Skip to content

Commit

Permalink
Update documentation
Browse files Browse the repository at this point in the history
  • Loading branch information
kthpanor committed Dec 7, 2023
1 parent 6663e2e commit ec0bf8d
Show file tree
Hide file tree
Showing 86 changed files with 9,045 additions and 8,652 deletions.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file not shown.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file not shown.
Binary file not shown.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file not shown.
146 changes: 90 additions & 56 deletions _sources/docs/spec_prop/cubic_resp.ipynb

Large diffs are not rendered by default.

23 changes: 16 additions & 7 deletions _sources/docs/spec_prop/finite_field.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -178,7 +178,16 @@
"remove-output"
]
},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"* Warning * Environment variable OMP_NUM_THREADS not set.\n",
"* Warning * Setting OMP_NUM_THREADS to 4.\n"
]
}
],
"source": [
"import numpy as np\n",
"import veloxchem as vlx"
Expand Down Expand Up @@ -481,7 +490,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 9,
"id": "db20b247-3fd5-4a39-bbb4-8cb96a9204eb",
"metadata": {
"editable": true,
Expand Down Expand Up @@ -516,10 +525,10 @@
" alpha[F] = -lrf_results[\"response_functions\"][(\"z\", \"z\", 0.0)]\n",
"\n",
" qrf_results = qrf_drv.compute(molecule, basis, scf_results)\n",
" beta[F] = -qrf_results[('qrf', 0.0, 0.0)]\n",
" beta[F] = -qrf_results[('qrf', 0.0, 0.0)].real\n",
"\n",
" crf_results = crf_drv.compute(molecule, basis, scf_results)\n",
" gamma[F] = -crf_results[('crf', 0.0, 0.0, 0.0)]"
" gamma[F] = -crf_results[('crf', 0.0, 0.0, 0.0)].real"
]
},
{
Expand Down Expand Up @@ -594,7 +603,7 @@
" 0.744762 9.34779 -6.73492 999.154\n",
"\n",
"Numerical differentiation\n",
" -energy 0.744763 9.34779 -6.71196 1046.601\n",
" -energy 0.744763 9.34779 -6.71209 1047.823\n",
" -mu 9.34781 -6.73532 999.819\n",
" -alpha -6.73499 999.151\n",
" -beta 999.159\n",
Expand All @@ -609,12 +618,12 @@
"print(f\"{'Method':10s}{'mu':>10s}{'alpha':>10s}{'beta':>10s}{'gamma':>10s}\")\n",
"print(\"-\"*50)\n",
"print(\"Analytic derivatives\")\n",
"print(f\"{'':10s}{mu[0.0]:10.6f}{alpha[0.0]:10.5f}{beta[0.0].real:10.5f}{gamma[0.0].real:10.3f}\")\n",
"print(f\"{'':10s}{mu[0.0]:10.6f}{alpha[0.0]:10.5f}{beta[0.0]:10.5f}{gamma[0.0]:10.3f}\")\n",
"print(\"\\nNumerical differentiation\")\n",
"print(f\"{' -energy':10s}{-dE[0]:10.6f}{-dE[1]:10.5f}{-dE[2]:10.5f}{-dE[3]:10.3f}\")\n",
"print(f\"{' -mu':10s}{'':10s}{dmu[0]:10.5f}{dmu[1]:10.5f}{dmu[2]:10.3f}\")\n",
"print(f\"{' -alpha':10s}{'':10s}{'':10s}{dalpha[0]:10.5f}{dalpha[1]:10.3f}\")\n",
"print(f\"{' -beta':10s}{'':10s}{'':10s}{'':10s}{dbeta[0].real:10.3f}\")\n",
"print(f\"{' -beta':10s}{'':10s}{'':10s}{'':10s}{dbeta[0]:10.3f}\")\n",
"print(\"-\"*50)"
]
},
Expand Down
266 changes: 146 additions & 120 deletions _sources/docs/spec_prop/linear_resp.ipynb

Large diffs are not rendered by default.

125 changes: 60 additions & 65 deletions _sources/docs/spec_prop/quad_resp.ipynb

Large diffs are not rendered by default.

54 changes: 27 additions & 27 deletions docs/basics_notebook.html

Large diffs are not rendered by default.

