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<h1 class="pageTitle"><a href="/sandbox/acastillo/output_fields/xdmf/output_xdmf.h">sandbox/acastillo/output_fields/xdmf/output_xdmf.h</a></h1>
<ul class="messages" id="messages"></ul>
<div id="status"></div>
<div id="TOC">
<ul>
<li><a href="#xdmf-file-format">XDMF File Format</a><ul>
<li><a href="#preamble-define-some-useful-macros">preamble: define some useful macros</a></li>
<li><a href="#write_xdmf_light_data-write-an-.xdmf-file-containing-the-light-data">write_xdmf_light_data(): write an <code>.xdmf</code> file containing the light data</a></li>
<li><a href="#output_xmf-exports-full-2d-or-3d-fields.">output_xmf(): Exports full 2D (or 3D) fields.</a></li>
<li><a href="#output_xmf_slice-exports-a-2d-slice-of-a-3d-field-along-x-y-or-z.">output_xmf_slice(): Exports a 2D slice of a 3D field along x, y, or z.</a></li>
<li><a href="#postamble-delete-macros">postamble: delete macros</a></li>
</ul></li>
</ul>
</div>
<h1 id="xdmf-file-format">XDMF File Format</h1>
<p>These routines are compatible with the <code>XDMF Model and Format</code> which can be read using Paraview or Visit. Data is split in two categories: Light data and Heavy data.</p>
<ul>
<li><p>Light data is stored using eXtensible Markup Language (<code>XML</code>) to describe the data model and the data format.</p></li>
<li><p>Heavy data is composed of large datasets stored using the Hierarchical Data Format HDF5. As the name implies, data is organized following a hierarchical structure. HDF5 files can be read without any prior knowledge of the stored data. The type, rank, dimension and other properties of each array are stored inside the file in the form of meta-data. Additional features include support for a large number of objects, file compression, a parallel I/O implementation through the MPI-IO or MPI POSIX drivers. Using this format requires the HDF5 library, which is usually installed in most computing centers or may be installed locally through a repository. Linking is automatic but requires the environment variables <code>HDF5_INCDIR</code> and <code>HDF5_LIBDIR</code>, which are usually set when you load the module hdf5. You might also add something like this to your <code>Makefile</code></p></li>
</ul>
<pre><code> HDFLIBS=-I$(HDF5_INCDIR) -L$(HDF5_LIBDIR) -lhdf5 -lhdf5_hl
LIBS+=$(HDFLIBS)</code></pre>
<p><strong>To use HDF5 we need to “declare” the library in the qcc system</strong>. This should not be the case, but HDF5 is a messy library that just won’t pass through <code>qcc</code></p>
<pre><code> echo "@include <hdf5.h>" > $BASILISK/ast/std/hdf5.h
echo "@include <hdf5_hl.h>" > $BASILISK/ast/std/hdf5_hl.h</code></pre>
<p><strong>We also need to declare the datatypes at the end of <code>$BASILISK/ast/defaults.h</code></strong></p>
<pre><code> echo "typedef hid_t, hsize_t, herr_t, H5L_info_t;" >> $BASILISK/ast/defaults.h</code></pre>
<p>An explanation can be found <a href="https://groups.google.com/g/basilisk-fr/c/CM270hBSfWo">here</a></p>
<div class="sourceCode"><pre class="sourceCode c"><code class="sourceCode c"><span class="pp">#pragma autolink -lhdf5<span id=46></span></span>
<span class="pp">#include </span><span class="im"><hdf5.h></span><span class="pp"><span id=47></span><span id=48></span></span></code></pre></div>
<h2 id="preamble-define-some-useful-macros">preamble: define some useful macros</h2>
<div class="sourceCode"><pre class="sourceCode c"><code class="sourceCode c"><span class="pp">#define shortcut_slice(n, _alpha) \<span id=52></span></span>
<span class="dt">double</span> alpha = (_alpha - n.x * x - n.y * y - n.z * z) / Delta; \<span id=53></span>
<span class="cf">if</span> (fabs(alpha) > <span class="fl">0.87</span>) \<span id=54></span>
<span class="cf">continue</span>;<span id=55></span>
<span id=56></span>
<span class="pp">#include </span><span class="im">"<a href=./output_xdmf_helpers.h>output_xdmf_helpers.h</a>"</span><span class="pp"><span id=57></span><span id=58></span></span></code></pre></div>
