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xdmf_file.hh
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/**
* @file xdmf_file.hh
*
* @author Nicolas Richart
*
* @date creation Thu Oct 12 2017
*
* @brief A Documented file.
*
* @section LICENSE
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_file_base.hh"
#include "xml_helper.hh"
/* -------------------------------------------------------------------------- */
#include <boost/filesystem.hpp>
#include <sstream>
#include <tuple>
#include <typeindex>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace {
#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
static const auto ENDIAN{"Little"};
#elif __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__
static const auto ENDIAN{"Big"};
#else
#error "Does not know from which end to open the eggs"
#endif
} // namespace
#ifndef __AKANTU_XDMF_FILE_HH__
#define __AKANTU_XDMF_FILE_HH__
namespace akantu {
namespace dumper {
namespace {
std::string xdmf_type(const ElementType & type) {
static std::map<ElementType, std::string> element_map{
{_triangle_3, "Triangle"}, {_quadrangle_4, "Quadrilateral"},
{_tetrahedron_4, "Tetrahedron"}, {_pentahedron_6, "Wedge"},
{_hexahedron_8, "Hexahedron"}, {_triangle_6, "Tri_6"},
{_quadrangle_8, "Quad_8"}, {_tetrahedron_10, "Tet_10"},
{_pentahedron_15, "Wedge_15"}, {_hexahedron_20, "Hex_20"}};
return element_map[type];
}
#define TIDX(x) std::type_index(typeid(x))
auto xdmf_datatype(const std::type_index & type_idx) {
const static std::unordered_map<std::type_index,
std::pair<std::string, std::size_t>>
type_ids{
{TIDX(int), {"Int", 4}}, {TIDX(unsigned int), {"UInt", 4}},
{TIDX(int32_t), {"Int", 4}}, {TIDX(int64_t), {"Int", 8}},
{TIDX(uint32_t), {"UInt", 4}}, {TIDX(uint64_t), {"Int", 8}},
{TIDX(bool), {"UChar", 1}}, {TIDX(float), {"Float", 4}},
{TIDX(double), {"Float", 8}},
};
return type_ids.at(type_idx);
}
std::string xdmf_geometry(char dim) {
switch (dim) {
case 1:
//[[gnu::fallthrougth]];
case 2:
return "XY";
case 3:
return "XYZ";
default:
AKANTU_EXCEPTION("Dim " << dim << " is not a recognized geometry");
}
}
} // namespace
namespace XDMF {
namespace fs = boost::filesystem;
class File : public XML::File, public dumper::FileBase {
using Tag = XML::Tag;
using CloseTag = XML::CloseTag;
public:
/* ----------------------------------------------------------------------
*/
File(SupportBase & support, const boost::filesystem::path & path)
: XML::File(path), FileBase(support), path(path) {
*this << "<?xml version=\"1.0\" encoding=\"utf-8\" ?>\n";
*this << "<!DOCTYPE Xdmf SYSTEM \"Xdmf.dtd\" []>\n";
current_xdmf_element.push_back(1);
*this << Tag("Xdmf")("Version", "3.0")(
"xmlns:xi", "http://www.w3.org/2001/XInclude");
*this << Tag("Domain");
support.addProperty("xdmf_file", path.string());
if (not support.hasProperty("dump_count"))
return;
auto mesh_name = support.getName();
*this << Tag("Grid")("Name", mesh_name + ":all")(
"GridType", "Collection")("CollectionType", "Temporal");
}
/* -------------------------------------------------------------------- */
File(SupportBase & support, const boost::filesystem::path & path,
const std::vector<std::string> & current_xdmf_path,
const std::vector<int> & current_xdmf_element)
: XML::File(path), FileBase(support), include(true),
current_xdmf_path(current_xdmf_path),
current_xdmf_element(current_xdmf_element), path(path) {}
/* -------------------------------------------------------------------- */
~File() = default;
/* -------------------------------------------------------------------- */
XML::File & operator<<(const std::string & str) override {
return XML::File::operator<<(str);
}
/* -------------------------------------------------------------------- */
XML::File & operator<<(const Tag & tag) override {
XML::File::operator<<(tag);
if (tag.autoclosing()) {
