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README.html
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 09:38</p>
<p class="date">Created: 2022-06-16 Thu 15:20</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title>
@ -333,24 +333,24 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org291f4b2">1. Accessing sparse quantities</a>
<li><a href="#orgab17b52">1. Accessing sparse quantities</a>
<ul>
<li><a href="#orgfcf3e82">1.1. Fortran</a>
<li><a href="#org3181d3f">1.1. Fortran</a>
<ul>
<li><a href="#org7b2b2a5">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org0bab32d">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga7bee5c">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org043faa3">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgdcf8569">1.1.5. Allocate memory</a></li>
<li><a href="#orgbfcab42">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org884edc5">1.1.7. Read two-electron quantities</a>
<li><a href="#org7b49d62">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgddfc2aa">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgeb734b8">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgdd4e07d">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgb62c7d7">1.1.5. Allocate memory</a></li>
<li><a href="#org66047b1">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orga9e0ec7">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org85d004a">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgbecc791">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org8424b81">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgb190bc8">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgfee49cf">1.1.8. Compute the energy</a></li>
<li><a href="#orgfd558a2">1.1.9. Terminate</a></li>
<li><a href="#orgbbc7be3">1.1.8. Compute the energy</a></li>
<li><a href="#orgc2c66c9">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
@ -360,12 +360,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org291f4b2" class="outline-2">
<h2 id="org291f4b2"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-orgab17b52" class="outline-2">
<h2 id="orgab17b52"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgfcf3e82" class="outline-3">
<h3 id="orgfcf3e82"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org3181d3f" class="outline-3">
<h3 id="org3181d3f"><span class="section-number-3">1.1</span> Fortran</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
@ -411,8 +411,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org7b2b2a5" class="outline-4">
<h4 id="org7b2b2a5"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org7b49d62" class="outline-4">
<h4 id="org7b49d62"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div class="outline-text-4" id="text-1-1-1">
<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>
@ -427,8 +427,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org0bab32d" class="outline-4">
<h4 id="org0bab32d"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-orgddfc2aa" class="outline-4">
<h4 id="orgddfc2aa"><span class="section-number-4">1.1.2</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-1-1-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
@ -444,8 +444,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orga7bee5c" class="outline-4">
<h4 id="orga7bee5c"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgeb734b8" class="outline-4">
<h4 id="orgeb734b8"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-1-1-3">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
@ -459,8 +459,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org043faa3" class="outline-4">
<h4 id="org043faa3"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgdd4e07d" class="outline-4">
<h4 id="orgdd4e07d"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-1-1-4">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
@ -474,8 +474,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgdcf8569" class="outline-4">
<h4 id="orgdcf8569"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-orgb62c7d7" class="outline-4">
<h4 id="orgb62c7d7"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div class="outline-text-4" id="text-1-1-5">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
@ -487,8 +487,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-orgbfcab42" class="outline-4">
<h4 id="orgbfcab42"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org66047b1" class="outline-4">
<h4 id="org66047b1"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-1-1-6">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@ -520,8 +520,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-org884edc5" class="outline-4">
<h4 id="org884edc5"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orga9e0ec7" class="outline-4">
<h4 id="orga9e0ec7"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-1-1-7">
<p>
Reading is done with OpenMP. Each thread reads its own buffer, and
@ -537,8 +537,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org85d004a" class="outline-5">
<h5 id="org85d004a"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org8424b81" class="outline-5">
<h5 id="org8424b81"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-1-1-7-1">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
@ -587,8 +587,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-orgbecc791" class="outline-5">
<h5 id="orgbecc791"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgb190bc8" class="outline-5">
<h5 id="orgb190bc8"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-1-1-7-2">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
@ -632,8 +632,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-orgfee49cf" class="outline-4">
<h4 id="orgfee49cf"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-orgbbc7be3" class="outline-4">
<h4 id="orgbbc7be3"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-1-1-8">
<p>
When the orbitals are real, we can use
@ -679,8 +679,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-orgfd558a2" class="outline-4">
<h4 id="orgfd558a2"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgc2c66c9" class="outline-4">
<h4 id="orgc2c66c9"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div class="outline-text-4" id="text-1-1-9">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
@ -695,7 +695,7 @@ E = E + E_nn
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 09:38</p>
<p class="date">Created: 2022-06-16 Thu 15:20</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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index.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-06-03 Fri 09:38 -->
<!-- 2022-06-16 Thu 15:20 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 09:38</p>
<p class="date">Created: 2022-06-16 Thu 15:20</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-06-03 Fri 09:38 -->
<!-- 2022-06-16 Thu 15:20 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>HDF5 back end</title>
@ -311,23 +311,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9e732ea">1. Template for HDF5 definitions</a></li>
<li><a href="#org29ccaf4">2. Template for HDF5 structures</a></li>
