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@ -3,7 +3,7 @@
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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<head>
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||||
<!-- 2022-01-07 Fri 10:04 -->
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<!-- 2022-01-07 Fri 10:09 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<meta name=google-site-verification content=jdDnuP2rYGJVy8AHSd-8LkmOmvK_dyz5buZ98wilYII />
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@ -348,7 +348,7 @@ and bug reports should be submitted at
|
||||
</div>
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||||
<div id="postamble" class="status">
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<p class="author">Author: TREX-CoE</p>
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<p class="date">Created: 2022-01-07 Fri 10:04</p>
|
||||
<p class="date">Created: 2022-01-07 Fri 10:09</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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||||
<head>
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<!-- 2022-01-07 Fri 10:04 -->
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||||
<!-- 2022-01-07 Fri 10:09 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Examples</title>
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||||
@ -333,24 +333,24 @@ 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="#orgba56890">1. Accessing sparse quantities</a>
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<li><a href="#orge047690">1. Accessing sparse quantities</a>
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<ul>
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<li><a href="#org9f5890e">1.1. Fortran</a>
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<li><a href="#orgcc8a140">1.1. Fortran</a>
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<ul>
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<li><a href="#orga2a41cc">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org8485afa">1.1.2. 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="#orge46293d">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#org119ccb8">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#orgc8118f7">1.1.5. Allocate memory</a></li>
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<li><a href="#orgbe12704">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org9e1f674">1.1.7. Read two-electron quantities</a>
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<li><a href="#org63b8dc0">1.1.1. Declare Temporary variables</a></li>
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<li><a href="#org2cdf6c1">1.1.2. 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="#org0854a31">1.1.3. Read the nuclear repulsion energy</a></li>
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<li><a href="#orgd926fe1">1.1.4. Read the number of molecular orbitals</a></li>
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<li><a href="#org1db9484">1.1.5. Allocate memory</a></li>
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<li><a href="#orge713f22">1.1.6. Read one-electron quantities</a></li>
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<li><a href="#org0507a4f">1.1.7. Read two-electron quantities</a>
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<ul>
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<li><a href="#org8a0ec69">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#orgc6b0c44">1.1.7.2. Reduced density matrix</a></li>
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<li><a href="#org7e61001">1.1.7.1. Electron repulsion integrals</a></li>
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<li><a href="#org5703c42">1.1.7.2. Reduced density matrix</a></li>
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</ul>
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</li>
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<li><a href="#org4cb2714">1.1.8. Compute the energy</a></li>
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<li><a href="#org174bdc8">1.1.9. Terminate</a></li>
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<li><a href="#org2adc532">1.1.8. Compute the energy</a></li>
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<li><a href="#org1cb02dd">1.1.9. Terminate</a></li>
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</ul>
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</li>
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</ul>
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@ -360,12 +360,12 @@ for the JavaScript code in this tag.
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</div>
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<div id="outline-container-orgba56890" class="outline-2">
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<h2 id="orgba56890"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
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<div id="outline-container-orge047690" class="outline-2">
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<h2 id="orge047690"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
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<div class="outline-text-2" id="text-1">
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</div>
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<div id="outline-container-org9f5890e" class="outline-3">
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<h3 id="org9f5890e"><span class="section-number-3">1.1</span> Fortran</h3>
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<div id="outline-container-orgcc8a140" class="outline-3">
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<h3 id="orgcc8a140"><span class="section-number-3">1.1</span> Fortran</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-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
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@ -413,8 +413,8 @@ 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-orga2a41cc" class="outline-4">
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<h4 id="orga2a41cc"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div id="outline-container-org63b8dc0" class="outline-4">
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<h4 id="org63b8dc0"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
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<div class="outline-text-4" id="text-1-1-1">
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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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@ -429,8 +429,8 @@ 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-org8485afa" class="outline-4">
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<h4 id="org8485afa"><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>
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<div id="outline-container-org2cdf6c1" class="outline-4">
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<h4 id="org2cdf6c1"><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>
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<div class="outline-text-4" id="text-1-1-2">
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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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@ -446,8 +446,8 @@ 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-orge46293d" class="outline-4">
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<h4 id="orge46293d"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div id="outline-container-org0854a31" class="outline-4">
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<h4 id="org0854a31"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
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<div class="outline-text-4" id="text-1-1-3">
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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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@ -461,8 +461,8 @@ 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-org119ccb8" class="outline-4">
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<h4 id="org119ccb8"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div id="outline-container-orgd926fe1" class="outline-4">
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<h4 id="orgd926fe1"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
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<div class="outline-text-4" id="text-1-1-4">
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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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@ -476,8 +476,8 @@ 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-orgc8118f7" class="outline-4">
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<h4 id="orgc8118f7"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div id="outline-container-org1db9484" class="outline-4">
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<h4 id="org1db9484"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
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<div class="outline-text-4" id="text-1-1-5">
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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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@ -489,8 +489,8 @@ W(:,:,:,:) = 0.d0
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</div>
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</div>
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<div id="outline-container-orgbe12704" class="outline-4">
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<h4 id="orgbe12704"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div id="outline-container-orge713f22" class="outline-4">
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<h4 id="orge713f22"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
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<div class="outline-text-4" id="text-1-1-6">
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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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@ -522,8 +522,8 @@ 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-org9e1f674" class="outline-4">
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<h4 id="org9e1f674"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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<div id="outline-container-org0507a4f" class="outline-4">
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||||
<h4 id="org0507a4f"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
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<div class="outline-text-4" id="text-1-1-7">
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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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@ -539,8 +539,8 @@ 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-org8a0ec69" class="outline-5">
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<h5 id="org8a0ec69"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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<div id="outline-container-org7e61001" class="outline-5">
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<h5 id="org7e61001"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
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<div class="outline-text-5" id="text-1-1-7-1">
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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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@ -589,8 +589,8 @@ icount = BUFSIZE
