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README.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2024-03-15 Fri 16:53 --> <!-- 2024-03-22 Fri 14:46 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title> <title>TREXIO source code documentation</title>
@ -406,7 +406,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-03-15 Fri 16:53</p> <p class="date">Created: 2024-03-22 Fri 14:46</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>

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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2024-03-15 Fri 16:53 --> <!-- 2024-03-22 Fri 14:46 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title> <title>Examples</title>
@ -346,61 +346,61 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#org448993e">1. Writing nuclear coordinates</a> <li><a href="#org987e4fa">1. Writing nuclear coordinates</a>
<ul> <ul>
<li><a href="#org222874e">1.1. C</a></li> <li><a href="#org824f665">1.1. C</a></li>
<li><a href="#org6034fe5">1.2. Python</a></li> <li><a href="#org6d7311a">1.2. Python</a></li>
<li><a href="#org0580e7a">1.3. Fortran</a></li> <li><a href="#org89331ff">1.3. Fortran</a></li>
</ul> </ul>
</li> </li>
<li><a href="#org2c6eb7b">2. Accessing sparse quantities (integrals)</a> <li><a href="#orgf4b95b0">2. Accessing sparse quantities (integrals)</a>
<ul> <ul>
<li><a href="#orga548050">2.1. Fortran</a> <li><a href="#orgb211c84">2.1. Fortran</a>
<ul> <ul>
<li><a href="#org49cf300">2.1.1. Declare Temporary variables</a></li> <li><a href="#orgfc497ca">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgb779a41">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li> <li><a href="#orgc0f803d">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgd7f6a21">2.1.3. Read the nuclear repulsion energy</a></li> <li><a href="#org0bd82ef">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgb7f56d0">2.1.4. Read the number of molecular orbitals</a></li> <li><a href="#orge781dc4">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org468113d">2.1.5. Allocate memory</a></li> <li><a href="#orgd24079e">2.1.5. Allocate memory</a></li>
<li><a href="#org97bf917">2.1.6. Read one-electron quantities</a></li> <li><a href="#orga047f0c">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orge5f9064">2.1.7. Read two-electron quantities</a> <li><a href="#org1854afe">2.1.7. Read two-electron quantities</a>
<ul> <ul>
<li><a href="#orgc02bffd">2.1.7.1. Electron repulsion integrals</a></li> <li><a href="#org1943d44">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgbc9a904">2.1.7.2. Reduced density matrix</a></li> <li><a href="#org414749d">2.1.7.2. Reduced density matrix</a></li>
</ul> </ul>
</li> </li>
<li><a href="#org3c12e83">2.1.8. Compute the energy</a></li> <li><a href="#org305fa57">2.1.8. Compute the energy</a></li>
<li><a href="#orge3546cb">2.1.9. Terminate</a></li> <li><a href="#orgefdea31">2.1.9. Terminate</a></li>
</ul> </ul>
</li> </li>
<li><a href="#org0f59a88">2.2. Python</a> <li><a href="#orged00879">2.2. Python</a>
<ul> <ul>
<li><a href="#orgc67f461">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li> <li><a href="#org1850d9f">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org288c1f9">2.2.2. Read the nuclear repulsion energy</a></li> <li><a href="#orgb33e2a0">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org657b8a7">2.2.3. Read the number of molecular orbitals</a></li> <li><a href="#orgb63f76f">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org44aebda">2.2.4. Read one-electron quantities</a></li> <li><a href="#org9d937a3">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org40b3e91">2.2.5. Read two-electron quantities</a> <li><a href="#org045b896">2.2.5. Read two-electron quantities</a>
<ul> <ul>
<li><a href="#orgfb5147e">2.2.5.1. Electron repulsion integrals</a></li> <li><a href="#org7e1df20">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org4cecc3f">2.2.5.2. Reduced density matrix</a></li> <li><a href="#orgfe66b43">2.2.5.2. Reduced density matrix</a></li>
</ul> </ul>
</li> </li>
<li><a href="#org58ef1b3">2.2.6. Compute the energy</a></li> <li><a href="#orgf56696a">2.2.6. Compute the energy</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
</li> </li>
<li><a href="#orgccabdc9">3. Reading determinants</a> <li><a href="#org66cc410">3. Reading determinants</a>
<ul> <ul>
<li><a href="#org5f5cdc3">3.1. Fortran</a></li> <li><a href="#org8d64da0">3.1. Fortran</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org448993e" class="outline-2"> <div id="outline-container-org987e4fa" class="outline-2">
<h2 id="org448993e"><span class="section-number-2">1</span> Writing nuclear coordinates</h2> <h2 id="org987e4fa"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div class="outline-text-2" id="text-1"> <div class="outline-text-2" id="text-1">
<p> <p>
Here is a demonstration of how to use TREXIO to write the nuclear Here is a demonstration of how to use TREXIO to write the nuclear
@ -410,8 +410,8 @@ as well as the necessary TREXIO functions to perform these actions.
</p> </p>
</div> </div>
<div id="outline-container-org222874e" class="outline-3"> <div id="outline-container-org824f665" class="outline-3">
<h3 id="org222874e"><span class="section-number-3">1.1</span> C</h3> <h3 id="org824f665"><span class="section-number-3">1.1</span> C</h3>
<div class="outline-text-3" id="text-1-1"> <div class="outline-text-3" id="text-1-1">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #483d8b;">#include</span> <span style="color: #8b2252;">&lt;stdio.h&gt;</span> <pre class="src src-c"><span style="color: #483d8b;">#include</span> <span style="color: #8b2252;">&lt;stdio.h&gt;</span>
@ -461,8 +461,8 @@ as well as the necessary TREXIO functions to perform these actions.
