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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="scatter-gather-operations">
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<h1><span class="section-number">1.1.6. </span>Scatter/gather operations<a class="headerlink" href="#scatter-gather-operations" title="Link to this heading"></a></h1>
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<p>This section has functions which gather per-atom data from one or more
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processors into a contiguous global list ordered by atom ID. The same
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list is returned to all calling processors. It also contains
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functions which scatter per-atom data from a contiguous global list
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across the processors that own those atom IDs. It also has a
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create_atoms() function which can create new atoms by scattering them
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appropriately to owning processors in the LAMMPS spatial
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decomposition.</p>
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<p>It documents the following functions:</p>
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<ul class="simple">
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<li><p><a class="reference internal" href="#_CPPv419lammps_gather_atomsPvPKciiPv" title="lammps_gather_atoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_atoms()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv426lammps_gather_atoms_concatPvPKciiPv" title="lammps_gather_atoms_concat"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_atoms_concat()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv426lammps_gather_atoms_subsetPvPKciiiPiPv" title="lammps_gather_atoms_subset"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_atoms_subset()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv420lammps_scatter_atomsPvPKciiPv" title="lammps_scatter_atoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_scatter_atoms()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv427lammps_scatter_atoms_subsetPvPKciiiPiPv" title="lammps_scatter_atoms_subset"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_scatter_atoms_subset()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv419lammps_gather_bondsPvPv" title="lammps_gather_bonds"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_bonds()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv420lammps_gather_anglesPvPv" title="lammps_gather_angles"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_angles()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv423lammps_gather_dihedralsPvPv" title="lammps_gather_dihedrals"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_dihedrals()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv423lammps_gather_impropersPvPv" title="lammps_gather_impropers"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_impropers()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv413lammps_gatherPvPKciiPv" title="lammps_gather"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv420lammps_gather_concatPvPKciiPv" title="lammps_gather_concat"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_concat()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv420lammps_gather_subsetPvPKciiiPiPv" title="lammps_gather_subset"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_subset()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv414lammps_scatterPvPKciiPv" title="lammps_scatter"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_scatter()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv421lammps_scatter_subsetPvPKciiiPiPv" title="lammps_scatter_subset"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_scatter_subset()</span></code></a></p></li>
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<li><p><a class="reference internal" href="#_CPPv419lammps_create_atomsPviPKiPKiPKdPKdPKii" title="lammps_create_atoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_create_atoms()</span></code></a></p></li>
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</ul>
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<hr class="docutils" />
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<dl class="cpp function">
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<dt class="sig sig-object cpp" id="_CPPv419lammps_gather_atomsPvPKciiPv">
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<span id="_CPPv319lammps_gather_atomsPvPKciiPv"></span><span id="_CPPv219lammps_gather_atomsPvPKciiPv"></span><span id="lammps_gather_atoms__voidP.cCP.i.i.voidP"></span><span class="target" id="library_8h_1ad3208ce7d03d54f74573a80565dc335d"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_gather_atoms</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">char</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">name</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">type</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">count</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv419lammps_gather_atomsPvPKciiPv" title="Link to this definition"></a><br /></dt>
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<dd><p>Gather the named atom-based entity for all atoms across all processes, in order.</p>
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<p><p>This subroutine gathers data for all atoms and stores them in a
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one-dimensional array allocated by the user. The data will be ordered by
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atom ID, which requires consecutive atom IDs (1 to <em>natoms</em>). If you need
|
||
a similar array but have non-consecutive atom IDs, see
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||
<a class="reference internal" href="#_CPPv426lammps_gather_atoms_concatPvPKciiPv" title="lammps_gather_atoms_concat"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_atoms_concat()</span></code></a>; for a similar array but for a subset
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||
of atoms, see <a class="reference internal" href="#_CPPv426lammps_gather_atoms_subsetPvPKciiiPiPv" title="lammps_gather_atoms_subset"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_atoms_subset()</span></code></a>.</p>
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<p>The <em>data</em> array will be ordered in groups of <em>count</em> values, sorted by atom ID
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(e.g., if <em>name</em> is <em>x</em> and <em>count</em> = 3, then <em>data</em> = x[0][0], x[0][1],
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x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], <span class="math notranslate nohighlight">\(\dots\)</span>);
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<em>data</em> must be pre-allocated by the caller to length (<em>count</em> <span class="math notranslate nohighlight">\(\times\)</span>
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<em>natoms</em>), as queried by <a class="reference internal" href="Library_properties.html#_CPPv417lammps_get_natomsPv" title="lammps_get_natoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_get_natoms()</span></code></a>,
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||
<a class="reference internal" href="Library_properties.html#_CPPv421lammps_extract_globalPvPKc" title="lammps_extract_global"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_global()</span></code></a>, or <a class="reference internal" href="Library_properties.html#_CPPv422lammps_extract_settingPvPKc" title="lammps_extract_setting"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_setting()</span></code></a>.</p>
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<div class="warning admonition">
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<p class="admonition-title">Restrictions</p>
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<p>This function is not compatible with <code class="docutils literal notranslate"><span class="pre">-DLAMMPS_BIGBIG</span></code>.</p>
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<p>Atom IDs must be defined and consecutive.</p>
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<p>The total number of atoms must not be more than 2147483647 (max 32-bit signed int).</p>
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</div>
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</p>
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<dl class="field-list simple">
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<dt class="field-odd">Parameters<span class="colon">:</span></dt>
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<dd class="field-odd"><ul class="simple">
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<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
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<li><p><strong>name</strong> – desired quantity (e.g., <em>x</em> or <em>charge</em>) </p></li>
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<li><p><strong>type</strong> – 0 for <code class="docutils literal notranslate"><span class="pre">int</span></code> values, 1 for <code class="docutils literal notranslate"><span class="pre">double</span></code> values </p></li>
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<li><p><strong>count</strong> – number of per-atom values (e.g., 1 for <em>type</em> or <em>charge</em>, 3 for <em>x</em> or <em>f</em>); use <em>count</em> = 3 with <em>image</em> if you want a single image flag unpacked into (<em>x</em>,<em>y</em>,<em>z</em>) components. </p></li>
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<li><p><strong>data</strong> – per-atom values packed in a 1-dimensional array of length <em>natoms</em> * <em>count</em>. </p></li>
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</ul>
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</dd>
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</dl>
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</dd></dl>
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<hr class="docutils" />
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<dl class="cpp function">
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<dt class="sig sig-object cpp" id="_CPPv426lammps_gather_atoms_concatPvPKciiPv">
|
||
<span id="_CPPv326lammps_gather_atoms_concatPvPKciiPv"></span><span id="_CPPv226lammps_gather_atoms_concatPvPKciiPv"></span><span id="lammps_gather_atoms_concat__voidP.cCP.i.i.voidP"></span><span class="target" id="library_8h_1a5e433d99895ca2aa9d87843bc7ee49d5"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_gather_atoms_concat</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">char</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">name</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">type</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">count</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv426lammps_gather_atoms_concatPvPKciiPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Gather the named atom-based entity for all atoms across all processes, unordered.</p>
|
||
<p><p>This subroutine gathers data for all atoms and stores them in a
|
||
one-dimensional array allocated by the user. The data will be a concatenation
|
||
of chunks from each processor’s owned atoms, in whatever order the atoms are
|
||
in on each processor. This process has no requirement that the atom IDs be
|
||
consecutive. If you need the ID of each atom, you can do another
|
||
<a class="reference internal" href="#_CPPv426lammps_gather_atoms_concatPvPKciiPv" title="lammps_gather_atoms_concat"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_atoms_concat()</span></code></a> call with <em>name</em> set to <code class="docutils literal notranslate"><span class="pre">id</span></code>.