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</div>
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</div>
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<div id="outline-container-orgc6b0c44" class="outline-5">
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<h5 id="orgc6b0c44"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div id="outline-container-org5703c42" class="outline-5">
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<h5 id="org5703c42"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
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<div class="outline-text-5" id="text-1-1-7-2">
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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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@ -634,8 +634,8 @@ icount = bufsize
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</div>
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</div>
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<div id="outline-container-org4cb2714" class="outline-4">
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<h4 id="org4cb2714"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div id="outline-container-org2adc532" class="outline-4">
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<h4 id="org2adc532"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
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<div class="outline-text-4" id="text-1-1-8">
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<p>
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As \((n,m)\) 2D arrays are stored in memory as \((\n times m)\) 1D
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@ -669,8 +669,8 @@ E = E + E_nn
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</div>
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</div>
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<div id="outline-container-org174bdc8" class="outline-4">
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<h4 id="org174bdc8"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div id="outline-container-org1cb02dd" class="outline-4">
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<h4 id="org1cb02dd"><span class="section-number-4">1.1.9</span> Terminate</h4>
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<div class="outline-text-4" id="text-1-1-9">
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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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@ -685,7 +685,7 @@ E = E + E_nn
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</div>
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<div id="postamble" class="status">
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<p class="author">Author: TREX-CoE</p>
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<p class="date">Created: 2022-01-07 Fri 10:04</p>
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<p class="date">Created: 2022-01-07 Fri 10:09</p>
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<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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</div>
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</body>
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@ -3,7 +3,7 @@
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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<head>
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<!-- 2022-01-07 Fri 10:04 -->
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<!-- 2022-01-07 Fri 10:09 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
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<meta name=google-site-verification content=jdDnuP2rYGJVy8AHSd-8LkmOmvK_dyz5buZ98wilYII />
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@ -348,7 +348,7 @@ and bug reports should be submitted at
|
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</div>
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<div id="postamble" class="status">
|
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<p class="author">Author: TREX-CoE</p>
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<p class="date">Created: 2022-01-07 Fri 10:04</p>
|
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<p class="date">Created: 2022-01-07 Fri 10:09</p>
|
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<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
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</div>
|
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</body>
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@ -3,7 +3,7 @@
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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<head>
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<!-- 2022-01-07 Fri 10:04 -->
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<!-- 2022-01-07 Fri 10:09 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Front end API</title>
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@ -333,137 +333,137 @@ 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="#org91dac6e">1. Coding conventions</a>
|
||||
<li><a href="#org674052c">1. Coding conventions</a>
|
||||
<ul>
|
||||
<li><a href="#org8a72cea">1.1. Memory allocation</a></li>
|
||||
<li><a href="#orgb0e2901">1.1. Memory allocation</a></li>
|
||||
</ul>
|
||||
</li>
|
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<li><a href="#org4e4eb90">2. Front end</a>
|
||||
<li><a href="#org3281918">2. Front end</a>
|
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<ul>
|
||||
<li><a href="#org1ef3cdd">2.1. Error handling</a>
|
||||
<li><a href="#org1d14c4c">2.1. Error handling</a>
|
||||
<ul>
|
||||
<li><a href="#org0e91585">2.1.1. Decoding errors</a>
|
||||
<li><a href="#org72bc610">2.1.1. Decoding errors</a>
|
||||
<ul>
|
||||
<li><a href="#orgb791b1a">2.1.1.1. C source code</a></li>
|
||||
<li><a href="#org78b69e9">2.1.1.2. Fortran interface</a></li>
|
||||
<li><a href="#org44cdee4">2.1.1.3. Python interface</a></li>
|
||||
<li><a href="#org1b19dde">2.1.1.1. C source code</a></li>
|
||||
<li><a href="#org099b711">2.1.1.2. Fortran interface</a></li>
|
||||
<li><a href="#org846a7c0">2.1.1.3. Python interface</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="#orgac0dcfc">2.2. Back ends</a>
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<li><a href="#orge248611">2.2. Back ends</a>
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<ul>
|
||||
<li><a href="#org70a1c67">2.2.1. C</a></li>
|
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<li><a href="#org6975549">2.2.2. Fortran</a></li>
|
||||
<li><a href="#org404e999">2.2.3. Python</a></li>
|
||||
<li><a href="#org52c1390">2.2.1. C</a></li>
|
||||
<li><a href="#org8c997b2">2.2.2. Fortran</a></li>
|
||||
<li><a href="#org641a47f">2.2.3. Python</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org4ee26c8">2.3. Read/write behavior</a></li>
|
||||
<li><a href="#orge55a3e9">2.4. TREXIO file type</a>
|
||||
<li><a href="#org6ec6e4d">2.3. Read/write behavior</a></li>
|
||||
<li><a href="#org2287fa5">2.4. TREXIO file type</a>
|
||||
<ul>
|
||||
<li><a href="#org47d08f0">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
|
||||
<li><a href="#org4315e9d">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org50ae385">2.5. Polymorphism of the file handle</a></li>
|
||||
<li><a href="#org90d8b8e">2.6. File opening</a>
|
||||
<li><a href="#org84f97cd">2.5. Polymorphism of the file handle</a></li>
|
||||
<li><a href="#org1a6b2f0">2.6. File opening</a>
|
||||
<ul>
|
||||
<li><a href="#orga11eaf9">2.6.1. C</a></li>
|
||||
<li><a href="#orga8e638c">2.6.2. Fortran</a></li>
|
||||
<li><a href="#org6ca8c7c">2.6.3. Python</a></li>
|
||||
<li><a href="#org2c34029">2.6.4. Zero-based versus one-based arrays of indices</a></li>
|
||||
<li><a href="#orge4c6dc7">2.6.1. C</a></li>
|
||||
<li><a href="#org58f47cf">2.6.2. Fortran</a></li>
|
||||
<li><a href="#org5d9b31c">2.6.3. Python</a></li>
|
||||
<li><a href="#org3c66b95">2.6.4. Zero-based versus one-based arrays of indices</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orge4d94ad">2.7. File closing</a>
|
||||
<li><a href="#org3ad95a5">2.7. File closing</a>
|
||||
<ul>
|
||||
<li><a href="#orgb4002b6">2.7.1. C</a></li>
|
||||
<li><a href="#org09893b6">2.7.2. Fortran</a></li>
|
||||
<li><a href="#org5d501f4">2.7.3. Python</a></li>
|
||||
<li><a href="#orga507d38">2.7.1. C</a></li>
|
||||
<li><a href="#orgffe4c03">2.7.2. Fortran</a></li>
|
||||
<li><a href="#org864ebbe">2.7.3. Python</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org90a5af6">3. Templates for front end</a>
|
||||
<li><a href="#orgc737a93">3. Templates for front end</a>
|
||||
<ul>
|
||||
<li><a href="#org01eee4e">3.1. Description</a></li>
|
||||
<li><a href="#org7249eef">3.2. Templates for front end has/read/write a single numerical attribute</a>
|
||||
<li><a href="#org8edbb90">3.1. Description</a></li>
|
||||
<li><a href="#orgfb21b1c">3.2. Templates for front end has/read/write a single numerical attribute</a>
|
||||
<ul>
|
||||
<li><a href="#org01db7b7">3.2.1. Introduction</a></li>
|
||||
<li><a href="#orgd30dde5">3.2.2. C templates for front end</a>
|
||||
<li><a href="#orgca21e87">3.2.1. Introduction</a></li>
|
||||
<li><a href="#orgc989826">3.2.2. C templates for front end</a>
|
||||
<ul>
|
||||
<li><a href="#org7e8c8f1">3.2.2.1. Function declarations</a></li>
|
||||
<li><a href="#org6380375">3.2.2.2. Source code for double precision functions</a></li>
|
||||
<li><a href="#org476fc95">3.2.2.3. Source code for single precision functions</a></li>
|
||||
<li><a href="#org5656beb">3.2.2.4. Source code for default functions</a></li>
|
||||
<li><a href="#orgc449af5">3.2.2.1. Function declarations</a></li>
|
||||
<li><a href="#org70f98ff">3.2.2.2. Source code for double precision functions</a></li>
|
||||
<li><a href="#org29bb58c">3.2.2.3. Source code for single precision functions</a></li>
|
||||
<li><a href="#org31a603d">3.2.2.4. Source code for default functions</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org6b29195">3.2.3. Fortran templates for front end</a></li>
|
||||
<li><a href="#org3da8c5f">3.2.4. Python templates for front end</a></li>
|
||||
<li><a href="#orgf29fda3">3.2.3. Fortran templates for front end</a></li>
|
||||
<li><a href="#orgce3f738">3.2.4. Python templates for front end</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org2b2aff1">3.3. Templates for front end has/read/write a dataset of numerical data</a>
|
||||
<li><a href="#org8be96ad">3.3. Templates for front end has/read/write a dataset of numerical data</a>
|
||||
<ul>
|
||||
<li><a href="#org5536c5b">3.3.1. Introduction</a></li>
|
||||
<li><a href="#org5385d5c">3.3.2. C templates for front end</a>
|
||||
<li><a href="#orga767f08">3.3.1. Introduction</a></li>
|
||||
<li><a href="#orga2e3222">3.3.2. C templates for front end</a>
|
||||
<ul>
|
||||
<li><a href="#org35660fa">3.3.2.1. Function declarations</a></li>
|
||||
<li><a href="#org0c2fc5d">3.3.2.2. Source code for double precision functions</a></li>
|
||||
<li><a href="#org5a8bf9f">3.3.2.3. Source code for single precision functions</a></li>
|
||||
<li><a href="#orgbb52468">3.3.2.4. Source code for memory-safe functions</a></li>
|
||||
<li><a href="#org773f6c1">3.3.2.5. Source code for default functions</a></li>
|
||||
<li><a href="#orgf02533a">3.3.2.1. Function declarations</a></li>
|
||||
<li><a href="#orge8f6fb9">3.3.2.2. Source code for double precision functions</a></li>