</div> </div>
</div> </div>
<div id="outline-container-org6034fe5" class="outline-3"> <div id="outline-container-org6d7311a" class="outline-3">
<h3 id="org6034fe5"><span class="section-number-3">1.2</span> Python</h3> <h3 id="org6d7311a"><span class="section-number-3">1.2</span> Python</h3>
<div class="outline-text-3" id="text-1-2"> <div class="outline-text-3" id="text-1-2">
<p> <p>
This code uses the TREXIO Python binding to create a new TREXIO file named This code uses the TREXIO Python binding to create a new TREXIO file named
@ -509,8 +509,8 @@ coordinates of the system.
</div> </div>
</div> </div>
<div id="outline-container-org0580e7a" class="outline-3"> <div id="outline-container-org89331ff" class="outline-3">
<h3 id="org0580e7a"><span class="section-number-3">1.3</span> Fortran</h3> <h3 id="org89331ff"><span class="section-number-3">1.3</span> Fortran</h3>
<div class="outline-text-3" id="text-1-3"> <div class="outline-text-3" id="text-1-3">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">trexio_water</span> <pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">trexio_water</span>
@ -567,12 +567,12 @@ coordinates of the system.
</div> </div>
</div> </div>
<div id="outline-container-org2c6eb7b" class="outline-2"> <div id="outline-container-orgf4b95b0" class="outline-2">
<h2 id="org2c6eb7b"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2> <h2 id="orgf4b95b0"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div class="outline-text-2" id="text-2"> <div class="outline-text-2" id="text-2">
</div> </div>
<div id="outline-container-orga548050" class="outline-3"> <div id="outline-container-orgb211c84" class="outline-3">
<h3 id="orga548050"><span class="section-number-3">2.1</span> Fortran</h3> <h3 id="orgb211c84"><span class="section-number-3">2.1</span> Fortran</h3>
<div class="outline-text-3" id="text-2-1"> <div class="outline-text-3" id="text-2-1">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span> <pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
@ -618,8 +618,8 @@ One needs to read from the TREXIO file:
</div> </div>
</div> </div>
<div id="outline-container-org49cf300" class="outline-4"> <div id="outline-container-orgfc497ca" class="outline-4">
<h4 id="org49cf300"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4> <h4 id="orgfc497ca"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div class="outline-text-4" id="text-2-1-1"> <div class="outline-text-4" id="text-2-1-1">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span> <pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span>
@ -634,8 +634,8 @@ One needs to read from the TREXIO file:
</div> </div>
</div> </div>
<div id="outline-container-orgb779a41" class="outline-4"> <div id="outline-container-orgc0f803d" class="outline-4">
<h4 id="orgb779a41"><span class="section-number-4">2.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4> <h4 id="orgc0f803d"><span class="section-number-4">2.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div class="outline-text-4" id="text-2-1-2"> <div class="outline-text-4" id="text-2-1-2">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename) <pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
@ -651,8 +651,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div> </div>
</div> </div>
<div id="outline-container-orgd7f6a21" class="outline-4"> <div id="outline-container-org0bd82ef" class="outline-4">
<h4 id="orgd7f6a21"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4> <h4 id="org0bd82ef"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-2-1-3"> <div class="outline-text-4" id="text-2-1-3">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn) <pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
@ -666,8 +666,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div> </div>
</div> </div>
<div id="outline-container-orgb7f56d0" class="outline-4"> <div id="outline-container-orge781dc4" class="outline-4">
<h4 id="orgb7f56d0"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4> <h4 id="orge781dc4"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-2-1-4"> <div class="outline-text-4" id="text-2-1-4">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_mo_num(f, n) <pre class="src src-f90">rc = trexio_read_mo_num(f, n)
@ -681,8 +681,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div> </div>
</div> </div>
<div id="outline-container-org468113d" class="outline-4"> <div id="outline-container-orgd24079e" class="outline-4">
<h4 id="org468113d"><span class="section-number-4">2.1.5</span> Allocate memory</h4> <h4 id="orgd24079e"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div class="outline-text-4" id="text-2-1-5"> <div class="outline-text-4" id="text-2-1-5">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) ) <pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
@ -694,8 +694,8 @@ W(:,:,:,:) = 0.d0
</div> </div>
</div> </div>
<div id="outline-container-org97bf917" class="outline-4"> <div id="outline-container-orga047f0c" class="outline-4">
<h4 id="org97bf917"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4> <h4 id="orga047f0c"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-2-1-6"> <div class="outline-text-4" id="text-2-1-6">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f) <pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@ -727,8 +727,8 @@ rc = trexio_read_rdm_1e(f, D)
</div> </div>
</div> </div>
<div id="outline-container-orge5f9064" class="outline-4"> <div id="outline-container-org1854afe" class="outline-4">
<h4 id="orge5f9064"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4> <h4 id="org1854afe"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-2-1-7"> <div class="outline-text-4" id="text-2-1-7">
<p> <p>
Reading is done with OpenMP. Each thread reads its own buffer, and Reading is done with OpenMP. Each thread reads its own buffer, and
@ -744,8 +744,8 @@ to be protected in the critical section when modified.