|
||
If you have consecutive IDs and want the data to be in order, use
|
||
<a class="reference internal" href="#_CPPv419lammps_gather_atomsPvPKciiPv" title="lammps_gather_atoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_atoms()</span></code></a>; for a similar array but for a subset
|
||
of atoms, use <a class="reference internal" href="#_CPPv426lammps_gather_atoms_subsetPvPKciiiPiPv" title="lammps_gather_atoms_subset"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_atoms_subset()</span></code></a>.</p>
|
||
<p>The <em>data</em> array will be in groups of <em>count</em> values, with <em>natoms</em>
|
||
groups total, but not in order by atom ID (e.g., if <em>name</em> is <em>x</em> and <em>count</em>
|
||
is 3, then <em>data</em> might be something like x[10][0], x[10][1], x[10][2],
|
||
x[2][0], x[2][1], x[2][2], x[4][0], <span class="math notranslate nohighlight">\(\dots\)</span>); <em>data</em> must be
|
||
pre-allocated by the caller to length (<em>count</em> <span class="math notranslate nohighlight">\(\times\)</span> <em>natoms</em>), as
|
||
queried by <a class="reference internal" href="Library_properties.html#_CPPv417lammps_get_natomsPv" title="lammps_get_natoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_get_natoms()</span></code></a>, <a class="reference internal" href="Library_properties.html#_CPPv421lammps_extract_globalPvPKc" title="lammps_extract_global"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_global()</span></code></a>,
|
||
or <a class="reference internal" href="Library_properties.html#_CPPv422lammps_extract_settingPvPKc" title="lammps_extract_setting"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_setting()</span></code></a>.</p>
|
||
<div class="warning admonition">
|
||
<p class="admonition-title">Restrictions</p>
|
||
<p>This function is not compatible with <code class="docutils literal notranslate"><span class="pre">-DLAMMPS_BIGBIG</span></code>.</p>
|
||
<p>Atom IDs must be defined.</p>
|
||
<p>The total number of atoms must not be more than 2147483647 (max 32-bit signed int).</p>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>name</strong> – desired quantity (e.g., <em>x</em> or <em>charge</em>\ ) </p></li>
|
||
<li><p><strong>type</strong> – 0 for <code class="docutils literal notranslate"><span class="pre">int</span></code> values, 1 for <code class="docutils literal notranslate"><span class="pre">double</span></code> values </p></li>
|
||
<li><p><strong>count</strong> – number of per-atom values (e.g., 1 for <em>type</em> or <em>charge</em>, 3 for <em>x</em> or <em>f</em>); use <em>count</em> = 3 with “image” if you want single image flags unpacked into (<em>x</em>,<em>y</em>,<em>z</em>) </p></li>
|
||
<li><p><strong>data</strong> – per-atom values packed in a 1-dimensional array of length <em>natoms</em> * <em>count</em>. </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv426lammps_gather_atoms_subsetPvPKciiiPiPv">
|
||
<span id="_CPPv326lammps_gather_atoms_subsetPvPKciiiPiPv"></span><span id="_CPPv226lammps_gather_atoms_subsetPvPKciiiPiPv"></span><span id="lammps_gather_atoms_subset__voidP.cCP.i.i.i.iP.voidP"></span><span class="target" id="library_8h_1adb2aa14375aa277b1c32ad17a5f4a39f"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_gather_atoms_subset</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">char</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">name</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">type</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">count</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">ndata</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">ids</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv426lammps_gather_atoms_subsetPvPKciiiPiPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Gather the named atom-based entity for a subset of atoms.</p>
|
||
<p><p>This subroutine gathers data for the requested atom IDs and stores them in a
|
||
one-dimensional array allocated by the user. The data will be ordered by atom
|
||
ID, but there is no requirement that the IDs be consecutive. If you wish to
|
||
return a similar array for <em>all</em> the atoms, use <a class="reference internal" href="#_CPPv419lammps_gather_atomsPvPKciiPv" title="lammps_gather_atoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_atoms()</span></code></a>
|
||
or <a class="reference internal" href="#_CPPv426lammps_gather_atoms_concatPvPKciiPv" title="lammps_gather_atoms_concat"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_atoms_concat()</span></code></a>.</p>
|
||
<p>The <em>data</em> array will be in groups of <em>count</em> values, sorted by atom ID
|
||
in the same order as the array <em>ids</em> (e.g., if <em>name</em> is <em>x</em>, <em>count</em> = 3, and
|
||
<em>ids</em> is {100, 57, 210}, then <em>data</em> might look like {x[100][0], x[100][1],
|
||
x[100][2], x[57][0], x[57][1], x[57][2], x[210][0], <span class="math notranslate nohighlight">\(\dots\)</span>);
|
||
<em>ids</em> must be provided by the user with length <em>ndata</em>, and
|
||
<em>data</em> must be pre-allocated by the caller to length
|
||
(<em>count</em> <span class="math notranslate nohighlight">\(\times\)</span> <em>ndata</em>).</p>
|
||
<div class="warning admonition">
|
||
<p class="admonition-title">Restrictions</p>
|
||
<p>This function is not compatible with <code class="docutils literal notranslate"><span class="pre">-DLAMMPS_BIGBIG</span></code>.</p>
|
||
<p>Atom IDs must be defined and an <a class="reference internal" href="atom_modify.html"><span class="doc">atom map must be enabled</span></a></p>
|
||
<p>The total number of atoms must not be more than 2147483647 (max 32-bit signed int).</p>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>name</strong> – desired quantity (e.g., <em>x</em> or <em>charge</em>) </p></li>
|
||
<li><p><strong>type</strong> – 0 for <code class="docutils literal notranslate"><span class="pre">int</span></code> values, 1 for <code class="docutils literal notranslate"><span class="pre">double</span></code> values </p></li>
|
||
<li><p><strong>count</strong> – number of per-atom values (e.g., 1 for <em>type</em> or <em>charge</em>, 3 for <em>x</em> or <em>f</em>); use <em>count</em> = 3 with “image” if you want single image flags unpacked into (<em>x</em>,<em>y</em>,<em>z</em>) </p></li>
|
||
<li><p><strong>ndata</strong> – number of atoms for which to return data (can be all of them) </p></li>
|
||
<li><p><strong>ids</strong> – list of <em>ndata</em> atom IDs for which to return data </p></li>
|
||
<li><p><strong>data</strong> – per-atom values packed in a 1-dimensional array of length <em>ndata</em> * <em>count</em>. </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv420lammps_scatter_atomsPvPKciiPv">
|
||
<span id="_CPPv320lammps_scatter_atomsPvPKciiPv"></span><span id="_CPPv220lammps_scatter_atomsPvPKciiPv"></span><span id="lammps_scatter_atoms__voidP.cCP.i.i.voidP"></span><span class="target" id="library_8h_1a912e450e211db31d9396ad5f421d500d"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_scatter_atoms</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">char</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">name</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">type</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">count</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv420lammps_scatter_atomsPvPKciiPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Scatter the named atom-based entities in <em>data</em> to all processes.</p>
|
||
<p><p>This subroutine takes data stored in a one-dimensional array supplied by the
|
||
user and scatters them to all atoms on all processes. The data must be
|
||
ordered by atom ID, with the requirement that the IDs be consecutive.
|
||
Use <a class="reference internal" href="#_CPPv427lammps_scatter_atoms_subsetPvPKciiiPiPv" title="lammps_scatter_atoms_subset"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_scatter_atoms_subset()</span></code></a> to scatter data for some (or all)
|
||
atoms, unordered.</p>
|
||
<p>The <em>data</em> array needs to be ordered in groups of <em>count</em> values, sorted by
|
||
atom ID (e.g., if <em>name</em> is <em>x</em> and <em>count</em> = 3, then
|
||
<em>data</em> = {x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], x[1][2], x[2][0],
|
||
<span class="math notranslate nohighlight">\(\dots\)</span>}); <em>data</em> must be of length (<em>count</em> <span class="math notranslate nohighlight">\(\times\)</span> <em>natoms</em>).</p>
|
||
<div class="warning admonition">
|
||
<p class="admonition-title">Restrictions</p>
|
||
<p>This function is not compatible with <code class="docutils literal notranslate"><span class="pre">-DLAMMPS_BIGBIG</span></code>.</p>
|
||
<p>Atom IDs must be defined, must be consecutive, and an
|
||
<a class="reference internal" href="atom_modify.html"><span class="doc">atom map must be enabled</span></a></p>
|
||
<p>The total number of atoms must not be more than 2147483647 (max 32-bit signed int).</p>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>name</strong> – desired quantity (e.g., <em>x</em> or <em>charge</em>) </p></li>
|
||
<li><p><strong>type</strong> – 0 for <code class="docutils literal notranslate"><span class="pre">int</span></code> values, 1 for <code class="docutils literal notranslate"><span class="pre">double</span></code> values </p></li>
|
||
<li><p><strong>count</strong> – number of per-atom values (e.g., 1 for <em>type</em> or <em>charge</em>, 3 for <em>x</em> or <em>f</em>); use <em>count</em> = 3 with <em>image</em> if you have a single image flag packed into (<em>x</em>,<em>y</em>,<em>z</em>) components. </p></li>
|
||
<li><p><strong>data</strong> – per-atom values packed in a one-dimensional array of length <em>natoms</em> * <em>count</em>. </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv427lammps_scatter_atoms_subsetPvPKciiiPiPv">
|
||
<span id="_CPPv327lammps_scatter_atoms_subsetPvPKciiiPiPv"></span><span id="_CPPv227lammps_scatter_atoms_subsetPvPKciiiPiPv"></span><span id="lammps_scatter_atoms_subset__voidP.cCP.i.i.i.iP.voidP"></span><span class="target" id="library_8h_1a42726943d284b0edad9b8f3cd3129398"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_scatter_atoms_subset</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">char</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">name</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">type</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">count</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">ndata</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">ids</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv427lammps_scatter_atoms_subsetPvPKciiiPiPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Scatter the named atom-based entities in <em>data</em> from a subset of atoms to all processes.</p>
|
||
<p><p>This subroutine takes data stored in a one-dimensional array supplied by the
|
||
user and scatters them to a subset of atoms on all processes. The array
|
||
<em>data</em> contains data associated with atom IDs, but there is no requirement that
|
||
the IDs be consecutive, as they are provided in a separate array.
