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examples.html
@ -346,46 +346,46 @@ for the JavaScript code in this tag.
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<h2>Table of Contents</h2>
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<div id="text-table-of-contents">
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<ul>
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<li><a href="#org5d9a5fe">1. Writing nuclear coordinates</a>
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<li><a href="#orge06a6e8">1. Writing nuclear coordinates</a>
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<ul>
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<li><a href="#org7f48233">1.1. C</a></li>
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<li><a href="#org4c4689f">1.2. Python</a></li>
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<li><a href="#org9bcb80c">1.3. Fortran</a></li>
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<li><a href="#orgfe135ce">1.1. C</a></li>
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<li><a href="#org8e1dd0f">1.2. Python</a></li>
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<li><a href="#org9ba64ad">1.3. Fortran</a></li>
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</ul>
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</li>
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<li><a href="#org806cab2">2. Accessing sparse quantities (integrals)</a>
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<li><a href="#org9a554fa">2. Accessing sparse quantities (integrals)</a>
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<ul>
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<li><a href="#org104068b">2.1. Fortran</a>
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<li><a href="#org6ed9117">2.1. Fortran</a>
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<ul>
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<li><a href="#org91fe63b">2.1.1. Declare Temporary variables</a></li>
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<li><a href="#org028371d">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
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<li><a href="#org04c40ec">2.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org9021dde">2.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org342014f">2.1.5. Allocate memory</a></li>
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<li><a href="#org839d2f9">2.1.6. Read one-electron quantities</a></li>
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<li><a href="#org86a4789">2.1.7. Read two-electron quantities</a>
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<li><a href="#orgbe87089">2.1.1. Declare Temporary variables</a></li>
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<li><a href="#orgc0e34fb">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
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<li><a href="#org4e11356">2.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org5a2ff51">2.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orgd416314">2.1.5. Allocate memory</a></li>
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<li><a href="#org63406c5">2.1.6. Read one-electron quantities</a></li>
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<li><a href="#org952f86f">2.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#orgede440d">2.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orgf8fd74d">2.1.7.2. Reduced density matrix</a></li>
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<li><a href="#orgb7fb044">2.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org3f75546">2.1.7.2. Reduced density matrix</a></li>
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</ul>
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</li>
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<li><a href="#org6515804">2.1.8. Compute the energy</a></li>
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<li><a href="#org683eeb9">2.1.9. Terminate</a></li>
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<li><a href="#org0b5e18a">2.1.8. Compute the energy</a></li>
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<li><a href="#org1951a51">2.1.9. Terminate</a></li>
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</ul>
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</li>
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</ul>
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</li>
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<li><a href="#org7431fe5">3. Reading determinants</a>
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<li><a href="#orgc7bd965">3. Reading determinants</a>
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<ul>
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<li><a href="#org5c24c72">3.1. Fortran</a></li>
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<li><a href="#orgc4bcd55">3.1. Fortran</a></li>
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</ul>
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</li>
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</ul>
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</div>
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</div>
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<div id="outline-container-org5d9a5fe" class="outline-2">
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<h2 id="org5d9a5fe"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
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<div id="outline-container-orge06a6e8" class="outline-2">
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<h2 id="orge06a6e8"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
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<div class="outline-text-2" id="text-1">
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<p>
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Here is a demonstration of how to use TREXIO to write the nuclear
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@ -395,8 +395,8 @@ as well as the necessary TREXIO functions to perform these actions.
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</p>
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</div>
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<div id="outline-container-org7f48233" class="outline-3">
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<h3 id="org7f48233"><span class="section-number-3">1.1</span> C</h3>
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<div id="outline-container-orgfe135ce" class="outline-3">
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<h3 id="orgfe135ce"><span class="section-number-3">1.1</span> C</h3>
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<div class="outline-text-3" id="text-1-1">
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<div class="org-src-container">
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<pre class="src src-c"><span style="color: #483d8b;">#include</span> <span style="color: #8b2252;"><stdio.h></span>
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@ -446,8 +446,8 @@ as well as the necessary TREXIO functions to perform these actions.
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</div>
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</div>
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<div id="outline-container-org4c4689f" class="outline-3">
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<h3 id="org4c4689f"><span class="section-number-3">1.2</span> Python</h3>
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<div id="outline-container-org8e1dd0f" class="outline-3">
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<h3 id="org8e1dd0f"><span class="section-number-3">1.2</span> Python</h3>
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<div class="outline-text-3" id="text-1-2">
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<p>
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This code uses the TREXIO Python binding to create a new TREXIO file named
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@ -494,8 +494,8 @@ coordinates of the system.
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</div>
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</div>
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<div id="outline-container-org9bcb80c" class="outline-3">
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<h3 id="org9bcb80c"><span class="section-number-3">1.3</span> Fortran</h3>
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<div id="outline-container-org9ba64ad" class="outline-3">
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<h3 id="org9ba64ad"><span class="section-number-3">1.3</span> Fortran</h3>
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<div class="outline-text-3" id="text-1-3">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">trexio_water</span>
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@ -552,12 +552,12 @@ coordinates of the system.