</p> </p>
</div> </div>
<div id="outline-container-orgc02bffd" class="outline-5"> <div id="outline-container-org1943d44" class="outline-5">
<h5 id="orgc02bffd"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5> <h5 id="org1943d44"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-2-1-7-1"> <div class="outline-text-5" id="text-2-1-7-1">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f) <pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
@ -794,8 +794,8 @@ icount = BUFSIZE
</div> </div>
</div> </div>
<div id="outline-container-orgbc9a904" class="outline-5"> <div id="outline-container-org414749d" class="outline-5">
<h5 id="orgbc9a904"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5> <h5 id="org414749d"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-2-1-7-2"> <div class="outline-text-5" id="text-2-1-7-2">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_rdm_2e(f) <pre class="src src-f90">rc = trexio_has_rdm_2e(f)
@ -839,8 +839,8 @@ icount = bufsize
</div> </div>
</div> </div>
<div id="outline-container-org3c12e83" class="outline-4"> <div id="outline-container-org305fa57" class="outline-4">
<h4 id="org3c12e83"><span class="section-number-4">2.1.8</span> Compute the energy</h4> <h4 id="org305fa57"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-2-1-8"> <div class="outline-text-4" id="text-2-1-8">
<p> <p>
When the orbitals are real, we can use When the orbitals are real, we can use
@ -886,8 +886,8 @@ E = E + E_nn
</div> </div>
</div> </div>
<div id="outline-container-orge3546cb" class="outline-4"> <div id="outline-container-orgefdea31" class="outline-4">
<h4 id="orge3546cb"><span class="section-number-4">2.1.9</span> Terminate</h4> <h4 id="orgefdea31"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div class="outline-text-4" id="text-2-1-9"> <div class="outline-text-4" id="text-2-1-9">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W ) <pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
@ -899,8 +899,8 @@ E = E + E_nn
</div> </div>
</div> </div>
<div id="outline-container-org0f59a88" class="outline-3"> <div id="outline-container-orged00879" class="outline-3">
<h3 id="org0f59a88"><span class="section-number-3">2.2</span> Python</h3> <h3 id="orged00879"><span class="section-number-3">2.2</span> Python</h3>
<div class="outline-text-3" id="text-2-2"> <div class="outline-text-3" id="text-2-2">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">import</span> sys <pre class="src src-python"><span style="color: #a020f0;">import</span> sys
@ -934,8 +934,8 @@ One needs to read from the TREXIO file:
</dl> </dl>
</div> </div>
<div id="outline-container-orgc67f461" class="outline-4"> <div id="outline-container-org1850d9f" class="outline-4">
<h4 id="orgc67f461"><span class="section-number-4">2.2.1</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4> <h4 id="org1850d9f"><span class="section-number-4">2.2.1</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div class="outline-text-4" id="text-2-2-1"> <div class="outline-text-4" id="text-2-2-1">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">filename</span> = sys.argv[1] <pre class="src src-python"><span style="color: #a0522d;">filename</span> = sys.argv[1]
@ -945,8 +945,8 @@ One needs to read from the TREXIO file:
</div> </div>
</div> </div>
<div id="outline-container-org288c1f9" class="outline-4"> <div id="outline-container-orgb33e2a0" class="outline-4">
<h4 id="org288c1f9"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4> <h4 id="orgb33e2a0"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-2-2-2"> <div class="outline-text-4" id="text-2-2-2">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">E_nn</span> = trexio.read_nucleus_repulsion(f) <pre class="src src-python"><span style="color: #a0522d;">E_nn</span> = trexio.read_nucleus_repulsion(f)
@ -955,8 +955,8 @@ One needs to read from the TREXIO file:
</div> </div>
</div> </div>
<div id="outline-container-org657b8a7" class="outline-4"> <div id="outline-container-orgb63f76f" class="outline-4">
<h4 id="org657b8a7"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4> <h4 id="orgb63f76f"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-2-2-3"> <div class="outline-text-4" id="text-2-2-3">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">n</span> = trexio.read_mo_num(f) <pre class="src src-python"><span style="color: #a0522d;">n</span> = trexio.read_mo_num(f)
@ -965,8 +965,8 @@ One needs to read from the TREXIO file:
</div> </div>
</div> </div>
<div id="outline-container-org44aebda" class="outline-4"> <div id="outline-container-org9d937a3" class="outline-4">
<h4 id="org44aebda"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4> <h4 id="org9d937a3"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-2-2-4"> <div class="outline-text-4" id="text-2-2-4">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_mo_1e_int_core_hamiltonian(f): <pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_mo_1e_int_core_hamiltonian(f):
@ -985,12 +985,12 @@ One needs to read from the TREXIO file:
</div> </div>
</div> </div>
<div id="outline-container-org40b3e91" class="outline-4"> <div id="outline-container-org045b896" class="outline-4">
<h4 id="org40b3e91"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4> <h4 id="org045b896"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-2-2-5"> <div class="outline-text-4" id="text-2-2-5">
</div> </div>
<div id="outline-container-orgfb5147e" class="outline-5"> <div id="outline-container-org7e1df20" class="outline-5">
<h5 id="orgfb5147e"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5> <h5 id="org7e1df20"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-2-2-5-1"> <div class="outline-text-5" id="text-2-2-5-1">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_mo_2e_int_eri(f): <pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_mo_2e_int_eri(f):
