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_sources/docs/tutorials/correlation.ipynb

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   {
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-    "slideshow": {
-     "slide_type": ""
-    },
-    "tags": []
-   },
+   "metadata": {},
    "source": [
     "# Static versus dynamic correlation correlation\n",
     "\n",
@@ -23,10 +17,6 @@
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    "id": "7f25f196-3ea5-45af-88a3-2051826e6972",
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@@ -3709,7 +3695,7 @@
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+   "version": "3.11.3"
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_sources/docs/tutorials/dire_xps.ipynb

@@ -13,7 +13,7 @@
    },
    "source": [
     "# Core-hole localization\n",
-    "A special aspect of X-ray spectroscopy calculations which involve an explicit core-hole, e.g. X-ray photoelectron spectroscopy (XPS) or X-ray emission spectroscopy (XES), is the delocalization-induced relaxation error (DIRE). DIRE affects symmetric molecules where care must be taken to localize the core-hole, especially when HF or DFT theory levels are used. Below follows an illustration of DIRE in the case of the ethylene molecule. We will calculate the ionization energy of the C 1s core orbitals. The ionization energy is calculated as:\n",
+    "A special aspect of X-ray spectroscopy calculations which involve an explicit core-hole, e.g. X-ray photoelectron spectroscopy (XPS) or X-ray emission spectroscopy (XES), is the delocalization-induced relaxation error (DIRE) {cite}`dire2022`. DIRE affects symmetric molecules where care must be taken to localize the core-hole, especially when HF or DFT theory levels are used. Below follows an illustration of DIRE in the case of the ethylene molecule. We will calculate the ionization energy of the C 1s core orbitals. The ionization energy is calculated as:\n",
     "\n",
     "$$\n",
     "\\textrm{IE} = E_\\textrm{FCH} - E_\\textrm{GS}\n",
@@ -522,7 +522,7 @@
     "tags": []
    },
    "source": [
-    "Now that we have calculated the ionization energies for both the localized and delocalized CH, let us plot the results. The dotted line marks the measured ionization energy."
+    "Now that we have calculated the ionization energies for both the localized and delocalized CH, let us plot the results. The dotted line marks the measured ionization energy {cite}`xpsethylene2011`."
    ]
   },
   {
@@ -580,7 +580,7 @@
      "slide_type": ""
     },
     "tags": [
-     "remove-cell"
+     "hide-input"
     ]
    },
    "outputs": [

_sources/docs/tutorials/uv_vis_analysis.ipynb

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   {
    "cell_type": "markdown",
    "id": "96b5371a",
-   "metadata": {
-    "editable": true,
-    "slideshow": {
-     "slide_type": ""
-    },
-    "tags": []
-   },
+   "metadata": {},
    "source": [
     "# Analysis\n",
     "\n",
@@ -743,7 +737,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.11.4"
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_sources/docs/tutorials/uv_vis_exercises.ipynb

@@ -2,13 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "metadata": {
-    "editable": true,
-    "slideshow": {
-     "slide_type": ""
-    },
-    "tags": []
-   },
+   "metadata": {},
    "source": [
     "# Exercises\n",
     "\n",
@@ -104,7 +98,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.9.14"
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_sources/docs/tutorials/xray_aspects.ipynb

@@ -2,13 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "metadata": {
-    "editable": true,
-    "slideshow": {
-     "slide_type": ""
-    },
-    "tags": []
-   },
+   "metadata": {},
    "source": [
     "# Special aspects\n",
     "\n",
@@ -3035,7 +3029,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.11.4"
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  "nbformat": 4,

docs/title.html

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docs/tutorials/openshells.html

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docs/tutorials/uv_vis.html

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docs/tutorials/uv_vis_exercises.html

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docs/tutorials/xray.html

@@ -32,7 +32,7 @@
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@@ -655,7 +655,7 @@ <h1>X-ray spectroscopies</h1>
 