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</div>
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</div>
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<div id="outline-container-org806cab2" class="outline-2">
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<h2 id="org806cab2"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
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<div id="outline-container-org9a554fa" class="outline-2">
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<h2 id="org9a554fa"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
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<div class="outline-text-2" id="text-2">
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</div>
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<div id="outline-container-org104068b" class="outline-3">
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<h3 id="org104068b"><span class="section-number-3">2.1</span> Fortran</h3>
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<div id="outline-container-org6ed9117" class="outline-3">
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<h3 id="org6ed9117"><span class="section-number-3">2.1</span> Fortran</h3>
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<div class="outline-text-3" id="text-2-1">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
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@ -603,8 +603,8 @@ One needs to read from the TREXIO file:
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</div>
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</div>
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<div id="outline-container-org91fe63b" class="outline-4">
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<h4 id="org91fe63b"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-orgbe87089" class="outline-4">
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<h4 id="orgbe87089"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
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<div class="outline-text-4" id="text-2-1-1">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span>
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@ -619,8 +619,8 @@ One needs to read from the TREXIO file:
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</div>
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</div>
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<div id="outline-container-org028371d" class="outline-4">
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<h4 id="org028371d"><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>
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<div id="outline-container-orgc0e34fb" class="outline-4">
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<h4 id="orgc0e34fb"><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>
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<div class="outline-text-4" id="text-2-1-2">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
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@ -636,8 +636,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-org04c40ec" class="outline-4">
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<h4 id="org04c40ec"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-org4e11356" class="outline-4">
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<h4 id="org4e11356"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
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<div class="outline-text-4" id="text-2-1-3">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
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@ -651,8 +651,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-org9021dde" class="outline-4">
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<h4 id="org9021dde"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-org5a2ff51" class="outline-4">
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<h4 id="org5a2ff51"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
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<div class="outline-text-4" id="text-2-1-4">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
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@ -666,8 +666,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
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</div>
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</div>
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<div id="outline-container-org342014f" class="outline-4">
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<h4 id="org342014f"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
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<div id="outline-container-orgd416314" class="outline-4">
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<h4 id="orgd416314"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
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<div class="outline-text-4" id="text-2-1-5">
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<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
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@ -679,8 +679,8 @@ W(:,:,:,:) = 0.d0
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</div>
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</div>
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<div id="outline-container-org839d2f9" class="outline-4">
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<h4 id="org839d2f9"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-org63406c5" class="outline-4">
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<h4 id="org63406c5"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
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<div class="outline-text-4" id="text-2-1-6">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
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@ -712,8 +712,8 @@ rc = trexio_read_rdm_1e(f, D)
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</div>
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</div>
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<div id="outline-container-org86a4789" class="outline-4">
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<h4 id="org86a4789"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
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<div id="outline-container-org952f86f" class="outline-4">
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<h4 id="org952f86f"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
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<div class="outline-text-4" id="text-2-1-7">
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<p>
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Reading is done with OpenMP. Each thread reads its own buffer, and
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@ -729,8 +729,8 @@ to be protected in the critical section when modified.
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</p>
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</div>
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<div id="outline-container-orgede440d" class="outline-5">
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<h5 id="orgede440d"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
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<div id="outline-container-orgb7fb044" class="outline-5">
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<h5 id="orgb7fb044"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
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<div class="outline-text-5" id="text-2-1-7-1">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
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@ -779,8 +779,8 @@ icount = BUFSIZE
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</div>
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</div>
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<div id="outline-container-orgf8fd74d" class="outline-5">
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<h5 id="orgf8fd74d"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-org3f75546" class="outline-5">
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<h5 id="org3f75546"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
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<div class="outline-text-5" id="text-2-1-7-2">
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<div class="org-src-container">
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<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
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@ -824,8 +824,8 @@ icount = bufsize
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</div>
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</div>
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<div id="outline-container-org6515804" class="outline-4">
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<h4 id="org6515804"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
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<div id="outline-container-org0b5e18a" class="outline-4">
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<h4 id="org0b5e18a"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
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<div class="outline-text-4" id="text-2-1-8">
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<p>
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When the orbitals are real, we can use
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@ -871,8 +871,8 @@ E = E + E_nn
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</div>
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</div>
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<div id="outline-container-org683eeb9" class="outline-4">
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<h4 id="org683eeb9"><span class="section-number-4">2.1.9</span> Terminate</h4>
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<div id="outline-container-org1951a51" class="outline-4">
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<h4 id="org1951a51"><span class="section-number-4">2.1.9</span> Terminate</h4>
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<div class="outline-text-4" id="text-2-1-9">
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<div class="org-src-container">
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<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
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@ -885,12 +885,12 @@ E = E + E_nn
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</div>
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</div>
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<div id="outline-container-org7431fe5" class="outline-2">
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<h2 id="org7431fe5"><span class="section-number-2">3</span> Reading determinants</h2>
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<div id="outline-container-orgc7bd965" class="outline-2">
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<h2 id="orgc7bd965"><span class="section-number-2">3</span> Reading determinants</h2>
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<div class="outline-text-2" id="text-3">
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</div>
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<div id="outline-container-org5c24c72" class="outline-3">
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<h3 id="org5c24c72"><span class="section-number-3">3.1</span> Fortran</h3>
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<div id="outline-container-orgc4bcd55" class="outline-3">
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<h3 id="orgc4bcd55"><span class="section-number-3">3.1</span> Fortran</h3>
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<div class="outline-text-3" id="text-3-1">
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||||
<div class="org-src-container">
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<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
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54
lib.html
54
lib.html
@ -346,19 +346,19 @@ for the JavaScript code in this tag.
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<h2>Table of Contents</h2>
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<div id="text-table-of-contents">
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<ul>
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<li><a href="#org353e63c">1. Format specification</a>
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<li><a href="#orgcbc0053">1. Format specification</a>
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<ul>
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<li><a href="#org92c20d4">1.1. Organization of the data</a></li>
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<li><a href="#org91a5566">1.2. Data types</a></li>
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<li><a href="#orgdf44d18">1.1. Organization of the data</a></li>
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<li><a href="#org2ccb0a2">1.2. Data types</a></li>
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</ul>
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</li>
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<li><a href="#org8e47f99">2. The TREXIO library</a>
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<li><a href="#orgebc2d8b">2. The TREXIO library</a>
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<ul>
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<li><a href="#org7d1f83a">2.1. The front-end</a></li>
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<li><a href="#org2173eeb">2.2. The back-end</a></li>
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<li><a href="#orge32b237">2.3. Supported languages</a></li>
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<li><a href="#org70bfc9c">2.4. Source code generation and documentation</a></li>
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<li><a href="#org11eb882">2.5. Availability</a></li>
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<li><a href="#org960da81">2.1. The front-end</a></li>
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<li><a href="#org9097857">2.2. The back-end</a></li>
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||||
<li><a href="#org92097c5">2.3. Supported languages</a></li>
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||||
<li><a href="#orgcee8493">2.4. Source code generation and documentation</a></li>
|
||||
<li><a href="#org0197943">2.5. Availability</a></li>
|
||||
</ul>
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</li>
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</ul>
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@ -366,8 +366,8 @@ for the JavaScript code in this tag.
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</div>
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<div id="outline-container-org353e63c" class="outline-2">
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<h2 id="org353e63c"><span class="section-number-2">1</span> Format specification</h2>
|
||||
<div id="outline-container-orgcbc0053" class="outline-2">
|
||||
<h2 id="orgcbc0053"><span class="section-number-2">1</span> Format specification</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
</td>
|
||||
<td>
|
||||
@ -388,8 +388,8 @@ calculation are stored.
