Yes, why not. Could you send a sample output in the xy format? -- Anders
On Wed, Sep 08, 2010 at 06:11:22PM +0100, [email protected] 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: n...@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: [email protected] > # > # 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 > > # Begin bundle > IyBCYXphYXIgcmV2aXNpb24gYnVuZGxlIHY0CiMKQlpoOTFBWSZTWfjaqNUABrtfgEwQe////3/n > z+6////7YA29r5WttCNnVx3NUAjV0tbtXbYUXaba0MrYbWOgHCSRJhA0U8ym0TZTTEGIIaMammjN > QBoBoyCUQExNAIJiano0o/VD1PRGmg0NAaAADQHMJoyNDQyGEaGQ00aADEZMgGEAwCQohqaaqH5J > 6NAp41T1NpB+VHojJp6j1Gg00A9TRppocwmjI0NDIYRoZDTRoAMRkyAYQDAJEghMEaRkJk1N6k8n > lDUyGpoeU8k009Q0yaaaGmlKpJNcxzZQjSPW0Hcw/7n3bKz8acvVG2b1+tqn8Sh/B2djl50oTzPq > xY0ldJRM1+2GCkRwuijRiiKik9c6ms/cRZXkG2sYZUIx5sKXDoUK1MXdTgZha20XMJN94cceJYTI > 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