109 changes: 56 additions & 53 deletions docs/elec_struct/ci.html
Original file line number Diff line number Diff line change
Expand Up @@ -698,8 +698,8 @@ <h2>The <span class="math notranslate nohighlight">\(N\)</span>-electron basis<a
</div>
<div class="cell tag_remove-input docutils container">
<div class="cell_output docutils container">
<div class="output text_html"><div id="3dmolviewer_17018903831743739" style="position: relative; width: 300px; height: 200px;">
<p id="3dmolwarning_17018903831743739" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: <br>
<div class="output text_html"><div id="3dmolviewer_1701945889602607" style="position: relative; width: 300px; height: 200px;">
<p id="3dmolwarning_1701945889602607" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: <br>
<tt>jupyter labextension install jupyterlab_3dmol</tt></p>
</div>
<script>
Expand Down Expand Up @@ -731,19 +731,19 @@ <h2>The <span class="math notranslate nohighlight">\(N\)</span>-electron basis<a
$3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.4/3Dmol-min.js');
}

var viewer_17018903831743739 = null;
var warn = document.getElementById("3dmolwarning_17018903831743739");
var viewer_1701945889602607 = null;
var warn = document.getElementById("3dmolwarning_1701945889602607");
if(warn) {
warn.parentNode.removeChild(warn);
}
$3Dmolpromise.then(function() {
viewer_17018903831743739 = $3Dmol.createViewer(document.getElementById("3dmolviewer_17018903831743739"),{backgroundColor:"white"});
viewer_17018903831743739.zoomTo();
viewer_17018903831743739.addModel("2\nO2 \nO 0.000000000000 0.000000000000 -0.600000000000 \nO 0.000000000000 0.000000000000 0.600000000000 \n","xyz");
viewer_17018903831743739.setViewStyle({"style": "outline", "width": 0.05});
viewer_17018903831743739.setStyle({"stick": {}, "sphere": {"scale": 0.25}});
viewer_17018903831743739.rotate(90,"y");
viewer_17018903831743739.render();
viewer_1701945889602607 = $3Dmol.createViewer(document.getElementById("3dmolviewer_1701945889602607"),{backgroundColor:"white"});
viewer_1701945889602607.zoomTo();
viewer_1701945889602607.addModel("2\nO2 \nO 0.000000000000 0.000000000000 -0.600000000000 \nO 0.000000000000 0.000000000000 0.600000000000 \n","xyz");
viewer_1701945889602607.setViewStyle({"style": "outline", "width": 0.05});
viewer_1701945889602607.setStyle({"stick": {}, "sphere": {"scale": 0.25}});
viewer_1701945889602607.rotate(90,"y");
viewer_1701945889602607.render();
});
</script></div></div>
</div>
Expand Down Expand Up @@ -975,6 +975,9 @@ <h2>The CI Hamiltonian<a class="headerlink" href="#the-ci-hamiltonian" title="Pe
-144.99400313 -144.89601606 -144.89601606 -144.86160532 -144.86160532]
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
</div>
<p>Note how the first (and lowest) energy is indeed lower than the one found at the Hartree–Fock level, due to electron correlation. However, it is important to note that some of the states obtained here are not actually triplet but have a higher multiplicity.</p>
Expand All @@ -988,17 +991,17 @@ <h2>The CI Hamiltonian<a class="headerlink" href="#the-ci-hamiltonian" title="Pe
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[0.969 -0.000 -0.000 -0.000 -0.000 -0.000 -0.000 0.000 -0.000 0.176 -0.000
0.000 0.000 -0.032 0.065 0.000 0.065 0.032 0.000 -0.000 0.000 -0.000
-0.000 0.000 -0.000 0.000 0.000 -0.002 0.003 0.000 0.000 0.000 0.000
-0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000 0.000
0.000 0.000 0.000 0.003 0.002 0.000 -0.000 -0.000 -0.000 0.000 0.000
0.000 0.000 0.000 -0.000 0.000 -0.000 -0.000 0.034 -0.070 0.000 -0.070
-0.034 0.000 -0.000 -0.000 -0.066 -0.000 0.000 -0.000 -0.000 0.000 -0.000
-0.000 0.000 -0.036 -0.000 0.004 0.000 -0.000 -0.008 -0.000 -0.000 -0.000