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org92c20d4" class="outline-3">
|
||||
<h3 id="org92c20d4"><span class="section-number-3">1.1</span> Organization of the data</h3>
|
||||
<div id="outline-container-orgdf44d18" class="outline-3">
|
||||
<h3 id="orgdf44d18"><span class="section-number-3">1.1</span> Organization of the data</h3>
|
||||
<div class="outline-text-3" id="text-1-1">
|
||||
<p>
|
||||
The data in TREXIO are organized into <b>groups</b>, each containing
|
||||
@ -405,8 +405,8 @@ number of nuclei.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org91a5566" class="outline-3">
|
||||
<h3 id="org91a5566"><span class="section-number-3">1.2</span> Data types</h3>
|
||||
<div id="outline-container-org2ccb0a2" class="outline-3">
|
||||
<h3 id="org2ccb0a2"><span class="section-number-3">1.2</span> Data types</h3>
|
||||
<div class="outline-text-3" id="text-1-2">
|
||||
<p>
|
||||
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 id="outline-container-org8e47f99" class="outline-2">
|
||||
<h2 id="org8e47f99"><span class="section-number-2">2</span> The TREXIO library</h2>
|
||||
<div id="outline-container-orgebc2d8b" class="outline-2">
|
||||
<h2 id="orgebc2d8b"><span class="section-number-2">2</span> The TREXIO library</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
</td>
|
||||
<td>
|
||||
@ -497,8 +497,8 @@ interface between the library and the physical storage.
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7d1f83a" class="outline-3">
|
||||
<h3 id="org7d1f83a"><span class="section-number-3">2.1</span> The front-end</h3>
|
||||
<div id="outline-container-org960da81" class="outline-3">
|
||||
<h3 id="org960da81"><span class="section-number-3">2.1</span> The front-end</h3>
|
||||
<div class="outline-text-3" id="text-2-1">
|
||||
<p>
|
||||
By using the TREXIO library, users can store and extract data in a
|
||||
@ -539,8 +539,8 @@ made are safe.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2173eeb" class="outline-3">
|
||||
<h3 id="org2173eeb"><span class="section-number-3">2.2</span> The back-end</h3>
|
||||
<div id="outline-container-org9097857" class="outline-3">
|
||||
<h3 id="org9097857"><span class="section-number-3">2.2</span> The back-end</h3>
|
||||
<div class="outline-text-3" id="text-2-2">
|
||||
<p>
|
||||
At present, TREXIO supports two back-ends: one relying only on the
|
||||
@ -610,8 +610,8 @@ repositories.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge32b237" class="outline-3">
|
||||
<h3 id="orge32b237"><span class="section-number-3">2.3</span> Supported languages</h3>
|
||||
<div id="outline-container-org92097c5" class="outline-3">
|
||||
<h3 id="org92097c5"><span class="section-number-3">2.3</span> Supported languages</h3>
|
||||
<div class="outline-text-3" id="text-2-3">
|
||||
<p>
|
||||
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 id="outline-container-org70bfc9c" class="outline-3">
|
||||
<h3 id="org70bfc9c"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
|
||||
<div id="outline-container-orgcee8493" class="outline-3">
|
||||
<h3 id="orgcee8493"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
|
||||
<div class="outline-text-3" id="text-2-4">
|
||||
<p>
|
||||
Source code generation is a valuable technique that can significantly
|
||||
@ -723,8 +723,8 @@ regardless of their programming skills.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org11eb882" class="outline-3">
|
||||
<h3 id="org11eb882"><span class="section-number-3">2.5</span> Availability</h3>
|
||||
<div id="outline-container-org0197943" class="outline-3">
|
||||
<h3 id="org0197943"><span class="section-number-3">2.5</span> Availability</h3>
|
||||
<div class="outline-text-3" id="text-2-5">
|
||||
<p>
|
||||
The TREXIO library is designed to be portable and easy to install
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -324,25 +324,25 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org1140de7">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#orgf7153ab">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgdbab6e1">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org9251edb">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#orge6a1e7d">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org960eac3">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org60046ba">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#org7926126">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
|
||||
<li><a href="#orgb9ee959">9. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgba418ae">10. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgb7db89a">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgfeacb4f">12. Source code for the determinant part</a></li>
|
||||
<li><a href="#orgaf8fe90">13. Helper functions</a></li>
|
||||
<li><a href="#orgd346e1b">1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#orgdfb40fd">2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgffa5f91">3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orga5d3953">4. Template for HDF5 has a group</a></li>
|
||||
<li><a href="#org4c3b44a">5. Template for HDF5 has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgb41c96e">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org86b7bba">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
|
||||
<li><a href="#orgb092493">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
|
||||
<li><a href="#org2abcc52">9. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgc13ff2f">10. Template for HDF5 has/read/write a string attribute</a></li>
|
||||
<li><a href="#org4ffde08">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgeb7980d">12. Source code for the determinant part</a></li>
|
||||
<li><a href="#org2c2f24c">13. Helper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1140de7" class="outline-2">
|
||||
<h2 id="org1140de7"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div id="outline-container-orgd346e1b" class="outline-2">
|
||||
<h2 id="orgd346e1b"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<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>
|
||||
@ -354,8 +354,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf7153ab" class="outline-2">
|
||||
<h2 id="orgf7153ab"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div id="outline-container-orgdfb40fd" class="outline-2">
|
||||
<h2 id="orgdfb40fd"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
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 id="outline-container-orgdbab6e1" class="outline-2">
|
||||
<h2 id="orgdbab6e1"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div id="outline-container-orgffa5f91" class="outline-2">
|
||||
<h2 id="orgffa5f91"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
<div class="org-src-container">
|
||||
<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 id="outline-container-org9251edb" class="outline-2">
|
||||
<h2 id="org9251edb"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<div id="outline-container-orga5d3953" class="outline-2">
|
||||
<h2 id="orga5d3953"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
<div class="org-src-container">
|
||||
<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 id="outline-container-orge6a1e7d" class="outline-2">
|
||||
<h2 id="orge6a1e7d"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org4c3b44a" class="outline-2">
|
||||
<h2 id="org4c3b44a"><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="org-src-container">
|
||||
<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 id="outline-container-org960eac3" class="outline-2">
|
||||
<h2 id="org960eac3"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-orgb41c96e" class="outline-2">
|
||||
<h2 id="orgb41c96e"><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="org-src-container">
|
||||
<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 id="outline-container-org60046ba" class="outline-2">
|
||||
<h2 id="org60046ba"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
||||
<div id="outline-container-org86b7bba" class="outline-2">
|
||||
<h2 id="org86b7bba"><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">
|
||||
<p>
|
||||
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
|
||||
@ -973,8 +973,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7926126" class="outline-2">
|
||||
<h2 id="org7926126"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
|
||||
<div id="outline-container-orgb092493" class="outline-2">
|
||||
<h2 id="orgb092493"><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">