|
||
Use <a class="reference internal" href="#_CPPv420lammps_scatter_atomsPvPKciiPv" title="lammps_scatter_atoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_scatter_atoms()</span></code></a> to scatter data for all atoms, in order.</p>
|
||
<p>The <em>data</em> array needs to be organized in groups of <em>count</em> values, with the
|
||
groups in the same order as the array <em>ids</em>. For example, if you want <em>data</em>
|
||
to be the array {x[1][0], x[1][1], x[1][2], x[100][0], x[100][1], x[100][2],
|
||
x[57][0], x[57][1], x[57][2]}, then <em>count</em> = 3, <em>ndata</em> = 3, and <em>ids</em> would
|
||
be {1, 100, 57}.</p>
|
||
<div class="warning admonition">
|
||
<p class="admonition-title">Restrictions</p>
|
||
<p>This function is not compatible with <code class="docutils literal notranslate"><span class="pre">-DLAMMPS_BIGBIG</span></code>.</p>
|
||
<p>Atom IDs must be defined and an <a class="reference internal" href="atom_modify.html"><span class="doc">atom map must be enabled</span></a></p>
|
||
<p>The total number of atoms must not be more than 2147483647 (max 32-bit signed int).</p>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>name</strong> – desired quantity (e.g., <em>x</em> or <em>charge</em>) </p></li>
|
||
<li><p><strong>type</strong> – 0 for <code class="docutils literal notranslate"><span class="pre">int</span></code> values, 1 for <code class="docutils literal notranslate"><span class="pre">double</span></code> values </p></li>
|
||
<li><p><strong>count</strong> – number of per-atom values (e.g., 1 for <em>type</em> or <em>charge</em>, 3 for <em>x</em> or <em>f</em>); use <em>count</em> = 3 with “image” if you have all the image flags packed into (<em>xyz</em>) </p></li>
|
||
<li><p><strong>ndata</strong> – number of atoms listed in <em>ids</em> and <em>data</em> arrays </p></li>
|
||
<li><p><strong>ids</strong> – list of <em>ndata</em> atom IDs to scatter data to </p></li>
|
||
<li><p><strong>data</strong> – per-atom values packed in a 1-dimensional array of length <em>ndata</em> * <em>count</em>. </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv419lammps_gather_bondsPvPv">
|
||
<span id="_CPPv319lammps_gather_bondsPvPv"></span><span id="_CPPv219lammps_gather_bondsPvPv"></span><span id="lammps_gather_bonds__voidP.voidP"></span><span class="target" id="library_8h_1a360d274b56e28d7a9fd0e195ff2171af"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_gather_bonds</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv419lammps_gather_bondsPvPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Gather type and constituent atom info for all bonds</p>
|
||
<p><div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This function copies the list of all bonds into a buffer provided by
|
||
the calling code. The buffer will be filled with bond type, bond atom 1,
|
||
bond atom 2 for each bond. Thus the buffer has to be allocated to the
|
||
dimension of 3 times the <strong>total</strong> number of bonds times the size of
|
||
the LAMMPS “tagint” type, which is either 4 or 8 bytes depending on
|
||
whether they are stored in 32-bit or 64-bit integers, respectively.
|
||
This size depends on the compile time settings used when compiling
|
||
the LAMMPS library and can be queried by calling
|
||
<a class="reference internal" href="Library_properties.html#_CPPv422lammps_extract_settingPvPKc" title="lammps_extract_setting"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_setting()</span></code></a> with the keyword “tagint”.</p>
|
||
<p>When running in parallel, the data buffer must be allocated on <strong>all</strong>
|
||
MPI ranks and will be filled with the information for <strong>all</strong> bonds
|
||
in the system.</p>
|
||
<p>Below is a brief C code demonstrating accessing this collected bond information.</p>
|
||
<div class="highlight-c notranslate"><div class="highlight"><pre><span></span><span class="cp">#include</span><span class="w"> </span><span class="cpf">"library.h"</span>
|
||
|
||
<span class="cp">#include</span><span class="w"> </span><span class="cpf"><stdint.h></span>
|
||
<span class="cp">#include</span><span class="w"> </span><span class="cpf"><stdio.h></span>
|
||
<span class="cp">#include</span><span class="w"> </span><span class="cpf"><stdlib.h></span>
|
||
|
||
<span class="kt">int</span><span class="w"> </span><span class="nf">main</span><span class="p">(</span><span class="kt">int</span><span class="w"> </span><span class="n">argc</span><span class="p">,</span><span class="w"> </span><span class="kt">char</span><span class="w"> </span><span class="o">**</span><span class="n">argv</span><span class="p">)</span>
|
||
<span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">tagintsize</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="kt">int64_t</span><span class="w"> </span><span class="n">i</span><span class="p">,</span><span class="w"> </span><span class="n">nbonds</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="kt">void</span><span class="w"> </span><span class="o">*</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="o">*</span><span class="n">bonds</span><span class="p">;</span>
|
||
|
||
<span class="w"> </span><span class="n">handle</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">lammps_open_no_mpi</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="nb">NULL</span><span class="p">,</span><span class="w"> </span><span class="nb">NULL</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">lammps_file</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"in.some_input"</span><span class="p">);</span>
|
||
|
||
<span class="w"> </span><span class="n">tagintsize</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">lammps_extract_setting</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"tagint"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">tagintsize</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">4</span><span class="p">)</span>
|
||
<span class="w"> </span><span class="n">nbonds</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="o">*</span><span class="p">(</span><span class="kt">int32_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">lammps_extract_global</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"nbonds"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">else</span>
|
||
<span class="w"> </span><span class="n">nbonds</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="o">*</span><span class="p">(</span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">lammps_extract_global</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"nbonds"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">bonds</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">malloc</span><span class="p">(</span><span class="n">nbonds</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">3</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">tagintsize</span><span class="p">);</span>
|
||
|
||
<span class="w"> </span><span class="n">lammps_gather_bonds</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="n">bonds</span><span class="p">);</span>
|
||
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">lammps_extract_setting</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"world_rank"</span><span class="p">)</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">0</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">tagintsize</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">4</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int32_t</span><span class="w"> </span><span class="o">*</span><span class="n">bonds_real</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="kt">int32_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">bonds</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="p">(</span><span class="n">i</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o"><</span><span class="w"> </span><span class="n">nbonds</span><span class="p">;</span><span class="w"> </span><span class="o">++</span><span class="n">i</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="n">printf</span><span class="p">(</span><span class="s">"bond % 4ld: type = %d, atoms: % 4d % 4d</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="n">bonds_real</span><span class="p">[</span><span class="mi">3</span><span class="o">*</span><span class="n">i</span><span class="p">],</span><span class="w"> </span><span class="n">bonds_real</span><span class="p">[</span><span class="mi">3</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="w"> </span><span class="n">bonds_real</span><span class="p">[</span><span class="mi">3</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">]);</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="n">bonds_real</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">bonds</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="p">(</span><span class="n">i</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o"><</span><span class="w"> </span><span class="n">nbonds</span><span class="p">;</span><span class="w"> </span><span class="o">++</span><span class="n">i</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="n">printf</span><span class="p">(</span><span class="s">"bond % 4ld: type = %ld, atoms: % 4ld % 4ld</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="n">bonds_real</span><span class="p">[</span><span class="mi">3</span><span class="o">*</span><span class="n">i</span><span class="p">],</span><span class="w"> </span><span class="n">bonds_real</span><span class="p">[</span><span class="mi">3</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="w"> </span><span class="n">bonds_real</span><span class="p">[</span><span class="mi">3</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">]);</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
|
||
<span class="w"> </span><span class="n">lammps_close</span><span class="p">(</span><span class="n">handle</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">lammps_mpi_finalize</span><span class="p">();</span>
|
||
<span class="w"> </span><span class="n">free</span><span class="p">(</span><span class="n">bonds</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">return</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span>
|
||
<span class="p">}</span>
|
||
</pre></div>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>data</strong> – pointer to data to copy the result to </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv420lammps_gather_anglesPvPv">
|
||
<span id="_CPPv320lammps_gather_anglesPvPv"></span><span id="_CPPv220lammps_gather_anglesPvPv"></span><span id="lammps_gather_angles__voidP.voidP"></span><span class="target" id="library_8h_1a6f8c39008d113b5c3450c2cffaadcf3c"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_gather_angles</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv420lammps_gather_anglesPvPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Gather type and constituent atom info for all angles</p>
|
||
<p><div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 8Feb2023.</span></p>
|
||
</div>
|
||
<p>This function copies the list of all angles into a buffer provided by
|
||
the calling code. The buffer will be filled with angle type, angle atom 1,
|
||
angle atom 2, angle atom 3 for each angle. Thus the buffer has to be allocated to the
|
||
dimension of 4 times the <strong>total</strong> number of angles times the size of
|
||
the LAMMPS “tagint” type, which is either 4 or 8 bytes depending on
|
||
whether they are stored in 32-bit or 64-bit integers, respectively.