|
||||
<li><a href="#org053e094">3.3.2.3. Source code for single precision functions</a></li>
|
||||
<li><a href="#orgdf16646">3.3.2.4. Source code for memory-safe functions</a></li>
|
||||
<li><a href="#org4df579d">3.3.2.5. Source code for default functions</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgf8d38fe">3.3.3. Fortran templates for front end</a></li>
|
||||
<li><a href="#org6f7ed5b">3.3.4. Python templates for front end</a></li>
|
||||
<li><a href="#orgb6ea5d1">3.3.3. Fortran templates for front end</a></li>
|
||||
<li><a href="#org1be71e9">3.3.4. Python templates for front end</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org8478b9c">3.4. Templates for front end has/read/write a dataset of sparse data</a>
|
||||
<li><a href="#orgdc8727c">3.4. Templates for front end has/read/write a dataset of sparse data</a>
|
||||
<ul>
|
||||
<li><a href="#org76a2bc9">3.4.1. Introduction</a></li>
|
||||
<li><a href="#org2c84ecb">3.4.2. C templates for front end</a>
|
||||
<li><a href="#orgcec261a">3.4.1. Introduction</a></li>
|
||||
<li><a href="#org8c6b047">3.4.2. C templates for front end</a>
|
||||
<ul>
|
||||
<li><a href="#org69b5916">3.4.2.1. Function declarations</a></li>
|
||||
<li><a href="#orgf1af77b">3.4.2.2. Source code for default functions</a></li>
|
||||
<li><a href="#org5d1147e">3.4.2.1. Function declarations</a></li>
|
||||
<li><a href="#orge421735">3.4.2.2. Source code for default functions</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#orgfff4945">3.4.3. Fortran templates for front end</a></li>
|
||||
<li><a href="#org8211703">3.4.4. Python templates for front end</a></li>
|
||||
<li><a href="#orgc5501f5">3.4.3. Fortran templates for front end</a></li>
|
||||
<li><a href="#org16e220f">3.4.4. Python templates for front end</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org362505b">3.5. Templates for front end has/read/write a dataset of strings</a>
|
||||
<li><a href="#orgb33f51b">3.5. Templates for front end has/read/write a dataset of strings</a>
|
||||
<ul>
|
||||
<li><a href="#orge773a87">3.5.1. Introduction</a></li>
|
||||
<li><a href="#orgdbed956">3.5.2. C templates for front end</a>
|
||||
<li><a href="#orga97c2c1">3.5.1. Introduction</a></li>
|
||||
<li><a href="#org416d81b">3.5.2. C templates for front end</a>
|
||||
<ul>
|
||||
<li><a href="#org2f5e022">3.5.2.1. Function declarations</a></li>
|
||||
<li><a href="#org60f070c">3.5.2.2. Source code for default functions</a></li>
|
||||
<li><a href="#orgf331270">3.5.2.1. Function declarations</a></li>
|
||||
<li><a href="#org64dfa7d">3.5.2.2. Source code for default functions</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org0021a42">3.5.3. Fortran templates for front end</a></li>
|
||||
<li><a href="#orgeede3cf">3.5.4. Python templates for front end</a></li>
|
||||
<li><a href="#orgef2d07a">3.5.3. Fortran templates for front end</a></li>
|
||||
<li><a href="#org913fac8">3.5.4. Python templates for front end</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org5df1a14">3.6. Templates for front end has/read/write a single string attribute</a>
|
||||
<li><a href="#orgeb59d52">3.6. Templates for front end has/read/write a single string attribute</a>
|
||||
<ul>
|
||||
<li><a href="#orgb334699">3.6.1. Introduction</a></li>
|
||||
<li><a href="#org51b2cad">3.6.2. C templates for front end</a>
|
||||
<li><a href="#org7616e59">3.6.1. Introduction</a></li>
|
||||
<li><a href="#org063fd7d">3.6.2. C templates for front end</a>
|
||||
<ul>
|
||||
<li><a href="#org9770263">3.6.2.1. Function declarations</a></li>
|
||||
<li><a href="#orgad1425c">3.6.2.2. Source code for default functions</a></li>
|
||||
<li><a href="#org2f0ab0f">3.6.2.1. Function declarations</a></li>
|
||||
<li><a href="#org98a10cb">3.6.2.2. Source code for default functions</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org4e318d7">3.6.3. Fortran templates for front end</a></li>
|
||||
<li><a href="#org0a03f94">3.6.4. Python templates for front end</a></li>
|
||||
<li><a href="#org1b18340">3.6.3. Fortran templates for front end</a></li>
|
||||
<li><a href="#org8f04f17">3.6.4. Python templates for front end</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org1e08b49">4. Fortran helper/wrapper functions</a></li>
|
||||
<li><a href="#org4a2a6b3">4. Fortran helper/wrapper functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org91dac6e" class="outline-2">
|
||||
<h2 id="org91dac6e"><span class="section-number-2">1</span> Coding conventions</h2>
|
||||
<div id="outline-container-org674052c" class="outline-2">
|
||||
<h2 id="org674052c"><span class="section-number-2">1</span> Coding conventions</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<ul class="org-ul">
|
||||
<li>integer types will be defined using types given in <code>stdint.h</code></li>
|
||||
@ -478,8 +478,8 @@ for the JavaScript code in this tag.
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8a72cea" class="outline-3">
|
||||
<h3 id="org8a72cea"><span class="section-number-3">1.1</span> Memory allocation</h3>
|
||||
<div id="outline-container-orgb0e2901" class="outline-3">
|
||||
<h3 id="orgb0e2901"><span class="section-number-3">1.1</span> Memory allocation</h3>
|
||||
<div class="outline-text-3" id="text-1-1">
|
||||
<p>
|
||||
Memory allocation of structures can be facilitated by using the
|
||||
@ -514,8 +514,8 @@ The maximum string size for the filenames is 4096 characters.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4e4eb90" class="outline-2">
|
||||
<h2 id="org4e4eb90"><span class="section-number-2">2</span> Front end</h2>
|
||||
<div id="outline-container-org3281918" class="outline-2">
|
||||
<h2 id="org3281918"><span class="section-number-2">2</span> Front end</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
All calls to TREXIO are thread-safe.
|
||||
@ -523,10 +523,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1ef3cdd" class="outline-3">
|
||||
<h3 id="org1ef3cdd"><span class="section-number-3">2.1</span> Error handling</h3>
|
||||
<div id="outline-container-org1d14c4c" class="outline-3">
|
||||
<h3 id="org1d14c4c"><span class="section-number-3">2.1</span> Error handling</h3>
|
||||
<div class="outline-text-3" id="text-2-1">
|
||||
<table id="orge87bf74" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2775876" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -767,8 +767,8 @@ and the corresponding message are not propagated to the source code.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0e91585" class="outline-4">
|
||||
<h4 id="org0e91585"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
|
||||
<div id="outline-container-org72bc610" class="outline-4">
|
||||
<h4 id="org72bc610"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
|
||||
<div class="outline-text-4" id="text-2-1-1">
|
||||
<p>
|
||||
The <code>trexio_string_of_error</code> converts an exit code into a string. The
|
||||
@ -794,8 +794,8 @@ and the corresponding message are not propagated to the source code.
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb791b1a" class="outline-5">
|
||||
<h5 id="orgb791b1a"><span class="section-number-5">2.1.1.1</span> C source code</h5>
|
||||
<div id="outline-container-org1b19dde" class="outline-5">
|
||||
<h5 id="org1b19dde"><span class="section-number-5">2.1.1.1</span> C source code</h5>
|
||||
<div class="outline-text-5" id="text-2-1-1-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span>*
|
||||
@ -906,8 +906,8 @@ and the corresponding message are not propagated to the source code.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org78b69e9" class="outline-5">
|
||||
<h5 id="org78b69e9"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
|
||||
<div id="outline-container-org099b711" class="outline-5">
|
||||
<h5 id="org099b711"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
|
||||
<div class="outline-text-5" id="text-2-1-1-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-f90"><span style="color: #a020f0;">interface</span>
|
||||
@ -923,8 +923,8 @@ and the corresponding message are not propagated to the source code.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org44cdee4" class="outline-5">
|
||||
<h5 id="org44cdee4"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
|
||||
<div id="outline-container-org846a7c0" class="outline-5">
|
||||
<h5 id="org846a7c0"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
|
||||
<div class="outline-text-5" id="text-2-1-1-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-python"><span style="color: #a020f0;">class</span> <span style="color: #228b22;">Error</span>(<span style="color: #228b22;">Exception</span>):
|
||||
@ -963,8 +963,8 @@ and the corresponding message are not propagated to the source code.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgac0dcfc" class="outline-3">
|
||||
<h3 id="orgac0dcfc"><span class="section-number-3">2.2</span> Back ends</h3>
|
||||
<div id="outline-container-orge248611" class="outline-3">
|
||||
<h3 id="orge248611"><span class="section-number-3">2.2</span> Back ends</h3>
|
||||
<div class="outline-text-3" id="text-2-2">
|
||||
<p>
|
||||
TREXIO has several back ends:
|
||||
@ -988,8 +988,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org70a1c67" class="outline-4">
|
||||
<h4 id="org70a1c67"><span class="section-number-4">2.2.1</span> C</h4>
|
||||
<div id="outline-container-org52c1390" class="outline-4">
|
||||
<h4 id="org52c1390"><span class="section-number-4">2.2.1</span> C</h4>
|
||||
<div class="outline-text-4" id="text-2-2-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #228b22;">int32_t</span> <span style="color: #228b22;">back_end_t</span>;
|
||||
@ -1032,8 +1032,8 @@ This is useful due to the fact that HDF5 back end can be disabled at configure s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6975549" class="outline-4">
|
||||
<h4 id="org6975549"><span class="section-number-4">2.2.2</span> Fortran</h4>
|
||||
<div id="outline-container-org8c997b2" class="outline-4">
|
||||
<h4 id="org8c997b2"><span class="section-number-4">2.2.2</span> Fortran</h4>
|
||||
<div class="outline-text-4" id="text-2-2-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-f90"> <span style="color: #228b22;">integer</span>(trexio_backend), <span style="color: #a020f0;">parameter</span> ::<span style="color: #a0522d;"> TREXIO_HDF5 = 0</span>
|
||||
@ -1059,8 +1059,8 @@ The function below is a Fortran interface for the aforementioned C-compatible <c
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org404e999" class="outline-4">
|
||||
<h4 id="org404e999"><span class="section-number-4">2.2.3</span> Python</h4>
|
||||
<div id="outline-container-org641a47f" class="outline-4">
|
||||
<h4 id="org641a47f"><span class="section-number-4">2.2.3</span> Python</h4>
|
||||
<div class="outline-text-4" id="text-2-2-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-python"># <span style="color: #b22222;">define TREXIO back ends</span>
|
||||
@ -1074,8 +1074,8 @@ The function below is a Fortran interface for the aforementioned C-compatible <c
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4ee26c8" class="outline-3">
|
||||
<h3 id="org4ee26c8"><span class="section-number-3">2.3</span> Read/write behavior</h3>
|
||||
<div id="outline-container-org6ec6e4d" class="outline-3">
|
||||
<h3 id="org6ec6e4d"><span class="section-number-3">2.3</span> Read/write behavior</h3>
|
||||
<div class="outline-text-3" id="text-2-3">
|
||||
<p>
|
||||
Every time a reading function is called, the data is read from the
|
||||
@ -1103,8 +1103,8 @@ concurrent programs, the behavior is not specified.
