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<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
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<li><a href="#org2379e3e">1. Context</a>
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<ul>
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<li><a href="#org8b955ad">1.1. Data structure</a></li>
<li><a href="#org0fbaa5e">1.2. Access functions</a></li>
<li><a href="#org3f2250b">1.3. Initialization functions</a></li>
<li><a href="#org4bb7623">1.4. Test</a></li>
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</ul>
</li>
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<li><a href="#orgead9976">2. Computation</a>
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<ul>
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<li><a href="#orgd58caca">2.1. Nucleus-nucleus distances</a>
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<ul>
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<li><a href="#org4abfc83">2.1.1. Get</a></li>
<li><a href="#orga1f1505">2.1.2. Compute</a></li>
<li><a href="#orgb3e4a24">2.1.3. Test</a></li>
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</ul>
</li>
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<li><a href="#orgda6dc52">2.2. Nuclear repulsion energy</a>
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<ul>
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<li><a href="#org7483570">2.2.1. Get</a></li>
<li><a href="#orgecb367a">2.2.2. Compute</a></li>
<li><a href="#orgcf592cd">2.2.3. Test</a></li>
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</ul>
</li>
</ul>
</li>
</ul>
</div>
</div>
<p>
#i+TITLE: Nucleus
</p>
<p>
A ll the data relative to the molecular geometry is described here.
</p>
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<div id="outline-container-org2379e3e" class="outline-2">
<h2 id="org2379e3e"><span class="section-number-2">1</span> Context</h2>
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<div class="outline-text-2" id="text-1">
<p>
The following data stored in the context:
</p>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left"><code>uninitialized</code></td>
<td class="org-left">int32<sub>t</sub></td>
<td class="org-left">Keeps bit set for uninitialized data</td>
</tr>
<tr>
<td class="org-left"><code>num</code></td>
<td class="org-left">int64<sub>t</sub></td>
<td class="org-left">Total number of nuclei</td>
</tr>
<tr>
<td class="org-left"><code>provided</code></td>
<td class="org-left">bool</td>
<td class="org-left">If true, <code>nucleus</code> is valid</td>
</tr>
<tr>
<td class="org-left"><code>charge</code></td>
<td class="org-left">double[num]</td>
<td class="org-left">Nuclear charges</td>
</tr>
<tr>
<td class="org-left"><code>coord</code></td>
<td class="org-left">double[3][num]</td>
<td class="org-left">Nuclear coordinates</td>
</tr>
<tr>
<td class="org-left"><code>nn_distance</code></td>
<td class="org-left">double[num][num]</td>
<td class="org-left">Nucleus-nucleus distances</td>
</tr>
<tr>
<td class="org-left"><code>nn_distance_date</code></td>
<td class="org-left">int64<sub>t</sub></td>
<td class="org-left">Date when Nucleus-nucleus distances were computed</td>
</tr>
<tr>
<td class="org-left"><code>repulsion</code></td>
<td class="org-left">double</td>
<td class="org-left">Nuclear repulsion energy</td>
</tr>
<tr>
<td class="org-left"><code>repulsion_date</code></td>
<td class="org-left">int64<sub>t</sub></td>
<td class="org-left">Date when the nuclear repulsion energy was computed</td>
</tr>
</tbody>
</table>
</div>
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<div id="outline-container-org8b955ad" class="outline-3">
<h3 id="org8b955ad"><span class="section-number-3">1.1</span> Data structure</h3>
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<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">qmckl_nucleus_struct</span> {
<span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">num</span>;
<span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">repulsion_date</span>;
<span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">nn_distance_date</span>;
<span style="color: #228b22;">double</span>* <span style="color: #a0522d;">coord</span>;
<span style="color: #228b22;">double</span>* <span style="color: #a0522d;">charge</span>;
<span style="color: #228b22;">double</span>* <span style="color: #a0522d;">nn_distance</span>;
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">repulsion</span>;
<span style="color: #228b22;">int32_t</span> <span style="color: #a0522d;">uninitialized</span>;
<span style="color: #228b22;">bool</span> <span style="color: #a0522d;">provided</span>;
} <span style="color: #228b22;">qmckl_nucleus_struct</span>;
</pre>
</div>
<p>
The <code>uninitialized</code> integer contains one bit set to one for each
initialization function which has not bee called. It becomes equal
to zero after all initialization functions have been called. The
struct is then initialized and <code>provided == true</code>.
</p>
</div>
</div>
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<div id="outline-container-org0fbaa5e" class="outline-3">
<h3 id="org0fbaa5e"><span class="section-number-3">1.2</span> Access functions</h3>
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<div class="outline-text-3" id="text-1-2">
<p>
When all the data relative to nuclei have been set, the following
function returns <code>true</code>.
