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commit
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@ -3,7 +3,7 @@
|
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
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<head>
|
||||
<!-- 2021-09-16 Thu 14:47 -->
|
||||
<!-- 2021-09-22 Wed 11:34 -->
|
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
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<title>TREXIO source code documentation</title>
|
||||
@ -343,7 +343,7 @@ and bug reports should be submitted at
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2021-09-16 Thu 14:47</p>
|
||||
<p class="date">Created: 2021-09-22 Wed 11:34</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
16
Sparse.html
16
Sparse.html
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2021-09-16 Thu 14:47 -->
|
||||
<!-- 2021-09-22 Wed 11:34 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>‎</title>
|
||||
@ -232,8 +232,8 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org39414f4">1. Text back end</a></li>
|
||||
<li><a href="#orge8df5f1">2. HDF5 Back end</a></li>
|
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<li><a href="#org3bac473">1. Text back end</a></li>
|
||||
<li><a href="#orge8cbf73">2. HDF5 Back end</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -241,8 +241,8 @@ for the JavaScript code in this tag.
|
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See templator<sub>front.org</sub>
|
||||
</p>
|
||||
|
||||
<div id="outline-container-org39414f4" class="outline-2">
|
||||
<h2 id="org39414f4"><span class="section-number-2">1</span> Text back end</h2>
|
||||
<div id="outline-container-org3bac473" class="outline-2">
|
||||
<h2 id="org3bac473"><span class="section-number-2">1</span> Text back end</h2>
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<div class="outline-text-2" id="text-1">
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<p>
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As the size of the dataset should be extensible, the simplest
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@ -256,8 +256,8 @@ The offset can be used with <code>fseek(69L*offset, SEEK_SET)</code>
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||||
</div>
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||||
</div>
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||||
|
||||
<div id="outline-container-orge8df5f1" class="outline-2">
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<h2 id="orge8df5f1"><span class="section-number-2">2</span> HDF5 Back end</h2>
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<div id="outline-container-orge8cbf73" class="outline-2">
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<h2 id="orge8cbf73"><span class="section-number-2">2</span> HDF5 Back end</h2>
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<div class="outline-text-2" id="text-2">
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<p>
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We need to declare the number of rows of the dataset as
|
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@ -278,7 +278,7 @@ If the offset+num > nmax, we need to extend the dataset.
|
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</div>
|
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</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="date">Created: 2021-09-16 Thu 14:47</p>
|
||||
<p class="date">Created: 2021-09-22 Wed 11:34</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2021-09-16 Thu 14:47 -->
|
||||
<!-- 2021-09-22 Wed 11:34 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TREXIO source code documentation</title>
|
||||
@ -343,7 +343,7 @@ and bug reports should be submitted at
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2021-09-16 Thu 14:47</p>
|
||||
<p class="date">Created: 2021-09-22 Wed 11:34</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2021-09-16 Thu 14:47 -->
|
||||
<!-- 2021-09-22 Wed 11:34 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>HDF5 back end</title>
|
||||
@ -311,27 +311,27 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org26617cc">1. HDF5 back end</a>
|
||||
<li><a href="#org4f96d3c">1. HDF5 back end</a>
|
||||
<ul>
|
||||
<li><a href="#org61e9dc2">1.1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org07b6511">1.2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org6d62c11">1.3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orgd4e29e2">1.4. Template for HDF5 has/read/write a single dimensioning variable</a></li>
|
||||
<li><a href="#org1996ea4">1.5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org9f4f182">1.6. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgb952d9b">1.7. Template for HDF5 has/read/write a single string attribute</a></li>
|
||||
<li><a href="#org935b3d3">1.1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org3f84f22">1.2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org4c83b5a">1.3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orgcaaa384">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
|
||||
<li><a href="#orgaa02987">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
|
||||
<li><a href="#orgd1e0d5c">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
|
||||
<li><a href="#org560a3cb">1.7. Template for HDF5 has/read/write the string attribute</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
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||||
|
||||
<div id="outline-container-org26617cc" class="outline-2">
|
||||
<h2 id="org26617cc"><span class="section-number-2">1</span> HDF5 back end</h2>
|
||||
<div id="outline-container-org4f96d3c" class="outline-2">
|
||||
<h2 id="org4f96d3c"><span class="section-number-2">1</span> HDF5 back end</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
</div>
|
||||
<div id="outline-container-org61e9dc2" class="outline-3">
|
||||
<h3 id="org61e9dc2"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
|
||||
<div id="outline-container-org935b3d3" class="outline-3">
|
||||
<h3 id="org935b3d3"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
|
||||
<div class="outline-text-3" id="text-1-1">
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||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #483d8b;">#define</span> $GROUP$_GROUP_NAME <span style="color: #8b2252;">"$group$"</span>
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@ -343,8 +343,8 @@ for the JavaScript code in this tag.
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||||
</div>
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||||
</div>
|
||||
|
||||
<div id="outline-container-org07b6511" class="outline-3">
|
||||
<h3 id="org07b6511"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
|
||||
<div id="outline-container-org3f84f22" class="outline-3">
|
||||
<h3 id="org3f84f22"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
|
||||
<div class="outline-text-3" id="text-1-2">
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||||
<div class="org-src-container">
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||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_hdf5_s</span> {
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@ -358,8 +358,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
|
||||
|
||||
<div id="outline-container-org6d62c11" class="outline-3">
|
||||
<h3 id="org6d62c11"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
|
||||
<div id="outline-container-org4c83b5a" class="outline-3">
|
||||
<h3 id="org4c83b5a"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
|
||||
<div class="outline-text-3" id="text-1-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
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||||
@ -439,12 +439,12 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd4e29e2" class="outline-3">
|
||||
<h3 id="orgd4e29e2"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write a single dimensioning variable</h3>
|
||||
<div id="outline-container-orgcaaa384" class="outline-3">
|
||||
<h3 id="orgcaaa384"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
|
||||
<div class="outline-text-3" id="text-1-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
<span style="color: #0000ff;">trexio_hdf5_read_$group_num$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #228b22;">uint64_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">num</span>)
|
||||
<span style="color: #0000ff;">trexio_hdf5_read_$group_num$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, $group_num_dtype_double$* <span style="color: #a020f0;">const</span> num)
|
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{
|
||||
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||||
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
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@ -458,7 +458,7 @@ for the JavaScript code in this tag.