|
||||
<p>
|
||||
Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
@ -1108,8 +1108,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb9ee959" class="outline-2">
|
||||
<h2 id="orgb9ee959"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-org2abcc52" class="outline-2">
|
||||
<h2 id="org2abcc52"><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="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgba418ae" class="outline-2">
|
||||
<h2 id="orgba418ae"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
|
||||
<div id="outline-container-orgc13ff2f" class="outline-2">
|
||||
<h2 id="orgc13ff2f"><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="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1434,8 +1434,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgb7db89a" class="outline-2">
|
||||
<h2 id="orgb7db89a"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-org4ffde08" class="outline-2">
|
||||
<h2 id="org4ffde08"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
||||
<div class="outline-text-2" id="text-11">
|
||||
<p>
|
||||
<b><b>Note:</b></b> in early versions of the HDF5 library (v < 1.10) unlinking an object was not working as expected
|
||||
@ -1475,8 +1475,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgfeacb4f" class="outline-2">
|
||||
<h2 id="orgfeacb4f"><span class="section-number-2">12</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-orgeb7980d" class="outline-2">
|
||||
<h2 id="orgeb7980d"><span class="section-number-2">12</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-12">
|
||||
<p>
|
||||
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
|
||||
@ -1578,8 +1578,8 @@ Size specifies the number of data items (e.g. determinants) to process.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgaf8fe90" class="outline-2">
|
||||
<h2 id="orgaf8fe90"><span class="section-number-2">13</span> Helper functions</h2>
|
||||
<div id="outline-container-org2c2f24c" class="outline-2">
|
||||
<h2 id="org2c2f24c"><span class="section-number-2">13</span> Helper functions</h2>
|
||||
<div class="outline-text-2" id="text-13">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
|
||||
@ -324,23 +324,23 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orgc876d43">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#orgfac9df1">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org1ba6f4e">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org67bd216">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orgd16d930">5. Flush function (templated part)</a></li>
|
||||
<li><a href="#org02ad7e5">6. Template for text read a group</a></li>
|
||||
<li><a href="#orgc6bd602">7. Template for text has a group</a></li>
|
||||
<li><a href="#orgef5aa07">8. Template for text flush a group</a></li>
|
||||
<li><a href="#orgfeddaea">9. Template for text free memory</a></li>
|
||||
<li><a href="#org99d1b70">10. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#orgda0455b">11. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org118263f">12. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgc656e7a">13. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#org75c9759">14. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org4ef1685">15. Template for has/read/write a buffered vector</a></li>
|
||||
<li><a href="#orgb0f6dcc">16. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgda8d8b2">17. Source code for the determinant part</a></li>
|
||||
<li><a href="#org5fa48f3">1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org5f6e568">2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org5a351a6">3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orgbf9ab4c">4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org12cb28f">5. Flush function (templated part)</a></li>
|
||||
<li><a href="#org4b6a18a">6. Template for text read a group</a></li>
|
||||
<li><a href="#orgf1fb1f6">7. Template for text has a group</a></li>
|
||||
<li><a href="#org7f1db96">8. Template for text flush a group</a></li>
|
||||
<li><a href="#orge22be5f">9. Template for text free memory</a></li>
|
||||
<li><a href="#org357c6fd">10. Template for has/read/write a numerical attribute</a></li>
|
||||
<li><a href="#org83902c2">11. Template for has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#orgb2951e7">12. Template for has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org6313d8c">13. Template for has/read/write a string attribute</a></li>
|
||||
<li><a href="#orgb600ce8">14. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org5e9da21">15. Template for has/read/write a buffered vector</a></li>
|
||||
<li><a href="#orgec7a394">16. Template for text delete a group (UNSAFE mode)</a></li>
|
||||
<li><a href="#orgda128fc">17. Source code for the determinant part</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -362,8 +362,8 @@ directory.
|
||||
The file is written when closed, or when the flush function is called.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-orgc876d43" class="outline-2">
|
||||
<h2 id="orgc876d43"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
|
||||
<div id="outline-container-org5fa48f3" class="outline-2">
|
||||
<h2 id="org5fa48f3"><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="org-src-container">
|
||||
<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 id="outline-container-orgfac9df1" class="outline-2">
|
||||
<h2 id="orgfac9df1"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div id="outline-container-org5f6e568" class="outline-2">
|
||||
<h2 id="org5f6e568"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
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 id="outline-container-org1ba6f4e" class="outline-2">
|
||||
<h2 id="org1ba6f4e"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div id="outline-container-org5a351a6" class="outline-2">
|
||||
<h2 id="org5a351a6"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">bool</span>
|
||||
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org67bd216" class="outline-2">
|
||||
<h2 id="org67bd216"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div id="outline-container-orgbf9ab4c" class="outline-2">
|
||||
<h2 id="orgbf9ab4c"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -594,8 +594,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd16d930" class="outline-2">
|
||||
<h2 id="orgd16d930"><span class="section-number-2">5</span> Flush function (templated part)</h2>
|
||||
<div id="outline-container-org12cb28f" class="outline-2">
|
||||
<h2 id="org12cb28f"><span class="section-number-2">5</span> Flush function (templated part)</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -618,8 +618,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org02ad7e5" class="outline-2">
|
||||
<h2 id="org02ad7e5"><span class="section-number-2">6</span> Template for text read a group</h2>
|
||||
<div id="outline-container-org4b6a18a" class="outline-2">
|
||||
<h2 id="org4b6a18a"><span class="section-number-2">6</span> Template for text read a group</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c">$group$_t*
|
||||
@ -845,8 +845,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc6bd602" class="outline-2">
|
||||
<h2 id="orgc6bd602"><span class="section-number-2">7</span> Template for text has a group</h2>
|
||||
<div id="outline-container-orgf1fb1f6" class="outline-2">
|
||||
<h2 id="orgf1fb1f6"><span class="section-number-2">7</span> Template for text has a group</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -886,8 +886,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgef5aa07" class="outline-2">
|
||||
<h2 id="orgef5aa07"><span class="section-number-2">8</span> Template for text flush a group</h2>
|
||||
<div id="outline-container-org7f1db96" class="outline-2">
|
||||
<h2 id="org7f1db96"><span class="section-number-2">8</span> Template for text flush a group</h2>
|
||||
<div class="outline-text-2" id="text-8">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -951,8 +951,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgfeddaea" class="outline-2">
|
||||
<h2 id="orgfeddaea"><span class="section-number-2">9</span> Template for text free memory</h2>
|
||||
<div id="outline-container-orge22be5f" class="outline-2">
|
||||
<h2 id="orge22be5f"><span class="section-number-2">9</span> Template for text free memory</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<p>
|
||||
Memory is allocated when reading. The following function frees memory.