<h2 id="write_xdmf_light_data-write-an-.xdmf-file-containing-the-light-data">write_xdmf_light_data(): write an <code>.xdmf</code> file containing the light data</h2>
<div class="sourceCode"><pre class="sourceCode c"><code class="sourceCode c"><span class="dt">void</span> <a id=write_xdmf_light_data>write_xdmf_light_data</a>(scalar *slist, vector *vlist, <span class="dt">char</span> *file_name, <span class="dt">char</span> *subname, <span class="dt">int</span> num_cells = <span class="dv">0</span>, <span class="dt">int</span> num_points = <span class="dv">0</span>, <span class="dt">int</span> dim = dimension){<span id=63></span>
<span id=64></span>
<span class="pp">#if defined(_OPENMP)<span id=65></span></span>
<span class="dt">int</span> num_omp = omp_get_max_threads();<span id=66></span>
omp_set_num_threads(<span class="dv">1</span>);<span id=67></span>
<span class="pp">#endif<span id=68></span></span>
<span id=69></span>
<span class="co">// Open a file for writing<span id=70></span></span>
<span class="dt">char</span> name[<span class="dv">111</span>];<span id=71></span>
<a href=http://man7.org/linux/man-pages/man3/sprintf.3.html>sprintf</a>(name, <span class="st">"%s.xmf"</span>, subname);<span id=72></span>
FILE *fp = <a href=http://man7.org/linux/man-pages/man3/fopen.3.html>fopen</a>(name, <span class="st">"w"</span>);<span id=73></span>
<span id=74></span>
<span class="co">// Write the header of the xdmf file.<span id=75></span></span>
<a href=./output_xdmf_helpers.h#write_xdmf_header>write_xdmf_header</a>(fp, file_name);<span id=76></span>
<a href=./output_xdmf_helpers.h#write_xdmf_topology>write_xdmf_topology</a>(fp, dim, num_cells, num_points, t);<span id=77></span>
<a href=./output_xdmf_helpers.h#write_xdmf_attributes>write_xdmf_attributes</a>(fp, num_cells, slist, vlist);<span id=78></span>
<a href=./output_xdmf_helpers.h#write_xdmf_footer>write_xdmf_footer</a>(fp);<span id=79></span>
<span id=80></span>
<span class="co">// Close the file<span id=81></span></span>
<a href=http://man7.org/linux/man-pages/man3/fflush.3.html>fflush</a>(fp);<span id=82></span>
<a href=http://man7.org/linux/man-pages/man3/fclose.3.html>fclose</a>(fp);<span id=83></span>
<span id=84></span>
<span class="pp">#if defined(_OPENMP)<span id=85></span></span>
omp_set_num_threads(num_omp);<span id=86></span>
<span class="pp">#endif<span id=87></span></span>
}<span id=88></span><span id=89></span></code></pre></div>
<h2 id="output_xmf-exports-full-2d-or-3d-fields.">output_xmf(): Exports full 2D (or 3D) fields.</h2>
<p>This function performs the following steps:</p>
<ol style="list-style-type: decimal">
<li>Constructs the HDF5 file name based on the input subname.</li>
<li>Counts the number of points and cells in the data and calculates offsets for parallel I/O.</li>
<li>Initializes a marker for topology reconstruction.</li>
<li>Writes the light data to the XDMF file.</li>
<li>Sets up file access template with parallel I/O access and creates a new HDF5 file collectively.</li>
<li>Populates and writes the topology, points, and cell data datasets to the HDF5 file.</li>
<li>Closes the HDF5 resources.</li>
</ol>
<p>The arguments and their default values are:</p>
<ul>
<li><strong>slist</strong> : Pointer to an array of <span class="dt">scalar</span> data.</li>
<li><strong>vlist</strong> : Pointer to an array of <span class="dt">vector</span> data.</li>
<li><strong>subname</strong> : String used to construct the HDF5 file name.</li>
<li><strong>compression_level</strong> : Level of compression to use when writing data to the HDF5 file.</li>
</ul>
<div class="sourceCode"><pre class="sourceCode c"><code class="sourceCode c"><a href=/Basilisk%20C#tracing-and-profiling>trace</a> <span class="dt">void</span> <a id=output_xmf>output_xmf</a>(scalar *slist, vector *vlist, <span class="dt">char</span> *subname, <span class="dt">int</span> compression_level = <span class="dv">9</span>){<span id=111></span>