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">num_id</span> = H5Aopen(f->$group$_group, $GROUP_NUM$_NAME, H5P_DEFAULT);
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<span style="color: #a020f0;">if</span> (num_id <= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Aread(num_id, H5T_NATIVE_UINT64, num);
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Aread(num_id, H5T_$GROUP_NUM_H5_DTYPE$, num);
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H5Aclose(num_id);
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@ -473,60 +473,38 @@ for the JavaScript code in this tag.
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<div class="org-src-container">
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<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
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<span style="color: #0000ff;">trexio_hdf5_write_$group_num$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">num</span>)
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<span style="color: #0000ff;">trexio_hdf5_write_$group_num$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #a020f0;">const</span> $group_num_dtype_double$ num)
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{
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<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
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<span style="color: #a020f0;">if</span> (num == 0L ) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
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<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
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<span style="color: #a020f0;">if</span> (H5Aexists(f->$group$_group, $GROUP_NUM$_NAME) == 0) {
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/* <span style="color: #b22222;">Write the dimensioning variables </span>*/
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype</span> = H5Tcopy(H5T_NATIVE_UINT64);
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace</span> = H5Screate(H5S_SCALAR);
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">num_id</span> = H5Acreate(f->$group$_group, $GROUP_NUM$_NAME, dtype, dspace,
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H5P_DEFAULT, H5P_DEFAULT);
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<span style="color: #a020f0;">if</span> (num_id <= 0) {
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H5Sclose(dspace);
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H5Tclose(dtype);
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<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
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}
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Awrite(num_id, dtype, &(num));
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<span style="color: #a020f0;">if</span> (status < 0) {
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H5Aclose(num_id);
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H5Sclose(dspace);
|
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H5Tclose(dtype);
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<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
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}
|
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/* <span style="color: #b22222;">Write the dimensioning variables </span>*/
|
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype</span> = H5Tcopy(H5T_$GROUP_NUM_H5_DTYPE$);
|
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace</span> = H5Screate(H5S_SCALAR);
|
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|
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">num_id</span> = H5Acreate(f->$group$_group, $GROUP_NUM$_NAME,
|
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dtype, dspace, H5P_DEFAULT, H5P_DEFAULT);
|
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<span style="color: #a020f0;">if</span> (num_id <= 0) {
|
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H5Sclose(dspace);
|
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H5Aclose(num_id);
|
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H5Tclose(dtype);
|
||||
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
|
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|
||||
} <span style="color: #a020f0;">else</span> {
|
||||
|
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<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">infile_num</span>;
|
||||
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span> = trexio_hdf5_read_$group_num$(file, &(infile_num));
|
||||
<span style="color: #a020f0;">if</span> (rc != TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> rc;
|
||||
|
||||
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype</span> = H5Tcopy(H5T_NATIVE_UINT64);
|
||||
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">num_id</span> = H5Aopen(f->$group$_group, $GROUP_NUM$_NAME, H5P_DEFAULT);
|
||||
<span style="color: #a020f0;">if</span> (num_id <= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
|
||||
|
||||
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Awrite(num_id, dtype, &(num));
|
||||
<span style="color: #a020f0;">if</span> (status < 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
||||
|
||||
H5Aclose(num_id);
|
||||
H5Tclose(dtype);
|
||||
|
||||
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
|
||||
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
|
||||
}
|
||||
|
||||
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Awrite(num_id, dtype, &(num));
|
||||
<span style="color: #a020f0;">if</span> (status < 0) {
|
||||
H5Aclose(num_id);
|
||||
H5Sclose(dspace);
|
||||
H5Tclose(dtype);
|
||||
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
||||
}
|
||||
|
||||
H5Sclose(dspace);
|
||||
H5Aclose(num_id);
|
||||
H5Tclose(dtype);
|
||||
|
||||
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
|
||||
}
|
||||
</pre>
|
||||
</div>
|
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@ -556,8 +534,8 @@ for the JavaScript code in this tag.
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</div>
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</div>
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|
||||
<div id="outline-container-org1996ea4" class="outline-3">
|
||||
<h3 id="org1996ea4"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write a dataset of numerical data</h3>
|
||||
<div id="outline-container-orgaa02987" class="outline-3">
|
||||
<h3 id="orgaa02987"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
|
||||
<div class="outline-text-3" id="text-1-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -623,12 +601,6 @@ for the JavaScript code in this tag.
|
||||
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
|
||||
<span style="color: #a020f0;">if</span> ($group_dset$ == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
|
||||
|
||||
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
|
||||
uint64_t $group_dset_dim$;
|
||||
// <span style="color: #b22222;">error handling for rc is added by the generator</span>
|
||||
rc = trexio_hdf5_read_$group_dset_dim$(file, &($group_dset_dim$));
|
||||
<span style="color: #a020f0;">if</span> ($group_dset_dim$ == 0L) <span style="color: #a020f0;">return</span> TREXIO_INVALID_NUM;
|
||||
|
||||
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
|
||||
|
||||
<span style="color: #a020f0;">if</span> ( H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) != 1 ) {
|
||||
@ -686,8 +658,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9f4f182" class="outline-3">
|
||||
<h3 id="org9f4f182"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write a dataset of strings</h3>
|
||||
<div id="outline-container-orgd1e0d5c" class="outline-3">
|
||||
<h3 id="orgd1e0d5c"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of strings</h3>
|
||||
<div class="outline-text-3" id="text-1-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -805,12 +777,6 @@ for the JavaScript code in this tag.
