dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

Yes, why not. Could you send a sample output in the xy format?

--
Anders


On Wed, Sep 08, 2010 at 06:11:22PM +0100, ndlopes@xxxxxxxxx wrote:
> Hi,
>
> Is it possible to consider a new output format for 1D problems?
> I'm using it for some time and now I've updated it to dolfin-0.9.9.
>
> The solutions file contain a list of  x y  coordinates.
> (analogous to the xyz format)
> It could be used directly with Xgraphic (wich is part of Xd3d),   gnuplot or
> with simple python/matplotlib  scripts for instance.
>
> Hope it works.
>
> Nuno Lopes
>

> # Bazaar merge directive format 2 (Bazaar 0.90)
> # revision_id: ndl@an9-20100908165948-xqvxgx0834mlrkpt
> # target_branch: bzr+ssh://bazaar.launchpad.net/~dolfin-\
> #   core/dolfin/main/
> # testament_sha1: 1a4383b33310156a890260ef4c35ceba6d7930e8
> # timestamp: 2010-09-08 18:01:16 +0100
> # base_revision_id: johannr@xxxxxxxxx-20100908084437-u2bw3adyeepm4de3
> #
> # Begin patch
> === modified file 'dolfin/io/File.cpp'
> --- dolfin/io/File.cpp	2010-09-06 15:19:48 +0000
> +++ dolfin/io/File.cpp	2010-09-08 16:59:48 +0000
> @@ -9,19 +9,20 @@
>  // Modified by Ola Skavhaug 2009.
>  //
>  // First added:  2002-11-12
> -// Last changed: 2010-09-06
> +// Last changed: 2010-09-08
>
> +#include <boost/filesystem.hpp>
>  #include <fstream>
> -#include <boost/filesystem.hpp>
> +#include <dolfin/main/MPI.h>
> +#include <dolfin/log/dolfin_log.h>
>  #include <dolfin/function/Function.h>
> -#include <dolfin/log/dolfin_log.h>
> -#include <dolfin/main/MPI.h>
>  #include "File.h"
>  #include "XMLFile.h"
>  #include "PythonFile.h"
>  #include "VTKFile.h"
>  #include "RAWFile.h"
>  #include "XYZFile.h"
> +#include "XYFile.h"
>  #include "BinaryFile.h"
>
>  using namespace dolfin;
> @@ -34,14 +35,11 @@
>    const std::string extension = boost::filesystem::extension(path);
>
>    // Create directory if we have a parent path
> -  if (path.has_parent_path())
> +  if ( path.has_parent_path() )
>    {
>      const boost::filesystem::path directory = path.parent_path();
> -    if (!boost::filesystem::is_directory(directory))
> -    {
> -      cout << "Creating directory \"" << directory.string() << "\"." << endl;
> -      boost::filesystem::create_directories(directory);
> -    }
> +    cout << "Creating directory \"" << directory.string() << "\"." << endl;
> +    boost::filesystem::create_directories(directory);
>    }
>
>    // Choose format based on extension
> @@ -64,6 +62,8 @@
>      file.reset(new RAWFile(filename));
>    else if (extension == ".xyz")
>      file.reset(new XYZFile(filename));
> +  else if (extension == ".xy")
> +    file.reset(new XYFile(filename));
>    else if (extension == ".bin")
>      file.reset(new BinaryFile(filename));
>    else
> @@ -89,6 +89,9 @@
>    case xyz:
>      file.reset(new XYZFile(filename));
>      break;
> +  case xy:
> +    file.reset(new XYFile(filename));
> +    break;
>    case binary:
>      file.reset(new BinaryFile(filename));
>      break;
>
> === modified file 'dolfin/io/File.h'
> --- dolfin/io/File.h	2010-08-26 21:44:34 +0000
> +++ dolfin/io/File.h	2010-09-08 16:59:48 +0000
> @@ -7,7 +7,7 @@
>  // Modified by Ola Skavhaug 2009
>  //
>  // First added:  2002-11-12
> -// Last changed: 2010-02-10
> +// Last changed: 2010-09-08
>
>  #ifndef __FILE_H
>  #define __FILE_H
> @@ -33,7 +33,7 @@
>    public:
>
>      /// File formats
> -    enum Type {xml, vtk, python, raw, xyz, binary};
> +    enum Type {xml, vtk, python, raw, xyz, xy, binary};
>
>      /// Create a file with given name
>      File(const std::string filename, std::string encoding = "ascii");
>
> === added file 'dolfin/io/XYFile.cpp'
> --- dolfin/io/XYFile.cpp	1970-01-01 00:00:00 +0000
> +++ dolfin/io/XYFile.cpp	2010-09-08 16:59:48 +0000
> @@ -0,0 +1,143 @@
> +// Copyright (C) 2005-2007 Garth N.Wells.
> +// Licensed under the GNU LGPL Version 2.1.
> +//
> +// Modified by Nuno Lopes 2010.
> +//
> +// First added:  2010-09-08
> +
> +#include <sstream>
> +#include <fstream>
> +#include <dolfin/fem/FiniteElement.h>
> +#include <dolfin/mesh/Mesh.h>
> +#include <dolfin/mesh/MeshFunction.h>
> +#include <dolfin/mesh/Vertex.h>
> +#include <dolfin/mesh/Cell.h>
> +#include <dolfin/function/Function.h>
> +#include <dolfin/function/FunctionSpace.h>
> +#include <dolfin/la/Vector.h>
> +#include "XYFile.h"
> +
> +using namespace dolfin;
> +
> +//----------------------------------------------------------------------------
> +XYFile::XYFile(const std::string filename) : GenericFile(filename)
> +{
> +  type = "XY";
> +}
> +//----------------------------------------------------------------------------
> +XYFile::~XYFile()
> +{
> +  // Do nothing
> +}
> +//----------------------------------------------------------------------------
