Hurray! -- Marie
On 2. juli 2011, at 13:12, [email protected] wrote: > Merge authors: > Garth Wells (garth-wells) > ------------------------------------------------------------ > revno: 6015 [merge] > committer: Garth N. Wells <[email protected]> > branch nick: dolfin-main > timestamp: Sat 2011-07-02 12:11:14 +0100 > message: > merge > modified: > dolfin/io/GenericFile.cpp > dolfin/io/GenericFile.h > dolfin/io/XMLFile.cpp > dolfin/io/XMLFile.h > dolfin/io/XMLIndent.cpp > dolfin/io/XMLIndent.h > dolfin/io/XMLMesh.cpp > dolfin/io/XMLMesh.h > dolfin/io/XMLVector.cpp > dolfin/io/XMLVector.h > dolfin/la/GenericMatrix.h > dolfin/mesh/Mesh.h > test/unit/io/python/xml_vector.py > > > -- > lp:dolfin > https://code.launchpad.net/~dolfin-core/dolfin/main > > Your team DOLFIN Core Team is subscribed to branch lp:dolfin. > To unsubscribe from this branch go to > https://code.launchpad.net/~dolfin-core/dolfin/main/+edit-subscription > === modified file 'dolfin/io/GenericFile.cpp' --- dolfin/io/GenericFile.cpp > 2011-06-21 00:01:06 +0000 +++ dolfin/io/GenericFile.cpp 2011-07-02 09:11:13 > +0000 @@ -42,6 +42,11 @@ // Do nothing } > //----------------------------------------------------------------------------- > +GenericFile::~GenericFile() +{ + // Do nothing +} > +//----------------------------------------------------------------------------- > void GenericFile::operator>> (Mesh& mesh) { read_not_impl("Mesh"); === > modified file 'dolfin/io/GenericFile.h' --- dolfin/io/GenericFile.h > 2011-06-21 00:01:06 +0000 +++ dolfin/io/GenericFile.h 2011-07-02 09:11:13 > +0000 @@ -48,6 +48,9 @@ /// Constructor GenericFile(const std::string > filename); + /// Destructor + virtual ~GenericFile(); + // Input virtual > void operator>> (Mesh& mesh); virtual void operator>> (GenericVector& x); === > modified file 'dolfin/io/XMLFile.cpp' --- dolfin/io/XMLFile.cpp > 2011-07-01 21:55:17 +0000 +++ dolfin/io/XMLFile.cpp 2011-07-02 11:11:14 > +0000 @@ -57,6 +57,11 @@ // Do nothing } > //----------------------------------------------------------------------------- > +XMLFile::~XMLFile() +{ + // Do nothing +} > +//----------------------------------------------------------------------------- > void XMLFile::operator>> (Mesh& input_mesh) { // Create XML doc and get > DOLFIN node @@ -72,16 +77,12 @@ if (MPI::num_processes() > 1) error("Mesh XML > output in parallel not yet supported"); - // Open file on process 0 for > distributed objects and on all processes - // for local objects - > open_file(); - - // Note: 'write' is being called on all processes since > collective MPI - // calls might be used. - XMLMesh::write(output_mesh, > *outstream, 1); - - // Close file - close_file(); + pugi::xml_document doc; + > pugi::xml_node node = write_dolfin(doc); + XMLMesh::write(output_mesh, node); > + + // FIXME: Implement copy to stream + doc.save_file(filename.c_str(), " > "); } > //----------------------------------------------------------------------------- > void XMLFile::operator>> (LocalMeshData& input_data) @@ -148,15 +149,19 @@ > // Open file on process 0 for distributed objects and on all processes // for > local objects if (MPI::process_number() == 0) - open_file(); - - // Note: > 'write' is being called on all processes since collective MPI - // calls > might be used. - XMLVector::write(output, *outstream, 1); - - // Close file - > if (MPI::process_number() == 0) - close_file(); + { + pugi::xml_document doc; > + pugi::xml_node node = write_dolfin(doc); + XMLVector::write(output, node, > true); + + // FIXME: Implement copy to stream + > doc.save_file(filename.c_str(), " "); + } + else + { + pugi::xml_node > node(0); + XMLVector::write(output, node, false); + } } > //----------------------------------------------------------------------------- > void