-0.000 -0.000 -0.000 -0.019 -0.000 0.000 0.000 -0.000 0.000 0.000 -0.000
-0.000 0.000 -0.008 0.000 0.000 -0.004 0.000 -0.000 -0.000 -0.000 0.000
-0.000 -0.000 -0.019 0.000 0.000 0.000 -0.000 0.000 0.000 -0.000]
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[-0.969 0.000 0.000 -0.000 0.000 -0.000 -0.000 -0.000 0.000 -0.176 -0.000
0.000 -0.000 -0.022 0.069 0.000 0.069 0.022 -0.000 -0.000 0.000 -0.000
-0.000 -0.000 -0.000 -0.000 0.000 -0.001 0.004 0.000 0.000 0.000 0.000
0.000 -0.000 0.000 -0.000 -0.000 0.000 0.000 0.000 -0.000 -0.000 0.000
-0.000 0.000 0.000 0.004 0.001 -0.000 0.000 0.000 -0.000 0.000 0.000
0.000 -0.000 -0.000 0.000 -0.000 -0.000 0.000 0.023 -0.074 0.000 -0.074
-0.023 0.000 -0.000 0.000 0.066 0.000 0.000 0.000 -0.000 0.000 0.000
-0.000 -0.000 0.036 0.000 0.003 0.000 -0.000 -0.009 -0.000 -0.000 -0.000
0.000 0.000 0.000 0.019 -0.000 -0.000 -0.000 -0.000 -0.000 0.000 -0.000
0.000 0.000 -0.009 0.000 -0.000 -0.003 -0.000 -0.000 -0.000 -0.000 0.000
0.000 -0.000 0.019 0.000 -0.000 -0.000 -0.000 -0.000 0.000 0.000]
</pre></div>
</div>
</div>
Expand Down Expand Up @@ -1408,23 +1411,23 @@ <h2>Direct CI<a class="headerlink" href="#direct-ci" title="Permalink to this he
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Energy at step 1 = -147.62953840021837
Energy at step 2 = -147.71950117839978
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Energy at step 1 = -147.62953840021845
Energy at step 2 = -147.71961084786736
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Energy at step 3 = -147.72319723321348
Energy at step 4 = -147.7233704307375
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Energy at step 3 = -147.72320976530582
Energy at step 4 = -147.72337266908193
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Energy at step 5 = -147.72338910986724
Energy at step 6 = -147.72339144388854
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Energy at step 5 = -147.72338945745622
Energy at step 6 = -147.72339149545613
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Energy at step 7 = -147.7233918490659
Energy at step 8 = -147.72339192120353
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Energy at step 7 = -147.72339185645623
Energy at step 8 = -147.72339192219124
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Energy at step 9 = -147.7233919345466
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Energy at step 9 = -147.72339193465749
</pre></div>
</div>
</div>
Expand Down Expand Up @@ -1482,19 +1485,19 @@ <h2>Direct CI<a class="headerlink" href="#direct-ci" title="Permalink to this he
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 1 -147.629538400 0.0e+00 1.6e-01 0:00:00
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 2 -147.719501269 -9.0e-02 8.3e-03 0:00:00
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 2 -147.719610931 -9.0e-02 8.2e-03 0:00:00
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 3 -147.723350936 -3.8e-03 4.8e-05 0:00:00
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 3 -147.723354794 -3.7e-03 4.4e-05 0:00:00
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 4 -147.723390664 -4.0e-05 1.9e-06 0:00:00
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 4 -147.723390696 -3.6e-05 1.7e-06 0:00:00
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 5 -147.723391934 -1.3e-06 5.0e-09 0:00:00
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 5 -147.723391934 -1.2e-06 5.2e-09 0:00:00
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 6 -147.723391938 -3.4e-09 2.8e-11 0:00:00
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 6 -147.723391938 -3.7e-09 3.5e-11 0:00:00
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>
Expand All @@ -1505,7 +1508,7 @@ <h2>Direct CI<a class="headerlink" href="#direct-ci" title="Permalink to this he