hid_t acc_tpl1; <span class="co">// File access template<span id=112></span></span>
hid_t file_id; <span class="co">// HDF5 file ID<span id=113></span></span>
hid_t group_id; <span class="co">// HDF5 group ID<span id=114></span></span>
hsize_t count[<span class="dv">2</span>]; <span class="co">// Hyperslab selection parameters<span id=115></span></span>
hsize_t offset[<span class="dv">2</span>]; <span class="co">// Offset for hyperslab<span id=116></span></span>
<span id=117></span>
<span class="dt">char</span> name[<span class="dv">111</span>]; <span class="co">// Buffer for file name construction<span id=118></span></span>
<a href=http://man7.org/linux/man-pages/man3/sprintf.3.html>sprintf</a>(name, <span class="st">"%s.h5"</span>, subname); <span class="co">// Construct the HDF5 file name<span id=119></span></span>
<span id=120></span>
<span class="co">// Define a <span class="dt">scalar</span> <a href=/Basilisk%20C#complex-domains>mask</a> for <a href=/Basilisk%20C#periodic-boundaries>periodic</a> conditions<span id=121></span></span>
<span class="dt">scalar</span> per_mask[];<span id=122></span>
<a href=/Basilisk%20C#iterators>foreach</a> () {<span id=123></span>
per_mask[] = <span class="dv">1</span>.;<span id=124></span>
}<span id=125></span>
<span id=126></span>
<span class="co">// Obtain the number of points and cells and get a marker to reconstruct the topology<span id=127></span></span>
<span class="dt">int</span> num_points = <span class="dv">0</span>, num_cells = <span class="dv">0</span>, num_points_loc = <span class="dv">0</span>, num_cells_loc = <span class="dv">0</span>;<span id=128></span>
<a href=./output_xdmf_helpers.h#count_points_and_cells>count_points_and_cells</a>(&num_points, &num_cells, &num_points_loc, &num_cells_loc, per_mask);<span id=129></span>
<span id=130></span>
<span class="co">// Calculate offsets for parallel I/O<span id=131></span></span>
<span class="dt">int</span> offset_points[npe()], offset_cells[npe()];<span id=132></span>
<a href=./output_xdmf_helpers.h#calculate_offsets>calculate_offsets</a>(offset_points, offset_cells, num_points_loc, num_cells_loc, offset);<span id=133></span>
<span id=134></span>
<span class="co">// Initialize marker for topology reconstruction<span id=135></span></span>
<a href=/Basilisk%20C#face-and-vertex-fields>vertex</a> <span class="dt">scalar</span> marker[];<span id=136></span>
<a href=./output_xdmf_helpers.h#initialize_marker>initialize_marker</a>(marker, offset);<span id=137></span>
<span id=138></span>
<span class="co">// Write the light data<span id=139></span></span>
<span class="cf">if</span> (pid() == <span class="dv">0</span>) {<span id=140></span>
<a href=output_xdmf.h#write_xdmf_light_data>write_xdmf_light_data</a>(slist, vlist, name, subname, num_cells, num_points);<span id=141></span>
}<span id=142></span>
<span id=143></span>
<span class="co">// Write the heavy data<span id=144></span></span>
<span class="co">// Setup file access template with parallel I/O access<span id=145></span></span>
acc_tpl1 = H5Pcreate(H5P_FILE_ACCESS);<span id=146></span>
H5Pset_fapl_mpio(acc_tpl1, MPI_COMM_WORLD, MPI_INFO_NULL);<span id=147></span>
<span id=148></span>
<span class="co">// Create a new HDF5 file collectively<span id=149></span></span>
file_id = H5Fcreate(name, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl1);<span id=150></span>
<span id=151></span>
<span class="co">// Release file-access template<span id=152></span></span>
H5Pclose(acc_tpl1);<span id=153></span>
<span id=154></span>
<span class="co">// Define chunk size for parallel I/O<span id=155></span></span>
hsize_t chunk_size = num_cells / npe() / <span class="dv">8</span>;<span id=156></span>
<span id=157></span>
<span class="co">// Populate and write the topology dataset<span id=158></span></span>
<span class="dt">long</span> *topo_dset;<span id=159></span>