|
||
This size depends on the compile time settings used when compiling
|
||
the LAMMPS library and can be queried by calling
|
||
<a class="reference internal" href="Library_properties.html#_CPPv422lammps_extract_settingPvPKc" title="lammps_extract_setting"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_setting()</span></code></a> with the keyword “tagint”.</p>
|
||
<p>When running in parallel, the data buffer must be allocated on <strong>all</strong>
|
||
MPI ranks and will be filled with the information for <strong>all</strong> angles
|
||
in the system.</p>
|
||
<p>Below is a brief C code demonstrating accessing this collected angle information.</p>
|
||
<div class="highlight-c notranslate"><div class="highlight"><pre><span></span><span class="cp">#include</span><span class="w"> </span><span class="cpf">"library.h"</span>
|
||
|
||
<span class="cp">#include</span><span class="w"> </span><span class="cpf"><stdint.h></span>
|
||
<span class="cp">#include</span><span class="w"> </span><span class="cpf"><stdio.h></span>
|
||
<span class="cp">#include</span><span class="w"> </span><span class="cpf"><stdlib.h></span>
|
||
|
||
<span class="kt">int</span><span class="w"> </span><span class="nf">main</span><span class="p">(</span><span class="kt">int</span><span class="w"> </span><span class="n">argc</span><span class="p">,</span><span class="w"> </span><span class="kt">char</span><span class="w"> </span><span class="o">**</span><span class="n">argv</span><span class="p">)</span>
|
||
<span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">tagintsize</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="kt">int64_t</span><span class="w"> </span><span class="n">i</span><span class="p">,</span><span class="w"> </span><span class="n">nangles</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="kt">void</span><span class="w"> </span><span class="o">*</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="o">*</span><span class="n">angles</span><span class="p">;</span>
|
||
|
||
<span class="w"> </span><span class="n">handle</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">lammps_open_no_mpi</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="nb">NULL</span><span class="p">,</span><span class="w"> </span><span class="nb">NULL</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">lammps_file</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"in.some_input"</span><span class="p">);</span>
|
||
|
||
<span class="w"> </span><span class="n">tagintsize</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">lammps_extract_setting</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"tagint"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">tagintsize</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">4</span><span class="p">)</span>
|
||
<span class="w"> </span><span class="n">nangles</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="o">*</span><span class="p">(</span><span class="kt">int32_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">lammps_extract_global</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"nangles"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">else</span>
|
||
<span class="w"> </span><span class="n">nangles</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="o">*</span><span class="p">(</span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">lammps_extract_global</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"nangles"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">angles</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">malloc</span><span class="p">(</span><span class="n">nangles</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">4</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">tagintsize</span><span class="p">);</span>
|
||
|
||
<span class="w"> </span><span class="n">lammps_gather_angles</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="n">angles</span><span class="p">);</span>
|
||
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">lammps_extract_setting</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"world_rank"</span><span class="p">)</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">0</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">tagintsize</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">4</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int32_t</span><span class="w"> </span><span class="o">*</span><span class="n">angles_real</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="kt">int32_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">angles</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="p">(</span><span class="n">i</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o"><</span><span class="w"> </span><span class="n">nangles</span><span class="p">;</span><span class="w"> </span><span class="o">++</span><span class="n">i</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="n">printf</span><span class="p">(</span><span class="s">"angle % 4ld: type = %d, atoms: % 4d % 4d % 4d</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="n">angles_real</span><span class="p">[</span><span class="mi">4</span><span class="o">*</span><span class="n">i</span><span class="p">],</span><span class="w"> </span><span class="n">angles_real</span><span class="p">[</span><span class="mi">4</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="w"> </span><span class="n">angles_real</span><span class="p">[</span><span class="mi">4</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">],</span><span class="w"> </span><span class="n">angles_real</span><span class="p">[</span><span class="mi">4</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">3</span><span class="p">]);</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="n">angles_real</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">angles</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="p">(</span><span class="n">i</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o"><</span><span class="w"> </span><span class="n">nangles</span><span class="p">;</span><span class="w"> </span><span class="o">++</span><span class="n">i</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="n">printf</span><span class="p">(</span><span class="s">"angle % 4ld: type = %ld, atoms: % 4ld % 4ld % 4ld</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="n">angles_real</span><span class="p">[</span><span class="mi">4</span><span class="o">*</span><span class="n">i</span><span class="p">],</span><span class="w"> </span><span class="n">angles_real</span><span class="p">[</span><span class="mi">4</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="w"> </span><span class="n">angles_real</span><span class="p">[</span><span class="mi">4</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">],</span><span class="w"> </span><span class="n">angles_real</span><span class="p">[</span><span class="mi">4</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">3</span><span class="p">]);</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
|
||
<span class="w"> </span><span class="n">lammps_close</span><span class="p">(</span><span class="n">handle</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">lammps_mpi_finalize</span><span class="p">();</span>
|
||
<span class="w"> </span><span class="n">free</span><span class="p">(</span><span class="n">angles</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">return</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span>
|
||
<span class="p">}</span>
|
||
</pre></div>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>data</strong> – pointer to data to copy the result to </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv423lammps_gather_dihedralsPvPv">
|
||
<span id="_CPPv323lammps_gather_dihedralsPvPv"></span><span id="_CPPv223lammps_gather_dihedralsPvPv"></span><span id="lammps_gather_dihedrals__voidP.voidP"></span><span class="target" id="library_8h_1a93dac1f42646ebfa89521fc77a38a785"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_gather_dihedrals</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv423lammps_gather_dihedralsPvPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Gather type and constituent atom info for all dihedrals</p>
|
||
<p><div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 8Feb2023.</span></p>
|
||
</div>
|
||
<p>This function copies the list of all dihedrals into a buffer provided by
|
||
the calling code. The buffer will be filled with dihedral type, dihedral atom 1,
|
||
dihedral atom 2, dihedral atom 3, dihedral atom 4 for each dihedral.
|
||
Thus the buffer has to be allocated to the
|
||
dimension of 5 times the <strong>total</strong> number of dihedrals times the size of
|
||
the LAMMPS “tagint” type, which is either 4 or 8 bytes depending on
|
||
whether they are stored in 32-bit or 64-bit integers, respectively.