<li><a href="#org1c830bd">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org0d1167c">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org0e8f46c">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgcaa240d">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org8a08453">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org7fb4dc1">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org49bd850">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org72fb750">10. Source code for the determinant part</a></li>
<li><a href="#org0e36795">11. Helper functions</a></li>
<li><a href="#orge9f6a0f">1. Template for HDF5 definitions</a></li>
<li><a href="#org2c9bff7">2. Template for HDF5 structures</a></li>
<li><a href="#org892cb54">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org7899a5c">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org8ff7550">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org0bf1f27">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org749b264">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org2fa726d">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org3933942">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orge227156">10. Source code for the determinant part</a></li>
<li><a href="#org3e62049">11. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org9e732ea" class="outline-2">
<h2 id="org9e732ea"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orge9f6a0f" class="outline-2">
<h2 id="orge9f6a0f"><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>
@ -339,8 +339,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org29ccaf4" class="outline-2">
<h2 id="org29ccaf4"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org2c9bff7" class="outline-2">
<h2 id="org2c9bff7"><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
@ -360,8 +360,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org1c830bd" class="outline-2">
<h2 id="org1c830bd"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org892cb54" class="outline-2">
<h2 id="org892cb54"><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>
@ -466,8 +466,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org0d1167c" class="outline-2">
<h2 id="org0d1167c"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org7899a5c" class="outline-2">
<h2 id="org7899a5c"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</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>
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org0e8f46c" class="outline-2">
<h2 id="org0e8f46c"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org8ff7550" class="outline-2">
<h2 id="org8ff7550"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</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>
@ -706,8 +706,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgcaa240d" class="outline-2">
<h2 id="orgcaa240d"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org0bf1f27" class="outline-2">
<h2 id="org0bf1f27"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-6">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -910,8 +910,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org8a08453" class="outline-2">
<h2 id="org8a08453"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org749b264" class="outline-2">
<h2 id="org749b264"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</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>
@ -1109,8 +1109,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org7fb4dc1" class="outline-2">
<h2 id="org7fb4dc1"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org2fa726d" class="outline-2">
<h2 id="org2fa726d"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</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>
@ -1237,8 +1237,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-org49bd850" class="outline-2">
<h2 id="org49bd850"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org3933942" class="outline-2">
<h2 id="org3933942"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-9">
<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
@ -1278,8 +1278,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org72fb750" class="outline-2">
<h2 id="org72fb750"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div id="outline-container-orge227156" class="outline-2">
<h2 id="orge227156"><span class="section-number-2">10</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-10">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1532,8 +1532,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org0e36795" class="outline-2">
<h2 id="org0e36795"><span class="section-number-2">11</span> Helper functions</h2>
<div id="outline-container-org3e62049" class="outline-2">
<h2 id="org3e62049"><span class="section-number-2">11</span> Helper functions</h2>
<div class="outline-text-2" id="text-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1796,7 +1796,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 09:38</p>
<p class="date">Created: 2022-06-16 Thu 15:20</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

88
templator_text.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-06-03 Fri 09:38 -->
<!-- 2022-06-16 Thu 15:20 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
@ -311,20 +311,20 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org96b8fb3">1. Template for group-related structures in text back end</a></li>
<li><a href="#org0c0c67c">2. Template for general structure in text back end</a></li>
<li><a href="#org72cad81">3. Initialize function (constant part)</a></li>
<li><a href="#org223f6d4">4. Deinitialize function (templated part)</a></li>
<li><a href="#org0f00d08">5. Template for text read a group</a></li>
<li><a href="#orgf8358ce">6. Template for text flush a group</a></li>
<li><a href="#orgf40863d">7. Template for text free memory</a></li>
<li><a href="#org2d7dc10">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgf2166d6">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgd8f4993">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgb93f363">11. Template for has/read/write a string attribute</a></li>
<li><a href="#orgf061347">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org77d9750">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org0bf830b">14. Source code for the determinant part</a></li>
<li><a href="#org07a98a4">1. Template for group-related structures in text back end</a></li>
<li><a href="#org39482aa">2. Template for general structure in text back end</a></li>
<li><a href="#org3252c3f">3. Initialize function (constant part)</a></li>
<li><a href="#orgcb1b765">4. Deinitialize function (templated part)</a></li>
<li><a href="#org69ae094">5. Template for text read a group</a></li>
<li><a href="#org75d7ccd">6. Template for text flush a group</a></li>
<li><a href="#org57ebc40">7. Template for text free memory</a></li>
<li><a href="#org48466ef">8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgc4c810b">9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgcdd7f94">10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org395b4f8">11. Template for has/read/write a string attribute</a></li>
<li><a href="#org90d0d62">12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org0ece64c">13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org14a2635">14. Source code for the determinant part</a></li>
</ul>
</div>
</div>
@ -346,8 +346,8 @@ directory.