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orge55a3e9" class="outline-3">
|
||||
<h3 id="orge55a3e9"><span class="section-number-3">2.4</span> TREXIO file type</h3>
|
||||
<div id="outline-container-org2287fa5" class="outline-3">
|
||||
<h3 id="org2287fa5"><span class="section-number-3">2.4</span> TREXIO file type</h3>
|
||||
<div class="outline-text-3" id="text-2-4">
|
||||
<p>
|
||||
<code>trexio_s</code> is the the main type for TREXIO files, visible to the users
|
||||
@ -1138,8 +1138,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org47d08f0" class="outline-4">
|
||||
<h4 id="org47d08f0"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
|
||||
<div id="outline-container-org4315e9d" class="outline-4">
|
||||
<h4 id="org4315e9d"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
|
||||
<div class="outline-text-4" id="text-2-4-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-python"><span style="color: #a020f0;">class</span> <span style="color: #228b22;">File</span>:
|
||||
@ -1212,8 +1212,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org50ae385" class="outline-3">
|
||||
<h3 id="org50ae385"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
|
||||
<div id="outline-container-org84f97cd" class="outline-3">
|
||||
<h3 id="org84f97cd"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
|
||||
<div class="outline-text-3" id="text-2-5">
|
||||
<p>
|
||||
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
|
||||
@ -1232,8 +1232,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org90d8b8e" class="outline-3">
|
||||
<h3 id="org90d8b8e"><span class="section-number-3">2.6</span> File opening</h3>
|
||||
<div id="outline-container-org1a6b2f0" class="outline-3">
|
||||
<h3 id="org1a6b2f0"><span class="section-number-3">2.6</span> File opening</h3>
|
||||
<div class="outline-text-3" id="text-2-6">
|
||||
<p>
|
||||
<code>trexio_open</code> creates a new TREXIO file or opens existing one.
|
||||
@ -1272,8 +1272,8 @@ renaming the <code>.txt</code> data files.
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga11eaf9" class="outline-4">
|
||||
<h4 id="orga11eaf9"><span class="section-number-4">2.6.1</span> C</h4>
|
||||
<div id="outline-container-orge4c6dc7" class="outline-4">
|
||||
<h4 id="orge4c6dc7"><span class="section-number-4">2.6.1</span> C</h4>
|
||||
<div class="outline-text-4" id="text-2-6-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_t</span>*
|
||||
@ -1459,8 +1459,8 @@ renaming the <code>.txt</code> data files.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga8e638c" class="outline-4">
|
||||
<h4 id="orga8e638c"><span class="section-number-4">2.6.2</span> Fortran</h4>
|
||||
<div id="outline-container-org58f47cf" class="outline-4">
|
||||
<h4 id="org58f47cf"><span class="section-number-4">2.6.2</span> Fortran</h4>
|
||||
<div class="outline-text-4" id="text-2-6-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-f90"><span style="color: #a020f0;">interface</span>
|
||||
@ -1478,8 +1478,8 @@ renaming the <code>.txt</code> data files.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6ca8c7c" class="outline-4">
|
||||
<h4 id="org6ca8c7c"><span class="section-number-4">2.6.3</span> Python</h4>
|
||||
<div id="outline-container-org5d9b31c" class="outline-4">
|
||||
<h4 id="org5d9b31c"><span class="section-number-4">2.6.3</span> Python</h4>
|
||||
<div class="outline-text-4" id="text-2-6-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">open</span>(file_name: <span style="color: #483d8b;">str</span>, mode: <span style="color: #483d8b;">str</span>, back_end: <span style="color: #483d8b;">int</span>):
|
||||
@ -1527,8 +1527,8 @@ renaming the <code>.txt</code> data files.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2c34029" class="outline-4">
|
||||
<h4 id="org2c34029"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
|
||||
<div id="outline-container-org3c66b95" class="outline-4">
|
||||
<h4 id="org3c66b95"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
|
||||
<div class="outline-text-4" id="text-2-6-4">
|
||||
<p>
|
||||
Because arrays are zero-based in Fortran, we need to set a flag to
|
||||
@ -1561,8 +1561,8 @@ know if we need to shift by 1 arrays of indices.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge4d94ad" class="outline-3">
|
||||
<h3 id="orge4d94ad"><span class="section-number-3">2.7</span> File closing</h3>
|
||||
<div id="outline-container-org3ad95a5" class="outline-3">
|
||||
<h3 id="org3ad95a5"><span class="section-number-3">2.7</span> File closing</h3>
|
||||
<div class="outline-text-3" id="text-2-7">
|
||||
<p>
|
||||
<code>trexio_close</code> closes an existing <code>trexio_t</code> file.
|
||||
@ -1579,8 +1579,8 @@ output:
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb4002b6" class="outline-4">
|
||||
<h4 id="orgb4002b6"><span class="section-number-4">2.7.1</span> C</h4>
|
||||
<div id="outline-container-orga507d38" class="outline-4">
|
||||
<h4 id="orga507d38"><span class="section-number-4">2.7.1</span> C</h4>
|
||||
<div class="outline-text-4" id="text-2-7-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1659,8 +1659,8 @@ output:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org09893b6" class="outline-4">
|
||||
<h4 id="org09893b6"><span class="section-number-4">2.7.2</span> Fortran</h4>
|
||||
<div id="outline-container-orgffe4c03" class="outline-4">
|
||||
<h4 id="orgffe4c03"><span class="section-number-4">2.7.2</span> Fortran</h4>
|
||||
<div class="outline-text-4" id="text-2-7-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-f90"><span style="color: #a020f0;">interface</span>
|
||||
@ -1674,8 +1674,8 @@ output:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5d501f4" class="outline-4">
|
||||
<h4 id="org5d501f4"><span class="section-number-4">2.7.3</span> Python</h4>
|
||||
<div id="outline-container-org864ebbe" class="outline-4">
|
||||
<h4 id="org864ebbe"><span class="section-number-4">2.7.3</span> Python</h4>
|
||||
<div class="outline-text-4" id="text-2-7-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">close</span>(trexio_file):
|
||||
@ -1697,12 +1697,12 @@ output:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org90a5af6" class="outline-2">
|
||||
<h2 id="org90a5af6"><span class="section-number-2">3</span> Templates for front end</h2>
|
||||
<div id="outline-container-orgc737a93" class="outline-2">
|
||||
<h2 id="orgc737a93"><span class="section-number-2">3</span> Templates for front end</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
</div>
|
||||
<div id="outline-container-org01eee4e" class="outline-3">
|
||||
<h3 id="org01eee4e"><span class="section-number-3">3.1</span> Description</h3>
|
||||
<div id="outline-container-org8edbb90" class="outline-3">
|
||||
<h3 id="org8edbb90"><span class="section-number-3">3.1</span> Description</h3>
|
||||
<div class="outline-text-3" id="text-3-1">
|
||||
<p>
|
||||
Consider the following block of <code>trex.json</code>:
|
||||
@ -1923,12 +1923,12 @@ value will result in <code>TREXIO_INVALID_ARG_2</code> exit code.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7249eef" class="outline-3">
|
||||
<h3 id="org7249eef"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
|
||||
<div id="outline-container-orgfb21b1c" class="outline-3">
|
||||
<h3 id="orgfb21b1c"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
|
||||
<div class="outline-text-3" id="text-3-2">
|
||||
</div>
|
||||
<div id="outline-container-org01db7b7" class="outline-4">
|
||||
<h4 id="org01db7b7"><span class="section-number-4">3.2.1</span> Introduction</h4>
|
||||
<div id="outline-container-orgca21e87" class="outline-4">
|
||||
<h4 id="orgca21e87"><span class="section-number-4">3.2.1</span> Introduction</h4>
|
||||
<div class="outline-text-4" id="text-3-2-1">
|
||||
<p>
|
||||
This section concerns API calls related to numerical attributes,
|
||||
@ -1999,8 +1999,8 @@ namely single value of int/float types.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd30dde5" class="outline-4">
|
||||
<h4 id="orgd30dde5"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
|
||||
<div id="outline-container-orgc989826" class="outline-4">
|
||||
<h4 id="orgc989826"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-2-2">
|
||||
<p>
|
||||
The <code>C</code> templates that correspond to each of the abovementioned
|
||||
@ -2014,12 +2014,12 @@ precision (see Table above).