</p>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">bool</span> <span style="color: #0000ff;">qmckl_nucleus_provided</span> (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>);
</pre>
</div>
</div>
</div>
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<div id="outline-container-org3f2250b" class="outline-3">
<h3 id="org3f2250b"><span class="section-number-3">1.3</span> Initialization functions</h3>
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<div class="outline-text-3" id="text-1-3">
<p>
To set the data relative to the nuclei in the context, the
following functions need to be called.
</p>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_set_nucleus_num</span> (<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">num</span>);
<span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_set_nucleus_charge</span> (<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">charge</span>);
<span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_set_nucleus_coord</span> (<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">coord</span>);
</pre>
</div>
<p>
To set the number of nuclei, use
</p>
<p>
The following function sets the nuclear charges of all the atoms.
</p>
<p>
The following function sets the nuclear coordinates of all the
atoms. The coordinates should be given in atomic units.
</p>
</div>
</div>
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<h3 id="org4bb7623"><span class="section-number-3">1.4</span> Test</h3>
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<div class="outline-text-3" id="text-1-4">
<div class="org-src-container">
<pre class="src src-c">/* <span style="color: #b22222;">Reference input data </span>*/
<span style="color: #483d8b;">#define</span> <span style="color: #a0522d;">num</span> ((<span style="color: #228b22;">int64_t</span>) 9)
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">charge</span>[num] = { 6., 6., 6., 7., 7., 1., 1., 1., 1. };
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">coord</span>[3*num] =
{ 4.166279566732572e-01, -1.526183863767697e+00, 1.041604719335635e+00,
-1.903457631371503e+00, 2.242154435363994e+00, 6.550163404813796e-01,
-3.575005445908036e+00, -3.063638942318878e+00, 2.086739409279095e+00,
2.060062599100338e+00, -1.623431626827498e+00, -1.930074272670425e+00,
9.491495662916423e-01, 3.808343139803397e-01, 4.077482772289367e+00,
1.841031662652821e+00, -2.945591662994877e+00, -3.670011011125464e+00,
0.000000000000000e+00, 0.000000000000000e+00, 0.000000000000000e+00,
0.000000000000000e+00, 0.000000000000000e+00, 0.000000000000000e+00,
0.000000000000000e+00, 0.000000000000000e+00, 0.000000000000000e+00};
/* <span style="color: #b22222;">--- </span>*/
<span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #a0522d;">rc</span>;
assert(!qmckl_nucleus_provided(context));
<span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">n</span>;
rc = qmckl_get_nucleus_num (context, &amp;n);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_NOT_PROVIDED);
rc = qmckl_set_nucleus_num (context, num);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
assert(!qmckl_nucleus_provided(context));
rc = qmckl_get_nucleus_num (context, &amp;n);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
<span style="color: #0000ff;">assert</span>(n == num);
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">coord2</span>[3*num];
rc = qmckl_get_nucleus_coord (context, coord2);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_NOT_PROVIDED);
rc = qmckl_set_nucleus_coord (context, coord);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
rc = qmckl_get_nucleus_coord (context, coord2);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">i</span>=0 ; i&lt;3*num ; ++i) {
assert( coord[i] == coord2[i] );
}
assert(!qmckl_nucleus_provided(context));
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">charge2</span>[num];
rc = qmckl_get_nucleus_charge(context, charge2);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_NOT_PROVIDED);
rc = qmckl_set_nucleus_charge(context, charge);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
rc = qmckl_get_nucleus_charge(context, charge2);
<span style="color: #0000ff;">assert</span>(rc == QMCKL_SUCCESS);
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">i</span>=0 ; i&lt;num ; ++i) {
assert( charge[i] == charge2[i] );
}
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">qmckl_nucleus_provided</span>(<span style="color: #a0522d;">context</span>));
</pre>
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<h2 id="orgead9976"><span class="section-number-2">2</span> Computation</h2>
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<div class="outline-text-2" id="text-2">
<p>
The computed data is stored in the context so that it can be reused
by different kernels. To ensure that the data is valid, for each
computed data the date of the context is stored when it is computed.
To know if some data needs to be recomputed, we check if the date of
the dependencies are more recent than the date of the data to
compute. If it is the case, then the data is recomputed and the
current date is stored.