The file is written when closed, or when the flush function is called.
</p>
<div id="outline-container-org96b8fb3" class="outline-2">
<h2 id="org96b8fb3"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org07a98a4" class="outline-2">
<h2 id="org07a98a4"><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 {
@ -366,8 +366,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org0c0c67c" class="outline-2">
<h2 id="org0c0c67c"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org39482aa" class="outline-2">
<h2 id="org39482aa"><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
@ -387,8 +387,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org72cad81" class="outline-2">
<h2 id="org72cad81"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org3252c3f" class="outline-2">
<h2 id="org3252c3f"><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;">trexio_exit_code</span>
@ -531,8 +531,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org223f6d4" class="outline-2">
<h2 id="org223f6d4"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgcb1b765" class="outline-2">
<h2 id="orgcb1b765"><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>
@ -554,8 +554,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org0f00d08" class="outline-2">
<h2 id="org0f00d08"><span class="section-number-2">5</span> Template for text read a group</h2>
<div id="outline-container-org69ae094" class="outline-2">
<h2 id="org69ae094"><span class="section-number-2">5</span> Template for text read a group</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -779,8 +779,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgf8358ce" class="outline-2">
<h2 id="orgf8358ce"><span class="section-number-2">6</span> Template for text flush a group</h2>
<div id="outline-container-org75d7ccd" class="outline-2">
<h2 id="org75d7ccd"><span class="section-number-2">6</span> Template for text flush a group</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>
@ -844,8 +844,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgf40863d" class="outline-2">
<h2 id="orgf40863d"><span class="section-number-2">7</span> Template for text free memory</h2>
<div id="outline-container-org57ebc40" class="outline-2">
<h2 id="org57ebc40"><span class="section-number-2">7</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-7">
<p>
Memory is allocated when reading. The following function frees memory.
@ -914,8 +914,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org2d7dc10" class="outline-2">
<h2 id="org2d7dc10"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org48466ef" class="outline-2">
<h2 id="org48466ef"><span class="section-number-2">8</span> Template for has/read/write a numerical attribute</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>
@ -978,8 +978,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgf2166d6" class="outline-2">
<h2 id="orgf2166d6"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgc4c810b" class="outline-2">
<h2 id="orgc4c810b"><span class="section-number-2">9</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-9">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1075,8 +1075,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgd8f4993" class="outline-2">
<h2 id="orgd8f4993"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgcdd7f94" class="outline-2">
<h2 id="orgcdd7f94"><span class="section-number-2">10</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-10">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1177,8 +1177,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgb93f363" class="outline-2">
<h2 id="orgb93f363"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org395b4f8" class="outline-2">
<h2 id="org395b4f8"><span class="section-number-2">11</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1252,8 +1252,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgf061347" class="outline-2">
<h2 id="orgf061347"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org90d0d62" class="outline-2">
<h2 id="org90d0d62"><span class="section-number-2">12</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-12">
<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
@ -1526,8 +1526,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org77d9750" class="outline-2">
<h2 id="org77d9750"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org0ece64c" class="outline-2">
<h2 id="org0ece64c"><span class="section-number-2">13</span> Template for text delete a group (UNSAFE mode)</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>
@ -1555,8 +1555,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org0bf830b" class="outline-2">
<h2 id="org0bf830b"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div id="outline-container-org14a2635" class="outline-2">
<h2 id="org14a2635"><span class="section-number-2">14</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-14">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -1960,7 +1960,7 @@ Size specifies the number of data items, e.g. determinants.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 09:38</p>
<p class="date">Created: 2022-06-16 Thu 15:20</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

150
trex.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-06-03 Fri 09:38 -->
<!-- 2022-06-16 Thu 15:20 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREX Configuration file</title>
@ -333,37 +333,37 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgc835ef9">1. Metadata (metadata group)</a></li>
<li><a href="#org9c080de">2. Electron (electron group)</a></li>
<li><a href="#org67c71de">3. Nucleus (nucleus group)</a></li>
<li><a href="#org5305d95">4. Effective core potentials (ecp group)</a>
<li><a href="#orgc98157b">1. Metadata (metadata group)</a></li>
<li><a href="#org6f76b6e">2. Electron (electron group)</a></li>
<li><a href="#orgac182eb">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgf70cf0c">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org1265448">4.1. Example</a></li>
<li><a href="#orgaa32ede">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org13c8c89">5. Basis set (basis group)</a>