|
||||
@ -1021,8 +1021,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org99d1b70" class="outline-2">
|
||||
<h2 id="org99d1b70"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
|
||||
<div id="outline-container-org357c6fd" class="outline-2">
|
||||
<h2 id="org357c6fd"><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="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1085,8 +1085,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgda0455b" class="outline-2">
|
||||
<h2 id="orgda0455b"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
|
||||
<div id="outline-container-org83902c2" class="outline-2">
|
||||
<h2 id="org83902c2"><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">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1182,8 +1182,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org118263f" class="outline-2">
|
||||
<h2 id="org118263f"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
|
||||
<div id="outline-container-orgb2951e7" class="outline-2">
|
||||
<h2 id="orgb2951e7"><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">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1284,8 +1284,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgc656e7a" class="outline-2">
|
||||
<h2 id="orgc656e7a"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
|
||||
<div id="outline-container-org6313d8c" class="outline-2">
|
||||
<h2 id="org6313d8c"><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="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1359,8 +1359,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org75c9759" class="outline-2">
|
||||
<h2 id="org75c9759"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
|
||||
<div id="outline-container-orgb600ce8" class="outline-2">
|
||||
<h2 id="orgb600ce8"><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">
|
||||
<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
|
||||
@ -1650,8 +1650,8 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4ef1685" class="outline-2">
|
||||
<h2 id="org4ef1685"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
|
||||
<div id="outline-container-org5e9da21" class="outline-2">
|
||||
<h2 id="org5e9da21"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
|
||||
<div class="outline-text-2" id="text-15">
|
||||
<p>
|
||||
Each array is stored in a separate <code>.txt</code> file due to the fact that buffered I/O has to be decoupled
|
||||
@ -1881,8 +1881,8 @@ Size specifies the number of vector elements to be written.
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgb0f6dcc" class="outline-2">
|
||||
<h2 id="orgb0f6dcc"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
|
||||
<div id="outline-container-orgec7a394" class="outline-2">
|
||||
<h2 id="orgec7a394"><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="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1910,8 +1910,8 @@ Size specifies the number of vector elements to be written.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgda8d8b2" class="outline-2">
|
||||
<h2 id="orgda8d8b2"><span class="section-number-2">17</span> Source code for the determinant part</h2>
|
||||
<div id="outline-container-orgda128fc" class="outline-2">
|
||||
<h2 id="orgda128fc"><span class="section-number-2">17</span> Source code for the determinant part</h2>
|
||||
<div class="outline-text-2" id="text-17">
|
||||
<p>
|
||||
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
|
||||
|
||||
238
trex.html
238
trex.html
@ -346,70 +346,70 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org8133886">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orgfea590a">2. System</a>
|
||||
<li><a href="#org8c12314">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#orge42966e">2. System</a>
|
||||
<ul>
|
||||
<li><a href="#orgfe96830">2.1. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org0967c10">2.2. Cell (cell group)</a></li>
|
||||
<li><a href="#org9f2f9e2">2.3. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#org6acf969">2.4. Electron (electron group)</a></li>
|
||||
<li><a href="#orge6025f7">2.5. Ground or excited states (state group)</a></li>
|
||||
<li><a href="#orgd4875f6">2.1. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org369ef24">2.2. Cell (cell group)</a></li>
|
||||
<li><a href="#org1966111">2.3. Periodic boundary calculations (pbc group)</a></li>
|
||||
<li><a href="#orgf69244c">2.4. Electron (electron group)</a></li>
|
||||
<li><a href="#org82444d9">2.5. Ground or excited states (state group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org82f69e0">3. Basis functions</a>
|
||||
<li><a href="#org41a8b8d">3. Basis functions</a>
|
||||
<ul>
|
||||
<li><a href="#org890fc4d">3.1. Basis set (basis group)</a>
|
||||
<li><a href="#org9407181">3.1. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgc12a995">3.1.1. Gaussian and Slater-type orbitals</a></li>
|
||||
<li><a href="#org00b87d4">3.1.2. Plane waves</a></li>
|
||||
<li><a href="#org4ced59f">3.1.3. Data definitions</a></li>
|
||||
<li><a href="#org85a88bb">3.1.4. Example</a></li>
|
||||
<li><a href="#org4cd1641">3.1.1. Gaussian and Slater-type orbitals</a></li>
|
||||
<li><a href="#orgb659df2">3.1.2. Plane waves</a></li>
|
||||
<li><a href="#org43d96df">3.1.3. Data definitions</a></li>
|
||||
<li><a href="#org8a1ebdb">3.1.4. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org941c45d">3.2. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#orgf07e829">3.2. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#org7be0e55">3.2.1. Example</a></li>
|
||||
<li><a href="#orga9c0db4">3.2.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org0deb84b">3.3. Numerical integration grid (grid group)</a></li>
|
||||
<li><a href="#org5746bdb">3.3. Numerical integration grid (grid group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgf3ab92a">4. Orbitals</a>
|
||||
<li><a href="#org6ecaf13">4. Orbitals</a>
|
||||
<ul>
|
||||
<li><a href="#org7fea497">4.1. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#org98ca1b7">4.1. Atomic orbitals (ao group)</a>
|
||||
<ul>
|
||||
<li><a href="#ao_one_e">4.1.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
|
||||