|
||||
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
|
||||
<span style="color: #a020f0;">if</span> ($group_dset$ == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
|
||||
|
||||
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
|
||||
uint64_t $group_dset_dim$;
|
||||
// <span style="color: #b22222;">error handling for rc is added by the generator</span>
|
||||
rc = trexio_hdf5_read_$group_dset_dim$(file, &($group_dset_dim$));
|
||||
<span style="color: #a020f0;">if</span> ($group_dset_dim$ == 0L) <span style="color: #a020f0;">return</span> TREXIO_INVALID_NUM;
|
||||
|
||||
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
|
||||
|
||||
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span>;
|
||||
@ -898,8 +864,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb952d9b" class="outline-3">
|
||||
<h3 id="orgb952d9b"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write a single string attribute</h3>
|
||||
<div id="outline-container-org560a3cb" class="outline-3">
|
||||
<h3 id="org560a3cb"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the string attribute</h3>
|
||||
<div class="outline-text-3" id="text-1-7">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1026,7 +992,7 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2021-09-16 Thu 14:47</p>
|
||||
<p class="date">Created: 2021-09-22 Wed 11:34</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2021-09-16 Thu 14:47 -->
|
||||
<!-- 2021-09-22 Wed 11:34 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TEXT back end</title>
|
||||
@ -311,26 +311,26 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org52f7e07">1. TEXT back end</a>
|
||||
<li><a href="#orga4d2401">1. TEXT back end</a>
|
||||
<ul>
|
||||
<li><a href="#org9ec603c">1.1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org1aaf4f6">1.2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org838d52e">1.3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org3106705">1.4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org7810f25">1.5. Template for text read struct</a></li>
|
||||
<li><a href="#orga899e45">1.6. Template for text flush struct</a></li>
|
||||
<li><a href="#org4704bff">1.7. Template for text free memory</a></li>
|
||||
<li><a href="#org98dc9f8">1.8. Template for has/read/write the num attribute</a></li>
|
||||
<li><a href="#org4e36999">1.9. Template for has/read/write the dataset of numerical data</a></li>
|
||||
<li><a href="#org62fd780">1.10. Template for has/read/write the dataset of strings</a></li>
|
||||
<li><a href="#org21d2224">1.11. Template for has/read/write the string attribute</a></li>
|
||||
<li><a href="#orgaf090f2">1.12. RDM struct (hard-coded)</a>
|
||||
<li><a href="#orge21a8c1">1.1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#orgf6a2e80">1.2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org7acd3e2">1.3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orgcb97c8c">1.4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org626a4b9">1.5. Template for text read struct</a></li>
|
||||
<li><a href="#orgbd6f77e">1.6. Template for text flush struct</a></li>
|
||||
<li><a href="#org64836c8">1.7. Template for text free memory</a></li>
|
||||
<li><a href="#org5570dff">1.8. Template for has/read/write the numerical attribute</a></li>
|
||||
<li><a href="#org80fd31f">1.9. Template for has/read/write the dataset of numerical data</a></li>
|
||||
<li><a href="#org674f937">1.10. Template for has/read/write the dataset of strings</a></li>
|
||||
<li><a href="#org717b30b">1.11. Template for has/read/write the string attribute</a></li>
|
||||
<li><a href="#org00fb9fd">1.12. RDM struct (hard-coded)</a>
|
||||
<ul>
|
||||
<li><a href="#orgcb0d605">1.12.1. Read the complete struct</a></li>
|
||||
<li><a href="#org58df0ff">1.12.2. Flush the complete struct</a></li>
|
||||
<li><a href="#org6db163c">1.12.3. Free memory</a></li>
|
||||
<li><a href="#org750d656">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
|
||||
<li><a href="#org6f559f9">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
|
||||
<li><a href="#org5d5a720">1.12.1. Read the complete struct</a></li>
|
||||
<li><a href="#orge037de5">1.12.2. Flush the complete struct</a></li>
|
||||
<li><a href="#org8974291">1.12.3. Free memory</a></li>
|
||||
<li><a href="#org6c7c856">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
|
||||
<li><a href="#org62e0f4e">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
@ -339,8 +339,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org52f7e07" class="outline-2">
|
||||
<h2 id="org52f7e07"><span class="section-number-2">1</span> TEXT back end</h2>
|
||||
<div id="outline-container-orga4d2401" class="outline-2">
|
||||
<h2 id="orga4d2401"><span class="section-number-2">1</span> TEXT back end</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<p>
|
||||
The "file" produced by the text back end is a directory with one
|
||||
@ -361,12 +361,13 @@ The file is written when closed, or when the flush function is called.