@ -1020,8 +1020,8 @@ One needs to read from the TREXIO file:
</div> </div>
</div> </div>
<div id="outline-container-org4cecc3f" class="outline-5"> <div id="outline-container-orgfe66b43" class="outline-5">
<h5 id="org4cecc3f"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5> <h5 id="orgfe66b43"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-2-2-5-2"> <div class="outline-text-5" id="text-2-2-5-2">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_rdm_2e(f): <pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_rdm_2e(f):
@ -1043,8 +1043,8 @@ One needs to read from the TREXIO file:
</div> </div>
</div> </div>
<div id="outline-container-org58ef1b3" class="outline-4"> <div id="outline-container-orgf56696a" class="outline-4">
<h4 id="org58ef1b3"><span class="section-number-4">2.2.6</span> Compute the energy</h4> <h4 id="orgf56696a"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div class="outline-text-4" id="text-2-2-6"> <div class="outline-text-4" id="text-2-2-6">
<p> <p>
When the orbitals are real, we can use When the orbitals are real, we can use
@ -1073,12 +1073,12 @@ E &=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,
</div> </div>
</div> </div>
<div id="outline-container-orgccabdc9" class="outline-2"> <div id="outline-container-org66cc410" class="outline-2">
<h2 id="orgccabdc9"><span class="section-number-2">3</span> Reading determinants</h2> <h2 id="org66cc410"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3"> <div class="outline-text-2" id="text-3">
</div> </div>
<div id="outline-container-org5f5cdc3" class="outline-3"> <div id="outline-container-org8d64da0" class="outline-3">
<h3 id="org5f5cdc3"><span class="section-number-3">3.1</span> Fortran</h3> <h3 id="org8d64da0"><span class="section-number-3">3.1</span> Fortran</h3>
<div class="outline-text-3" id="text-3-1"> <div class="outline-text-3" id="text-3-1">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span> <pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
@ -1157,7 +1157,7 @@ end
</div> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-03-15 Fri 16:53</p> <p class="date">Created: 2024-03-22 Fri 14:46</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>

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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2024-03-15 Fri 16:53 --> <!-- 2024-03-22 Fri 14:46 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title> <title>TREXIO source code documentation</title>
@ -406,7 +406,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-03-15 Fri 16:53</p> <p class="date">Created: 2024-03-22 Fri 14:46</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>

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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2024-03-15 Fri 16:53 --> <!-- 2024-03-22 Fri 14:46 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Motivation</title> <title>Motivation</title>
@ -384,7 +384,7 @@ still lacking, and the purpose of the TREXIO library is to fill this gap.
</div> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-03-15 Fri 16:53</p> <p class="date">Created: 2024-03-22 Fri 14:46</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>

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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2024-03-15 Fri 16:53 --> <!-- 2024-03-22 Fri 14:46 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>The TREXIO library</title> <title>The TREXIO library</title>
@ -346,19 +346,19 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#orge00d982">1. Format specification</a> <li><a href="#orgb3f7d06">1. Format specification</a>
<ul> <ul>
<li><a href="#org5422001">1.1. Organization of the data</a></li> <li><a href="#org53e8951">1.1. Organization of the data</a></li>
<li><a href="#orgf61338a">1.2. Data types</a></li> <li><a href="#orga907b6b">1.2. Data types</a></li>
</ul> </ul>
</li> </li>
<li><a href="#orgffb2a1e">2. The TREXIO library</a> <li><a href="#org4970b5c">2. The TREXIO library</a>
<ul> <ul>
<li><a href="#orgd581542">2.1. The front-end</a></li> <li><a href="#org8109a11">2.1. The front-end</a></li>
<li><a href="#orgc98a524">2.2. The back-end</a></li> <li><a href="#org528d29a">2.2. The back-end</a></li>
<li><a href="#org91e5928">2.3. Supported languages</a></li> <li><a href="#org732c621">2.3. Supported languages</a></li>
<li><a href="#org34c8122">2.4. Source code generation and documentation</a></li> <li><a href="#orgc0c195c">2.4. Source code generation and documentation</a></li>
<li><a href="#org6de72c4">2.5. Availability</a></li> <li><a href="#orgc5e179f">2.5. Availability</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div> </div>
<div id="outline-container-orge00d982" class="outline-2"> <div id="outline-container-orgb3f7d06" class="outline-2">
<h2 id="orge00d982"><span class="section-number-2">1</span> Format specification</h2> <h2 id="orgb3f7d06"><span class="section-number-2">1</span> Format specification</h2>
<div class="outline-text-2" id="text-1"> <div class="outline-text-2" id="text-1">
</td> </td>
<td> <td>
@ -388,8 +388,8 @@ calculation are stored.
</p> </p>
</div> </div>
<div id="outline-container-org5422001" class="outline-3"> <div id="outline-container-org53e8951" class="outline-3">
<h3 id="org5422001"><span class="section-number-3">1.1</span> Organization of the data</h3> <h3 id="org53e8951"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div class="outline-text-3" id="text-1-1"> <div class="outline-text-3" id="text-1-1">
<p> <p>
The data in TREXIO are organized into <b>groups</b>, each containing The data in TREXIO are organized into <b>groups</b>, each containing
@ -405,8 +405,8 @@ number of nuclei.