<li><a href="#ao_two_e">4.1.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org861bd51">4.2. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org226bf37">4.2. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#orge94b898">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orga4232a8">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#org5ea5ee3">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org2b365a1">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org11acd12">5. Multi-determinant information</a>
|
||||
<li><a href="#org8d80fe8">5. Multi-determinant information</a>
|
||||
<ul>
|
||||
<li><a href="#org4a67946">5.1. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org9719ea8">5.2. Configuration state functions (csf group)</a></li>
|
||||
<li><a href="#org410b43b">5.3. Amplitudes (amplitude group)</a></li>
|
||||
<li><a href="#orgdf109ef">5.4. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#orge667954">5.1. Slater determinants (determinant group)</a></li>
|
||||
<li><a href="#org739ce84">5.2. Configuration state functions (csf group)</a></li>
|
||||
<li><a href="#org1e2afb0">5.3. Amplitudes (amplitude group)</a></li>
|
||||
<li><a href="#org112b0ee">5.4. Reduced density matrices (rdm group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org4b0f6f2">6. Correlation factors</a>
|
||||
<li><a href="#orgcde404f">6. Correlation factors</a>
|
||||
<ul>
|
||||
<li><a href="#org663f8eb">6.1. Jastrow factor (jastrow group)</a>
|
||||
<li><a href="#org9b2751c">6.1. Jastrow factor (jastrow group)</a>
|
||||
<ul>
|
||||
<li><a href="#org86a9e2d">6.1.1. CHAMP</a></li>
|
||||
<li><a href="#orgd60bb9a">6.1.2. Mu</a></li>
|
||||
<li><a href="#orgdc226be">6.1.3. Table of values</a></li>
|
||||
<li><a href="#org4dd9c0d">6.1.1. CHAMP</a></li>
|
||||
<li><a href="#orge45e8f0">6.1.2. Mu</a></li>
|
||||
<li><a href="#orgc9a764e">6.1.3. Table of values</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org8c70ec8">7. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
<li><a href="#org2b94634">7. Quantum Monte Carlo data (qmc group)</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -422,8 +422,8 @@ is reversed in the produced <code>trex.json</code> configuration file as the
|
||||
library is written in C.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-org8133886" class="outline-2">
|
||||
<h2 id="org8133886"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-org8c12314" class="outline-2">
|
||||
<h2 id="org8c12314"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<p>
|
||||
As we expect TREXIO files to be archived in open-data repositories,
|
||||
@ -433,7 +433,7 @@ have participated to the creation of the file, a list of authors of
|
||||
the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="org5a58349" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org0963927" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -516,19 +516,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgfea590a" class="outline-2">
|
||||
<h2 id="orgfea590a"><span class="section-number-2">2</span> System</h2>
|
||||
<div id="outline-container-orge42966e" class="outline-2">
|
||||
<h2 id="orge42966e"><span class="section-number-2">2</span> System</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
</div>
|
||||
<div id="outline-container-orgfe96830" class="outline-3">
|
||||
<h3 id="orgfe96830"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
|
||||
<div id="outline-container-orgd4875f6" class="outline-3">
|
||||
<h3 id="orgd4875f6"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
|
||||
<div class="outline-text-3" id="text-2-1">
|
||||
<p>
|
||||
The nuclei are considered as fixed point charges. Coordinates are
|
||||
given in Cartesian \((x,y,z)\) format.
|
||||
</p>
|
||||
|
||||
<table id="org3376c0b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org427b2ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -595,15 +595,15 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0967c10" class="outline-3">
|
||||
<h3 id="org0967c10"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
|
||||
<div id="outline-container-org369ef24" class="outline-3">
|
||||
<h3 id="org369ef24"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
|
||||
<div class="outline-text-3" id="text-2-2">
|
||||
<p>
|
||||
3 Lattice vectors to define a box containing the system, for example
|
||||
used in periodic calculations.
|
||||
</p>
|
||||
|
||||
<table id="orgbd71d5d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org8d53bfa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -677,15 +677,15 @@ used in periodic calculations.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9f2f9e2" class="outline-3">
|
||||
<h3 id="org9f2f9e2"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
|
||||
<div id="outline-container-org1966111" class="outline-3">
|
||||
<h3 id="org1966111"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
|
||||
<div class="outline-text-3" id="text-2-3">
|
||||
<p>
|
||||
A single $k$-point per TREXIO file can be stored. The $k$-point is
|
||||
defined in this group.
|
||||
</p>
|
||||
|
||||
<table id="org9cf55bd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org5f7f4a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -724,8 +724,8 @@ defined in this group.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6acf969" class="outline-3">
|
||||
<h3 id="org6acf969"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
|
||||
<div id="outline-container-orgf69244c" class="outline-3">
|
||||
<h3 id="orgf69244c"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
|
||||
<div class="outline-text-3" id="text-2-4">
|
||||
<p>
|
||||
The chemical system consists of nuclei and electrons, where the
|
||||
@ -744,7 +744,7 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</p>
|
||||
|
||||
|
||||
<table id="orgd615ffe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org4d56c8e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -790,8 +790,8 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge6025f7" class="outline-3">
|
||||
<h3 id="orge6025f7"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
|
||||
<div id="outline-container-org82444d9" class="outline-3">
|
||||
<h3 id="org82444d9"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
|
||||
<div class="outline-text-3" id="text-2-5">
|
||||
<p>
|
||||
This group contains information about excited states. Since only a
|
||||
@ -808,7 +808,7 @@ integrals, etc.