<li><a href="#org1371c4b">5. Basis set (basis group)</a>
<ul>
<li><a href="#org30462a9">5.1. Example</a></li>
<li><a href="#orgbf532ab">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org6ae942e">6. Atomic orbitals (ao group)</a>
<li><a href="#orgb956148">6. Atomic orbitals (ao group)</a>
<ul>
<li><a href="#ao_one_e">6.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
<li><a href="#ao_two_e">6.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org1131f83">7. Molecular orbitals (mo group)</a>
<li><a href="#org84fad74">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orge4c0724">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org7c17825">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org4ca8797">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org8be84e9">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org5732738">8. Slater determinants (determinant group)</a></li>
<li><a href="#orgd68f40b">9. Excited states (state group)</a></li>
<li><a href="#org63e088b">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#orga334aa2">11. Cell (cell group)</a></li>
<li><a href="#org841485f">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgb3b0d10">13. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#orgcfb1606">8. Slater determinants (determinant group)</a></li>
<li><a href="#org08f365d">9. Excited states (state group)</a></li>
<li><a href="#org79b5e15">10. Reduced density matrices (rdm group)</a></li>
<li><a href="#org35c56e1">11. Cell (cell group)</a></li>
<li><a href="#org0e7aa9b">12. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgdc82494">13. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -413,8 +413,8 @@ the <a href="./examples.html">examples</a>.
</p>
<div id="outline-container-orgc835ef9" class="outline-2">
<h2 id="orgc835ef9"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgc98157b" class="outline-2">
<h2 id="orgc98157b"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect our files to be archived in open-data repositories, we
@ -424,7 +424,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org28b3b00" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org37159bd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -505,15 +505,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-org9c080de" class="outline-2">
<h2 id="org9c080de"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org6f76b6e" class="outline-2">
<h2 id="org6f76b6e"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div class="outline-text-2" id="text-2">
<p>
We consider wave functions expressed in the spin-free formalism, where
the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org1d705e2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7b12c50" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -559,15 +559,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org67c71de" class="outline-2">
<h2 id="org67c71de"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-orgac182eb" class="outline-2">
<h2 id="orgac182eb"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div class="outline-text-2" id="text-3">
<p>
The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format.
</p>
<table id="org1f5ed16" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org02fbb69" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -634,8 +634,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org5305d95" class="outline-2">
<h2 id="org5305d95"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgf70cf0c" class="outline-2">
<h2 id="orgf70cf0c"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div class="outline-text-2" id="text-4">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -668,7 +668,7 @@ The functions \(V_{A\ell}\) are parameterized as:
See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.4984046</a> or <a href="https://doi.org/10.1063/1.5121006">https://doi.org/10.1063/1.5121006</a> for more info.
</p>
<table id="orga269ad1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga21e7aa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -770,8 +770,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-org1265448" class="outline-3">
<h3 id="org1265448"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orgaa32ede" class="outline-3">
<h3 id="orgaa32ede"><span class="section-number-3">4.1</span> Example</h3>
<div class="outline-text-3" id="text-4-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -834,8 +834,8 @@ power = [
</div>
</div>
<div id="outline-container-org13c8c89" class="outline-2">
<h2 id="org13c8c89"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org1371c4b" class="outline-2">
<h2 id="org1371c4b"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div class="outline-text-2" id="text-5">
<p>
We consider here basis functions centered on nuclei. Hence, we enable
@ -888,7 +888,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
All the basis set parameters are stored in one-dimensional arrays:
</p>
<table id="orgc4e122b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org710b215" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -982,8 +982,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-org30462a9" class="outline-3">
<h3 id="org30462a9"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-orgbf532ab" class="outline-3">
<h3 id="orgbf532ab"><span class="section-number-3">5.1</span> Example</h3>
<div class="outline-text-3" id="text-5-1">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1061,8 +1061,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org6ae942e" class="outline-2">
<h2 id="org6ae942e"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-orgb956148" class="outline-2">
<h2 id="orgb956148"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div class="outline-text-2" id="text-6">
<p>
Going from the atomic basis set to AOs implies a systematic
@ -1115,13 +1115,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org13c8c89">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org1371c4b">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
normalization factor of the atomic orbitals in spherical coordinates.