</p>
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<h3 id="orgd58caca"><span class="section-number-3">2.1</span> Nucleus-nucleus distances</h3>
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<div class="outline-text-3" id="text-2-1">
</div>
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<div id="outline-container-org4abfc83" class="outline-4">
<h4 id="org4abfc83"><span class="section-number-4">2.1.1</span> Get</h4>
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<div class="outline-text-4" id="text-2-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_get_nucleus_nn_distance</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">distance</span>);
</pre>
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<h4 id="orga1f1505"><span class="section-number-4">2.1.2</span> Compute</h4>
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<div class="outline-text-4" id="text-2-1-2">
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<table id="orgc1b87f5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
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<colgroup>
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left">qmckl<sub>context</sub></td>
<td class="org-left">context</td>
<td class="org-left">in</td>
<td class="org-left">Global state</td>
</tr>
<tr>
<td class="org-left">int64<sub>t</sub></td>
<td class="org-left">nucl<sub>num</sub></td>
<td class="org-left">in</td>
<td class="org-left">Number of nuclei</td>
</tr>
<tr>
<td class="org-left">double</td>
<td class="org-left">coord[3][nucl<sub>num</sub>]</td>
<td class="org-left">in</td>
<td class="org-left">Nuclear coordinates (au)</td>
</tr>
<tr>
<td class="org-left">double</td>
<td class="org-left">nn<sub>distance</sub>[nucl<sub>num</sub>][nucl<sub>num</sub>]</td>
<td class="org-left">out</td>
<td class="org-left">Nucleus-nucleus distances (au)</td>
</tr>
</tbody>
</table>
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer </span><span style="color: #a020f0;">function</span><span style="color: #a0522d;"> </span><span style="color: #0000ff;">qmckl_compute_nn_distance_f</span><span style="color: #000000; background-color: #ffffff;">(context, nucl_num, coord, nn_distance)</span><span style="color: #a0522d;"> </span><span style="color: #a020f0;">&amp;</span>
<span style="color: #a020f0;">result</span>(info)
<span style="color: #a020f0;">use</span> <span style="color: #0000ff;">qmckl</span>
<span style="color: #a020f0;">implicit</span> <span style="color: #228b22;">none</span>
<span style="color: #228b22;">integer</span>(qmckl_context), <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> context</span>
<span style="color: #228b22;">integer</span>*8 , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> nucl_num</span>
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> coord(nucl_num,3)</span>
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(out) ::<span style="color: #a0522d;"> nn_distance(nucl_num,nucl_num)</span>
<span style="color: #228b22;">integer</span>*8 ::<span style="color: #a0522d;"> k</span>
info = QMCKL_SUCCESS
<span style="color: #a020f0;">if</span> (context == QMCKL_NULL_CONTEXT) <span style="color: #a020f0;">then</span>
info = QMCKL_INVALID_CONTEXT
<span style="color: #a020f0;">return</span>
<span style="color: #a020f0;">endif</span>
<span style="color: #a020f0;">if</span> (nucl_num &lt;= 0) <span style="color: #a020f0;">then</span>
info = QMCKL_INVALID_ARG_2
<span style="color: #a020f0;">return</span>
<span style="color: #a020f0;">endif</span>
info = qmckl_distance(context, <span style="color: #8b2252;">'T'</span>, <span style="color: #8b2252;">'T'</span>, nucl_num, nucl_num, <span style="color: #a020f0;">&amp;</span>
coord, nucl_num, <span style="color: #a020f0;">&amp;</span>
coord, nucl_num, <span style="color: #a020f0;">&amp;</span>
nn_distance, nucl_num)
<span style="color: #a020f0;">end function</span> <span style="color: #0000ff;">qmckl_compute_nn_distance_f</span>
</pre>
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<h4 id="orgb3e4a24"><span class="section-number-4">2.1.3</span> Test</h4>
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<div class="outline-text-4" id="text-2-1-3">
<div class="org-src-container">
<pre class="src src-c">/* <span style="color: #b22222;">Reference input data </span>*/
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">qmckl_nucleus_provided</span>(<span style="color: #a0522d;">context</span>));
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">distance</span>[num*num];
rc = qmckl_get_nucleus_nn_distance(context, distance);
rc = qmckl_get_nucleus_nn_distance(context, distance);
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">distance</span>[0] == 0.);
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">distance</span>[1] == distance[num]);
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<span style="color: #0000ff;">assert</span>(fabs(<span style="color: #228b22;">distance</span>[1]-4.164450441785663) &lt; 1.e-12);
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</pre>
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<div id="outline-container-orgda6dc52" class="outline-3">
<h3 id="orgda6dc52"><span class="section-number-3">2.2</span> Nuclear repulsion energy</h3>