|
||
This size depends on the compile time settings used when compiling
|
||
the LAMMPS library and can be queried by calling
|
||
<a class="reference internal" href="Library_properties.html#_CPPv422lammps_extract_settingPvPKc" title="lammps_extract_setting"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_setting()</span></code></a> with the keyword “tagint”.</p>
|
||
<p>When running in parallel, the data buffer must be allocated on <strong>all</strong>
|
||
MPI ranks and will be filled with the information for <strong>all</strong> dihedrals
|
||
in the system.</p>
|
||
<p>Below is a brief C code demonstrating accessing this collected dihedral information.</p>
|
||
<div class="highlight-c notranslate"><div class="highlight"><pre><span></span><span class="cp">#include</span><span class="w"> </span><span class="cpf">"library.h"</span>
|
||
|
||
<span class="cp">#include</span><span class="w"> </span><span class="cpf"><stdint.h></span>
|
||
<span class="cp">#include</span><span class="w"> </span><span class="cpf"><stdio.h></span>
|
||
<span class="cp">#include</span><span class="w"> </span><span class="cpf"><stdlib.h></span>
|
||
|
||
<span class="kt">int</span><span class="w"> </span><span class="nf">main</span><span class="p">(</span><span class="kt">int</span><span class="w"> </span><span class="n">argc</span><span class="p">,</span><span class="w"> </span><span class="kt">char</span><span class="w"> </span><span class="o">**</span><span class="n">argv</span><span class="p">)</span>
|
||
<span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">tagintsize</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="kt">int64_t</span><span class="w"> </span><span class="n">i</span><span class="p">,</span><span class="w"> </span><span class="n">ndihedrals</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="kt">void</span><span class="w"> </span><span class="o">*</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="o">*</span><span class="n">dihedrals</span><span class="p">;</span>
|
||
|
||
<span class="w"> </span><span class="n">handle</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">lammps_open_no_mpi</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="nb">NULL</span><span class="p">,</span><span class="w"> </span><span class="nb">NULL</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">lammps_file</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"in.some_input"</span><span class="p">);</span>
|
||
|
||
<span class="w"> </span><span class="n">tagintsize</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">lammps_extract_setting</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"tagint"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">tagintsize</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">4</span><span class="p">)</span>
|
||
<span class="w"> </span><span class="n">ndihedrals</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="o">*</span><span class="p">(</span><span class="kt">int32_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">lammps_extract_global</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"ndihedrals"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">else</span>
|
||
<span class="w"> </span><span class="n">ndihedrals</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="o">*</span><span class="p">(</span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">lammps_extract_global</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"ndihedrals"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">dihedrals</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">malloc</span><span class="p">(</span><span class="n">ndihedrals</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">5</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">tagintsize</span><span class="p">);</span>
|
||
|
||
<span class="w"> </span><span class="n">lammps_gather_dihedrals</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="n">dihedrals</span><span class="p">);</span>
|
||
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">lammps_extract_setting</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"world_rank"</span><span class="p">)</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">0</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">tagintsize</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">4</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int32_t</span><span class="w"> </span><span class="o">*</span><span class="n">dihedrals_real</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="kt">int32_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">dihedrals</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="p">(</span><span class="n">i</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o"><</span><span class="w"> </span><span class="n">ndihedrals</span><span class="p">;</span><span class="w"> </span><span class="o">++</span><span class="n">i</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="n">printf</span><span class="p">(</span><span class="s">"dihedral % 4ld: type = %d, atoms: % 4d % 4d % 4d % 4d</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="n">dihedrals_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="p">],</span><span class="w"> </span><span class="n">dihedrals_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="w"> </span><span class="n">dihedrals_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">],</span><span class="w"> </span><span class="n">dihedrals_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">3</span><span class="p">],</span><span class="w"> </span><span class="n">dihedrals_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">4</span><span class="p">]);</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="n">dihedrals_real</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">dihedrals</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="p">(</span><span class="n">i</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o"><</span><span class="w"> </span><span class="n">ndihedrals</span><span class="p">;</span><span class="w"> </span><span class="o">++</span><span class="n">i</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="n">printf</span><span class="p">(</span><span class="s">"dihedral % 4ld: type = %ld, atoms: % 4ld % 4ld % 4ld % 4ld</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="n">dihedrals_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="p">],</span><span class="w"> </span><span class="n">dihedrals_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="w"> </span><span class="n">dihedrals_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">],</span><span class="w"> </span><span class="n">dihedrals_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">3</span><span class="p">],</span><span class="w"> </span><span class="n">dihedrals_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">4</span><span class="p">]);</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
|
||
<span class="w"> </span><span class="n">lammps_close</span><span class="p">(</span><span class="n">handle</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">lammps_mpi_finalize</span><span class="p">();</span>
|
||
<span class="w"> </span><span class="n">free</span><span class="p">(</span><span class="n">dihedrals</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">return</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span>
|
||
<span class="p">}</span>
|
||
</pre></div>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>data</strong> – pointer to data to copy the result to </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv423lammps_gather_impropersPvPv">
|
||
<span id="_CPPv323lammps_gather_impropersPvPv"></span><span id="_CPPv223lammps_gather_impropersPvPv"></span><span id="lammps_gather_impropers__voidP.voidP"></span><span class="target" id="library_8h_1abf81ea4427e375c6605fb7362e995b92"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_gather_impropers</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv423lammps_gather_impropersPvPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Gather type and constituent atom info for all impropers</p>
|
||
<p><div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 8Feb2023.</span></p>
|
||
</div>
|
||
<p>This function copies the list of all impropers into a buffer provided by
|
||
the calling code. The buffer will be filled with improper type, improper atom 1,
|
||
improper atom 2, improper atom 3, improper atom 4 for each improper.
|
||
Thus the buffer has to be allocated to the
|
||
dimension of 5 times the <strong>total</strong> number of impropers times the size of
|
||
the LAMMPS “tagint” type, which is either 4 or 8 bytes depending on
|
||
whether they are stored in 32-bit or 64-bit integers, respectively.
|
||
This size depends on the compile time settings used when compiling
|
||
the LAMMPS library and can be queried by calling
|
||
<a class="reference internal" href="Library_properties.html#_CPPv422lammps_extract_settingPvPKc" title="lammps_extract_setting"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_setting()</span></code></a> with the keyword “tagint”.</p>
|
||
<p>When running in parallel, the data buffer must be allocated on <strong>all</strong>
|
||
MPI ranks and will be filled with the information for <strong>all</strong> impropers
|
||
in the system.</p>
|
||
<p>Below is a brief C code demonstrating accessing this collected improper information.</p>
|
||
<div class="highlight-c notranslate"><div class="highlight"><pre><span></span><span class="cp">#include</span><span class="w"> </span><span class="cpf">"library.h"</span>
|
||
|
||
<span class="cp">#include</span><span class="w"> </span><span class="cpf"><stdint.h></span>
|
||
<span class="cp">#include</span><span class="w"> </span><span class="cpf"><stdio.h></span>
|
||
<span class="cp">#include</span><span class="w"> </span><span class="cpf"><stdlib.h></span>
|
||
|
||
<span class="kt">int</span><span class="w"> </span><span class="nf">main</span><span class="p">(</span><span class="kt">int</span><span class="w"> </span><span class="n">argc</span><span class="p">,</span><span class="w"> </span><span class="kt">char</span><span class="w"> </span><span class="o">**</span><span class="n">argv</span><span class="p">)</span>
|
||
<span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">tagintsize</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="kt">int64_t</span><span class="w"> </span><span class="n">i</span><span class="p">,</span><span class="w"> </span><span class="n">nimpropers</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="kt">void</span><span class="w"> </span><span class="o">*</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="o">*</span><span class="n">impropers</span><span class="p">;</span>
|
||
|
||
<span class="w"> </span><span class="n">handle</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">lammps_open_no_mpi</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="nb">NULL</span><span class="p">,</span><span class="w"> </span><span class="nb">NULL</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">lammps_file</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"in.some_input"</span><span class="p">);</span>
|
||
|
||