The normalization factor of the \(xy\) function which should be
introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</p>
<table id="orgdf1ae45" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org721e71b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1173,8 +1173,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org04a8a68" class="outline-3">
<h3 id="ao_one_e"><a id="org04a8a68"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgd40844c" class="outline-3">
<h3 id="ao_one_e"><a id="orgd40844c"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_one_e">
<ul class="org-ul">
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
@ -1191,7 +1191,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org223365e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge46c38d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1286,8 +1286,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org946f27c" class="outline-3">
<h3 id="ao_two_e"><a id="org946f27c"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org61e7028" class="outline-3">
<h3 id="ao_two_e"><a id="org61e7028"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_two_e">
<p>
The two-electron integrals for a two-electron operator \(\hat{O}\) are
@ -1308,7 +1308,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="orgceb3a60" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd8d104d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1348,10 +1348,10 @@ notation.
</div>
</div>
<div id="outline-container-org1131f83" class="outline-2">
<h2 id="org1131f83"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org84fad74" class="outline-2">
<h2 id="org84fad74"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org4efb13f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdfd5d28" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1424,8 +1424,8 @@ notation.
</table>
</div>
<div id="outline-container-orge4c0724" class="outline-3">
<h3 id="orge4c0724"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org4ca8797" class="outline-3">
<h3 id="org4ca8797"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-1">
<p>
The operators as the same as those defined in the
@ -1433,7 +1433,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgf0a401c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org06f940e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1528,8 +1528,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org7c17825" class="outline-3">
<h3 id="org7c17825"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org8be84e9" class="outline-3">
<h3 id="org8be84e9"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-2">
<p>
The operators as the same as those defined in the
@ -1537,7 +1537,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org6a00c52" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7d65746" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1577,8 +1577,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org5732738" class="outline-2">
<h2 id="org5732738"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div id="outline-container-orgcfb1606" class="outline-2">
<h2 id="orgcfb1606"><span class="section-number-2">8</span> Slater determinants (determinant group)</h2>
<div class="outline-text-2" id="text-8">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -1611,7 +1611,7 @@ where \(\alpha\) and \(\beta\) denote $&uarr;$-spin and $&darr;$-spin electrons,
\(n\uparrow\) and \(n\downarrow\) correspond to <code>electron.up_num</code> and <code>electron.dn_num</code>, respectively.
</p>
<table id="org0f03bc6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org20508c6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1657,8 +1657,8 @@ where \(\alpha\) and \(\beta\) denote $&uarr;$-spin and $&darr;$-spin electrons,
</div>
</div>
<div id="outline-container-orgd68f40b" class="outline-2">
<h2 id="orgd68f40b"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div id="outline-container-org08f365d" class="outline-2">
<h2 id="org08f365d"><span class="section-number-2">9</span> Excited states (state group)</h2>
<div class="outline-text-2" id="text-9">
<p>
By default, the <code>determinant</code> group corresponds to the ground state.
@ -1667,7 +1667,7 @@ correspond to excited state wave functions for the same set of
determinants. This is the goal of the present group
</p>
<table id="org5df6a40" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org04ac219" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1706,8 +1706,8 @@ determinants. This is the goal of the present group
</div>
</div>
<div id="outline-container-org63e088b" class="outline-2">
<h2 id="org63e088b"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org79b5e15" class="outline-2">
<h2 id="org79b5e15"><span class="section-number-2">10</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-10">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1760,7 +1760,7 @@ The total energy can be computed as:
\]
</p>
<table id="org8e165d1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3148dac" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1841,10 +1841,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-orga334aa2" class="outline-2">
<h2 id="orga334aa2"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div id="outline-container-org35c56e1" class="outline-2">
<h2 id="org35c56e1"><span class="section-number-2">11</span> Cell (cell group)</h2>
<div class="outline-text-2" id="text-11">
<table id="orgffd90a0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd0de25a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1890,10 +1890,10 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-org841485f" class="outline-2">
<h2 id="org841485f"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div id="outline-container-org0e7aa9b" class="outline-2">
<h2 id="org0e7aa9b"><span class="section-number-2">12</span> Periodic boundary calculations (pbc group)</h2>
<div class="outline-text-2" id="text-12">
<table id="org34eb831" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge172734" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1932,8 +1932,8 @@ The total energy can be computed as:
</div>
</div>
<div id="outline-container-orgb3b0d10" class="outline-2">
<h2 id="orgb3b0d10"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-orgdc82494" class="outline-2">
<h2 id="orgdc82494"><span class="section-number-2">13</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-13">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -1947,7 +1947,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orge8ae3d4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga3ffdb3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2002,7 +2002,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-06-03 Fri 09:38</p>
<p class="date">Created: 2022-06-16 Thu 15:20</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>