<a href=./output_xdmf_helpers.h#populate_topo_dset>populate_topo_dset</a>(&topo_dset, num_cells_loc, offset_cells, count, offset, per_mask, marker);<span id=160></span>
<a href=./output_xdmf_helpers.h#create_chunked_dataset>create_chunked_dataset</a>(file_id, count, offset, <span class="st">"/Topology"</span>, num_cells, num_cells_loc, pow(<span class="dv">2</span>, dimension), topo_dset, H5T_NATIVE_LONG, chunk_size, compression_level);<span id=161></span>
<a href=http://man7.org/linux/man-pages/man3/free.3.html>free</a>(topo_dset);<span id=162></span>
<span id=163></span>
<span class="co">// Create group for mesh geometry data<span id=164></span></span>
group_id = H5Gcreate(file_id, <span class="st">"Geometry"</span>, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);<span id=165></span>
<span id=166></span>
<span class="co">// Populate and write the points dataset<span id=167></span></span>
<span class="dt">double</span> *points_dset;<span id=168></span>
<a href=./output_xdmf_helpers.h#populate_points_dset>populate_points_dset</a>(&points_dset, num_points_loc, offset_points, count, offset);<span id=169></span>
<a href=./output_xdmf_helpers.h#create_chunked_dataset>create_chunked_dataset</a>(group_id, count, offset, <span class="st">"/Geometry/Points"</span>, num_points, num_points_loc, <span class="dv">3</span>, points_dset, H5T_NATIVE_DOUBLE, chunk_size, compression_level);<span id=170></span>
<a href=http://man7.org/linux/man-pages/man3/free.3.html>free</a>(points_dset);<span id=171></span>
H5Gclose(group_id);<span id=172></span>
<span id=173></span>
<span class="co">// Create group for cell data<span id=174></span></span>
group_id = H5Gcreate(file_id, <span class="st">"Cells"</span>, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);<span id=175></span>
<span id=176></span>
<span class="co">// Allocate memory and write <span class="dt">scalar</span> datasets<span id=177></span></span>
<span class="dt">double</span> *scalar_dset = (<span class="dt">double</span> *)<a href=http://man7.org/linux/man-pages/man3/malloc.3.html>malloc</a>(num_cells_loc * <span class="kw">sizeof</span>(<span class="dt">double</span>));<span id=178></span>
<span class="cf">for</span> (<span class="dt">scalar</span> s in slist) {<span id=179></span>
<span class="dt">char</span> substamp[<span class="dv">1024</span>];<span id=180></span>
<a href=http://man7.org/linux/man-pages/man3/sprintf.3.html>sprintf</a>(substamp, <span class="st">"/Cells/%s"</span>, s.name);<span id=181></span>
<a href=./output_xdmf_helpers.h#populate_scalar_dset>populate_scalar_dset</a>(s, scalar_dset, num_cells_loc, offset_cells, count, offset, per_mask);<span id=182></span>
<a href=./output_xdmf_helpers.h#create_chunked_dataset>create_chunked_dataset</a>(group_id, count, offset, substamp, num_cells, num_cells_loc, <span class="dv">1</span>, scalar_dset, H5T_NATIVE_DOUBLE, chunk_size, compression_level);<span id=183></span>
}<span id=184></span>
<a href=http://man7.org/linux/man-pages/man3/free.3.html>free</a>(scalar_dset);<span id=185></span>
<span id=186></span>
<span class="co">// Allocate memory and write <span class="dt">vector</span> datasets<span id=187></span></span>
<span class="dt">double</span> *vector_dset = (<span class="dt">double</span> *)<a href=http://man7.org/linux/man-pages/man3/malloc.3.html>malloc</a>(num_cells_loc * <span class="dv">3</span> * <span class="kw">sizeof</span>(<span class="dt">double</span>));<span id=188></span>
<span class="cf">for</span> (<span class="dt">vector</span> v in vlist) {<span id=189></span>
<span class="dt">char</span> substamp[<span class="dv">1024</span>];<span id=190></span>
<a href=http://man7.org/linux/man-pages/man3/sprintf.3.html>sprintf</a>(substamp, <span class="st">"/Cells/%s"</span>, v.x.name);<span id=191></span>
<a href=./output_xdmf_helpers.h#populate_vector_dset>populate_vector_dset</a>(v, vector_dset, num_cells_loc, offset_cells, count, offset, per_mask);<span id=192></span>