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9ec603c" class="outline-3">
|
||||
<h3 id="org9ec603c"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
|
||||
<div id="outline-container-orge21a8c1" class="outline-3">
|
||||
<h3 id="orge21a8c1"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
|
||||
<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> $group$_s {
|
||||
uint64_t $group_num$;
|
||||
$group_num_dtype_double$ $group_num$;
|
||||
bool $group_num$_isSet;
|
||||
$group_dset_dtype$* $group_dset$;
|
||||
<span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">rank_$group_dset$</span>;
|
||||
<span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">to_flush</span>;
|
||||
@ -380,8 +381,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1aaf4f6" class="outline-3">
|
||||
<h3 id="org1aaf4f6"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
|
||||
<div id="outline-container-orgf6a2e80" class="outline-3">
|
||||
<h3 id="orgf6a2e80"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
|
||||
<div class="outline-text-3" id="text-1-2">
|
||||
<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;">rdm_s</span> {
|
||||
@ -407,8 +408,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org838d52e" class="outline-3">
|
||||
<h3 id="org838d52e"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
|
||||
<div id="outline-container-org7acd3e2" class="outline-3">
|
||||
<h3 id="org7acd3e2"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
|
||||
<div class="outline-text-3" id="text-1-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -509,8 +510,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3106705" class="outline-3">
|
||||
<h3 id="org3106705"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
|
||||
<div id="outline-container-orgcb97c8c" class="outline-3">
|
||||
<h3 id="orgcb97c8c"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
|
||||
<div class="outline-text-3" id="text-1-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -535,8 +536,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7810f25" class="outline-3">
|
||||
<h3 id="org7810f25"><span class="section-number-3">1.5</span> Template for text read struct</h3>
|
||||
<div id="outline-container-org626a4b9" class="outline-3">
|
||||
<h3 id="org626a4b9"><span class="section-number-3">1.5</span> Template for text read struct</h3>
|
||||
<div class="outline-text-3" id="text-1-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c">$group$_t*
|
||||
@ -633,18 +634,21 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
}
|
||||
// <span style="color: #b22222;">END REPEAT GROUP_DSET_ALL</span>
|
||||
|
||||
<span style="color: #228b22;">unsigned</span> <span style="color: #228b22;">int</span> <span style="color: #a0522d;">local_isSet</span>;
|
||||
// <span style="color: #b22222;">START REPEAT GROUP_NUM</span>
|
||||
/* <span style="color: #b22222;">Read data </span>*/
|
||||
rc = fscanf(f, <span style="color: #8b2252;">"%1023s"</span>, buffer);
|
||||
assert(!((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_num$"</span>) != 0)));
|
||||
<span style="color: #a020f0;">if</span> ((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_num$"</span>) != 0)) {
|
||||
assert(!((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_num$_isSet"</span>) != 0)));
|
||||
<span style="color: #a020f0;">if</span> ((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_num$_isSet"</span>) != 0)) {
|
||||
FREE(buffer);
|
||||
fclose(f);
|
||||
FREE($group$);
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
|
||||
}
|
||||
|
||||
rc = fscanf(f, <span style="color: #8b2252;">"%"</span> SCNu64 <span style="color: #8b2252;">""</span>, &($group$->$group_num$));
|
||||
/* <span style="color: #b22222;">additional parameter local_isSet is needed to suppress warning when fscanf into bool variable using %u or %d </span>*/
|
||||
rc = fscanf(f, <span style="color: #8b2252;">"%u"</span>, &(local_isSet));
|
||||
$group$->$group_num$_isSet = (<span style="color: #228b22;">bool</span>) local_isSet;
|
||||
assert(!(rc != 1));
|
||||
<span style="color: #a020f0;">if</span> (rc != 1) {
|
||||
FREE(buffer);
|
||||
@ -652,6 +656,26 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
FREE($group$);
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
|
||||
}
|
||||
|
||||
<span style="color: #a020f0;">if</span> ($group$->$group_num$_isSet == <span style="color: #008b8b;">true</span>) {
|
||||
rc = fscanf(f, <span style="color: #8b2252;">"%1023s"</span>, buffer);
|
||||
assert(!((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_num$"</span>) != 0)));
|
||||
<span style="color: #a020f0;">if</span> ((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_num$"</span>) != 0)) {
|
||||
FREE(buffer);
|
||||
fclose(f);
|
||||
FREE($group$);
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
|
||||
}
|
||||
|
||||
rc = fscanf(f, <span style="color: #8b2252;">"%$group_num_std_dtype_in$"</span>, &($group$->$group_num$));
|
||||
assert(!(rc != 1));
|
||||
<span style="color: #a020f0;">if</span> (rc != 1) {
|
||||
FREE(buffer);
|
||||
fclose(f);
|
||||
FREE($group$);
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
|
||||
}
|
||||
}
|
||||
// <span style="color: #b22222;">END REPEAT GROUP_NUM</span>
|
||||
|
||||
// <span style="color: #b22222;">START REPEAT GROUP_ATTR_STR</span>
|
||||
@ -745,40 +769,10 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
|
||||
// <span style="color: #b22222;">START REPEAT GROUP_DSET_STR</span>
|
||||
/* <span style="color: #b22222;">Allocate arrays </span>*/
|
||||
$group$->$group_dset$ = CALLOC(size_$group_dset$, $group_dset_dtype$);
|
||||
assert (!($group$->$group_dset$ == <span style="color: #008b8b;">NULL</span>));
|
||||
<span style="color: #a020f0;">if</span> ($group$->$group_dset$ == <span style="color: #008b8b;">NULL</span>) {
|
||||
FREE(buffer);
|
||||
fclose(f);
|
||||
FREE($group$->$group_dset$);
|
||||
FREE($group$);
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
|
||||
}
|
||||
|
||||
rc = fscanf(f, <span style="color: #8b2252;">"%1023s"</span>, buffer);
|
||||
assert(!((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_dset$"</span>) != 0)));
|
||||
<span style="color: #a020f0;">if</span> ((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_dset$"</span>) != 0)) {
|
||||
FREE(buffer);
|
||||
fclose(f);
|
||||
FREE($group$->$group_dset$);
|
||||
FREE($group$);
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
|
||||
}
|
||||
|
||||
/* <span style="color: #b22222;">WARNING: this tmp array allows to avoid allocation of space for each element of array of string</span>
|
||||
<span style="color: #b22222;"> , BUT it's size has to be number_of_str*max_len_str where max_len_str is somewhat arbitrary, e.g. 32.</span>