|
||||
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
|
||||
</p>
|
||||
|
||||
<table id="org8a73d5f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1caebba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -869,16 +869,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org82f69e0" class="outline-2">
|
||||
<h2 id="org82f69e0"><span class="section-number-2">3</span> Basis functions</h2>
|
||||
<div id="outline-container-org41a8b8d" class="outline-2">
|
||||
<h2 id="org41a8b8d"><span class="section-number-2">3</span> Basis functions</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
</div>
|
||||
<div id="outline-container-org890fc4d" class="outline-3">
|
||||
<h3 id="org890fc4d"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
|
||||
<div id="outline-container-org9407181" class="outline-3">
|
||||
<h3 id="org9407181"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
|
||||
<div class="outline-text-3" id="text-3-1">
|
||||
</div>
|
||||
<div id="outline-container-orgc12a995" class="outline-4">
|
||||
<h4 id="orgc12a995"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
|
||||
<div id="outline-container-org4cd1641" class="outline-4">
|
||||
<h4 id="org4cd1641"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
|
||||
<div class="outline-text-4" id="text-3-1-1">
|
||||
<p>
|
||||
We consider here basis functions centered on nuclei. Hence, it is
|
||||
@ -932,8 +932,8 @@ All the basis set parameters are stored in one-dimensional arrays.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org00b87d4" class="outline-4">
|
||||
<h4 id="org00b87d4"><span class="section-number-4">3.1.2</span> Plane waves</h4>
|
||||
<div id="outline-container-orgb659df2" class="outline-4">
|
||||
<h4 id="orgb659df2"><span class="section-number-4">3.1.2</span> Plane waves</h4>
|
||||
<div class="outline-text-4" id="text-3-1-2">
|
||||
<p>
|
||||
A plane wave is defined as
|
||||
@ -954,10 +954,10 @@ plane waves.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4ced59f" class="outline-4">
|
||||
<h4 id="org4ced59f"><span class="section-number-4">3.1.3</span> Data definitions</h4>
|
||||
<div id="outline-container-org43d96df" class="outline-4">
|
||||
<h4 id="org43d96df"><span class="section-number-4">3.1.3</span> Data definitions</h4>
|
||||
<div class="outline-text-4" id="text-3-1-3">
|
||||
<table id="orgbce2216" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org30c66d7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1066,8 +1066,8 @@ plane waves.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org85a88bb" class="outline-4">
|
||||
<h4 id="org85a88bb"><span class="section-number-4">3.1.4</span> Example</h4>
|
||||
<div id="outline-container-org8a1ebdb" class="outline-4">
|
||||
<h4 id="org8a1ebdb"><span class="section-number-4">3.1.4</span> Example</h4>
|
||||
<div class="outline-text-4" id="text-3-1-4">
|
||||
<p>
|
||||
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
|
||||
@ -1145,8 +1145,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org941c45d" class="outline-3">
|
||||
<h3 id="org941c45d"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
|
||||
<div id="outline-container-orgf07e829" class="outline-3">
|
||||
<h3 id="orgf07e829"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
|
||||
<div class="outline-text-3" id="text-3-2">
|
||||
<p>
|
||||
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
|
||||
@ -1178,7 +1178,7 @@ All 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> or <a href="https://doi.org/10.1063/1.5121006">https://doi.org/10.1063/1.5121006</a> for more info.
|
||||
</p>
|
||||
|
||||
<table id="org28eb3d4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org9902894" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1282,8 +1282,8 @@ If you encounter the aforementioned issue, please report it to our
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7be0e55" class="outline-4">
|
||||
<h4 id="org7be0e55"><span class="section-number-4">3.2.1</span> Example</h4>
|
||||
<div id="outline-container-orga9c0db4" class="outline-4">
|
||||
<h4 id="orga9c0db4"><span class="section-number-4">3.2.1</span> Example</h4>
|
||||
<div class="outline-text-4" id="text-3-2-1">
|
||||
<p>
|
||||
For example, consider H<sub>2</sub> molecule with the following
|
||||
@ -1346,8 +1346,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0deb84b" class="outline-3">
|
||||
<h3 id="org0deb84b"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
|
||||
<div id="outline-container-org5746bdb" class="outline-3">
|
||||
<h3 id="org5746bdb"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
|
||||
<div class="outline-text-3" id="text-3-3">
|
||||
<p>
|
||||
In some applications, such as DFT calculations, integrals have to
|
||||
@ -1362,7 +1362,7 @@ The structure of this group is adapted for the <a href="https://github.com/dftli
|
||||
Feel free to submit a PR if you find missing options/functionalities.
|
||||
</p>
|
||||
|
||||
<table id="orgb9150a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgbedd617" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1479,12 +1479,12 @@ Feel free to submit a PR if you find missing options/functionalities.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf3ab92a" class="outline-2">
|
||||
<h2 id="orgf3ab92a"><span class="section-number-2">4</span> Orbitals</h2>
|
||||
<div id="outline-container-org6ecaf13" class="outline-2">
|
||||
<h2 id="org6ecaf13"><span class="section-number-2">4</span> Orbitals</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
</div>
|
||||
<div id="outline-container-org7fea497" class="outline-3">
|
||||
<h3 id="org7fea497"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
|
||||
<div id="outline-container-org98ca1b7" class="outline-3">
|
||||
<h3 id="org98ca1b7"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
|
||||
<div class="outline-text-3" id="text-4-1">
|
||||
<p>
|
||||
AOs are defined as
|
||||
@ -1565,7 +1565,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
|
||||
</p>
|
||||
|
||||
|
||||
<table id="org1676901" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org3c18df2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1617,7 +1617,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgcce7db2" class="outline-4">
|
||||
<div id="outline-container-org811d8c9" class="outline-4">
|
||||
<h4 id="ao_one_e"><span class="section-number-4">4.1.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h4>
|
||||
<div class="outline-text-4" id="text-ao_one_e">
|
||||
<ul class="org-ul">
|
||||
@ -1635,7 +1635,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orge9cbf1f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org556e56c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1730,7 +1730,7 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga7c03bb" class="outline-4">
|
||||
<div id="outline-container-orgb9da083" class="outline-4">
|
||||
<h4 id="ao_two_e"><span class="section-number-4">4.1.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h4>
|
||||
<div class="outline-text-4" id="text-ao_two_e">
|
||||
<p>
|
||||
@ -1756,7 +1756,7 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
\]
|
||||
</p>
|
||||
|
||||
<table id="org246f3a4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgb2e2c48" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1824,10 +1824,10 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org861bd51" class="outline-3">
|
||||
<h3 id="org861bd51"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
|
||||
<div id="outline-container-org226bf37" class="outline-3">
|
||||
<h3 id="org226bf37"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
|
||||
<div class="outline-text-3" id="text-4-2">
|
||||
<table id="org0953c87" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org0fd53df" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1914,8 +1914,8 @@ The Cholesky decomposition of the integrals can also be stored:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge94b898" class="outline-4">
|
||||
<h4 id="orge94b898"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
|
||||
<div id="outline-container-org5ea5ee3" class="outline-4">
|
||||
<h4 id="org5ea5ee3"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
|
||||
<div class="outline-text-4" id="text-4-2-1">
|
||||
<p>
|
||||
The operators as the same as those defined in the
|
||||
@ -1923,7 +1923,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orgcb3a214" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org8ec4e3e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2018,8 +2018,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga4232a8" class="outline-4">
|
||||
<h4 id="orga4232a8"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
|
||||
<div id="outline-container-org2b365a1" class="outline-4">
|
||||
<h4 id="org2b365a1"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
|
||||
<div class="outline-text-4" id="text-4-2-2">
|
||||
<p>
|
||||
The operators are the same as those defined in the
|
||||
@ -2027,7 +2027,7 @@ The operators are the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org6b5edb9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgdb75598" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2096,12 +2096,12 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org11acd12" class="outline-2">
|
||||
<h2 id="org11acd12"><span class="section-number-2">5</span> Multi-determinant information</h2>
|
||||
<div id="outline-container-org8d80fe8" class="outline-2">
|
||||
<h2 id="org8d80fe8"><span class="section-number-2">5</span> Multi-determinant information</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
</div>
|
||||
<div id="outline-container-org4a67946" class="outline-3">
|
||||
<h3 id="org4a67946"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
|
||||
<div id="outline-container-orge667954" class="outline-3">
|
||||
<h3 id="orge667954"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
|
||||
<div class="outline-text-3" id="text-5-1">
|
||||
<p>
|
||||
The configuration interaction (CI) wave function \(\Psi\)
|
||||
@ -2143,7 +2143,7 @@ produced by the code generator.