</div> </div>
</div> </div>
<div id="outline-container-orgf61338a" class="outline-3"> <div id="outline-container-orga907b6b" class="outline-3">
<h3 id="orgf61338a"><span class="section-number-3">1.2</span> Data types</h3> <h3 id="orga907b6b"><span class="section-number-3">1.2</span> Data types</h3>
<div class="outline-text-3" id="text-1-2"> <div class="outline-text-3" id="text-1-2">
<p> <p>
So that TREXIO can be used in any language, we use a limited number So that TREXIO can be used in any language, we use a limited number
@ -473,8 +473,8 @@ with the same name suffixed by <code>_im</code>.
</div> </div>
</div> </div>
<div id="outline-container-orgffb2a1e" class="outline-2"> <div id="outline-container-org4970b5c" class="outline-2">
<h2 id="orgffb2a1e"><span class="section-number-2">2</span> The TREXIO library</h2> <h2 id="org4970b5c"><span class="section-number-2">2</span> The TREXIO library</h2>
<div class="outline-text-2" id="text-2"> <div class="outline-text-2" id="text-2">
</td> </td>
<td> <td>
@ -497,8 +497,8 @@ interface between the library and the physical storage.
</p> </p>
</div> </div>
<div id="outline-container-orgd581542" class="outline-3"> <div id="outline-container-org8109a11" class="outline-3">
<h3 id="orgd581542"><span class="section-number-3">2.1</span> The front-end</h3> <h3 id="org8109a11"><span class="section-number-3">2.1</span> The front-end</h3>
<div class="outline-text-3" id="text-2-1"> <div class="outline-text-3" id="text-2-1">
<p> <p>
By using the TREXIO library, users can store and extract data in a By using the TREXIO library, users can store and extract data in a
@ -539,8 +539,8 @@ made are safe.
</div> </div>
</div> </div>
<div id="outline-container-orgc98a524" class="outline-3"> <div id="outline-container-org528d29a" class="outline-3">
<h3 id="orgc98a524"><span class="section-number-3">2.2</span> The back-end</h3> <h3 id="org528d29a"><span class="section-number-3">2.2</span> The back-end</h3>
<div class="outline-text-3" id="text-2-2"> <div class="outline-text-3" id="text-2-2">
<p> <p>
At present, TREXIO supports two back-ends: one relying only on the At present, TREXIO supports two back-ends: one relying only on the
@ -610,8 +610,8 @@ repositories.
</div> </div>
</div> </div>
<div id="outline-container-org91e5928" class="outline-3"> <div id="outline-container-org732c621" class="outline-3">
<h3 id="org91e5928"><span class="section-number-3">2.3</span> Supported languages</h3> <h3 id="org732c621"><span class="section-number-3">2.3</span> Supported languages</h3>
<div class="outline-text-3" id="text-2-3"> <div class="outline-text-3" id="text-2-3">
<p> <p>
One of the main benefits of using C as the interface for a library is One of the main benefits of using C as the interface for a library is
@ -668,8 +668,8 @@ via the Binder platform.
</div> </div>
<div id="outline-container-org34c8122" class="outline-3"> <div id="outline-container-orgc0c195c" class="outline-3">
<h3 id="org34c8122"><span class="section-number-3">2.4</span> Source code generation and documentation</h3> <h3 id="orgc0c195c"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div class="outline-text-3" id="text-2-4"> <div class="outline-text-3" id="text-2-4">
<p> <p>
Source code generation is a valuable technique that can significantly Source code generation is a valuable technique that can significantly
@ -723,8 +723,8 @@ regardless of their programming skills.
</div> </div>
</div> </div>
<div id="outline-container-org6de72c4" class="outline-3"> <div id="outline-container-orgc5e179f" class="outline-3">
<h3 id="org6de72c4"><span class="section-number-3">2.5</span> Availability</h3> <h3 id="orgc5e179f"><span class="section-number-3">2.5</span> Availability</h3>
<div class="outline-text-3" id="text-2-5"> <div class="outline-text-3" id="text-2-5">
<p> <p>
The TREXIO library is designed to be portable and easy to install The TREXIO library is designed to be portable and easy to install
@ -754,7 +754,7 @@ are available in Ubuntu 23.04.