|
||||
<span style="color: #b22222;"> </span>*/
|
||||
<span style="color: #228b22;">char</span>* <span style="color: #a0522d;">tmp_$group_dset$</span>;
|
||||
<span style="color: #a020f0;">if</span>(size_$group_dset$ != 0) tmp_$group_dset$ = CALLOC(size_$group_dset$*32, <span style="color: #228b22;">char</span>);
|
||||
|
||||
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">i</span>=0 ; i<size_$group_dset$ ; ++i) {
|
||||
$group$->$group_dset$[i] = tmp_$group_dset$;
|
||||
/* <span style="color: #b22222;">conventional fcanf with "%s" only return the string before the first space character </span>
|
||||
<span style="color: #b22222;"> * to read string with spaces use "%[^\n]" possible with space before or after, i.e. " %[^\n]"</span>
|
||||
<span style="color: #b22222;"> * Q: depending on what ? </span>*/
|
||||
rc = fscanf(f, <span style="color: #8b2252;">" %1023[^\n]"</span>, tmp_$group_dset$);
|
||||
assert(!(rc != 1));
|
||||
<span style="color: #a020f0;">if</span> (rc != 1) {
|
||||
<span style="color: #a020f0;">if</span>(size_$group_dset$ != 0) {
|
||||
$group$->$group_dset$ = CALLOC(size_$group_dset$, $group_dset_dtype$);
|
||||
assert (!($group$->$group_dset$ == <span style="color: #008b8b;">NULL</span>));
|
||||
<span style="color: #a020f0;">if</span> ($group$->$group_dset$ == <span style="color: #008b8b;">NULL</span>) {
|
||||
FREE(buffer);
|
||||
fclose(f);
|
||||
FREE($group$->$group_dset$);
|
||||
@ -786,8 +780,40 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
|
||||
}
|
||||
|
||||
<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">tmp_$group_dset$_len</span> = strlen($group$->$group_dset$[i]);
|
||||
tmp_$group_dset$ += tmp_$group_dset$_len + 1;
|
||||
rc = fscanf(f, <span style="color: #8b2252;">"%1023s"</span>, buffer);
|
||||
assert(!((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_dset$"</span>) != 0)));
|
||||
<span style="color: #a020f0;">if</span> ((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_dset$"</span>) != 0)) {
|
||||
FREE(buffer);
|
||||
fclose(f);
|
||||
FREE($group$->$group_dset$);
|
||||
FREE($group$);
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
|
||||
}
|
||||
|
||||
/* <span style="color: #b22222;">WARNING: this tmp array allows to avoid allocation of space for each element of array of string</span>
|
||||
<span style="color: #b22222;"> , BUT it's size has to be number_of_str*max_len_str where max_len_str is somewhat arbitrary, e.g. 32.</span>
|
||||
<span style="color: #b22222;"> </span>*/
|
||||
<span style="color: #228b22;">char</span>* <span style="color: #a0522d;">tmp_$group_dset$</span>;
|
||||
tmp_$group_dset$ = CALLOC(size_$group_dset$*32, <span style="color: #228b22;">char</span>);
|
||||
|
||||
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">i</span>=0 ; i<size_$group_dset$ ; ++i) {
|
||||
$group$->$group_dset$[i] = tmp_$group_dset$;
|
||||
/* <span style="color: #b22222;">conventional fcanf with "%s" only return the string before the first space character </span>
|
||||
<span style="color: #b22222;"> * to read string with spaces use "%[^\n]" possible with space before or after, i.e. " %[^\n]"</span>
|
||||
<span style="color: #b22222;"> * Q: depending on what ? </span>*/
|
||||
rc = fscanf(f, <span style="color: #8b2252;">" %1023[^\n]"</span>, tmp_$group_dset$);
|
||||
assert(!(rc != 1));
|
||||
<span style="color: #a020f0;">if</span> (rc != 1) {
|
||||
FREE(buffer);
|
||||
fclose(f);
|
||||
FREE($group$->$group_dset$);
|
||||
FREE($group$);
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
|
||||
}
|
||||
|
||||
<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">tmp_$group_dset$_len</span> = strlen($group$->$group_dset$[i]);
|
||||
tmp_$group_dset$ += tmp_$group_dset$_len + 1;
|
||||
}
|
||||
}
|
||||
// <span style="color: #b22222;">END REPEAT GROUP_DSET_STR</span>
|
||||
|
||||
@ -805,8 +831,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga899e45" class="outline-3">
|
||||
<h3 id="orga899e45"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
|
||||
<div id="outline-container-orgbd6f77e" class="outline-3">
|
||||
<h3 id="orgbd6f77e"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
|
||||
<div class="outline-text-3" id="text-1-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -842,7 +868,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
// <span style="color: #b22222;">END REPEAT GROUP_DSET_ALL</span>
|
||||
|
||||
// <span style="color: #b22222;">START REPEAT GROUP_NUM</span>
|
||||
fprintf(f, <span style="color: #8b2252;">"$group_num$ %"</span> PRIu64 <span style="color: #8b2252;">"\n"</span>, $group$->$group_num$);
|
||||
fprintf(f, <span style="color: #8b2252;">"$group_num$_isSet %u \n"</span>, $group$->$group_num$_isSet);
|
||||
<span style="color: #a020f0;">if</span> ($group$->$group_num$_isSet == <span style="color: #008b8b;">true</span>) fprintf(f, <span style="color: #8b2252;">"$group_num$ %$group_num_std_dtype_out$ \n"</span>, $group$->$group_num$);
|
||||
// <span style="color: #b22222;">END REPEAT GROUP_NUM</span>
|
||||
|
||||
// <span style="color: #b22222;">START REPEAT GROUP_ATTR_STR</span>
|
||||
@ -870,8 +897,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4704bff" class="outline-3">
|
||||
<h3 id="org4704bff"><span class="section-number-3">1.7</span> Template for text free memory</h3>
|
||||
<div id="outline-container-org64836c8" class="outline-3">
|
||||
<h3 id="org64836c8"><span class="section-number-3">1.7</span> Template for text free memory</h3>
|
||||
<div class="outline-text-3" id="text-1-7">
|
||||
<p>
|
||||
Memory is allocated when reading. The following function frees memory.
|
||||
@ -916,12 +943,12 @@ Memory is allocated when reading. The following function frees memory.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org98dc9f8" class="outline-3">
|
||||
<h3 id="org98dc9f8"><span class="section-number-3">1.8</span> Template for has/read/write the num attribute</h3>
|
||||
<div id="outline-container-org5570dff" class="outline-3">
|
||||
<h3 id="org5570dff"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
|
||||
<div class="outline-text-3" id="text-1-8">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
<span style="color: #0000ff;">trexio_text_read_$group_num$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #228b22;">uint64_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">num</span>)
|
||||
<span style="color: #0000ff;">trexio_text_read_$group_num$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, $group_num_dtype_double$* <span style="color: #a020f0;">const</span> num)
|
||||
{
|
||||
|
||||
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
|
||||
@ -940,7 +967,7 @@ Memory is allocated when reading. The following function frees memory.
