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Message #19641
xy format for solutions.
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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