</div> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-03-15 Fri 16:53</p> <p class="date">Created: 2024-03-22 Fri 14:46</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>

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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2024-03-15 Fri 16:53 --> <!-- 2024-03-22 Fri 14:46 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>HDF5 back end</title> <title>HDF5 back end</title>
@ -324,25 +324,25 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#orge71ff77">1. Template for HDF5 definitions</a></li> <li><a href="#org4fb494f">1. Template for HDF5 definitions</a></li>
<li><a href="#orgb01457a">2. Template for HDF5 structures</a></li> <li><a href="#org3682b83">2. Template for HDF5 structures</a></li>
<li><a href="#orgc7312a3">3. Template for HDF5 init/deinit</a></li> <li><a href="#org46b44c0">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org06543ad">4. Template for HDF5 has a group</a></li> <li><a href="#org0b6f6dc">4. Template for HDF5 has a group</a></li>
<li><a href="#orgd403c55">5. Template for HDF5 has/read/write a numerical attribute</a></li> <li><a href="#org1cf7a6c">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org203fed0">6. Template for HDF5 has/read/write a dataset of numerical data</a></li> <li><a href="#org99f5f16">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org080cdc1">7. Template for HDF5 has/read/write a dataset of sparse data</a></li> <li><a href="#org701fb9e">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org72dc1b5">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li> <li><a href="#orgbe0f710">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org1e7fa00">9. Template for HDF5 has/read/write a dataset of strings</a></li> <li><a href="#org8815ab5">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org57169f5">10. Template for HDF5 has/read/write a string attribute</a></li> <li><a href="#orgde1b27b">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org876317e">11. Template for HDF5 delete a group (UNSAFE mode)</a></li> <li><a href="#org7ffbe90">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org352aeb5">12. Source code for the determinant part</a></li> <li><a href="#orgd4277ca">12. Source code for the determinant part</a></li>
<li><a href="#org79b4ae2">13. Helper functions</a></li> <li><a href="#orge2c8fca">13. Helper functions</a></li>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-orge71ff77" class="outline-2"> <div id="outline-container-org4fb494f" class="outline-2">
<h2 id="orge71ff77"><span class="section-number-2">1</span> Template for HDF5 definitions</h2> <h2 id="org4fb494f"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div class="outline-text-2" id="text-1"> <div class="outline-text-2" id="text-1">
<div class="org-src-container"> <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> <pre class="src src-c"><span style="color: #483d8b;">#define</span> $GROUP$_GROUP_NAME <span style="color: #8b2252;">"$group$"</span>
@ -354,8 +354,8 @@ for the JavaScript code in this tag.
</div> </div>
</div> </div>
<div id="outline-container-orgb01457a" class="outline-2"> <div id="outline-container-org3682b83" class="outline-2">
<h2 id="orgb01457a"><span class="section-number-2">2</span> Template for HDF5 structures</h2> <h2 id="org3682b83"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div class="outline-text-2" id="text-2"> <div class="outline-text-2" id="text-2">
<p> <p>
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
@ -375,8 +375,8 @@ corresponding types for all back ends can be safely casted to
</div> </div>
</div> </div>
<div id="outline-container-orgc7312a3" class="outline-2"> <div id="outline-container-org46b44c0" class="outline-2">
<h2 id="orgc7312a3"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2> <h2 id="org46b44c0"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div class="outline-text-2" id="text-3"> <div class="outline-text-2" id="text-3">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -496,8 +496,8 @@ corresponding types for all back ends can be safely casted to
</div> </div>
</div> </div>
<div id="outline-container-org06543ad" class="outline-2"> <div id="outline-container-org0b6f6dc" class="outline-2">
<h2 id="org06543ad"><span class="section-number-2">4</span> Template for HDF5 has a group</h2> <h2 id="org0b6f6dc"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div class="outline-text-2" id="text-4"> <div class="outline-text-2" id="text-4">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -527,8 +527,8 @@ corresponding types for all back ends can be safely casted to
</div> </div>
</div> </div>
<div id="outline-container-orgd403c55" class="outline-2"> <div id="outline-container-org1cf7a6c" class="outline-2">
<h2 id="orgd403c55"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2> <h2 id="org1cf7a6c"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-5"> <div class="outline-text-2" id="text-5">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -632,8 +632,8 @@ corresponding types for all back ends can be safely casted to
</div> </div>
</div> </div>
<div id="outline-container-org203fed0" class="outline-2"> <div id="outline-container-org99f5f16" class="outline-2">
<h2 id="org203fed0"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2> <h2 id="org99f5f16"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-6"> <div class="outline-text-2" id="text-6">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -770,8 +770,8 @@ corresponding types for all back ends can be safely casted to
</div> </div>
</div> </div>
<div id="outline-container-org080cdc1" class="outline-2"> <div id="outline-container-org701fb9e" class="outline-2">
<h2 id="org080cdc1"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2> <h2 id="org701fb9e"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-7"> <div class="outline-text-2" id="text-7">
<p> <p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -976,8 +976,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div> </div>
</div> </div>
<div id="outline-container-org72dc1b5" class="outline-2"> <div id="outline-container-orgbe0f710" class="outline-2">
<h2 id="org72dc1b5"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2> <h2 id="orgbe0f710"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div class="outline-text-2" id="text-8"> <div class="outline-text-2" id="text-8">
<p> <p>
Chunked I/O in HDF5 for <code>buffered</code> data. Chunked I/O in HDF5 for <code>buffered</code> data.