> +void XYFile::operator<<(const Function& u)
> +{
> +  // Update xy file name and clear file
> +  xy_name_update(counter);
> +
> +  // Write results
> +  results_write(u);
> +
> +  // Increase the number of times we have saved the function
> +  counter++;
> +
> +  cout << "Saved function " << u.name() << " (" << u.label()
> +       << ") to file " << filename << " in xgraphic xy format." << endl;
> +}
> +//----------------------------------------------------------------------------
> +void XYFile::results_write(const Function& u) const
> +{
> +  // Open file
> +  std::ofstream fp(xy_filename.c_str(), std::ios_base::app);
> +  if (!fp)
> +    error("Unable to open file %s", filename.c_str());
> +
> +  const uint rank = u.function_space().element().value_rank();
> +  if(rank > 1)
> +    error("Only scalar functions can be saved in xy format.");
> +
> +  // Get number of components
> +  uint dim = 1;
> +  for (uint i = 0; i < rank; i++)
> +    dim *= u.function_space().element().value_dimension(i);
> +
> +  const Mesh& mesh = u.function_space().mesh();
> +
> +  // Allocate memory for function values at vertices
> +  const uint size = mesh.num_vertices()*dim;
> +  Array<double> values(size);
> +
> +  // Get function values at vertices
> +  u.compute_vertex_values(values,mesh);
> +
> +  // Write function data at mesh vertices
> +
> +  if ( dim > 1 )
> +    error("Cannot handle XY file for non-scalar functions. ");
> +
> +
> +
> +  std::ostringstream ss;
> +  ss << std::scientific;
> +  for (VertexIterator vertex(mesh); !vertex.end(); ++vertex)
> +  {
> +        ss.str("");
> +        ss<<vertex->x(0)<<" "<< values[ vertex->index()];
> +        ss<<std::endl;
> +        fp<<ss.str( );
> +  }
> +}
> +//----------------------------------------------------------------------------
> +void XYFile::xy_name_update(int counter)
> +{
> +  std::string filestart, extension;
> +  std::ostringstream fileid, newfilename;
> +
> +  fileid.fill('0');
> +  fileid.width(6);
> +
> +  filestart.assign(filename, 0, filename.find("."));
> +  extension.assign(filename, filename.find("."), filename.size());
> +
> +  fileid << counter;
> +  newfilename << filestart << fileid.str() << ".xy";
> +
> +  xy_filename = newfilename.str();
> +
> +  // Make sure file is empty
> +  FILE* fp = fopen(xy_filename.c_str(), "w");
> +  if (!fp)
> +    error("Unable to open file %s", filename.c_str());
> +  fclose(fp);
> +}
> +//----------------------------------------------------------------------------
> +template<class T>
> +void XYFile::mesh_function_write(T& meshfunction)
> +{
> +  // Update xy file name and clear file
> +  xy_name_update(counter);
> +
> +  Mesh& mesh = meshfunction.mesh();
> +
> +  if( meshfunction.dim() != mesh.topology().dim() )
> +    error("XY output of mesh functions is implemenetd for cell-based functions only.");
> +
> +  // Open file
> +  std::ofstream fp(xy_filename.c_str(), std::ios_base::app);
> +
> +  fp<<mesh.num_cells( ) <<std::endl;
> +  for (CellIterator cell(mesh); !cell.end(); ++cell)
> +    fp << meshfunction.get( cell->index() )  << std::endl;
> +
> +  // Close file
> +  fp.close();
> +
> +  // Increase the number of times we have saved the mesh function
> +  counter++;
> +
> +  cout << "saved mesh function " << counter << " times." << endl;
> +
> +  cout << "Saved mesh function " << mesh.name() << " (" << mesh.label()
> +       << ") to file " << filename << " in XY format." << endl;
> +}
> +//----------------------------------------------------------------------------
>
> === added file 'dolfin/io/XYFile.h'
> --- dolfin/io/XYFile.h	1970-01-01 00:00:00 +0000
> +++ dolfin/io/XYFile.h	2010-09-08 16:59:48 +0000
> @@ -0,0 +1,45 @@
> +// Copyright (C) 2005-2007 Garth N.Wells.
> +// Licensed under the GNU LGPL Version 2.1.
> +//
> +// Modified by Nuno Lopes 2010.
> +//
> +// First added:  2010-02-17
> +
> +#ifndef __XY_FILE_H
> +#define __XY_FILE_H
> +
> +#include <fstream>
> +#include "GenericFile.h"
> +
> +namespace dolfin
> +{
> +
> +  class XYFile : public GenericFile
> +  {
> +  public:
> +
> +    /// Simple and light file format for use with Xd3d. Supports
> +    /// scalar solution on 2D convex domains. The files only have a
> +    /// list of xy coordinates 'x , u(x)=y'
> +
> +    XYFile(const std::string filename);
> +    ~XYFile();
> +
> +    void operator<< (const Function& u);
> +
> +  private:
> +
> +    void results_write(const Function& u) const;
> +    void xy_name_update(const int counter);
> +
> +    template<class T>
> +    void mesh_function_write(T& meshfunction);
> +
> +    // raw filename
> +    std::string xy_filename;
> +
> +  };
> +
> +}
> +
> +#endif
>
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--
Anders