<span class="w"> </span><span class="n">tagintsize</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">lammps_extract_setting</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"tagint"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">tagintsize</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">4</span><span class="p">)</span>
|
||
<span class="w"> </span><span class="n">nimpropers</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="o">*</span><span class="p">(</span><span class="kt">int32_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">lammps_extract_global</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"nimpropers"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">else</span>
|
||
<span class="w"> </span><span class="n">nimpropers</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="o">*</span><span class="p">(</span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">lammps_extract_global</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"nimpropers"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">impropers</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">malloc</span><span class="p">(</span><span class="n">nimpropers</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">5</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">tagintsize</span><span class="p">);</span>
|
||
|
||
<span class="w"> </span><span class="n">lammps_gather_impropers</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="n">impropers</span><span class="p">);</span>
|
||
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">lammps_extract_setting</span><span class="p">(</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="s">"world_rank"</span><span class="p">)</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">0</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">tagintsize</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">4</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int32_t</span><span class="w"> </span><span class="o">*</span><span class="n">impropers_real</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="kt">int32_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">impropers</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="p">(</span><span class="n">i</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o"><</span><span class="w"> </span><span class="n">nimpropers</span><span class="p">;</span><span class="w"> </span><span class="o">++</span><span class="n">i</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="n">printf</span><span class="p">(</span><span class="s">"improper % 4ld: type = %d, atoms: % 4d % 4d % 4d % 4d</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="n">impropers_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="p">],</span><span class="w"> </span><span class="n">impropers_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="w"> </span><span class="n">impropers_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">],</span><span class="w"> </span><span class="n">impropers_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">3</span><span class="p">],</span><span class="w"> </span><span class="n">impropers_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">4</span><span class="p">]);</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="n">impropers_real</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="p">)</span><span class="n">impropers</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="p">(</span><span class="n">i</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o"><</span><span class="w"> </span><span class="n">nimpropers</span><span class="p">;</span><span class="w"> </span><span class="o">++</span><span class="n">i</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="n">printf</span><span class="p">(</span><span class="s">"improper % 4ld: type = %ld, atoms: % 4ld % 4ld % 4ld % 4ld</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="n">impropers_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="p">],</span><span class="w"> </span><span class="n">impropers_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="w"> </span><span class="n">impropers_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">],</span><span class="w"> </span><span class="n">impropers_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">3</span><span class="p">],</span><span class="w"> </span><span class="n">impropers_real</span><span class="p">[</span><span class="mi">5</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">4</span><span class="p">]);</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
|
||
<span class="w"> </span><span class="n">lammps_close</span><span class="p">(</span><span class="n">handle</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">lammps_mpi_finalize</span><span class="p">();</span>
|
||
<span class="w"> </span><span class="n">free</span><span class="p">(</span><span class="n">impropers</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">return</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span>
|
||
<span class="p">}</span>
|
||
</pre></div>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>data</strong> – pointer to data to copy the result to </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv413lammps_gatherPvPKciiPv">
|
||
<span id="_CPPv313lammps_gatherPvPKciiPv"></span><span id="_CPPv213lammps_gatherPvPKciiPv"></span><span id="lammps_gather__voidP.cCP.i.i.voidP"></span><span class="target" id="library_8h_1aeaf5356f9fafd2fd9dbab0958a0a8ac3"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_gather</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">char</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">name</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">type</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">count</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv413lammps_gatherPvPKciiPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes, in order by atom ID.</p>
|
||
<p><p>This subroutine gathers data from all processes and stores them in a one-dimensional array
|
||
allocated by the user. The array <em>data</em> will be ordered by atom ID, which requires consecutive IDs
|
||
(1 to <em>natoms</em>). If you need a similar array but for non-consecutive atom IDs, see
|
||
<a class="reference internal" href="#_CPPv420lammps_gather_concatPvPKciiPv" title="lammps_gather_concat"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_concat()</span></code></a>; for a similar array but for a subset of atoms, see
|
||
<a class="reference internal" href="#_CPPv420lammps_gather_subsetPvPKciiiPiPv" title="lammps_gather_subset"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_subset()</span></code></a>.</p>
|
||
<p>The <em>data</em> array will be ordered in groups of <em>count</em> values, sorted by atom ID (e.g., if <em>name</em> is
|
||
<em>x</em>, then <em>data</em> is {x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], x[1][2], x[2][0],
|
||
<span class="math notranslate nohighlight">\(\dots\)</span>}); <em>data</em> must be pre-allocated by the caller to the correct length
|
||
(<em>count</em><span class="math notranslate nohighlight">\({}\times{}\)</span><em>natoms</em>), as queried by <a class="reference internal" href="Library_properties.html#_CPPv417lammps_get_natomsPv" title="lammps_get_natoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_get_natoms()</span></code></a>,
|
||
<a class="reference internal" href="Library_properties.html#_CPPv421lammps_extract_globalPvPKc" title="lammps_extract_global"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_global()</span></code></a>, or <a class="reference internal" href="Library_properties.html#_CPPv422lammps_extract_settingPvPKc" title="lammps_extract_setting"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_setting()</span></code></a>.</p>
|
||
<p>This function will return an error if fix or compute data are requested and the fix or compute ID
|
||
given does not have per-atom data.</p>
|
||
<div class="warning admonition">
|
||
<p class="admonition-title">Restrictions</p>
|
||
<p>This function is not compatible with <code class="docutils literal notranslate"><span class="pre">-DLAMMPS_BIGBIG</span></code>.</p>
|
||
<p>Atom IDs must be defined and must be consecutive.</p>
|
||
<p>The total number of atoms must not be more than 2147483647 (max 32-bit signed int).</p>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>name</strong> – desired quantity (e.g., “x” or “f” for atom properties, “f_id” for per-atom fix data, “c_id” for per-atom compute data, “d_name” or “i_name” for fix property/atom vectors with <em>count</em> = 1, “d2_name” or “i2_name” for fix property/atom vectors with <em>count</em> > 1) </p></li>
|
||
<li><p><strong>type</strong> – 0 for <code class="docutils literal notranslate"><span class="pre">int</span></code> values, 1 for <code class="docutils literal notranslate"><span class="pre">double</span></code> values </p></li>
|
||
<li><p><strong>count</strong> – number of per-atom values (e.g., 1 for <em>type</em> or <em>charge</em>, 3 for <em>x</em> or <em>f</em>); use <em>count</em> = 3 with <em>image</em> if you want the image flags unpacked into (<em>x</em>,<em>y</em>,<em>z</em>) components. </p></li>
|
||
<li><p><strong>data</strong> – per-atom values packed into a one-dimensional array of length <em>natoms</em> * <em>count</em>. </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv420lammps_gather_concatPvPKciiPv">
|
||
<span id="_CPPv320lammps_gather_concatPvPKciiPv"></span><span id="_CPPv220lammps_gather_concatPvPKciiPv"></span><span id="lammps_gather_concat__voidP.cCP.i.i.voidP"></span><span class="target" id="library_8h_1add32cd75d71123448c752d69d96a9009"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_gather_concat</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">char</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">name</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">type</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">count</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv420lammps_gather_concatPvPKciiPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes, unordered.</p>
|
||
<p><p>This subroutine gathers data for all atoms and stores them in a one-dimensional array allocated by
|
||
the user. The data will be a concatenation of chunks from each processor’s owned atoms, in
|
||
whatever order the atoms are in on each processor. This process has no requirement that the atom
|
||
IDs be consecutive. If you need the ID of each atom, you can do another call to either
|
||
<a class="reference internal" href="#_CPPv426lammps_gather_atoms_concatPvPKciiPv" title="lammps_gather_atoms_concat"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_atoms_concat()</span></code></a> or <a class="reference internal" href="#_CPPv420lammps_gather_concatPvPKciiPv" title="lammps_gather_concat"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_concat()</span></code></a> with <em>name</em> set to
|
||
<code class="docutils literal notranslate"><span class="pre">id</span></code>. If you have consecutive IDs and want the data to be in order, use
|
||
<a class="reference internal" href="#_CPPv413lammps_gatherPvPKciiPv" title="lammps_gather"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather()</span></code></a>; for a similar array but for a subset of atoms, use
|
||