<a href=./output_xdmf_helpers.h#create_chunked_dataset>create_chunked_dataset</a>(group_id, count, offset, substamp, num_cells, num_cells_loc, <span class="dv">3</span>, vector_dset, H5T_NATIVE_DOUBLE, chunk_size, compression_level);<span id=193></span>
}<span id=194></span>
<a href=http://man7.org/linux/man-pages/man3/free.3.html>free</a>(vector_dset);<span id=195></span>
H5Gclose(group_id);<span id=196></span>
<span id=197></span>
<span class="co">// Close HDF5 resources<span id=198></span></span>
H5Fclose(file_id);<span id=199></span>
}<span id=200></span><span id=201></span></code></pre></div>
<h2 id="output_xmf_slice-exports-a-2d-slice-of-a-3d-field-along-x-y-or-z.">output_xmf_slice(): Exports a 2D slice of a 3D field along x, y, or z.</h2>
<p>This function performs the following steps:</p>
<ol style="list-style-type: decimal">
<li>Constructs the HDF5 file name based on the input subname.</li>
<li>Counts the number of points and cells in the data and calculates offsets for parallel I/O.</li>
<li>Initializes a marker for topology reconstruction.</li>
<li>Writes the light data to the XDMF file.</li>
<li>Sets up file access template with parallel I/O access and creates a new HDF5 file collectively.</li>
<li>Populates and writes the topology, points, and cell data datasets to the HDF5 file.</li>
<li>Closes the HDF5 resources.</li>
</ol>
<p>The arguments and their default values are:</p>
<ul>
<li><strong>slist</strong> : Pointer to an array of <span class="dt">scalar</span> data.</li>
<li><strong>vlist</strong> : Pointer to an array of <span class="dt">vector</span> data.</li>
<li><strong>subname</strong> : String used to construct the HDF5 file name.</li>
<li><strong>n</strong> : Vector defining the plane</li>
<li><strong>alpha</strong> : Intersect defining the plane</li>
<li><strong>compression_level</strong> : Level of compression to use when writing data to the HDF5 file.</li>
</ul>
<div class="sourceCode"><pre class="sourceCode c"><code class="sourceCode c"><span class="pp">#if dimension == 3<span id=226></span></span>
<a href=/Basilisk%20C#tracing-and-profiling>trace</a> <span class="dt">void</span> <a id=output_xmf_slice>output_xmf_slice</a>(scalar *slist, vector *vlist, <span class="dt">char</span> *subname, coord n = {<span class="dv">0</span>, <span class="dv">0</span>, <span class="dv">1</span>}, <span class="dt">double</span> _alpha = <span class="dv">0</span>, <span class="dt">int</span> compression_level = <span class="dv">9</span>){<span id=227></span>
hid_t acc_tpl1; <span class="co">// File access template<span id=228></span></span>
hid_t file_id; <span class="co">// HDF5 file ID<span id=229></span></span>
hid_t group_id; <span class="co">// HDF5 group ID<span id=230></span></span>
hsize_t count[<span class="dv">2</span>]; <span class="co">// Hyperslab selection parameters<span id=231></span></span>
hsize_t offset[<span class="dv">2</span>]; <span class="co">// Offset for hyperslab<span id=232></span></span>
<span id=233></span>
<span class="dt">char</span> name[<span class="dv">111</span>]; <span class="co">// Buffer for file name construction<span id=234></span></span>
<a href=http://man7.org/linux/man-pages/man3/sprintf.3.html>sprintf</a>(name, <span class="st">"%s.h5"</span>, subname); <span class="co">// Construct the HDF5 file name<span id=235></span></span>
<span id=236></span>
<span class="co">// Define a <span class="dt">scalar</span> <a href=/Basilisk%20C#complex-domains>mask</a> to deal with solids and <a href=/Basilisk%20C#periodic-boundaries>periodic</a> conditions<span id=237></span></span>
<span class="dt">scalar</span> per_mask[];<span id=238></span>
<a href=/Basilisk%20C#iterators>foreach</a> (){<span id=239></span>
per_mask[] = <span class="dv">0</span>.;<span id=240></span>
shortcut_slice(n, _alpha);<span id=241></span>
<span class="cf">if</span> (alpha > <span class="dv">0</span>.){<span id=242></span>
<span class="pp">#if EMBED<span id=243></span></span>