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7e8c8f1" class="outline-5">
|
||||
<h5 id="org7e8c8f1"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
|
||||
<div id="outline-container-orgc449af5" class="outline-5">
|
||||
<h5 id="orgc449af5"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6380375" class="outline-5">
|
||||
<h5 id="org6380375"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
|
||||
<div id="outline-container-org70f98ff" class="outline-5">
|
||||
<h5 id="org70f98ff"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
|
||||
<div class="outline-text-5" id="text-3-2-2-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -2088,8 +2088,8 @@ precision (see Table above).
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org476fc95" class="outline-5">
|
||||
<h5 id="org476fc95"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
|
||||
<div id="outline-container-org29bb58c" class="outline-5">
|
||||
<h5 id="org29bb58c"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
|
||||
<div class="outline-text-5" id="text-3-2-2-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -2165,8 +2165,8 @@ precision (see Table above).
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5656beb" class="outline-5">
|
||||
<h5 id="org5656beb"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
|
||||
<div id="outline-container-org31a603d" class="outline-5">
|
||||
<h5 id="org31a603d"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
|
||||
<div class="outline-text-5" id="text-3-2-2-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -2223,8 +2223,8 @@ precision (see Table above).
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6b29195" class="outline-4">
|
||||
<h4 id="org6b29195"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
|
||||
<div id="outline-container-orgf29fda3" class="outline-4">
|
||||
<h4 id="orgf29fda3"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-2-3">
|
||||
<p>
|
||||
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from Fortran.
|
||||
@ -2309,8 +2309,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3da8c5f" class="outline-4">
|
||||
<h4 id="org3da8c5f"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
|
||||
<div id="outline-container-orgce3f738" class="outline-4">
|
||||
<h4 id="orgce3f738"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-2-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_num$(trexio_file, num_w: $group_num_py_dtype$) -> <span style="color: #008b8b;">None</span>:
|
||||
@ -2395,12 +2395,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2b2aff1" class="outline-3">
|
||||
<h3 id="org2b2aff1"><span class="section-number-3">3.3</span> Templates for front end has/read/write a dataset of numerical data</h3>
|
||||
<div id="outline-container-org8be96ad" class="outline-3">
|
||||
<h3 id="org8be96ad"><span class="section-number-3">3.3</span> Templates for front end has/read/write a dataset of numerical data</h3>
|
||||
<div class="outline-text-3" id="text-3-3">
|
||||
</div>
|
||||
<div id="outline-container-org5536c5b" class="outline-4">
|
||||
<h4 id="org5536c5b"><span class="section-number-4">3.3.1</span> Introduction</h4>
|
||||
<div id="outline-container-orga767f08" class="outline-4">
|
||||
<h4 id="orga767f08"><span class="section-number-4">3.3.1</span> Introduction</h4>
|
||||
<div class="outline-text-4" id="text-3-3-1">
|
||||
<p>
|
||||
This section concerns API calls related to datasets.
|
||||
@ -2482,8 +2482,8 @@ This section concerns API calls related to datasets.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5385d5c" class="outline-4">
|
||||
<h4 id="org5385d5c"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
|
||||
<div id="outline-container-orga2e3222" class="outline-4">
|
||||
<h4 id="orga2e3222"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-3-2">
|
||||
<p>
|
||||
The C templates that correspond to each of the abovementioned functions can be found below.
|
||||
@ -2494,12 +2494,12 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org35660fa" class="outline-5">
|
||||
<h5 id="org35660fa"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
|
||||
<div id="outline-container-orgf02533a" class="outline-5">
|
||||
<h5 id="orgf02533a"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0c2fc5d" class="outline-5">
|
||||
<h5 id="org0c2fc5d"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
|
||||
<div id="outline-container-orge8f6fb9" class="outline-5">
|
||||
<h5 id="orge8f6fb9"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
|
||||
<div class="outline-text-5" id="text-3-3-2-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -2634,8 +2634,8 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5a8bf9f" class="outline-5">
|
||||
<h5 id="org5a8bf9f"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
|
||||
<div id="outline-container-org053e094" class="outline-5">
|
||||
<h5 id="org053e094"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
|
||||
<div class="outline-text-5" id="text-3-3-2-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -2784,11 +2784,11 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgbb52468" class="outline-5">
|
||||
<h5 id="orgbb52468"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
|
||||
<div id="outline-container-orgdf16646" class="outline-5">
|
||||
<h5 id="orgdf16646"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
|
||||
<div class="outline-text-5" id="text-3-3-2-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c" id="org1ebf588"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
|
||||
<pre class="src src-c" id="orgab59395"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
|
||||
int64_t $group_dset_dim$ = 0;
|
||||
|
||||
/* <span style="color: #b22222;">Error handling for this call is added by the generator </span>*/
|
||||
@ -2944,8 +2944,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org773f6c1" class="outline-5">
|
||||
<h5 id="org773f6c1"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
|
||||
<div id="outline-container-org4df579d" class="outline-5">
|
||||
<h5 id="org4df579d"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
|
||||
<div class="outline-text-5" id="text-3-3-2-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -3023,8 +3023,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf8d38fe" class="outline-4">
|
||||
<h4 id="orgf8d38fe"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
|
||||
<div id="outline-container-orgb6ea5d1" class="outline-4">
|
||||
<h4 id="orgb6ea5d1"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-3-3">
|
||||
<p>
|
||||
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from <code>Fortran</code>.
|
||||
@ -3109,8 +3109,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6f7ed5b" class="outline-4">
|
||||
<h4 id="org6f7ed5b"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
|
||||
<div id="outline-container-org1be71e9" class="outline-4">
|
||||
<h4 id="org1be71e9"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-3-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_dset$(trexio_file, dset_w) -> <span style="color: #008b8b;">None</span>:
|
||||
@ -3305,12 +3305,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8478b9c" class="outline-3">
|
||||
<h3 id="org8478b9c"><span class="section-number-3">3.4</span> Templates for front end has/read/write a dataset of sparse data</h3>
|
||||
<div id="outline-container-orgdc8727c" class="outline-3">
|
||||
<h3 id="orgdc8727c"><span class="section-number-3">3.4</span> Templates for front end has/read/write a dataset of sparse data</h3>
|
||||
<div class="outline-text-3" id="text-3-4">
|
||||
</div>
|
||||
<div id="outline-container-org76a2bc9" class="outline-4">
|
||||
<h4 id="org76a2bc9"><span class="section-number-4">3.4.1</span> Introduction</h4>
|
||||
<div id="outline-container-orgcec261a" class="outline-4">
|
||||
<h4 id="orgcec261a"><span class="section-number-4">3.4.1</span> Introduction</h4>
|
||||
<div class="outline-text-4" id="text-3-4-1">
|
||||
<p>
|
||||
Sparse data structures are used typically for large tensors such as
|
||||
@ -3471,16 +3471,16 @@ This section concerns API calls related to sparse data structures.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2c84ecb" class="outline-4">
|
||||
<h4 id="org2c84ecb"><span class="section-number-4">3.4.2</span> C templates for front end</h4>
|
||||
<div id="outline-container-org8c6b047" class="outline-4">
|
||||
<h4 id="org8c6b047"><span class="section-number-4">3.4.2</span> C templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-4-2">
|
||||
</div>
|
||||
<div id="outline-container-org69b5916" class="outline-5">
|
||||
<h5 id="org69b5916"><span class="section-number-5">3.4.2.1</span> Function declarations</h5>
|
||||
<div id="outline-container-org5d1147e" class="outline-5">
|
||||
<h5 id="org5d1147e"><span class="section-number-5">3.4.2.1</span> Function declarations</h5>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf1af77b" class="outline-5">
|
||||
<h5 id="orgf1af77b"><span class="section-number-5">3.4.2.2</span> Source code for default functions</h5>
|
||||
<div id="outline-container-orge421735" class="outline-5">
|
||||
<h5 id="orge421735"><span class="section-number-5">3.4.2.2</span> Source code for default functions</h5>
|
||||
<div class="outline-text-5" id="text-3-4-2-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #0000ff;">trexio_read_safe_$group_dset$</span>(<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>,
|
||||
@ -3725,8 +3725,8 @@ This section concerns API calls related to sparse data structures.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgfff4945" class="outline-4">
|
||||
<h4 id="orgfff4945"><span class="section-number-4">3.4.3</span> Fortran templates for front end</h4>
|
||||
<div id="outline-container-orgc5501f5" class="outline-4">
|
||||
<h4 id="orgc5501f5"><span class="section-number-4">3.4.3</span> Fortran templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-4-3">
|
||||
<p>
|
||||
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from <code>Fortran</code>.