<a class="reference internal" href="#_CPPv420lammps_gather_subsetPvPKciiiPiPv" title="lammps_gather_subset"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_subset()</span></code></a>.</p>
|
||
<p>The <em>data</em> array will be in groups of <em>count</em> values, with <em>natoms</em> groups total, but not in order
|
||
by atom ID (e.g., if <em>name</em> is <em>x</em> and <em>count</em> is 3, then <em>data</em> might be something like
|
||
{x[10][0], x[10][1], x[10][2], x[2][0], x[2][1], x[2][2], x[4][0], <span class="math notranslate nohighlight">\(\dots\)</span>}); <em>data</em> must be
|
||
pre-allocated by the caller to length (<em>count</em> <span class="math notranslate nohighlight">\(\times\)</span> <em>natoms</em>), as queried by
|
||
<a class="reference internal" href="Library_properties.html#_CPPv417lammps_get_natomsPv" title="lammps_get_natoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_get_natoms()</span></code></a>, <a class="reference internal" href="Library_properties.html#_CPPv421lammps_extract_globalPvPKc" title="lammps_extract_global"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_global()</span></code></a>, or
|
||
<a class="reference internal" href="Library_properties.html#_CPPv422lammps_extract_settingPvPKc" title="lammps_extract_setting"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_setting()</span></code></a>.</p>
|
||
<div class="warning admonition">
|
||
<p class="admonition-title">Restrictions</p>
|
||
<p>This function is not compatible with <code class="docutils literal notranslate"><span class="pre">-DLAMMPS_BIGBIG</span></code>.</p>
|
||
<p>Atom IDs must be defined.</p>
|
||
<p>The total number of atoms must be less than 2147483647 (max 32-bit signed int).</p>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>name</strong> – desired quantity (e.g., “x” or “f” for atom properties, “f_id” for per-atom fix data, “c_id” for per-atom compute data, “d_name” or “i_name” for fix property/atom vectors with count = 1, “d2_name” or “i2_name” for fix property/atom vectors with count > 1) </p></li>
|
||
<li><p><strong>type</strong> – 0 for <code class="docutils literal notranslate"><span class="pre">int</span></code> values, 1 for <code class="docutils literal notranslate"><span class="pre">double</span></code> values </p></li>
|
||
<li><p><strong>count</strong> – number of per-atom values (e.g., 1 for <em>type</em> or <em>charge</em>, 3 for <em>x</em> or <em>f</em>); use <em>count</em> = 3 with <em>image</em> if you want the image flags unpacked into (<em>x</em>,<em>y</em>,<em>z</em>) components. </p></li>
|
||
<li><p><strong>data</strong> – per-atom values packed into a one-dimensional array of length <em>natoms</em> * <em>count</em>. </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv420lammps_gather_subsetPvPKciiiPiPv">
|
||
<span id="_CPPv320lammps_gather_subsetPvPKciiiPiPv"></span><span id="_CPPv220lammps_gather_subsetPvPKciiiPiPv"></span><span id="lammps_gather_subset__voidP.cCP.i.i.i.iP.voidP"></span><span class="target" id="library_8h_1ab098fa5d18996508a54430ff5e3a0faf"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_gather_subset</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">char</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">name</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">type</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">count</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">ndata</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">ids</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv420lammps_gather_subsetPvPKciiiPiPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes for a subset of atoms.</p>
|
||
<p><p>This subroutine gathers data for the requested atom IDs and stores them in a one-dimensional array
|
||
allocated by the user. The data will be ordered by atom ID, but there is no requirement that the
|
||
IDs be consecutive. If you wish to return a similar array for <em>all</em> the atoms, use
|
||
<a class="reference internal" href="#_CPPv413lammps_gatherPvPKciiPv" title="lammps_gather"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather()</span></code></a> or <a class="reference internal" href="#_CPPv420lammps_gather_concatPvPKciiPv" title="lammps_gather_concat"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_concat()</span></code></a>.</p>
|
||
<p>The <em>data</em> array will be in groups of <em>count</em> values, sorted by atom ID in the same order as the
|
||
array <em>ids</em> (e.g., if <em>name</em> is <em>x</em>, <em>count</em> = 3, and <em>ids</em> is {100, 57, 210}, then <em>data</em> might
|
||
look like {x[100][0], x[100][1], x[100][2], x[57][0], x[57][1], x[57][2], x[210][0],
|
||
<span class="math notranslate nohighlight">\(\dots\)</span>}); <em>ids</em> must be provided by the user with length <em>ndata</em>, and <em>data</em> must be
|
||
pre-allocated by the caller to length (<em>count</em><span class="math notranslate nohighlight">\({}\times{}\)</span><em>ndata</em>).</p>
|
||
<div class="warning admonition">
|
||
<p class="admonition-title">Restrictions</p>
|
||
<p>This function is not compatible with <code class="docutils literal notranslate"><span class="pre">-DLAMMPS_BIGBIG</span></code>.</p>
|
||
<p>Atom IDs must be defined and an <a class="reference internal" href="atom_modify.html"><span class="doc">atom map must be enabled</span></a></p>
|
||
<p>The total number of atoms must not be more than 2147483647 (max 32-bit signed int).</p>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>name</strong> – desired quantity (e.g., “x” or “f” for atom properties, “f_id” for per-atom fix data, “c_id” for per-atom compute data, “d_name” or “i_name” for fix property/atom vectors with <em>count</em> = 1, “d2_name” or “i2_name” for fix property/atom vectors with <em>count</em> > 1) </p></li>
|
||
<li><p><strong>type</strong> – 0 for <code class="docutils literal notranslate"><span class="pre">int</span></code> values, 1 for <code class="docutils literal notranslate"><span class="pre">double</span></code> values </p></li>
|
||
<li><p><strong>count</strong> – number of per-atom values (e.g., 1 for <em>type</em> or <em>charge</em>, 3 for <em>x</em> or <em>f</em>); use <em>count</em> = 3 with <em>image</em> if you want the image flags unpacked into (<em>x</em>,<em>y</em>,<em>z</em>) components. </p></li>
|
||
<li><p><strong>ndata</strong> – number of atoms for which to return data (can be all of them) </p></li>
|
||
<li><p><strong>ids</strong> – list of <em>ndata</em> atom IDs for which to return data </p></li>
|
||
<li><p><strong>data</strong> – per-atom values packed into a one-dimensional array of length <em>ndata</em> * <em>count</em>. </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv414lammps_scatterPvPKciiPv">
|
||
<span id="_CPPv314lammps_scatterPvPKciiPv"></span><span id="_CPPv214lammps_scatterPvPKciiPv"></span><span id="lammps_scatter__voidP.cCP.i.i.voidP"></span><span class="target" id="library_8h_1a1251a6d15588762a6810ed4021bfce11"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_scatter</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">char</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">name</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">type</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">count</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv414lammps_scatterPvPKciiPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Scatter the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entity in <em>data</em> to all processes.</p>
|
||
<p><p>This subroutine takes data stored in a one-dimensional array supplied by the user and scatters
|
||
them to all atoms on all processes. The data must be ordered by atom ID, with the requirement that
|
||
the IDs be consecutive. Use <a class="reference internal" href="#_CPPv421lammps_scatter_subsetPvPKciiiPiPv" title="lammps_scatter_subset"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_scatter_subset()</span></code></a> to scatter data for some (or all)
|
||
atoms, unordered.</p>
|
||
<p>The <em>data</em> array needs to be ordered in groups of <em>count</em> values, sorted by atom ID (e.g., if
|
||
<em>name</em> is <em>x</em> and <em>count</em> = 3, then <em>data</em> = {x[0][0], x[0][1], x[0][2], x[1][0], x[1][1],
|
||
x[1][2], x[2][0], <span class="math notranslate nohighlight">\(\dots\)</span>}); <em>data</em> must be of length (<em>count</em> <span class="math notranslate nohighlight">\(\times\)</span> <em>natoms</em>).</p>
|
||
<div class="warning admonition">
|
||
<p class="admonition-title">Restrictions</p>
|
||
<p>This function is not compatible with <code class="docutils literal notranslate"><span class="pre">-DLAMMPS_BIGBIG</span></code>.</p>
|
||
<p>Atom IDs must be defined, must be consecutive, and an
|
||
<a class="reference internal" href="atom_modify.html"><span class="doc">atom map must be enabled</span></a></p>
|
||
<p>The total number of atoms must not be more than 2147483647 (max 32-bit signed int).</p>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>name</strong> – desired quantity (e.g., “x” or “f” for atom properties, “f_id” for per-atom fix data, “c_id” for per-atom compute data, “d_name” or “i_name” for fix property/atom vectors with <em>count</em> = 1, “d2_name” or “i2_name” for fix property/atom vectors with <em>count</em> > 1) </p></li>
|
||
<li><p><strong>type</strong> – 0 for <code class="docutils literal notranslate"><span class="pre">int</span></code> values, 1 for <code class="docutils literal notranslate"><span class="pre">double</span></code> values </p></li>
|
||
<li><p><strong>count</strong> – number of per-atom values (e.g., 1 for <em>type</em> or <em>charge</em>, 3 for <em>x</em> or <em>f</em>); use <em>count</em> = 3 with <em>image</em> if you have a single image flag packed into (<em>x</em>,<em>y</em>,<em>z</em>) components. </p></li>
|
||
<li><p><strong>data</strong> – per-atom values packed in a one-dimensional array of length <em>natoms</em> * <em>count</em>. </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv421lammps_scatter_subsetPvPKciiiPiPv">
|
||
<span id="_CPPv321lammps_scatter_subsetPvPKciiiPiPv"></span><span id="_CPPv221lammps_scatter_subsetPvPKciiiPiPv"></span><span id="lammps_scatter_subset__voidP.cCP.i.i.i.iP.voidP"></span><span class="target" id="library_8h_1ae379c37f2f8136e130030ddbe832695a"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_scatter_subset</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">char</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">name</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">type</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">count</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">ndata</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">ids</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv421lammps_scatter_subsetPvPKciiiPiPv" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Scatter the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities in <em>data</em> from a subset of atoms to all processes.</p>
|
||
<p><p>This subroutine takes data stored in a one-dimensional array supplied by the
|
||
user and scatters them to a subset of atoms on all processes. The array
|
||
<em>data</em> contains data associated with atom IDs, but there is no requirement that
|
||
the IDs be consecutive, as they are provided in a separate array.