per_mask[] = cs[];<span id=244></span>
<span class="pp">#else<span id=245></span></span>
per_mask[] = <span class="dv">1</span>.;<span id=246></span>
<span class="pp">#endif<span id=247></span></span>
}<span id=248></span>
}<span id=249></span>
<span id=250></span>
<span class="co">// Obtain the number of points and cells and get a marker to reconstruct the topology<span id=251></span></span>
<span class="dt">int</span> num_points = <span class="dv">0</span>, num_cells = <span class="dv">0</span>, num_points_loc = <span class="dv">0</span>, num_cells_loc = <span class="dv">0</span>;<span id=252></span>
<a href=./output_xdmf_helpers.h#count_points_and_cells_slice>count_points_and_cells_slice</a>(&num_points, &num_cells, &num_points_loc, &num_cells_loc, per_mask, n, _alpha);<span id=253></span>
<span id=254></span>
<span class="co">// Calculate offsets for parallel I/O<span id=255></span></span>
<span class="dt">int</span> offset_points[npe()], offset_cells[npe()];<span id=256></span>
<a href=./output_xdmf_helpers.h#calculate_offsets>calculate_offsets</a>(offset_points, offset_cells, num_points_loc, num_cells_loc, offset);<span id=257></span>
<span id=258></span>
<span class="co">// Initialize marker for topology reconstruction<span id=259></span></span>
<a href=/Basilisk%20C#face-and-vertex-fields>vertex</a> <span class="dt">scalar</span> marker[];<span id=260></span>
<a href=./output_xdmf_helpers.h#initialize_marker_slice>initialize_marker_slice</a>(marker, offset, n, _alpha);<span id=261></span>
<span id=262></span>
<span class="co">// Write the light data to an XDMF file<span id=263></span></span>
<span class="cf">if</span> (pid() == <span class="dv">0</span>)<span id=264></span>
<a href=output_xdmf.h#write_xdmf_light_data>write_xdmf_light_data</a>(slist, vlist, name, subname, num_cells, num_points, dim = dimension - <span class="dv">1</span>);<span id=265></span>
<span id=266></span>
<span class="co">// Setup file access template with parallel I/O access<span id=267></span></span>
acc_tpl1 = H5Pcreate(H5P_FILE_ACCESS);<span id=268></span>
H5Pset_fapl_mpio(acc_tpl1, MPI_COMM_WORLD, MPI_INFO_NULL);<span id=269></span>
<span id=270></span>
<span class="co">// Create a new HDF5 file collectively<span id=271></span></span>
file_id = H5Fcreate(name, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl1);<span id=272></span>
<span id=273></span>
<span class="co">// Release file-access template<span id=274></span></span>
H5Pclose(acc_tpl1);<span id=275></span>
<span id=276></span>
<span class="co">// Define chunk size for parallel I/O<span id=277></span></span>
hsize_t chunk_size = num_cells / npe() / <span class="dv">8</span>;<span id=278></span>
<span id=279></span>
<span class="co">// Populate and write the topology dataset<span id=280></span></span>
<span class="dt">long</span> *topo_dset;<span id=281></span>
<a href=./output_xdmf_helpers.h#populate_topo_dset_slice>populate_topo_dset_slice</a>(&topo_dset, num_cells_loc, offset_cells, count, offset, per_mask, marker, n, _alpha);<span id=282></span>
<a href=./output_xdmf_helpers.h#create_chunked_dataset>create_chunked_dataset</a>(file_id, count, offset, <span class="st">"/Topology"</span>, num_cells, num_cells_loc, pow(<span class="dv">2</span>, dimension - <span class="dv">1</span>), topo_dset, H5T_NATIVE_LONG, chunk_size, compression_level);<span id=283></span>
<a href=http://man7.org/linux/man-pages/man3/free.3.html>free</a>(topo_dset);<span id=284></span>
<span id=285></span>
<span class="co">// Create group for mesh geometry data<span id=286></span></span>
group_id = H5Gcreate(file_id, <span class="st">"Geometry"</span>, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);<span id=287></span>
<span id=288></span>
<span class="co">// Populate and write the points dataset<span id=289></span></span>
<span class="dt">double</span> *points_dset;<span id=290></span>