   <section class="tex2jax_ignore mathjax_ignore" id="x-ray-spectroscopies">
 <span id="sec-x-ray"></span><h1>X-ray spectroscopies<a class="headerlink" href="#x-ray-spectroscopies" title="Link to this heading">#</a></h1>
-<p>Tuning the photon energy to the X-ray regime, processes involving the transition of core electrons can be probed, providing measurements which are very sensitive to elements and local environment <span id="id1">[<a class="reference internal" href="../refs.html#id9" title="U. Bergmann, V. K. Yachandra, and J. Yano. X-Ray Free Electron Lasers: Applications in Materials, Chemistry, and Biology. The Royal Society of Chemistry, 2017. ISBN 978-1-84973-100-3. URL: https://doi.org/10.1039/9781782624097.">BYY17</a>, <a class="reference internal" href="../refs.html#id80" title="P. Norman and A. Dreuw. Simulating x-ray spectroscopies and calculating core-excited states of molecules. Chem. Rev., 118:7208-7248, 2018. URL: https://doi.org/10.1021/acs.chemrev.8b00156.">ND18</a>, <a class="reference internal" href="../refs.html#id118" title="J. A. van Bokhoven and C. Laberti. X-Ray Absorption and X-Ray Emission Spectroscopy: Theory and Applications. John Wiley &amp; Sons, 2016. ISBN 9781118844236. URL: https://doi.org/10.1002/9781118844243.">vBL16</a>]</span>. Here we will discuss the modeling of four such spectroscopies:</p>
+<p>Tuning the photon energy to the X-ray regime, processes involving the transition of core electrons can be probed, providing measurements which are very sensitive to elements and local environment <span id="id1">[<a class="reference internal" href="../refs.html#id9" title="U. Bergmann, V. K. Yachandra, and J. Yano. X-Ray Free Electron Lasers: Applications in Materials, Chemistry, and Biology. The Royal Society of Chemistry, 2017. ISBN 978-1-84973-100-3. URL: https://doi.org/10.1039/9781782624097.">BYY17</a>, <a class="reference internal" href="../refs.html#id82" title="P. Norman and A. Dreuw. Simulating x-ray spectroscopies and calculating core-excited states of molecules. Chem. Rev., 118:7208-7248, 2018. URL: https://doi.org/10.1021/acs.chemrev.8b00156.">ND18</a>, <a class="reference internal" href="../refs.html#id120" title="J. A. van Bokhoven and C. Laberti. X-Ray Absorption and X-Ray Emission Spectroscopy: Theory and Applications. John Wiley &amp; Sons, 2016. ISBN 9781118844236. URL: https://doi.org/10.1002/9781118844243.">vBL16</a>]</span>. Here we will discuss the modeling of four such spectroscopies:</p>
 <figure class="align-default" id="xray-processes">
 <img alt="../../_images/processes.svg" src="../../_images/processes.svg" />
 <figcaption>