if (not current_xdmf_element.empty()) {
++(current_xdmf_element.back());
}
return *this;
}
auto tag_ = tag.tag();
if (tag.hasProperty("Name")) {
tag_ += "[@Name=\"" + tag.getProperty("Name") + "\"]";
}
current_xdmf_path.push_back(tag_);
current_xdmf_element.push_back(1);
//*this << "<!-- element(" + currentXMFElement() + ") -->\n";
return *this;
}
/* -------------------------------------------------------------------- */
XML::File & operator<<(const CloseTag & tag) override {
XML::File::operator<<(tag);
current_xdmf_path.pop_back();
current_xdmf_element.pop_back();
if (not current_xdmf_element.empty()) {
++(current_xdmf_element.back());
}
return *this;
}
/* -------------------------------------------------------------------- */
void dump() override {
// if (include) {
auto count = support.getProperty<Int>("dump_count");
*this << Tag("Grid")("CollectionType", "Spatial")(
"GridType", "Collection")("Name", "model_" + std::to_string(count));
if (support.hasProperty("time")) {
*this << Tag("Information", true)("Name", "Time")(
"Value", support.getProperty<Real>("time"));
}
FileBase::dump();
*this << CloseTag{};
// return;
// }
// auto count = support.getProperty<Int>("dump_count");
// auto include_path = getIncludeFilename(count);
// File xdmf_include(support, include_path, current_xdmf_path);
// xdmf_include.dump();
// auto sub_path =
// fs::relative(include_path, fs::path(path).remove_filename());
// *this << Tag("xi:include", true)("href", sub_path.string());
}
private:
fs::path getIncludeFilename(std::size_t num) {
std::stringstream sstr;
sstr << std::setw(5) << std::setfill('0') << num;
auto include_path = path;
include_path.remove_filename();
include_path /= "xmfs";
include_path /=
path.stem().string() + '_' + sstr.str() + path.extension().string();
return include_path;
}
std::string currentXMFPath() const {
auto tmp = fs::path("/");
for (auto && tag : current_xdmf_path) {
tmp /= tag;
}
return tmp.generic_string<std::string>();
}
std::string currentXMFElement() const {
auto tmp = fs::path("/");
auto copy = current_xdmf_element;
copy.pop_back();
for (auto && tag : copy) {
tmp /= std::to_string(tag);
}
return tmp.generic_string<std::string>();
}
std::string getName(const ID & name,
const Qualified<ElementType> & type) const {
std::stringstream sstr;
sstr << name << ":" << type.type;
if (type.ghost_type != _not_ghost) {
sstr << ":" << type.ghost_type;
}
return sstr.str();
}
protected:
/* -------------------------------------------------------------------- */
void dump(FieldArrayBase & field) override {
auto && support = field.getSupport();
auto && tag = Tag("DataItem");
bool unchanged = true;
if (field.hasProperty("hdf5_path") and
field.hasProperty("xdmf_previous_hdf5_path")) {
unchanged =
(field.getProperty<std::string>("hdf5_path") ==
field.getProperty<std::string>("xdmf_previous_hdf5_path"));
}
if (field.hasProperty("xdmf_element") and unchanged) {
*this << Tag("xi:include", true)(
"xpointer", "element(" +
field.getProperty<std::string>("xdmf_element") +
")");
//*this << tag("Reference", "XML");
//*this << (field.getProperty<std::string>("xdmf_path")) << "\n";
} else if (field.hasProperty("hdf5_path")) {
auto && dims = std::make_tuple(field.size(), field.getNbComponent());
auto && hdf5_path =
fs::relative(
fs::path(support.getProperty<std::string>("hdf5_file")),
fs::path(support.getProperty<std::string>("xdmf_file"))
.remove_filename())
.string() +
":" + field.getProperty<std::string>("hdf5_path");
auto && xdmf_datatype_ = xdmf_datatype(field.type());
/* clang-format off */
*this << tag("Name", field.getName())
("Dimensions", dims)
("Format", "HDF")
("NumberType", xdmf_datatype_.first)
("Precision", xdmf_datatype_.second)
("Endian", ENDIAN);
/* clang-format on */
*this << hdf5_path << "\n";
field.addProperty("xdmf_path", currentXMFPath());