|
||||
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
<span style="color: #0000ff;">trexio_text_write_$group_num$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">num</span>)
|
||||
<span style="color: #0000ff;">trexio_text_write_$group_num$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #a020f0;">const</span> $group_num_dtype_double$ num)
|
||||
{
|
||||
|
||||
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
|
||||
@ -950,6 +977,7 @@ Memory is allocated when reading. The following function frees memory.
|
||||
<span style="color: #a020f0;">if</span> ($group$ == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
||||
|
||||
$group$->$group_num$ = num;
|
||||
$group$->$group_num$_isSet = <span style="color: #008b8b;">true</span>;
|
||||
$group$->to_flush = 1;
|
||||
|
||||
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
|
||||
@ -967,7 +995,7 @@ Memory is allocated when reading. The following function frees memory.
|
||||
$group$_t* $group$ = trexio_text_read_$group$((<span style="color: #228b22;">trexio_text_t</span>*) file);
|
||||
<span style="color: #a020f0;">if</span> ($group$ == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
||||
|
||||
<span style="color: #a020f0;">if</span> ($group$->$group_num$ > 0L){
|
||||
<span style="color: #a020f0;">if</span> ($group$->$group_num$_isSet == <span style="color: #008b8b;">true</span>){
|
||||
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
|
||||
} <span style="color: #a020f0;">else</span> {
|
||||
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
|
||||
@ -979,8 +1007,8 @@ Memory is allocated when reading. The following function frees memory.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4e36999" class="outline-3">
|
||||
<h3 id="org4e36999"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
|
||||
<div id="outline-container-org80fd31f" class="outline-3">
|
||||
<h3 id="org80fd31f"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
|
||||
<div class="outline-text-3" id="text-1-9">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1076,8 +1104,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org62fd780" class="outline-3">
|
||||
<h3 id="org62fd780"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
|
||||
<div id="outline-container-org674f937" class="outline-3">
|
||||
<h3 id="org674f937"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
|
||||
<div class="outline-text-3" id="text-1-10">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1178,8 +1206,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org21d2224" class="outline-3">
|
||||
<h3 id="org21d2224"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
|
||||
<div id="outline-container-org717b30b" class="outline-3">
|
||||
<h3 id="org717b30b"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
|
||||
<div class="outline-text-3" id="text-1-11">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1253,12 +1281,12 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgaf090f2" class="outline-3">
|
||||
<h3 id="orgaf090f2"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3>
|
||||
<div id="outline-container-org00fb9fd" class="outline-3">
|
||||
<h3 id="org00fb9fd"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3>
|
||||
<div class="outline-text-3" id="text-1-12">
|
||||
</div>
|
||||
<div id="outline-container-orgcb0d605" class="outline-4">
|
||||
<h4 id="orgcb0d605"><span class="section-number-4">1.12.1</span> Read the complete struct</h4>
|
||||
<div id="outline-container-org5d5a720" class="outline-4">
|
||||
<h4 id="org5d5a720"><span class="section-number-4">1.12.1</span> Read the complete struct</h4>
|
||||
<div class="outline-text-4" id="text-1-12-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">rdm_t</span>* <span style="color: #0000ff;">trexio_text_read_rdm</span>(<span style="color: #228b22;">trexio_text_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>);
|
||||
@ -1353,8 +1381,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org58df0ff" class="outline-4">
|
||||
<h4 id="org58df0ff"><span class="section-number-4">1.12.2</span> Flush the complete struct</h4>
|
||||
<div id="outline-container-orge037de5" class="outline-4">
|
||||
<h4 id="orge037de5"><span class="section-number-4">1.12.2</span> Flush the complete struct</h4>
|
||||
<div class="outline-text-4" id="text-1-12-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #0000ff;">trexio_text_flush_rdm</span>(<span style="color: #228b22;">trexio_text_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>);
|
||||
@ -1396,8 +1424,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6db163c" class="outline-4">
|
||||
<h4 id="org6db163c"><span class="section-number-4">1.12.3</span> Free memory</h4>
|
||||
<div id="outline-container-org8974291" class="outline-4">
|
||||
<h4 id="org8974291"><span class="section-number-4">1.12.3</span> Free memory</h4>
|
||||
<div class="outline-text-4" id="text-1-12-3">
|
||||
<p>
|
||||
Memory is allocated when reading. The followig function frees memory.
|
||||
@ -1433,8 +1461,8 @@ Memory is allocated when reading. The followig function frees memory.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org750d656" class="outline-4">
|
||||
<h4 id="org750d656"><span class="section-number-4">1.12.4</span> Read/Write the one<sub>e</sub> attribute</h4>
|
||||
<div id="outline-container-org6c7c856" class="outline-4">
|
||||
<h4 id="org6c7c856"><span class="section-number-4">1.12.4</span> Read/Write the one<sub>e</sub> attribute</h4>
|
||||
<div class="outline-text-4" id="text-1-12-4">
|
||||
<p>
|
||||
The <code>one_e</code> array is assumed allocated with the appropriate size.