|
||||
@ -3821,8 +3821,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8211703" class="outline-4">
|
||||
<h4 id="org8211703"><span class="section-number-4">3.4.4</span> Python templates for front end</h4>
|
||||
<div id="outline-container-org16e220f" class="outline-4">
|
||||
<h4 id="org16e220f"><span class="section-number-4">3.4.4</span> Python templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-4-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_dset$(trexio_file: File, offset_file: <span style="color: #483d8b;">int</span>, buffer_size: <span style="color: #483d8b;">int</span>, indices: <span style="color: #483d8b;">list</span>, values: <span style="color: #483d8b;">list</span>) -> <span style="color: #008b8b;">None</span>:
|
||||
@ -4043,12 +4043,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org362505b" class="outline-3">
|
||||
<h3 id="org362505b"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
|
||||
<div id="outline-container-orgb33f51b" class="outline-3">
|
||||
<h3 id="orgb33f51b"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
|
||||
<div class="outline-text-3" id="text-3-5">
|
||||
</div>
|
||||
<div id="outline-container-orge773a87" class="outline-4">
|
||||
<h4 id="orge773a87"><span class="section-number-4">3.5.1</span> Introduction</h4>
|
||||
<div id="outline-container-orga97c2c1" class="outline-4">
|
||||
<h4 id="orga97c2c1"><span class="section-number-4">3.5.1</span> Introduction</h4>
|
||||
<div class="outline-text-4" id="text-3-5-1">
|
||||
<p>
|
||||
This section concerns API calls related to datasets of strings.
|
||||
@ -4088,8 +4088,8 @@ This section concerns API calls related to datasets of strings.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdbed956" class="outline-4">
|
||||
<h4 id="orgdbed956"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
|
||||
<div id="outline-container-org416d81b" class="outline-4">
|
||||
<h4 id="org416d81b"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-5-2">
|
||||
<p>
|
||||
First parameter is the <code>TREXIO</code> file handle. Second parameter is the variable to be written/read
|
||||
@ -4097,12 +4097,12 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2f5e022" class="outline-5">
|
||||
<h5 id="org2f5e022"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
|
||||
<div id="outline-container-orgf331270" class="outline-5">
|
||||
<h5 id="orgf331270"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org60f070c" class="outline-5">
|
||||
<h5 id="org60f070c"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
|
||||
<div id="outline-container-org64dfa7d" class="outline-5">
|
||||
<h5 id="org64dfa7d"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
|
||||
<div class="outline-text-5" id="text-3-5-2-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -4356,8 +4356,8 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0021a42" class="outline-4">
|
||||
<h4 id="org0021a42"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
|
||||
<div id="outline-container-orgef2d07a" class="outline-4">
|
||||
<h4 id="orgef2d07a"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-5-3">
|
||||
<p>
|
||||
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from <code>Fortran</code>.
|
||||
@ -4453,8 +4453,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgeede3cf" class="outline-4">
|
||||
<h4 id="orgeede3cf"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
|
||||
<div id="outline-container-org913fac8" class="outline-4">
|
||||
<h4 id="org913fac8"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-5-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_dset$(trexio_file, dset_w: <span style="color: #483d8b;">list</span>) -> <span style="color: #008b8b;">None</span>:
|
||||
@ -4570,12 +4570,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5df1a14" class="outline-3">
|
||||
<h3 id="org5df1a14"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
|
||||
<div id="outline-container-orgeb59d52" class="outline-3">
|
||||
<h3 id="orgeb59d52"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
|
||||
<div class="outline-text-3" id="text-3-6">
|
||||
</div>
|
||||
<div id="outline-container-orgb334699" class="outline-4">
|
||||
<h4 id="orgb334699"><span class="section-number-4">3.6.1</span> Introduction</h4>
|
||||
<div id="outline-container-org7616e59" class="outline-4">
|
||||
<h4 id="org7616e59"><span class="section-number-4">3.6.1</span> Introduction</h4>
|
||||
<div class="outline-text-4" id="text-3-6-1">
|
||||
<p>
|
||||
This section concerns API calls related to string attributes.
|
||||
@ -4615,16 +4615,16 @@ This section concerns API calls related to string attributes.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org51b2cad" class="outline-4">
|
||||
<h4 id="org51b2cad"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
|
||||
<div id="outline-container-org063fd7d" class="outline-4">
|
||||
<h4 id="org063fd7d"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-6-2">
|
||||
</div>
|
||||
<div id="outline-container-org9770263" class="outline-5">
|
||||
<h5 id="org9770263"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
|
||||
<div id="outline-container-org2f0ab0f" class="outline-5">
|
||||
<h5 id="org2f0ab0f"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgad1425c" class="outline-5">
|
||||
<h5 id="orgad1425c"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
|
||||
<div id="outline-container-org98a10cb" class="outline-5">
|
||||
<h5 id="org98a10cb"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
|
||||
<div class="outline-text-5" id="text-3-6-2-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -4736,8 +4736,8 @@ This section concerns API calls related to string attributes.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4e318d7" class="outline-4">
|
||||
<h4 id="org4e318d7"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
|
||||
<div id="outline-container-org1b18340" class="outline-4">
|
||||
<h4 id="org1b18340"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-6-3">
|
||||
<p>
|
||||
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from Fortran.
|
||||
@ -4814,8 +4814,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0a03f94" class="outline-4">
|
||||
<h4 id="org0a03f94"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
|
||||
<div id="outline-container-org8f04f17" class="outline-4">
|
||||
<h4 id="org8f04f17"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-6-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_str$(trexio_file, str_w: <span style="color: #483d8b;">str</span>) -> <span style="color: #008b8b;">None</span>:
|
||||
@ -4905,8 +4905,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1e08b49" class="outline-2">
|
||||
<h2 id="org1e08b49"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
|
||||
<div id="outline-container-org4a2a6b3" class="outline-2">
|
||||
<h2 id="org4a2a6b3"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
<p>
|
||||
The function below adapts the original C-based <code>trexio_open</code> for Fortran.