field.addProperty("xdmf_element", currentXMFElement());
field.addProperty("xdmf_previous_hdf5_path",
field.getProperty<std::string>("hdf5_path"));
} else {
AKANTU_EXCEPTION("The XML and Binary format are not implemented yet");
}
*this << CloseTag{};
}
/* -------------------------------------------------------------------- */
void dump(FieldElementMapArrayBase & /*field*/) override {}
/* -------------------------------------------------------------------- */
void dump(Support<Mesh> & support) override {
auto && mesh_name = support.getName();
auto && nodes = support.getNodes();
if (support.hasProperty("xdmf_element")) {
auto element = support.getProperty<std::string>("xdmf_element");
*this << Tag("xi:include", true)("xpointer",
"element(" + element + ")");
} else {
*this << Tag("Grid")("CollectionType", "Spatial")(
"GridType", "Collection")("Name", mesh_name);
support.addProperty("xdmf_path", currentXMFPath());
support.addProperty("xdmf_element", currentXMFElement());
for (auto && type : support.elementTypes()) {
auto & connectivities = support.getConnectivities();
auto & conn = connectivities.array(type);
auto && conn_name = getName(mesh_name, type);
*this << Tag("Grid")("Name", conn_name)("GridType", "Uniform");
// Topology
if (conn.hasProperty("xdmf_element")) {
auto element =
fs::path(conn.getProperty<std::string>("xdmf_element"))
.parent_path()
.string();
*this << Tag("xi:include", true)("xpointer",
"element(" + element + ")");
} else {
*this << Tag("Topology")("TopologyType", xdmf_type(type))(
"NumberOfElements", conn.size());
dump(conn);
*this << CloseTag{};
}
// Geometry
if (nodes.hasProperty("xdmf_element")) {
auto element =
fs::path(nodes.getProperty<std::string>("xdmf_element"))
.parent_path()
.string();
*this << Tag("xi:include", true)("xpointer",
"element(" + element + ")");
} else {
*this << Tag("Geometry")("GeometryType",
xdmf_geometry(nodes.getNbComponent()));
dump(nodes);
*this << CloseTag{};
}
*this << CloseTag{};
}
*this << CloseTag{};
}
for (auto && support : support.getSubSupports()) {
dump(*support.second);
}
}
/* -------------------------------------------------------------------- */
void dump(Support<ElementGroup> & support) override {
const auto & parent_support = support.getParentSupport();
fs::path xdmf_parent =
parent_support.getProperty<std::string>("xdmf_path");
auto parent_name = parent_support.getName();
auto name = parent_name + ":" + support.getName();
if (support.hasProperty("xdmf_element")) {
auto element = support.getProperty<std::string>("xdmf_element");
*this << Tag("xi:include", true)("xpointer",
"element(" + element + ")");
return;
}
*this << Tag("Grid")("Name", name)("GridType", "Collection")(
"CollectionType", "Spatial");
support.addProperty("xdmf_path", currentXMFPath());
support.addProperty("xdmf_element", currentXMFElement());
support.addProperty(
"xdmf_file", parent_support.getProperty<std::string>("xdmf_file"));
auto & elements = support.getElements();
for (auto && type : support.elementTypes()) {
auto xdmf_path = xdmf_parent;
auto && name = getName(support.getName(), type);
*this << Tag("Grid")("Name", name)("GridType", "Subset")("Section",
"DataItem");
dump(elements.array(type));
*this << Tag("Grid")("Name", "Target")("Reference", "XML");
xdmf_path /= "Grid[@Name=\"" + getName(parent_name, type) + "\"]";
*this << xdmf_path.generic_string() << "\n";
*this << CloseTag{};
*this << CloseTag{};
}
*this << CloseTag{};
}
void dump(SupportBase & support) override { FileBase::dump(support); }
public:
bool include{false};
std::vector<std::string> current_xdmf_path;
std::vector<int> current_xdmf_element;
boost::filesystem::path path;
};
} // namespace XDMF
} // namespace dumper
} // namespace akantu
#endif /* __AKANTU_XDMF_FILE_HH__ */
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