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<div class="outline-text-3" id="text-2-2">
<p>
\[
V_{NN} = \sum_{A=1}^{N-1} \sum_{B>A}^N \frac{Q_A Q_B}{R_{AB}}
\]
</p>
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<h4 id="org7483570"><span class="section-number-4">2.2.1</span> Get</h4>
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<div class="outline-text-4" id="text-2-2-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">qmckl_exit_code</span> <span style="color: #0000ff;">qmckl_get_nucleus_repulsion</span>(<span style="color: #228b22;">qmckl_context</span> <span style="color: #a0522d;">context</span>, <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">energy</span>);
</pre>
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<h4 id="orgecb367a"><span class="section-number-4">2.2.2</span> Compute</h4>
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<div class="outline-text-4" id="text-2-2-2">
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<colgroup>
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left">qmckl<sub>context</sub></td>
<td class="org-left">context</td>
<td class="org-left">in</td>
<td class="org-left">Global state</td>
</tr>
<tr>
<td class="org-left">int64<sub>t</sub></td>
<td class="org-left">nucl<sub>num</sub></td>
<td class="org-left">in</td>
<td class="org-left">Number of nuclei</td>
</tr>
<tr>
<td class="org-left">double</td>
<td class="org-left">charge[nucl<sub>num</sub>]</td>
<td class="org-left">in</td>
<td class="org-left">Nuclear charges (au)</td>
</tr>
<tr>
<td class="org-left">double</td>
<td class="org-left">nn<sub>distance</sub>[nucl<sub>num</sub>][nucl<sub>num</sub>]</td>
<td class="org-left">in</td>
<td class="org-left">Nucleus-nucleus distances (au)</td>
</tr>
<tr>
<td class="org-left">double</td>
<td class="org-left">energy</td>
<td class="org-left">out</td>
<td class="org-left">Nuclear repulsion energy</td>
</tr>
</tbody>
</table>
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer </span><span style="color: #a020f0;">function</span><span style="color: #a0522d;"> </span><span style="color: #0000ff;">qmckl_compute_nucleus_repulsion_f</span><span style="color: #000000; background-color: #ffffff;">(context, nucl_num, charge, nn_distance, energy)</span><span style="color: #a0522d;"> </span><span style="color: #a020f0;">&amp;</span>
<span style="color: #a020f0;">result</span>(info)
<span style="color: #a020f0;">use</span> <span style="color: #0000ff;">qmckl</span>
<span style="color: #a020f0;">implicit</span> <span style="color: #228b22;">none</span>
<span style="color: #228b22;">integer</span>(qmckl_context), <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> context</span>
<span style="color: #228b22;">integer</span>*8 , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> nucl_num</span>
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> charge(nucl_num)</span>
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(in) ::<span style="color: #a0522d;"> nn_distance(nucl_num,nucl_num)</span>
<span style="color: #228b22;">double precision</span> , <span style="color: #a020f0;">intent</span>(out) ::<span style="color: #a0522d;"> energy</span>
<span style="color: #228b22;">integer</span>*8 ::<span style="color: #a0522d;"> i, j</span>
info = QMCKL_SUCCESS
<span style="color: #a020f0;">if</span> (context == QMCKL_NULL_CONTEXT) <span style="color: #a020f0;">then</span>
info = QMCKL_INVALID_CONTEXT
<span style="color: #a020f0;">return</span>
<span style="color: #a020f0;">endif</span>
<span style="color: #a020f0;">if</span> (nucl_num &lt;= 0) <span style="color: #a020f0;">then</span>
info = QMCKL_INVALID_ARG_2
<span style="color: #a020f0;">return</span>
<span style="color: #a020f0;">endif</span>
energy = 0.d0
<span style="color: #a020f0;">do</span> j=2, nucl_num
<span style="color: #a020f0;">do</span> i=1, j-1
energy = energy + charge(i) * charge(j) / nn_distance(i,j)
<span style="color: #a020f0;">end do</span>
<span style="color: #a020f0;">end do</span>
<span style="color: #a020f0;">print</span> *, energy
<span style="color: #a020f0;">end function</span> <span style="color: #0000ff;">qmckl_compute_nucleus_repulsion_f</span>
</pre>
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<div id="outline-container-orgcf592cd" class="outline-4">
<h4 id="orgcf592cd"><span class="section-number-4">2.2.3</span> Test</h4>
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<div class="outline-text-4" id="text-2-2-3">
<div class="org-src-container">
<pre class="src src-c">/* <span style="color: #b22222;">Reference input data </span>*/
<span style="color: #0000ff;">assert</span>(<span style="color: #228b22;">qmckl_nucleus_provided</span>(<span style="color: #a0522d;">context</span>));
<span style="color: #228b22;">double</span> <span style="color: #a0522d;">rep</span>;
rc = qmckl_get_nucleus_repulsion(context, &amp;rep);
<span style="color: #0000ff;">assert</span>(rep - 163.50434957121263 &lt; 1.e-10);
</pre>
</div>
</div>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
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<p class="date">Created: 2021-05-18 Tue 10:33</p>
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<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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