* State 1
- Energy: -147.72339193756662
- Energy: -147.72339193756164
- S^2 : 2.00 (multiplicity = 3.0 )
- Natural orbitals
1.95550 1.95550 1.96583 1.04380 1.04380 0.03557
Expand Down Expand Up @@ -1577,8 +1580,8 @@ <h3>Restricting the excitations<a class="headerlink" href="#restricting-the-exci
</div>
<div class="cell tag_remove-input docutils container">
<div class="cell_output docutils container">
<div class="output text_html"><div id="3dmolviewer_17018903855734441" style="position: relative; width: 300px; height: 200px;">
<p id="3dmolwarning_17018903855734441" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: <br>
<div class="output text_html"><div id="3dmolviewer_1701945892000584" style="position: relative; width: 300px; height: 200px;">
<p id="3dmolwarning_1701945892000584" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: <br>
<tt>jupyter labextension install jupyterlab_3dmol</tt></p>
</div>
<script>
Expand Down Expand Up @@ -1610,20 +1613,20 @@ <h3>Restricting the excitations<a class="headerlink" href="#restricting-the-exci
$3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.4/3Dmol-min.js');
}

var viewer_17018903855734441 = null;
var warn = document.getElementById("3dmolwarning_17018903855734441");
var viewer_1701945892000584 = null;
var warn = document.getElementById("3dmolwarning_1701945892000584");
if(warn) {
warn.parentNode.removeChild(warn);
}
$3Dmolpromise.then(function() {
viewer_17018903855734441 = $3Dmol.createViewer(document.getElementById("3dmolviewer_17018903855734441"),{backgroundColor:"white"});
viewer_17018903855734441.zoomTo();
viewer_17018903855734441.addModel("3\nwater \nO 0.000000000000 0.000000000000 0.000000000000 \nH 0.000000000000 0.740848095288 0.582094932012 \nH 0.000000000000 -0.740848095288 0.582094932012\n","xyz");
viewer_17018903855734441.setViewStyle({"style": "outline", "width": 0.05});
viewer_17018903855734441.setStyle({"stick": {}, "sphere": {"scale": 0.25}});
viewer_17018903855734441.rotate(90,"y");
viewer_17018903855734441.rotate(-90,"x");
viewer_17018903855734441.render();
viewer_1701945892000584 = $3Dmol.createViewer(document.getElementById("3dmolviewer_1701945892000584"),{backgroundColor:"white"});
viewer_1701945892000584.zoomTo();
viewer_1701945892000584.addModel("3\nwater \nO 0.000000000000 0.000000000000 0.000000000000 \nH 0.000000000000 0.740848095288 0.582094932012 \nH 0.000000000000 -0.740848095288 0.582094932012\n","xyz");
viewer_1701945892000584.setViewStyle({"style": "outline", "width": 0.05});
viewer_1701945892000584.setStyle({"stick": {}, "sphere": {"scale": 0.25}});
viewer_1701945892000584.rotate(90,"y");
viewer_1701945892000584.rotate(-90,"x");
viewer_1701945892000584.render();
});
</script></div></div>
</div>
Expand Down Expand Up @@ -1689,7 +1692,7 @@ <h3>Restricting the excitations<a class="headerlink" href="#restricting-the-exci
----------------------------------------------------------
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 1 -75.983338648 0.0e+00 2.3e-29 0:00:00
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 1 -75.983338648 0.0e+00 1.7e-28 0:00:00
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>
Expand All @@ -1700,10 +1703,10 @@ <h3>Restricting the excitations<a class="headerlink" href="#restricting-the-exci


* State 1
- Energy: -75.98333864834032
- S^2 : 0.00 (multiplicity = 1.0 )
- Energy: -75.98333864834028
- S^2 : -0.00 (multiplicity = 1.0 )
- Natural orbitals
2.00000 2.00000 2.00000 2.00000 2.00000 -0.00000 -0.00000 -0.00000 0.00000 0.00000 0.00000 0.00000 -0.00000
2.00000 2.00000 2.00000 2.00000 2.00000 0.00000 0.00000 0.00000 -0.00000 -0.00000 -0.00000 0.00000 -0.00000
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> Configuration Interaction Driver
Expand Down
Loading

0 comments on commit ec0bf8d

Please sign in to comment.