|
||
Use <a class="reference internal" href="#_CPPv414lammps_scatterPvPKciiPv" title="lammps_scatter"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_scatter()</span></code></a> to scatter data for all atoms, in order.</p>
|
||
<p>The <em>data</em> array needs to be organized in groups of <em>count</em> values, with the
|
||
groups in the same order as the array <em>ids</em>. For example, if you want <em>data</em>
|
||
to be the array {x[1][0], x[1][1], x[1][2], x[100][0], x[100][1], x[100][2],
|
||
x[57][0], x[57][1], x[57][2]}, then <em>count</em> = 3, <em>ndata</em> = 3, and <em>ids</em> would
|
||
be {1, 100, 57}.</p>
|
||
<div class="warning admonition">
|
||
<p class="admonition-title">Restrictions</p>
|
||
<p>This function is not compatible with <code class="docutils literal notranslate"><span class="pre">-DLAMMPS_BIGBIG</span></code>.</p>
|
||
<p>Atom IDs must be defined and an <a class="reference internal" href="atom_modify.html"><span class="doc">atom map must be enabled</span></a></p>
|
||
<p>The total number of atoms must not be more than 2147483647 (max 32-bit signed int).</p>
|
||
</div>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>name</strong> – desired quantity (e.g., “x” or “f” for atom properties, “f_id” for per-atom fix data, “c_id” for per-atom compute data, “d_name” or “i_name” for fix property/atom vectors with <em>count</em> = 1, “d2_name” or “i2_name” for fix property/atom vectors with <em>count</em> > 1) </p></li>
|
||
<li><p><strong>type</strong> – 0 for <code class="docutils literal notranslate"><span class="pre">int</span></code> values, 1 for <code class="docutils literal notranslate"><span class="pre">double</span></code> values </p></li>
|
||
<li><p><strong>count</strong> – number of per-atom values (e.g., 1 for <em>type</em> or <em>charge</em>, 3 for <em>x</em> or <em>f</em>); use <em>count</em> = 3 with “image” if you want single image flags unpacked into (<em>x</em>,<em>y</em>,<em>z</em>) </p></li>
|
||
<li><p><strong>ndata</strong> – number of atoms listed in <em>ids</em> and <em>data</em> arrays </p></li>
|
||
<li><p><strong>ids</strong> – list of <em>ndata</em> atom IDs to scatter data to </p></li>
|
||
<li><p><strong>data</strong> – per-atom values packed in a 1-dimensional array of length <em>ndata</em> * <em>count</em>. </p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<hr class="docutils" />
|
||
<dl class="cpp function">
|
||
<dt class="sig sig-object cpp" id="_CPPv419lammps_create_atomsPviPKiPKiPKdPKdPKii">
|
||
<span id="_CPPv319lammps_create_atomsPviPKiPKiPKdPKdPKii"></span><span id="_CPPv219lammps_create_atomsPviPKiPKiPKdPKdPKii"></span><span id="lammps_create_atoms__voidP.i.iCP.iCP.doubleCP.doubleCP.iCP.i"></span><span class="target" id="library_8h_1aeebd5ebadb0c014f80e2c25dd369ff44"></span><span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">lammps_create_atoms</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">handle</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">n</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">id</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">type</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">double</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">x</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">double</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">v</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">image</span></span>, <span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">bexpand</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv419lammps_create_atomsPviPKiPKiPKdPKdPKii" title="Link to this definition"></a><br /></dt>
|
||
<dd><p>Create N atoms from list of coordinates</p>
|
||
<p><p>The prototype for this function when compiling with <code class="docutils literal notranslate"><span class="pre">-DLAMMPS_BIGBIG</span></code>
|
||
is:</p>
|
||
<div class="highlight-c notranslate"><div class="highlight"><pre><span></span><span class="kt">int</span><span class="w"> </span><span class="nf">lammps_create_atoms</span><span class="p">(</span><span class="kt">void</span><span class="w"> </span><span class="o">*</span><span class="n">handle</span><span class="p">,</span><span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">n</span><span class="p">,</span><span class="w"> </span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="n">id</span><span class="p">,</span><span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="o">*</span><span class="n">type</span><span class="p">,</span><span class="w"> </span><span class="kt">double</span><span class="w"> </span><span class="o">*</span><span class="n">x</span><span class="p">,</span><span class="w"> </span><span class="kt">double</span><span class="w"> </span><span class="o">*</span><span class="n">v</span><span class="p">,</span><span class="w"> </span><span class="kt">int64_t</span><span class="w"> </span><span class="o">*</span><span class="n">image</span><span class="p">,</span><span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">bexpand</span><span class="p">);</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>This function creates additional atoms from a given list of coordinates
|
||
and a list of atom types. Additionally the atom-IDs, velocities, and
|
||
image flags may be provided. If atom-IDs are not provided, they will be
|
||
automatically created as a sequence following the largest existing
|
||
atom-ID.</p>
|
||
<p>This function is useful to add atoms to a simulation or - in tandem with
|
||
<a class="reference internal" href="Library_properties.html#_CPPv416lammps_reset_boxPvPdPdddd" title="lammps_reset_box"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_reset_box()</span></code></a> - to restore a previously extracted and
|
||
saved state of a simulation. Additional properties for the new atoms
|
||
can then be assigned via the <a class="reference internal" href="#_CPPv420lammps_scatter_atomsPvPKciiPv" title="lammps_scatter_atoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_scatter_atoms()</span></code></a>
|
||
<a class="reference internal" href="Library_atoms.html#_CPPv419lammps_extract_atomPvPKc" title="lammps_extract_atom"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_atom()</span></code></a> functions.</p>
|
||
<p>For non-periodic boundaries, atoms will <strong>not</strong> be created that have
|
||
coordinates outside the box unless it is a shrink-wrap boundary and the
|
||
shrinkexceed flag has been set to a non-zero value. For periodic
|
||
boundaries atoms will be wrapped back into the simulation cell and its
|
||
image flags adjusted accordingly, unless explicit image flags are
|
||
provided.</p>
|
||
<p>The function returns the number of atoms created or -1 on failure (e.g.,
|
||
when called before as box has been created).</p>
|
||
<p>Coordinates and velocities have to be given in a 1d-array in the order
|
||
X(1), Y(1), Z(1), X(2), Y(2), Z(2), …, X(N), Y(N), Z(N).</p>
|
||
</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>handle</strong> – pointer to a previously created LAMMPS instance </p></li>
|
||
<li><p><strong>n</strong> – number of atoms, N, to be added to the system </p></li>
|
||
<li><p><strong>id</strong> – pointer to N atom IDs; <code class="docutils literal notranslate"><span class="pre">NULL</span></code> will generate IDs </p></li>
|
||
<li><p><strong>type</strong> – pointer to N atom types (required) </p></li>
|
||
<li><p><strong>x</strong> – pointer to 3N doubles with x-,y-,z- positions of the new atoms (required) </p></li>
|
||
<li><p><strong>v</strong> – pointer to 3N doubles with x-,y-,z- velocities of the new atoms (set to 0.0 if <code class="docutils literal notranslate"><span class="pre">NULL</span></code>) </p></li>
|
||
<li><p><strong>image</strong> – pointer to N imageint sets of image flags, or <code class="docutils literal notranslate"><span class="pre">NULL</span></code></p></li>
|
||
<li><p><strong>bexpand</strong> – if 1, atoms outside of shrink-wrap boundaries will still be created and not dropped and the box extended </p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>number of atoms created on success; -1 on failure (no box, no atom IDs, etc.) </p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
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