|
||||
@ -5041,7 +5041,7 @@ two code are identical, i.e. if the <code>assert</code> statement pass.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-01-07 Fri 10:04</p>
|
||||
<p class="date">Created: 2022-01-07 Fri 10:09</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-01-07 Fri 10:04 -->
|
||||
<!-- 2022-01-07 Fri 10:09 -->
|
||||
<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>
|
||||
@ -311,29 +311,29 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orgda22059">1. HDF5 back end</a>
|
||||
<li><a href="#org13e8630">1. HDF5 back end</a>
|
||||
<ul>
|
||||
<li><a href="#orgdfd608b">1.1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#orgf09ea66">1.2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org5b49d68">1.3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org1b013c3">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
|
||||
<li><a href="#org8b6c751">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
|
||||
<li><a href="#org8373b00">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org3254e8c">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
|
||||
<li><a href="#org11d1c0a">1.8. Template for HDF5 has/read/write the string attribute</a></li>
|
||||
<li><a href="#orge7ebdec">1.9. Helper functions</a></li>
|
||||
<li><a href="#org02e6509">1.1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org0e326a4">1.2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#orgdbf3a8d">1.3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#orgd7c406d">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
|
||||
<li><a href="#org049c5fe">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
|
||||
<li><a href="#orge8bd226">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#orgfed449f">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
|
||||
<li><a href="#org50d49b9">1.8. Template for HDF5 has/read/write the string attribute</a></li>
|
||||
<li><a href="#orgd444d7d">1.9. Helper functions</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgda22059" class="outline-2">
|
||||
<h2 id="orgda22059"><span class="section-number-2">1</span> HDF5 back end</h2>
|
||||
<div id="outline-container-org13e8630" class="outline-2">
|
||||
<h2 id="org13e8630"><span class="section-number-2">1</span> HDF5 back end</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
</div>
|
||||
<div id="outline-container-orgdfd608b" class="outline-3">
|
||||
<h3 id="orgdfd608b"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
|
||||
<div id="outline-container-org02e6509" class="outline-3">
|
||||
<h3 id="org02e6509"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
|
||||
<div class="outline-text-3" id="text-1-1">
|
||||
<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>
|
||||
@ -345,8 +345,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf09ea66" class="outline-3">
|
||||
<h3 id="orgf09ea66"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
|
||||
<div id="outline-container-org0e326a4" class="outline-3">
|
||||
<h3 id="org0e326a4"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
|
||||
<div class="outline-text-3" id="text-1-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_hdf5_s</span> {
|
||||
@ -360,8 +360,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
|
||||
|
||||
<div id="outline-container-org5b49d68" class="outline-3">
|
||||
<h3 id="org5b49d68"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
|
||||
<div id="outline-container-orgdbf3a8d" class="outline-3">
|
||||
<h3 id="orgdbf3a8d"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
|
||||
<div class="outline-text-3" id="text-1-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -441,8 +441,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1b013c3" class="outline-3">
|
||||
<h3 id="org1b013c3"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
|
||||
<div id="outline-container-orgd7c406d" class="outline-3">
|
||||
<h3 id="orgd7c406d"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
|
||||
<div class="outline-text-3" id="text-1-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -536,8 +536,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8b6c751" class="outline-3">
|
||||
<h3 id="org8b6c751"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
|
||||
<div id="outline-container-org049c5fe" class="outline-3">
|
||||
<h3 id="org049c5fe"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
|
||||
<div class="outline-text-3" id="text-1-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -659,8 +659,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8373b00" class="outline-3">
|
||||
<h3 id="org8373b00"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
|
||||
<div id="outline-container-orge8bd226" class="outline-3">
|
||||
<h3 id="orge8bd226"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
|
||||
<div class="outline-text-3" id="text-1-6">
|
||||
<p>
|
||||
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
|
||||
@ -861,8 +861,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3254e8c" class="outline-3">
|
||||
<h3 id="org3254e8c"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</h3>
|
||||
<div id="outline-container-orgfed449f" class="outline-3">
|
||||
<h3 id="orgfed449f"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</h3>
|
||||
<div class="outline-text-3" id="text-1-7">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1066,8 +1066,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org11d1c0a" class="outline-3">
|
||||
<h3 id="org11d1c0a"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string attribute</h3>
|
||||
<div id="outline-container-org50d49b9" class="outline-3">
|
||||
<h3 id="org50d49b9"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string attribute</h3>
|
||||
<div class="outline-text-3" id="text-1-8">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1189,8 +1189,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orge7ebdec" class="outline-3">
|
||||
<h3 id="orge7ebdec"><span class="section-number-3">1.9</span> Helper functions</h3>
|
||||
<div id="outline-container-orgd444d7d" class="outline-3">
|
||||
<h3 id="orgd444d7d"><span class="section-number-3">1.9</span> Helper functions</h3>
|
||||
<div class="outline-text-3" id="text-1-9">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1452,7 +1452,7 @@ due to the fact that the sparse data will be written in chunks of user-defined s
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-01-07 Fri 10:04</p>
|
||||
<p class="date">Created: 2022-01-07 Fri 10:09</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-01-07 Fri 10:04 -->
|
||||
<!-- 2022-01-07 Fri 10:09 -->
|
||||
<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>
|
||||
@ -311,28 +311,28 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orgf2d5c38">1. TEXT back end</a>
|
||||
<li><a href="#org9c0503a">1. TEXT back end</a>
|
||||
<ul>
|
||||
<li><a href="#org42aeaa4">1.1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org847c0f5">1.2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#orgf868063">1.3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org8e6a798">1.4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org44448a5">1.5. Template for text read struct</a></li>
|
||||
<li><a href="#org645385d">1.6. Template for text flush struct</a></li>
|
||||
<li><a href="#orgedd425c">1.7. Template for text free memory</a></li>
|
||||
<li><a href="#org5f6235a">1.8. Template for has/read/write the numerical attribute</a></li>
|
||||
<li><a href="#org154f742">1.9. Template for has/read/write the dataset of numerical data</a></li>
|
||||
<li><a href="#orgbf841ec">1.10. Template for has/read/write the dataset of strings</a></li>
|
||||
<li><a href="#org0559160">1.11. Template for has/read/write the string attribute</a></li>
|
||||
<li><a href="#org74c0d53">1.12. Template for has/read/write the dataset of sparse data</a></li>
|
||||
<li><a href="#org650728f">1.1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#org4c91045">1.2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#orgc3e751f">1.3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orgf269df8">1.4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orgc349fc2">1.5. Template for text read struct</a></li>
|
||||
<li><a href="#orgf5bd67d">1.6. Template for text flush struct</a></li>
|
||||
<li><a href="#org5393033">1.7. Template for text free memory</a></li>
|
||||
<li><a href="#orgdba67d0">1.8. Template for has/read/write the numerical attribute</a></li>
|
||||
<li><a href="#org4105e1c">1.9. Template for has/read/write the dataset of numerical data</a></li>
|
||||
<li><a href="#orgf385435">1.10. Template for has/read/write the dataset of strings</a></li>
|
||||
<li><a href="#orgf071c4d">1.11. Template for has/read/write the string attribute</a></li>
|
||||
<li><a href="#orgef26ff9">1.12. Template for has/read/write the dataset of sparse data</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf2d5c38" class="outline-2">
|
||||
<h2 id="orgf2d5c38"><span class="section-number-2">1</span> TEXT back end</h2>
|
||||
<div id="outline-container-org9c0503a" class="outline-2">
|
||||
<h2 id="org9c0503a"><span class="section-number-2">1</span> TEXT back end</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<p>
|
||||
The "file" produced by the text back end is a directory with one
|
||||
@ -353,8 +353,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org42aeaa4" class="outline-3">
|
||||
<h3 id="org42aeaa4"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
|
||||
<div id="outline-container-org650728f" class="outline-3">
|
||||
<h3 id="org650728f"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
|
||||
<div class="outline-text-3" id="text-1-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
|
||||
@ -373,8 +373,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org847c0f5" class="outline-3">
|
||||
<h3 id="org847c0f5"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
|
||||
<div id="outline-container-org4c91045" class="outline-3">
|
||||
<h3 id="org4c91045"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
|
||||
<div class="outline-text-3" id="text-1-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_text_s</span> {
|
||||
@ -387,8 +387,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf868063" class="outline-3">
|
||||
<h3 id="orgf868063"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
|
||||
<div id="outline-container-orgc3e751f" class="outline-3">
|
||||
<h3 id="orgc3e751f"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
|
||||
<div class="outline-text-3" id="text-1-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -519,8 +519,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org8e6a798" class="outline-3">
|
||||
<h3 id="org8e6a798"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
|
||||
<div id="outline-container-orgf269df8" class="outline-3">
|
||||
<h3 id="orgf269df8"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
|
||||
<div class="outline-text-3" id="text-1-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -542,8 +542,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org44448a5" class="outline-3">
|
||||
<h3 id="org44448a5"><span class="section-number-3">1.5</span> Template for text read struct</h3>
|
||||
<div id="outline-container-orgc349fc2" class="outline-3">
|
||||
<h3 id="orgc349fc2"><span class="section-number-3">1.5</span> Template for text read struct</h3>
|
||||
<div class="outline-text-3" id="text-1-5">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c">$group$_t*
|
||||
@ -835,8 +835,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org645385d" class="outline-3">
|
||||
<h3 id="org645385d"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
|
||||
<div id="outline-container-orgf5bd67d" class="outline-3">
|
||||
<h3 id="orgf5bd67d"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
|
||||
<div class="outline-text-3" id="text-1-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -901,8 +901,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgedd425c" class="outline-3">
|
||||
<h3 id="orgedd425c"><span class="section-number-3">1.7</span> Template for text free memory</h3>
|
||||
<div id="outline-container-org5393033" class="outline-3">
|
||||
<h3 id="org5393033"><span class="section-number-3">1.7</span> Template for text free memory</h3>
|
||||
<div class="outline-text-3" id="text-1-7">
|
||||
<p>
|
||||
Memory is allocated when reading. The following function frees memory.
|
||||
@ -947,8 +947,8 @@ Memory is allocated when reading. The following function frees memory.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5f6235a" class="outline-3">
|
||||
<h3 id="org5f6235a"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
|
||||
<div id="outline-container-orgdba67d0" class="outline-3">
|
||||
<h3 id="orgdba67d0"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
|
||||
<div class="outline-text-3" id="text-1-8">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1011,8 +1011,8 @@ Memory is allocated when reading. The following function frees memory.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org154f742" class="outline-3">
|
||||
<h3 id="org154f742"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
|
||||
<div id="outline-container-org4105e1c" class="outline-3">
|
||||
<h3 id="org4105e1c"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
|
||||
<div class="outline-text-3" id="text-1-9">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1108,8 +1108,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgbf841ec" class="outline-3">
|
||||
<h3 id="orgbf841ec"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
|
||||
<div id="outline-container-orgf385435" class="outline-3">
|
||||
<h3 id="orgf385435"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
|
||||
<div class="outline-text-3" id="text-1-10">
|
||||
<p>
|
||||
The <code>group_dset</code> array is assumed allocated with the appropriate size.