|
||||
@ -1500,8 +1528,8 @@ The <code>one_e</code> array is assumed allocated with the appropriate size.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6f559f9" class="outline-4">
|
||||
<h4 id="org6f559f9"><span class="section-number-4">1.12.5</span> Read/Write the two<sub>e</sub> attribute</h4>
|
||||
<div id="outline-container-org62e0f4e" class="outline-4">
|
||||
<h4 id="org62e0f4e"><span class="section-number-4">1.12.5</span> Read/Write the two<sub>e</sub> attribute</h4>
|
||||
<div class="outline-text-4" id="text-1-12-5">
|
||||
<p>
|
||||
<code>two_e</code> is a sparse data structure, which can be too large to fit
|
||||
@ -1609,7 +1637,7 @@ file for each sparse float structure.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2021-09-16 Thu 14:47</p>
|
||||
<p class="date">Created: 2021-09-22 Wed 11:34</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
150
trex.html
150
trex.html
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2021-09-16 Thu 14:47 -->
|
||||
<!-- 2021-09-22 Wed 11:34 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>TREX Configuration file</title>
|
||||
@ -333,28 +333,28 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orgf01cc8b">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org6e07d76">2. Electron (electron group)</a></li>
|
||||
<li><a href="#orga389cc4">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#orge373450">4. Effective core potentials (ecp group)</a></li>
|
||||
<li><a href="#org9b59ff1">5. Basis set (basis group)</a></li>
|
||||
<li><a href="#orged437c1">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#orgc291cc2">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org73e1250">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org597fcf8">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org87488df">4. Effective core potentials (ecp group)</a></li>
|
||||
<li><a href="#org0791ffe">5. Basis set (basis group)</a></li>
|
||||
<li><a href="#org4666864">6. Atomic orbitals (ao group)</a>
|
||||
<ul>
|
||||
<li><a href="#ao_one_e">6.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
|
||||
<li><a href="#ao_two_e">6.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgbb85665">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#orgc2e724a">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgff9b4c2">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org6aedef6">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#org7dae4a0">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org68387d3">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgd7378f6">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
|
||||
<li><a href="#orgb3124cb">9. <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org951d21b">10. Appendix</a>
|
||||
<li><a href="#org7a75fad">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
|
||||
<li><a href="#orgf1a2f70">9. <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#orgf5c229e">10. Appendix</a>
|
||||
<ul>
|
||||
<li><a href="#orgbd76282">10.1. Python script from table to json</a></li>
|
||||
<li><a href="#orgf7576f4">10.1. Python script from table to json</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
@ -380,14 +380,24 @@ is reversed in the produced <code>trex.json</code> configuration file as the lib
|
||||
written in C.
|
||||
</p>
|
||||
|
||||
<p>
|
||||
TREXIO currently supports <code>int</code>, <code>float</code> and <code>str</code> types for both single attributes and arrays.
|
||||
Note, that some attributes might have <code>dim</code> type (e.g. <code>num</code> of the <code>nucleus</code> group).
|
||||
This type is treated exactly the same as <code>int</code> with the only difference that <code>dim</code> variables
|
||||
cannot be negative or zero. This additional constraint is required because <code>dim</code> attributes
|
||||
are used internally to allocate memory and to check array boundaries in the memory-safe API.
|
||||
Most of the times, the <code>dim</code> variables contain <code>num</code> suffix.
|
||||
</p>
|
||||
|
||||
|
||||
<p>
|
||||
In Fortran, the arrays are 1-based and in most other languages the
|
||||
arrays are 0-based. Hence, we introduce the <code>index</code> type which is an
|
||||
1-based <code>int</code> in the Fortran interface and 0-based otherwise.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-orgf01cc8b" class="outline-2">
|
||||
<h2 id="orgf01cc8b"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-orgc291cc2" class="outline-2">
|
||||
<h2 id="orgc291cc2"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<p>
|
||||
As we expect our files to be archived in open-data repositories, we
|
||||
@ -397,7 +407,7 @@ which have participated to the creation of the file, a list of
|
||||
authors of the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="orgae2a71e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org96a99b2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -420,7 +430,7 @@ authors of the file, and a textual description.
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left"><code>code_num</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Number of codes used to produce the file</td>
|
||||
</tr>
|
||||
@ -434,7 +444,7 @@ authors of the file, and a textual description.
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>author_num</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Number of authors of the file</td>
|
||||
</tr>
|
||||
@ -464,15 +474,15 @@ authors of the file, and a textual description.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6e07d76" class="outline-2">
|
||||
<h2 id="org6e07d76"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-org73e1250" class="outline-2">
|
||||
<h2 id="org73e1250"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
We consider wave functions expressed in the spin-free formalism, where
|
||||
the number of ↑ and ↓ electrons is fixed.
|
||||
</p>
|
||||
|
||||
<table id="orgbaec19d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgcf1029a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -495,14 +505,14 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left"><code>up_num</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Number of ↑-spin electrons</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>dn_num</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Number of ↓-spin electrons</td>
|
||||
</tr>
|
||||
@ -511,15 +521,15 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga389cc4" class="outline-2">
|
||||
<h2 id="orga389cc4"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-org597fcf8" class="outline-2">
|
||||
<h2 id="org597fcf8"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
<p>
|
||||
The nuclei are considered as fixed point charges. Coordinates are
|
||||
given in Cartesian \((x,y,z)\) format.
|
||||
</p>
|
||||
|
||||
<table id="org4271e24" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgc14b8fe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -542,7 +552,7 @@ given in Cartesian \((x,y,z)\) format.
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left"><code>num</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Number of nuclei</td>
|
||||
</tr>
|
||||
@ -579,8 +589,8 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge373450" class="outline-2">
|
||||
<h2 id="orge373450"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div id="outline-container-org87488df" class="outline-2">
|
||||
<h2 id="org87488df"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
<p>
|
||||
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
|
||||
@ -608,7 +618,7 @@ The functions \(V_{A\ell}\) are parameterized as:
|
||||
See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.4984046</a> for more info.