<a href=./output_xdmf_helpers.h#populate_points_dset_slice>populate_points_dset_slice</a>(&points_dset, num_points_loc, offset_points, count, offset, n, _alpha);<span id=291></span>
<a href=./output_xdmf_helpers.h#create_chunked_dataset>create_chunked_dataset</a>(group_id, count, offset, <span class="st">"/Geometry/Points"</span>, num_points, num_points_loc, <span class="dv">3</span>, points_dset, H5T_NATIVE_DOUBLE, chunk_size, compression_level);<span id=292></span>
<a href=http://man7.org/linux/man-pages/man3/free.3.html>free</a>(points_dset);<span id=293></span>
H5Gclose(group_id);<span id=294></span>
<span id=295></span>
<span class="co">// Create group for cell data<span id=296></span></span>
group_id = H5Gcreate(file_id, <span class="st">"Cells"</span>, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);<span id=297></span>
<span id=298></span>
<span class="co">// Allocate memory and write <span class="dt">scalar</span> datasets<span id=299></span></span>
<span class="dt">double</span> *scalar_dset = (<span class="dt">double</span> *)<a href=http://man7.org/linux/man-pages/man3/malloc.3.html>malloc</a>(num_cells_loc * <span class="kw">sizeof</span>(<span class="dt">double</span>));<span id=300></span>
<span class="cf">for</span> (<span class="dt">scalar</span> s in slist)<span id=301></span>
{<span id=302></span>
<span class="dt">char</span> substamp[<span class="dv">1024</span>];<span id=303></span>
<a href=http://man7.org/linux/man-pages/man3/sprintf.3.html>sprintf</a>(substamp, <span class="st">"/Cells/%s"</span>, s.name);<span id=304></span>
<a href=./output_xdmf_helpers.h#populate_scalar_dset_slice>populate_scalar_dset_slice</a>(s, scalar_dset, num_cells_loc, offset_cells, count, offset, per_mask, n, _alpha);<span id=305></span>
<a href=./output_xdmf_helpers.h#create_chunked_dataset>create_chunked_dataset</a>(group_id, count, offset, substamp, num_cells, num_cells_loc, <span class="dv">1</span>, scalar_dset, H5T_NATIVE_DOUBLE, chunk_size, compression_level);<span id=306></span>
}<span id=307></span>
<a href=http://man7.org/linux/man-pages/man3/free.3.html>free</a>(scalar_dset);<span id=308></span>
<span id=309></span>
<span class="co">// Allocate memory and write <span class="dt">vector</span> datasets<span id=310></span></span>
<span class="dt">double</span> *vector_dset = (<span class="dt">double</span> *)<a href=http://man7.org/linux/man-pages/man3/malloc.3.html>malloc</a>(num_cells_loc * <span class="dv">3</span> * <span class="kw">sizeof</span>(<span class="dt">double</span>));<span id=311></span>
<span class="cf">for</span> (<span class="dt">vector</span> v in vlist)<span id=312></span>
{<span id=313></span>
<span class="dt">char</span> substamp[<span class="dv">1024</span>];<span id=314></span>
<a href=http://man7.org/linux/man-pages/man3/sprintf.3.html>sprintf</a>(substamp, <span class="st">"/Cells/%s"</span>, v.x.name);<span id=315></span>
<a href=./output_xdmf_helpers.h#populate_vector_dset_slice>populate_vector_dset_slice</a>(v, vector_dset, num_cells_loc, offset_cells, count, offset, per_mask, n, _alpha);<span id=316></span>
<a href=./output_xdmf_helpers.h#create_chunked_dataset>create_chunked_dataset</a>(group_id, count, offset, substamp, num_cells, num_cells_loc, <span class="dv">3</span>, vector_dset, H5T_NATIVE_DOUBLE, chunk_size, compression_level);<span id=317></span>
}<span id=318></span>
<a href=http://man7.org/linux/man-pages/man3/free.3.html>free</a>(vector_dset);<span id=319></span>
H5Gclose(group_id);<span id=320></span>
<span id=321></span>
<span class="co">// Close HDF5 resources<span id=322></span></span>
H5Fclose(file_id);<span id=323></span>
}<span id=324></span>
<span class="pp">#endif<span id=325></span><span id=326></span></span></code></pre></div>
<h2 id="postamble-delete-macros">postamble: delete macros</h2>
<div class="sourceCode"><pre class="sourceCode c"><code class="sourceCode c"><span class="pp">#undef shortcut_slice<span id=328></span></span></code></pre></div>
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