@ -1111,8 +1111,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div> </div>
</div> </div>
<div id="outline-container-org1e7fa00" class="outline-2"> <div id="outline-container-org8815ab5" class="outline-2">
<h2 id="org1e7fa00"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2> <h2 id="org8815ab5"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-9"> <div class="outline-text-2" id="text-9">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1309,8 +1309,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div> </div>
</div> </div>
<div id="outline-container-org57169f5" class="outline-2"> <div id="outline-container-orgde1b27b" class="outline-2">
<h2 id="org57169f5"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2> <h2 id="orgde1b27b"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-10"> <div class="outline-text-2" id="text-10">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1437,8 +1437,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org876317e" class="outline-2"> <div id="outline-container-org7ffbe90" class="outline-2">
<h2 id="org876317e"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2> <h2 id="org7ffbe90"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-11"> <div class="outline-text-2" id="text-11">
<p> <p>
<b><b>Note:</b></b> in early versions of the HDF5 library (v &lt; 1.10) unlinking an object was not working as expected <b><b>Note:</b></b> in early versions of the HDF5 library (v &lt; 1.10) unlinking an object was not working as expected
@ -1478,8 +1478,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div> </div>
</div> </div>
<div id="outline-container-org352aeb5" class="outline-2"> <div id="outline-container-orgd4277ca" class="outline-2">
<h2 id="org352aeb5"><span class="section-number-2">12</span> Source code for the determinant part</h2> <h2 id="orgd4277ca"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-12"> <div class="outline-text-2" id="text-12">
<p> <p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled. Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1581,8 +1581,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div> </div>
</div> </div>
<div id="outline-container-org79b4ae2" class="outline-2"> <div id="outline-container-orge2c8fca" class="outline-2">
<h2 id="org79b4ae2"><span class="section-number-2">13</span> Helper functions</h2> <h2 id="orge2c8fca"><span class="section-number-2">13</span> Helper functions</h2>
<div class="outline-text-2" id="text-13"> <div class="outline-text-2" id="text-13">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1850,7 +1850,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-03-15 Fri 16:53</p> <p class="date">Created: 2024-03-22 Fri 14:46</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>

106
templator_text.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2024-03-15 Fri 16:53 --> <!-- 2024-03-22 Fri 14:46 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title> <title>TEXT back end</title>
@ -324,23 +324,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#org5d7334a">1. Template for group-related structures in text back end</a></li> <li><a href="#org4df028d">1. Template for group-related structures in text back end</a></li>
<li><a href="#org587767b">2. Template for general structure in text back end</a></li> <li><a href="#orgc9b82a6">2. Template for general structure in text back end</a></li>
<li><a href="#org780a448">3. Initialize function (constant part)</a></li> <li><a href="#org3c76758">3. Initialize function (constant part)</a></li>
<li><a href="#org9f43e0c">4. Deinitialize function (templated part)</a></li> <li><a href="#orgc95bb84">4. Deinitialize function (templated part)</a></li>
<li><a href="#org3bfbbd2">5. Flush function (templated part)</a></li> <li><a href="#org81bc72c">5. Flush function (templated part)</a></li>
<li><a href="#orgd2f508a">6. Template for text read a group</a></li> <li><a href="#orgf4581d0">6. Template for text read a group</a></li>
<li><a href="#org7b860c7">7. Template for text has a group</a></li> <li><a href="#org72ddd2a">7. Template for text has a group</a></li>
<li><a href="#orgabb4d97">8. Template for text flush a group</a></li> <li><a href="#orgb05cb1e">8. Template for text flush a group</a></li>
<li><a href="#org00dc58e">9. Template for text free memory</a></li> <li><a href="#org5db2cc5">9. Template for text free memory</a></li>
<li><a href="#orgf489738">10. Template for has/read/write a numerical attribute</a></li> <li><a href="#orgd5952af">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgf32402e">11. Template for has/read/write a dataset of numerical data</a></li> <li><a href="#org83b0719">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org3db7383">12. Template for has/read/write a dataset of strings</a></li> <li><a href="#org51f8d15">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org9d2678e">13. Template for has/read/write a string attribute</a></li> <li><a href="#org6dc57bc">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org938790b">14. Template for has/read/write the dataset of sparse data</a></li> <li><a href="#org8518c71">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org48a354d">15. Template for has/read/write a buffered vector</a></li> <li><a href="#org3cf6d51">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org16c6682">16. Template for text delete a group (UNSAFE mode)</a></li> <li><a href="#org98fe274">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org0ab6f9e">17. Source code for the determinant part</a></li> <li><a href="#orgac78bdb">17. Source code for the determinant part</a></li>
</ul> </ul>
</div> </div>
</div> </div>
@ -362,8 +362,8 @@ directory.
The file is written when closed, or when the flush function is called. The file is written when closed, or when the flush function is called.
</p> </p>
<div id="outline-container-org5d7334a" class="outline-2"> <div id="outline-container-org4df028d" class="outline-2">
<h2 id="org5d7334a"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2> <h2 id="org4df028d"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div class="outline-text-2" id="text-1"> <div class="outline-text-2" id="text-1">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s { <pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
@ -382,8 +382,8 @@ The file is written when closed, or when the flush function is called.