|
||||
</p>
|
||||
|
||||
<table id="org3e82be2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgfd7506b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -652,7 +662,7 @@ See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.49
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>local_num_n_max</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Maximum value of <code>local_n</code>, used for dimensioning arrays</td>
|
||||
</tr>
|
||||
@ -687,7 +697,7 @@ See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.49
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>non_local_num_n_max</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Maximum value of <code>non_local_n</code>, used for dimensioning arrays</td>
|
||||
</tr>
|
||||
@ -717,8 +727,8 @@ See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.49
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9b59ff1" class="outline-2">
|
||||
<h2 id="org9b59ff1"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-org0791ffe" class="outline-2">
|
||||
<h2 id="org0791ffe"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
<p>
|
||||
We consider here basis functions centered on nuclei. Hence, we enable
|
||||
@ -771,7 +781,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
|
||||
All the basis set parameters are stored in one-dimensional arrays:
|
||||
</p>
|
||||
|
||||
<table id="org7bbfbca" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org8a64b8c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -801,14 +811,14 @@ All the basis set parameters are stored in one-dimensional arrays:
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>num</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Total Number of shells</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>prim_num</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Total number of primitives</td>
|
||||
</tr>
|
||||
@ -940,8 +950,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orged437c1" class="outline-2">
|
||||
<h2 id="orged437c1"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-org4666864" class="outline-2">
|
||||
<h2 id="org4666864"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<p>
|
||||
Going from the atomic basis set to AOs implies a systematic
|
||||
@ -989,13 +999,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#org9b59ff1">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#org0791ffe">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
normalization factor of the atomic orbitals in spherical coordinates.
|
||||
The normalization factor of the \(xy\) function which should be
|
||||
introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</p>
|
||||
|
||||
<table id="orge2b99d5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgfdf45f4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1025,7 +1035,7 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>num</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Total number of atomic orbitals</td>
|
||||
</tr>
|
||||
@ -1047,8 +1057,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgcaa1ff2" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="orgcaa1ff2"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div id="outline-container-org15c6107" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org15c6107"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div class="outline-text-3" id="text-ao_one_e">
|
||||
<ul class="org-ul">
|
||||
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
|
||||
@ -1066,7 +1076,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org508a477" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org3bc1d9c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1133,8 +1143,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org19a3d73" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org19a3d73"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div id="outline-container-orgdf4e873" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="orgdf4e873"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div class="outline-text-3" id="text-ao_two_e">
|
||||
<p>
|
||||
The two-electron integrals for a two-electron operator \(\hat{O}\) are
|
||||
@ -1155,7 +1165,7 @@ notation.
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
|
||||
</ul>
|
||||
|
||||
<table id="org095dd51" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgc46ab51" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1195,10 +1205,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgbb85665" class="outline-2">
|
||||
<h2 id="orgbb85665"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-orgc2e724a" class="outline-2">
|
||||
<h2 id="orgc2e724a"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="orgad0e1ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgf858b0b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1228,7 +1238,7 @@ notation.
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>num</code></td>
|
||||
<td class="org-left"><code>int</code></td>
|
||||
<td class="org-left"><code>dim</code></td>
|
||||
<td class="org-left"> </td>
|
||||
<td class="org-left">Number of MOs</td>
|
||||
</tr>
|
||||
@ -1264,8 +1274,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgff9b4c2" class="outline-3">
|
||||
<h3 id="orgff9b4c2"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div id="outline-container-org7dae4a0" class="outline-3">
|
||||
<h3 id="org7dae4a0"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div class="outline-text-3" id="text-7-1">
|
||||
<p>
|
||||
The operators as the same as those defined in the
|
||||
@ -1273,7 +1283,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org276731f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org51eb58d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1340,8 +1350,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6aedef6" class="outline-3">
|
||||
<h3 id="org6aedef6"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div id="outline-container-org68387d3" class="outline-3">
|
||||
<h3 id="org68387d3"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div class="outline-text-3" id="text-7-2">
|
||||
<p>
|
||||
The operators as the same as those defined in the
|
||||
@ -1349,7 +1359,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org91cfad3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgb953cb5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1389,13 +1399,13 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd7378f6" class="outline-2">
|
||||
<h2 id="orgd7378f6"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
|
||||
<div id="outline-container-org7a75fad" class="outline-2">
|
||||
<h2 id="org7a75fad"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
|
||||
</div>
|
||||
<div id="outline-container-orgb3124cb" class="outline-2">
|
||||
<h2 id="orgb3124cb"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
|
||||
<div id="outline-container-orgf1a2f70" class="outline-2">
|
||||
<h2 id="orgf1a2f70"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<table id="orgf4ea161" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org7a1d0c4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1448,15 +1458,15 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org951d21b" class="outline-2">
|
||||
<h2 id="org951d21b"><span class="section-number-2">10</span> Appendix</h2>
|
||||
<div id="outline-container-orgf5c229e" class="outline-2">
|
||||
<h2 id="orgf5c229e"><span class="section-number-2">10</span> Appendix</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
</div>
|
||||
<div id="outline-container-orgbd76282" class="outline-3">
|
||||
<h3 id="orgbd76282"><span class="section-number-3">10.1</span> Python script from table to json</h3>
|
||||
<div id="outline-container-orgf7576f4" class="outline-3">
|
||||
<h3 id="orgf7576f4"><span class="section-number-3">10.1</span> Python script from table to json</h3>
|
||||
<div class="outline-text-3" id="text-10-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-python" id="org55db609"><span style="color: #a020f0;">print</span>(<span style="color: #8b2252;">"""#+begin_src python :tangle trex.json"""</span>)
|
||||
<pre class="src src-python" id="org6318b64"><span style="color: #a020f0;">print</span>(<span style="color: #8b2252;">"""#+begin_src python :tangle trex.json"""</span>)
|
||||
<span style="color: #a020f0;">print</span>(<span style="color: #8b2252;">""" "%s": {"""</span>%(title))
|
||||
<span style="color: #a0522d;">indent</span> = <span style="color: #8b2252;">" "</span>
|
||||
<span style="color: #a0522d;">f1</span> = 0 ; <span style="color: #a0522d;">f2</span> = 0 ; <span style="color: #a0522d;">f3</span> = 0
|
||||
@ -1509,7 +1519,7 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2021-09-16 Thu 14:47</p>
|
||||
<p class="date">Created: 2021-09-22 Wed 11:34</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
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Reference in New Issue
Block a user