|
||||
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
|
||||
</p>
|
||||
|
||||
<table id="org073d023" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org5253226" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2189,8 +2189,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9719ea8" class="outline-3">
|
||||
<h3 id="org9719ea8"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
|
||||
<div id="outline-container-org739ce84" class="outline-3">
|
||||
<h3 id="org739ce84"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
|
||||
<div class="outline-text-3" id="text-5-2">
|
||||
<p>
|
||||
The configuration interaction (CI) wave function \(\Psi\) can be
|
||||
@ -2212,7 +2212,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
|
||||
the basis of Slater determinants.
|
||||
</p>
|
||||
|
||||
<table id="org8c53149" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org384c25d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2258,8 +2258,8 @@ the basis of Slater determinants.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org410b43b" class="outline-3">
|
||||
<h3 id="org410b43b"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
|
||||
<div id="outline-container-org1e2afb0" class="outline-3">
|
||||
<h3 id="org1e2afb0"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
|
||||
<div class="outline-text-3" id="text-5-3">
|
||||
<p>
|
||||
The wave function may be expressed in terms of action of the cluster
|
||||
@ -2330,7 +2330,7 @@ The order of the indices is chosen such that
|
||||
<li>\(\dots\)</li>
|
||||
</ul>
|
||||
|
||||
<table id="org003b666" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org09f7f98" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2411,8 +2411,8 @@ The order of the indices is chosen such that
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdf109ef" class="outline-3">
|
||||
<h3 id="orgdf109ef"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
|
||||
<div id="outline-container-org112b0ee" class="outline-3">
|
||||
<h3 id="org112b0ee"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
|
||||
<div class="outline-text-3" id="text-5-4">
|
||||
<p>
|
||||
The reduced density matrices are defined in the basis of molecular
|
||||
@ -2484,7 +2484,7 @@ expressed in a basis of a one-electron function
|
||||
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
|
||||
</p>
|
||||
|
||||
<table id="orgdbc3a82" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org0e4a33b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2615,12 +2615,12 @@ expressed in a basis of a one-electron function
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4b0f6f2" class="outline-2">
|
||||
<h2 id="org4b0f6f2"><span class="section-number-2">6</span> Correlation factors</h2>
|
||||
<div id="outline-container-orgcde404f" class="outline-2">
|
||||
<h2 id="orgcde404f"><span class="section-number-2">6</span> Correlation factors</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
</div>
|
||||
<div id="outline-container-org663f8eb" class="outline-3">
|
||||
<h3 id="org663f8eb"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
|
||||
<div id="outline-container-org9b2751c" class="outline-3">
|
||||
<h3 id="org9b2751c"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
|
||||
<div class="outline-text-3" id="text-6-1">
|
||||
<p>
|
||||
The Jastrow factor is an $N$-electron function which multiplies the CI
|
||||
@ -2645,8 +2645,8 @@ following:
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org86a9e2d" class="outline-4">
|
||||
<h4 id="org86a9e2d"><span class="section-number-4">6.1.1</span> CHAMP</h4>
|
||||
<div id="outline-container-org4dd9c0d" class="outline-4">
|
||||
<h4 id="org4dd9c0d"><span class="section-number-4">6.1.1</span> CHAMP</h4>
|
||||
<div class="outline-text-4" id="text-6-1-1">
|
||||
<p>
|
||||
The first form of Jastrow factor is the one used in
|
||||
@ -2747,8 +2747,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
|
||||
</div>
|
||||
|
||||
|
||||
<div id="outline-container-orgd60bb9a" class="outline-4">
|
||||
<h4 id="orgd60bb9a"><span class="section-number-4">6.1.2</span> Mu</h4>
|
||||
<div id="outline-container-orge45e8f0" class="outline-4">
|
||||
<h4 id="orge45e8f0"><span class="section-number-4">6.1.2</span> Mu</h4>
|
||||
<div class="outline-text-4" id="text-6-1-2">
|
||||
<p>
|
||||
<a href="https://aip.scitation.org/doi/10.1063/5.0044683">Mu-Jastrow</a> is based on a one-parameter correlation factor that has
|
||||
@ -2845,10 +2845,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdc226be" class="outline-4">
|
||||
<h4 id="orgdc226be"><span class="section-number-4">6.1.3</span> Table of values</h4>
|
||||
<div id="outline-container-orgc9a764e" class="outline-4">
|
||||
<h4 id="orgc9a764e"><span class="section-number-4">6.1.3</span> Table of values</h4>
|
||||
<div class="outline-text-4" id="text-6-1-3">
|
||||
<table id="org3d4b7f6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org1306391" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -2952,8 +2952,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8c70ec8" class="outline-2">
|
||||
<h2 id="org8c70ec8"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div id="outline-container-org2b94634" class="outline-2">
|
||||
<h2 id="org2b94634"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<p>
|
||||
In quantum Monte Carlo calculations, the wave function is evaluated
|
||||
@ -2967,7 +2967,7 @@ By convention, the electron coordinates contain first all the electrons
|
||||
of $↑$-spin and then all the $↓$-spin.
|
||||
</p>
|
||||
|
||||
<table id="org432a1f9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga95b198" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user