include <dolfin/la/Scalar.h>
#include "Form.h"
#include "Assembler.h"
#include "assemble.h"

namespace dolfin
{
  
  using namespace dolfin;
  //--- Copies of assembly functions in Assembler.h ---
  
  /// Assemble tensor
  void assemble(GenericTensor& A,
                const Form& a,
                bool reset_tensor=true)
  {
    Assembler::assemble(A, a, reset_tensor);
  }

  /// Assemble tensor on sub domain
  void assemble(GenericTensor& A,
                const Form& a,
                const SubDomain& sub_domain,
                bool reset_tensor=true)
  {
    Assembler::assemble(A, a, sub_domain, reset_tensor);
  }

  /// Assemble tensor on sub domains
  void assemble(GenericTensor& A,
                const Form& a,
                const MeshFunction<uint>* cell_domains,
                const MeshFunction<uint>* exterior_facet_domains,
                const MeshFunction<uint>* interior_facet_domains,
                bool reset_tensor=true)
  {
    Assembler::assemble(A, a, cell_domains, exterior_facet_domains, interior_facet_domains);
  }

  /// Assemble system (A, b) and apply Dirichlet boundary condition
  void assemble_system(GenericMatrix& A,
                       GenericVector& b,
                       const Form& a,
                       const Form& L,
                       const DirichletBC& bc,
                       bool reset_tensors=true)
  {
    Assembler::assemble_system(A, b, a, L, bc, reset_tensors);
  }
 
  /// Assemble system (A, b) and apply Dirichlet boundary conditions
  void assemble_system(GenericMatrix& A,
                       GenericVector& b,
                       const Form& a,
                       const Form& L, 
                       std::vector<const DirichletBC*>& bcs,
                       bool reset_tensors=true)
  {
    Assembler::assemble_system(A, b, a, L, bcs, reset_tensors);
  }

  /// Assemble system (A, b) on sub domains and apply Dirichlet boundary conditions
  void assemble_system(GenericMatrix& A,
                       GenericVector& b,
                       const Form& a,
                       const Form& L,
                       std::vector<const DirichletBC*>& bcs,
                       const MeshFunction<uint>* cell_domains,
                       const MeshFunction<uint>* exterior_facet_domains,
                       const MeshFunction<uint>* interior_facet_domains,
                       const GenericVector* x0,
                       bool reset_tensors=true)
  {
    Assembler::assemble_system(A, b, a, L, bcs, 
                               cell_domains, exterior_facet_domains, interior_facet_domains,
                               x0, reset_tensors);
  }

  //--- Specialized versions for scalars ---

  /// Assemble scalar
  double assemble(const Form& a,
                  bool reset_tensor=true)
  {
    if (a.rank() != 0) error("Unable to assemble, form is not scalar.");
    Scalar s;
    Assembler::assemble(s, a, reset_tensor);
    return s;
  }

  /// Assemble scalar on sub domain
  double assemble(const Form& a,
                  const SubDomain& sub_domain,
                  bool reset_tensor=true)
  {
    if (a.rank() != 0) error("Unable to assemble, form is not scalar.");
    Scalar s;
    Assembler::assemble(s, a, sub_domain, reset_tensor);
    return s;
  }

  /// Assemble scalar on sub domains
  double assemble(const Form& a,
                  const MeshFunction<uint>* cell_domains,
                  const MeshFunction<uint>* exterior_facet_domains,
                  const MeshFunction<uint>* interior_facet_domains,
                  bool reset_tensor=true)
  {
    if (a.rank() != 0) error("Unable to assemble, form is not scalar.");
    Scalar s;
    Assembler::assemble(s, a, cell_domains, exterior_facet_domains, interior_facet_domains, reset_tensor);
    return s;
  }

}