XMLFile::operator>> (Parameters& input) @@ -172,12 +177,13 @@ void > XMLFile::operator<< (const Parameters& output) { if (MPI::process_number() == > 0) - open_file(); - - XMLParameters::write(output, *outstream, 1); - - if > (MPI::process_number() == 0) - close_file(); + { + open_write_file(); + > XMLParameters::write(output, *outstream, 1); + close_write_file(); + } + else > + XMLParameters::write(output, *outstream, 1); } > //----------------------------------------------------------------------------- > void XMLFile::operator>> (FunctionPlotData& input) @@ -193,12 +199,13 @@ > void XMLFile::operator<< (const FunctionPlotData& output) { if > (MPI::process_number() == 0) - open_file(); - - > XMLFunctionPlotData::write(output, *outstream, 1); - - if > (MPI::process_number() == 0) - close_file(); + { + open_write_file(); + > XMLFunctionPlotData::write(output, *outstream, 1); + close_write_file(); + } > + else + XMLFunctionPlotData::write(output, *outstream, 1); } > //----------------------------------------------------------------------------- > void XMLFile::write_start(std::ostream& outfile, uint indentation_level) @@ > -229,12 +236,13 @@ const std::string type) { if (MPI::process_number() == 0) > - open_file(); - - XMLMeshFunction::write(t, type, *outstream, 1); - - if > (MPI::process_number() == 0) - close_file(); + { + open_write_file(); + > XMLMeshFunction::write(t, type, *outstream, 1); + close_write_file(); + } + > else + XMLMeshFunction::write(t, type, *outstream, 1); } > //----------------------------------------------------------------------------- > const pugi::xml_node XMLFile::get_dolfin_xml_node(pugi::xml_document& > xml_doc, @@ -273,27 +281,38 @@ // Check that we have a DOLFIN XML file const > pugi::xml_node dolfin_node = xml_doc.child("dolfin"); if (!dolfin_node) - > error("Not a DOLFIN XML file"); + error("XMLFile::get_dolfin_xml_node: not a > DOLFIN XML file"); return dolfin_node; } > //----------------------------------------------------------------------------- > -void XMLFile::open_file() +pugi::xml_node > XMLFile::write_dolfin(pugi::xml_document& xml_doc) +{ + pugi::xml_node node = > xml_doc.append_child("dolfin"); + node.append_attribute("xmlns:dolfin") = > "http://www.fenicsproject.org";; + return node; +} > +//----------------------------------------------------------------------------- > +void XMLFile::open_write_file() { // Convert to ofstream std::ofstream* > outfile = dynamic_cast(outstream.get()); if (outfile) { - // Open file - > outfile->open(filename.c_str()); + // Open file (erase contents) + > outfile->open(filename.c_str(), std::ios::out | std::ios::trunc); + + if > (!outfile->is_open()) + error("Error opening XML file."); // Go to end of > file - outfile->seekp(0, std::ios::end); + //outfile->seekp(0, > std::ios::end); } + assert(outstream); XMLFile::write_start(*outstream); } > //----------------------------------------------------------------------------- > -void XMLFile::close_file() +void XMLFile::close_write_file() { > XMLFile::write_end(*outstream); @@ -301,15 +320,9 @@ const > boost::filesystem::path path(filename); const std::string extension = > boost::filesystem::extension(path); if (extension == ".gz") - { > error("Compressed XML output not yet supported."); - } - else - { - // > Convert to ofstream - std::ofstream* outfile = dynamic_cast(outstream.get()); > - if (outfile) - outfile->close(); - } + + // Finalise (closes file is stream > is a file stream) + outstream.reset(); } > //----------------------------------------------------------------------------- > === modified file 'dolfin/io/XMLFile.h' --- dolfin/io/XMLFile.h > 2011-06-30 12:57:51 +0000 +++ dolfin/io/XMLFile.h 2011-07-02 11:09:24 > +0000 @@ -53,6 +53,8 @@ /// Constructor from a stream XMLFile(std::ostream& > s); + ~XMLFile(); + // Mesh void operator>> (Mesh& input); void operator<< > (const Mesh& output); @@ -111,9 +113,11 @@ const pugi::xml_node > get_dolfin_xml_node(pugi::xml_document& xml_doc, const std::string filename) > const; + static pugi::xml_node write_dolfin(pugi::xml_document& doc); + // > Open/close files - void open_file(); - void close_file(); + void > open_write_file(); + void close_write_file(); boost::shared_ptr outstream; > === modified file 'dolfin/io/XMLIndent.cpp' --- dolfin/io/XMLIndent.cpp > 2011-06-30 12:57:51 +0000 +++ dolfin/io/XMLIndent.cpp 2011-07-02 09:11:13 > +0000 @@ -45,10 +45,8 @@ -- indentation_level; } > //----------------------------------------------------------------------------- > -std::string XMLIndent::operator()() +std::string XMLIndent::operator()() > const { - std::ostringstream ss; - ss << > std::setw(indentation_level*step_size) << ""; - return ss.str(); + return > std::string(indentation_level*step_size, ' '); } > //----------------------------------------------------------------------------- > === modified file 'dolfin/io/XMLIndent.h' --- dolfin/io/XMLIndent.h > 2011-06-30 12:57:51 +0000 +++ dolfin/io/XMLIndent.h 2011-07-02 09:11:13 > +0000 @@ -44,7 +44,7 @@ void operator--(); - std::string operator() (); + > std::string operator() () const; dolfin::uint level() { return > indentation_level; } === modified file 'dolfin/io/XMLMesh.cpp' --- > dolfin/io/XMLMesh.cpp 2011-06-30 12:57:51 +0000 +++ dolfin/io/XMLMesh.cpp > 2011-07-02 11:09:24 +0000 @@ -143,6 +143,85 @@ outfile << indent() << "" << > std::endl; } > //----------------------------------------------------------------------------- > +void XMLMesh::write(const Mesh& mesh, pugi::xml_node xml_node) +{ + // Add > mesh node + pugi::xml_node mesh_node = xml_node.append_child("mesh"); + + // > Add mesh attributes + const CellType::Type _cell_type = > mesh.type().cell_type(); + const std::string cell_type = > CellType::type2string(_cell_type); + mesh_node.append_attribute("celltype") = > cell_type.c_str(); + mesh_node.append_attribute("dim") = > mesh.geometry().dim(); + + // Add vertices node + pugi::xml_node > vertices_node = mesh_node.append_child("vertices"); + > vertices_node.append_attribute("size") = mesh.num_vertices(); + + // Write > each vertex + for(VertexIterator v(mesh); !v.end(); ++v) + { + pugi::xml_node > vertex_node = vertices_node.append_child("vertex"); + > vertex_node.append_attribute("index") = v->index(); + + const Point p = > v->point(); + switch (mesh.geometry().dim()) + { + case 1: + > vertex_node.append_attribute("x") = p.x(); + break; + case 2: + > vertex_node.append_attribute("x") = p.x(); + > vertex_node.append_attribute("y") = p.y(); + break; + case 3: + > vertex_node.append_attribute("x") = p.x(); + > vertex_node.append_attribute("y") = p.y(); + > vertex_node.append_attribute("z") = p.z(); + break; + default: + error("The > XML mesh file format only supports 1D, 2D and 3D meshes."); + } + } + + // > Add cells node + pugi::xml_node cells_node = mesh_node.append_child("cells"); > + cells_node.append_attribute("size") = mesh.num_cells(); + + // Add each > cell + for (CellIterator c(mesh); !c.end(); ++c) + { + pugi::xml_node > cell_node = cells_node.append_child(cell_type.c_str()); + > cell_node.append_attribute("index") = c->index(); + + const uint* vertices = > c->entities(0); + assert(vertices); + + switch (_cell_type) + { + case > CellType::interval: + cell_node.append_attribute("v0") = vertices[0]; + > cell_node.append_attribute("v1") = vertices[1]; + break; + case > CellType::triangle: + cell_node.append_attribute("v0") = vertices[0]; + > cell_node.append_attribute("v1") = vertices[1]; + > cell_node.append_attribute("v2") = vertices[2]; + break; + case > CellType::tetrahedron: + cell_node.append_attribute("v0") = vertices[0]; + > cell_node.append_attribute("v1") = vertices[1]; + > cell_node.append_attribute("v2") = vertices[2]; + > cell_node.append_attribute("v3") = vertices[3]; + break; + default: + > error("Unknown cell type: %u.", _cell_type); + } + } + + // FIXME: Write mesh > data +} > +//----------------------------------------------------------------------------- > void XMLMesh::read_mesh(Mesh& mesh, const pugi::xml_node xml_mesh) { // Get > cell type and geometric dimension === modified file 'dolfin/io/XMLMesh.h' --- > dolfin/io/XMLMesh.h 2011-06-30 12:57:51 +0000 +++ dolfin/io/XMLMesh.h > 2011-07-02 11:09:24 +0000 @@ -47,6 +47,8 @@ static void write(const Mesh& > mesh, std::ostream& outfile, unsigned int indentation_level=0); + /// Write > the XML file + static void write(const Mesh& mesh, pugi::xml_node xml_node); > private: === modified file 'dolfin/io/XMLVector.cpp' --- > dolfin/io/XMLVector.cpp 2011-06-30 13:30:14 +0000 +++ > dolfin/io/XMLVector.cpp 2011-07-02 11:09:24 +0000 @@ -37,12 +37,12 @@ // > Check that we have a XML Vector const pugi::xml_node xml_vector_node = > xml_dolfin.child("vector"); if (!xml_vector_node) - error("Not a DOLFIN > Vector file."); + error("XMLVector::read: not a DOLFIN Vector file."); // Get > type and size const pugi::xml_node array = xml_vector_node.child("array"); if > (!array) - error("Not a DOLFIN array inside Vector XML file."); + > error("XMLVector::read: not a DOLFIN array inside Vector XML file."); const > unsigned int size = array.attribute("size").as_uint(); const std::string type > = array.attribute("type").value(); @@ -68,37 +68,72 @@ // Check that we have > a XML Vector const pugi::xml_node xml_vector_node = > xml_dolfin.child("vector"); if (!xml_vector_node) - error("Not a DOLFIN > Vector file."); + error("XMLVector::read_size: not a DOLFIN Vector file."); > // Get size const pugi::xml_node array = xml_vector_node.child("array"); if > (!array) - std::cout << "Not a DOLFIN Array" << std::endl; + std::cout << > "XMLVector::read_size: not a DOLFIN Array" << std::endl; return > array.attribute("size").as_uint(); } > //----------------------------------------------------------------------------- > void XMLVector::write(const GenericVector& vector, std::ostream& outfile, - > unsigned int indentation_level) + bool write_to_stream, unsigned int > indentation_level) { - bool write_to_stream = false; + // Gather entries from > process i on process 0 + Array x; + if (MPI::num_processes() > 1) + > vector.gather_on_zero(x); + else + vector.get_local(x); + + const uint size = > vector.size(); if (MPI::process_number() == 0) - write_to_stream = true; - - > XMLIndent indent(indentation_level); - - // Write vector header + assert(size > == x.size()); + if (write_to_stream) { - outfile << indent() << "" << > std::endl; - ++indent; - - // Write array header - outfile << indent() << > "<< vector.size() - << "\">" << std::endl; - ++indent; + XMLIndent > indent(indentation_level); + + // Write vector header + if (write_to_stream) > + { + outfile << indent() << "" << std::endl; + ++indent; + + // Write array > header + outfile << indent() << "<< size + << "\">" << std::endl; + ++indent; > + } + + + // Write vector entries + if (write_to_stream) + { + for (uint i = > 0; i < x.size(); ++i) + { + outfile << indent() + << "<< i + _______________________________________________ Mailing list: https://launchpad.net/~dolfin Post to : [email protected] Unsubscribe : https://launchpad.net/~dolfin More help : https://help.launchpad.net/ListHelp