|
||||
@ -1210,8 +1210,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org0559160" class="outline-3">
|
||||
<h3 id="org0559160"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
|
||||
<div id="outline-container-orgf071c4d" class="outline-3">
|
||||
<h3 id="orgf071c4d"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
|
||||
<div class="outline-text-3" id="text-1-11">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1285,8 +1285,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org74c0d53" class="outline-3">
|
||||
<h3 id="org74c0d53"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
|
||||
<div id="outline-container-orgef26ff9" class="outline-3">
|
||||
<h3 id="orgef26ff9"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
|
||||
<div class="outline-text-3" id="text-1-12">
|
||||
<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
|
||||
@ -1563,7 +1563,7 @@ User provides indices and values of the sparse array as two separate variables.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-01-07 Fri 10:04</p>
|
||||
<p class="date">Created: 2022-01-07 Fri 10:09</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
116
trex.html
116
trex.html
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2022-01-07 Fri 10:04 -->
|
||||
<!-- 2022-01-07 Fri 10:09 -->
|
||||
<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>
|
||||
@ -333,33 +333,33 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org5646172">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org731f7d1">2. Electron (electron group)</a></li>
|
||||
<li><a href="#orge07fa88">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#orgceb34e1">4. Effective core potentials (ecp group)</a>
|
||||
<li><a href="#orgf734636">1. Metadata (metadata group)</a></li>
|
||||
<li><a href="#org5ee55d6">2. Electron (electron group)</a></li>
|
||||
<li><a href="#org21783a9">3. Nucleus (nucleus group)</a></li>
|
||||
<li><a href="#org8b65491">4. Effective core potentials (ecp group)</a>
|
||||
<ul>
|
||||
<li><a href="#org6702c12">4.1. Example</a></li>
|
||||
<li><a href="#org9ecea84">4.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org52fd660">5. Basis set (basis group)</a>
|
||||
<li><a href="#org78b7bb7">5. Basis set (basis group)</a>
|
||||
<ul>
|
||||
<li><a href="#org7fc3b36">5.1. Example</a></li>
|
||||
<li><a href="#orgbaae11c">5.1. Example</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org0186fca">6. Atomic orbitals (ao group)</a>
|
||||
<li><a href="#orgbcc938b">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="#org1b9dc1f">7. Molecular orbitals (mo group)</a>
|
||||
<li><a href="#org40e02e7">7. Molecular orbitals (mo group)</a>
|
||||
<ul>
|
||||
<li><a href="#orgcc6128a">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#org53f9856">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
<li><a href="#orgbc32fe6">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
|
||||
<li><a href="#orgd142f07">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org82aae62">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
|
||||
<li><a href="#orgc2dea78">9. Reduced density matrices (rdm group)</a></li>
|
||||
<li><a href="#org35d7b7c">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
|
||||
<li><a href="#org4f8aef0">9. Reduced density matrices (rdm group)</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@ -409,8 +409,8 @@ fetched using multiple function calls to perform I/O on buffers.
|
||||
</p>
|
||||
|
||||
|
||||
<div id="outline-container-org5646172" class="outline-2">
|
||||
<h2 id="org5646172"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
|
||||
<div id="outline-container-orgf734636" class="outline-2">
|
||||
<h2 id="orgf734636"><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
|
||||
@ -420,7 +420,7 @@ which have participated to the creation of the file, a list of
|
||||
authors of the file, and a textual description.
|
||||
</p>
|
||||
|
||||
<table id="org9403d4f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org29ba59b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -487,15 +487,15 @@ authors of the file, and a textual description.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org731f7d1" class="outline-2">
|
||||
<h2 id="org731f7d1"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div id="outline-container-org5ee55d6" class="outline-2">
|
||||
<h2 id="org5ee55d6"><span class="section-number-2">2</span> Electron (electron group)</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
We consider wave functions expressed in the spin-free formalism, where
|
||||
the number of ↑ and ↓ electrons is fixed.
|
||||
</p>
|
||||
|
||||
<table id="org1588f35" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org6500da9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -534,15 +534,15 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge07fa88" class="outline-2">
|
||||
<h2 id="orge07fa88"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
|
||||
<div id="outline-container-org21783a9" class="outline-2">
|
||||
<h2 id="org21783a9"><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="orga1f6b35" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga37b39d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -609,8 +609,8 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgceb34e1" class="outline-2">
|
||||
<h2 id="orgceb34e1"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
|
||||
<div id="outline-container-org8b65491" class="outline-2">
|
||||
<h2 id="org8b65491"><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
|
||||
@ -643,7 +643,7 @@ 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="org71089ac" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org0305fa4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -741,8 +741,8 @@ The latter causes issues when written before <code>ang_mom</code> in the TREXIO
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org6702c12" class="outline-3">
|
||||
<h3 id="org6702c12"><span class="section-number-3">4.1</span> Example</h3>
|
||||
<div id="outline-container-org9ecea84" class="outline-3">
|
||||
<h3 id="org9ecea84"><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
|
||||
@ -805,8 +805,8 @@ power = [
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org52fd660" class="outline-2">
|
||||
<h2 id="org52fd660"><span class="section-number-2">5</span> Basis set (basis group)</h2>
|
||||
<div id="outline-container-org78b7bb7" class="outline-2">
|
||||
<h2 id="org78b7bb7"><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
|
||||
@ -859,7 +859,7 @@ 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="org787645a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orga3f96b5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -953,8 +953,8 @@ All the basis set parameters are stored in one-dimensional arrays:
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7fc3b36" class="outline-3">
|
||||
<h3 id="org7fc3b36"><span class="section-number-3">5.1</span> Example</h3>
|
||||
<div id="outline-container-orgbaae11c" class="outline-3">
|
||||
<h3 id="orgbaae11c"><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
|
||||
@ -1032,8 +1032,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0186fca" class="outline-2">
|
||||
<h2 id="org0186fca"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
|
||||
<div id="outline-container-orgbcc938b" class="outline-2">
|
||||
<h2 id="orgbcc938b"><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
|
||||
@ -1081,13 +1081,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#org52fd660">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#org78b7bb7">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="org4b26df7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org0c7d98a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1139,8 +1139,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org827401c" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org827401c"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
|
||||
<div id="outline-container-org6067b96" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="org6067b96"></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}}
|
||||
@ -1158,7 +1158,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org758715b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orge7629e6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1225,8 +1225,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgabf0df5" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="orgabf0df5"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
|
||||
<div id="outline-container-orgeaa214a" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="orgeaa214a"></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
|
||||
@ -1247,7 +1247,7 @@ notation.
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
|
||||
</ul>
|
||||
|
||||
<table id="orgbc15a42" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org39c6f21" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1287,10 +1287,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1b9dc1f" class="outline-2">
|
||||
<h2 id="org1b9dc1f"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div id="outline-container-org40e02e7" class="outline-2">
|
||||
<h2 id="org40e02e7"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="org3fb029d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org91ed797" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1356,8 +1356,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgcc6128a" class="outline-3">
|
||||
<h3 id="orgcc6128a"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
|
||||
<div id="outline-container-orgbc32fe6" class="outline-3">
|
||||
<h3 id="orgbc32fe6"><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
|
||||
@ -1365,7 +1365,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="org537383c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org3b8aa5b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1432,8 +1432,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org53f9856" class="outline-3">
|
||||
<h3 id="org53f9856"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
|
||||
<div id="outline-container-orgd142f07" class="outline-3">
|
||||
<h3 id="orgd142f07"><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
|
||||
@ -1441,7 +1441,7 @@ The operators as the same as those defined in the
|
||||
the basis of molecular orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orge041ca1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org16b8565" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1481,13 +1481,13 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org82aae62" class="outline-2">
|
||||
<h2 id="org82aae62"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
|
||||
<div id="outline-container-org35d7b7c" class="outline-2">
|
||||
<h2 id="org35d7b7c"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
|
||||
</div>
|
||||
<div id="outline-container-orgc2dea78" class="outline-2">
|
||||
<h2 id="orgc2dea78"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
|
||||
<div id="outline-container-org4f8aef0" class="outline-2">
|
||||
<h2 id="org4f8aef0"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
|
||||
<div class="outline-text-2" id="text-9">
|
||||
<table id="orgd929e5c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgbab801f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1563,7 +1563,7 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2022-01-07 Fri 10:04</p>
|
||||
<p class="date">Created: 2022-01-07 Fri 10:09</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
Loading…
Reference in New Issue
Block a user