docs/tutorials/xray_aspects.html

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@@ -3742,7 +3742,7 @@ <h3>Spin-orbit coupling<a class="headerlink" href="#spin-orbit-coupling" title="
 <section id="spurious-valence-mixing-in-xas">
 <span id="sec-xray-cons-spur-val"></span><h2>Spurious valence mixing in XAS<a class="headerlink" href="#spurious-valence-mixing-in-xas" title="Link to this heading">#</a></h2>
 <p>Within a damped response theory framework or when performing explicit real-time propagation, a CVS-like scheme which separates core-transitions from the valence-continuum is usually not performed. If such calculations are run with an atom-centered basis set (as most are), this can then lead to spurious mixing with valence-excited states. What happens is that resonances in the valence-continuum occur close to core-excitations, leading to unphysical mixing which affects excitation energies and (more significantly) intensities. These issues occur both for methods featuring only single-excited configurations (<em>e.g.</em> TDDFT) and higher-excited configurations (<em>e.g.</em> ADC) and need to be avoided.</p>
-<p>These issues have been observed for, <em>e.g.</em>, <span class="math notranslate nohighlight">\(L_{2,3}\)</span>-edge of silicon <span id="id1">[<a class="reference internal" href="../refs.html#id31" title="T. Fransson, D. Burdakova, and P. Norman. K- and L-edge X-ray absorption spectrum calculations of closed-shell carbon, silicon, germanium, and sulfur compounds using damped four-component density functional response theory. Phys. Chem. Chem. Phys., 18:13591-13603, 2016. URL: https://doi.org/10.1039/C6CP00561F.">FBN16</a>, <a class="reference internal" href="../refs.html#id56" title="M. Kadek, L. Konecny, B. Gao, M. Repisky, and K. Ruud. X-ray absorption resonances near L2,3-edges from real-time propagation of the Dirac–Kohn–Sham density matrix. Phys. Chem. Chem. Phys., 17:22566-22570, 2015. URL: https://doi.org/10.1039/C5CP03712C.">KKG+15</a>]</span>, and are usually more common at lower energies. They can be identified by studying the amplitudes and the <span class="math notranslate nohighlight">\(t^2\)</span> values for post-HF methods, and can be avoided by chosing appropriate basis sets, freezing certain virtual orbitals, or by re-introducing the CVS approximation (or some other flavour) within the CPP/RT framework. The latter approach is recommended at least for CPP-ADC, as converging the response vectors has otherwise been seen to be difficult <span id="id2">[<a class="reference internal" href="../refs.html#id93" title="D. R. Rehn, Z. Rinkevicius, M. Herbst, M. Li, X. Scheurer, M. Brand, A. L. Dempwolff, I. E. Brumboiu, T. Fransson, A. Dreuw, and P. Norman. Gator: a Python-driven program for spectroscopy simulations using correlated wave functions. WIREs Comput. Mol. Sci., 2021. URL: https://doi.org/10.1002/wcms.1528.">RRH+21</a>]</span>.</p>
+<p>These issues have been observed for, <em>e.g.</em>, <span class="math notranslate nohighlight">\(L_{2,3}\)</span>-edge of silicon <span id="id1">[<a class="reference internal" href="../refs.html#id33" title="T. Fransson, D. Burdakova, and P. Norman. K- and L-edge X-ray absorption spectrum calculations of closed-shell carbon, silicon, germanium, and sulfur compounds using damped four-component density functional response theory. Phys. Chem. Chem. Phys., 18:13591-13603, 2016. URL: https://doi.org/10.1039/C6CP00561F.">FBN16</a>, <a class="reference internal" href="../refs.html#id58" title="M. Kadek, L. Konecny, B. Gao, M. Repisky, and K. Ruud. X-ray absorption resonances near L2,3-edges from real-time propagation of the Dirac–Kohn–Sham density matrix. Phys. Chem. Chem. Phys., 17:22566-22570, 2015. URL: https://doi.org/10.1039/C5CP03712C.">KKG+15</a>]</span>, and are usually more common at lower energies. They can be identified by studying the amplitudes and the <span class="math notranslate nohighlight">\(t^2\)</span> values for post-HF methods, and can be avoided by chosing appropriate basis sets, freezing certain virtual orbitals, or by re-introducing the CVS approximation (or some other flavour) within the CPP/RT framework. The latter approach is recommended at least for CPP-ADC, as converging the response vectors has otherwise been seen to be difficult <span id="id2">[<a class="reference internal" href="../refs.html#id95" title="D. R. Rehn, Z. Rinkevicius, M. Herbst, M. Li, X. Scheurer, M. Brand, A. L. Dempwolff, I. E. Brumboiu, T. Fransson, A. Dreuw, and P. Norman. Gator: a Python-driven program for spectroscopy simulations using correlated wave functions. WIREs Comput. Mol. Sci., 2021. URL: https://doi.org/10.1002/wcms.1528.">RRH+21</a>]</span>.</p>
 </section>
 </section>
 

genindex.html

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