</div> </div>
</div> </div>
<div id="outline-container-org587767b" class="outline-2"> <div id="outline-container-orgc9b82a6" class="outline-2">
<h2 id="org587767b"><span class="section-number-2">2</span> Template for general structure in text back end</h2> <h2 id="orgc9b82a6"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div class="outline-text-2" id="text-2"> <div class="outline-text-2" id="text-2">
<p> <p>
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
@ -403,8 +403,8 @@ corresponding types for all back ends can be safely casted to
</div> </div>
</div> </div>
<div id="outline-container-org780a448" class="outline-2"> <div id="outline-container-org3c76758" class="outline-2">
<h2 id="org780a448"><span class="section-number-2">3</span> Initialize function (constant part)</h2> <h2 id="org3c76758"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div class="outline-text-2" id="text-3"> <div class="outline-text-2" id="text-3">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">bool</span> <pre class="src src-c"><span style="color: #228b22;">bool</span>
@ -601,8 +601,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div> </div>
</div> </div>
<div id="outline-container-org9f43e0c" class="outline-2"> <div id="outline-container-orgc95bb84" class="outline-2">
<h2 id="org9f43e0c"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2> <h2 id="orgc95bb84"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div class="outline-text-2" id="text-4"> <div class="outline-text-2" id="text-4">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -624,8 +624,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div> </div>
</div> </div>
<div id="outline-container-org3bfbbd2" class="outline-2"> <div id="outline-container-org81bc72c" class="outline-2">
<h2 id="org3bfbbd2"><span class="section-number-2">5</span> Flush function (templated part)</h2> <h2 id="org81bc72c"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div class="outline-text-2" id="text-5"> <div class="outline-text-2" id="text-5">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -648,8 +648,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div> </div>
</div> </div>
<div id="outline-container-orgd2f508a" class="outline-2"> <div id="outline-container-orgf4581d0" class="outline-2">
<h2 id="orgd2f508a"><span class="section-number-2">6</span> Template for text read a group</h2> <h2 id="orgf4581d0"><span class="section-number-2">6</span> Template for text read a group</h2>
<div class="outline-text-2" id="text-6"> <div class="outline-text-2" id="text-6">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c">$group$_t* <pre class="src src-c">$group$_t*
@ -875,8 +875,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div> </div>
</div> </div>
<div id="outline-container-org7b860c7" class="outline-2"> <div id="outline-container-org72ddd2a" class="outline-2">
<h2 id="org7b860c7"><span class="section-number-2">7</span> Template for text has a group</h2> <h2 id="org72ddd2a"><span class="section-number-2">7</span> Template for text has a group</h2>
<div class="outline-text-2" id="text-7"> <div class="outline-text-2" id="text-7">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -916,8 +916,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div> </div>
</div> </div>
<div id="outline-container-orgabb4d97" class="outline-2"> <div id="outline-container-orgb05cb1e" class="outline-2">
<h2 id="orgabb4d97"><span class="section-number-2">8</span> Template for text flush a group</h2> <h2 id="orgb05cb1e"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div class="outline-text-2" id="text-8"> <div class="outline-text-2" id="text-8">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -981,8 +981,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div> </div>
</div> </div>
<div id="outline-container-org00dc58e" class="outline-2"> <div id="outline-container-org5db2cc5" class="outline-2">
<h2 id="org00dc58e"><span class="section-number-2">9</span> Template for text free memory</h2> <h2 id="org5db2cc5"><span class="section-number-2">9</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-9"> <div class="outline-text-2" id="text-9">
<p> <p>
Memory is allocated when reading. The following function frees memory. Memory is allocated when reading. The following function frees memory.
@ -1051,8 +1051,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div> </div>
</div> </div>
<div id="outline-container-orgf489738" class="outline-2"> <div id="outline-container-orgd5952af" class="outline-2">
<h2 id="orgf489738"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2> <h2 id="orgd5952af"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-10"> <div class="outline-text-2" id="text-10">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1115,8 +1115,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
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<div id="outline-container-orgf32402e" class="outline-2"> <div id="outline-container-org83b0719" class="outline-2">
<h2 id="orgf32402e"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2> <h2 id="org83b0719"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-11"> <div class="outline-text-2" id="text-11">
<p> <p>
The <code>group_dset</code> array is assumed allocated with the appropriate size. The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1212,8 +1212,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
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<div id="outline-container-org3db7383" class="outline-2"> <div id="outline-container-org51f8d15" class="outline-2">
<h2 id="org3db7383"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2> <h2 id="org51f8d15"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-12"> <div class="outline-text-2" id="text-12">
<p> <p>
The <code>group_dset</code> array is assumed allocated with the appropriate size. The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1314,8 +1314,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
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<div id="outline-container-org9d2678e" class="outline-2"> <div id="outline-container-org6dc57bc" class="outline-2">
<h2 id="org9d2678e"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2> <h2 id="org6dc57bc"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-13"> <div class="outline-text-2" id="text-13">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1389,8 +1389,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
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<div id="outline-container-org938790b" class="outline-2"> <div id="outline-container-org8518c71" class="outline-2">
<h2 id="org938790b"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2> <h2 id="org8518c71"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-14"> <div class="outline-text-2" id="text-14">
<p> <p>
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
@ -1680,8 +1680,8 @@ User provides indices and values of the sparse array as two separate variables.
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<div id="outline-container-org48a354d" class="outline-2"> <div id="outline-container-org3cf6d51" class="outline-2">
<h2 id="org48a354d"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2> <h2 id="org3cf6d51"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div class="outline-text-2" id="text-15"> <div class="outline-text-2" id="text-15">
<p> <p>
Each array is stored in a separate <code>.txt</code> file due to the fact that buffered I/O has to be decoupled Each array is stored in a separate <code>.txt</code> file due to the fact that buffered I/O has to be decoupled
@ -1911,8 +1911,8 @@ Size specifies the number of vector elements to be written.
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<h2 id="org16c6682"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2> <h2 id="org98fe274"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-16"> <div class="outline-text-2" id="text-16">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1940,8 +1940,8 @@ Size specifies the number of vector elements to be written.
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<h2 id="org0ab6f9e"><span class="section-number-2">17</span> Source code for the determinant part</h2> <h2 id="orgac78bdb"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-17"> <div class="outline-text-2" id="text-17">
<p> <p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -2133,7 +2133,7 @@ Size specifies the number of data items, e.g. determinants.
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<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-03-15 Fri 16:53</p> <p class="date">Created: 2024-03-22 Fri 14:46</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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