Update documentation

kthpanor · May 6, 2024 · bec99cf · bec99cf
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 1730e940bd0f5a51009b164991c631c2
+config: 6e2531388bad5c7431eb69dd2a4c263e
 tags: 645f666f9bcd5a90fca523b33c5a78b7
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diff --git a/...aa0fa92f3d0aea88025e2b82af06a08ead09f.png → ...8f193aeacf96347bfe860fb3196c28b03e152.png b/...aa0fa92f3d0aea88025e2b82af06a08ead09f.png → ...8f193aeacf96347bfe860fb3196c28b03e152.png
diff --git a/...154107d2325e4817602835d9ba242dd11761c.png → ...1c5fb8c474f9902486a043ad9d11a242d3a74.png b/...154107d2325e4817602835d9ba242dd11761c.png → ...1c5fb8c474f9902486a043ad9d11a242d3a74.png
diff --git a/...dcd4da275ecabd4f788fb791a0ab1aa8b0946.png → ...79c454ead06f53eee8b87dfdfa54976d9b536.png b/...dcd4da275ecabd4f788fb791a0ab1aa8b0946.png → ...79c454ead06f53eee8b87dfdfa54976d9b536.png
diff --git a/_images/fe2f58d25767a5ac37f0eae7f6687a687537a60925e92453550436bbef2e1ba3.png b/_images/fe2f58d25767a5ac37f0eae7f6687a687537a60925e92453550436bbef2e1ba3.png
diff --git a/_images/kahweol_normal_mode_slider.png b/_images/kahweol_normal_mode_slider.png
diff --git a/_images/kahweol_opt_slider.png b/_images/kahweol_opt_slider.png
diff --git a/_images/kahweol_slider.png b/_images/kahweol_slider.png
diff --git a/_images/linear_polarization.gif b/_images/linear_polarization.gif
diff --git a/_sources/docs/spec_prop/adc_exercises_new.ipynb b/_sources/docs/spec_prop/adc_exercises_new.ipynb
@@ -809,7 +809,10 @@
     "\n",
     "where $\\omega$ is the excitation energy of the corresponding excited state.\n",
     "\n",
-    "**In the CIS scheme, $\\gamma_{ia} = x_{ia}$ is correct through zeroth order only. As a matter of fact, this is the only place where the ADC(1) and CIS methods differ.**\n",
+    "`````{admonition} Note\n",
+    ":class: tip\n",
+    "In the CIS scheme, $\\gamma_{ia} = x_{ia}$ is correct through zeroth order only. As a matter of fact, this is the only place where the ADC(1) and CIS methods differ.\n",
+    "`````\n",
     "\n",
     "Let's use the excitation vectors to build the one-particle transition density matrices and calculate the oscillator strengths."
    ]
@@ -1770,7 +1773,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

diff --git a/_sources/docs/tutorials/colab.ipynb b/_sources/docs/tutorials/colab.ipynb
@@ -30,7 +30,7 @@
     "\n",
     "This serve as a convenient alternative if you just wish to try things out. Note, however, that session startup times will be in the order of minutes as software needs to be installed on the cloud resource made available to you (one typically gets two CPU cores). \n",
     "\n",
-    "If you are new to Colab, there is an abundance of introductory material such as the YouTube video below."
+    "If you are new to Colab, there is an abundance of introductory material on the internet such as the YouTube video below."
    ]
   },
   {

diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js
@@ -0,0 +1,134 @@
+/*
+ * _sphinx_javascript_frameworks_compat.js
+ * ~~~~~~~~~~
+ *
+ * Compatability shim for jQuery and underscores.js.
+ *
+ * WILL BE REMOVED IN Sphinx 6.0
+ * xref RemovedInSphinx60Warning
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}
diff --git a/_static/basic.css b/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -236,11 +236,17 @@ div.body p, div.body dd, div.body li, div.body blockquote {
 a.headerlink {
     visibility: hidden;
 }
+a.brackets:before,
+span.brackets > a:before{
+    content: "[";
+}
 
-a:visited {
-    color: #551A8B;
+a.brackets:after,
+span.brackets > a:after {
+    content: "]";
 }
 
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -328,17 +334,11 @@ aside.sidebar {
 p.sidebar-title {
     font-weight: bold;
 }
-
-nav.contents,
-aside.topic,
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
-
-nav.contents,
-aside.topic,
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -377,17 +377,13 @@ div.body p.centered {
 
 div.sidebar > :last-child,
 aside.sidebar > :last-child,
-nav.contents > :last-child,
-aside.topic > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
 aside.sidebar::after,
-nav.contents::after,
-aside.topic::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -613,6 +609,25 @@ ul.simple p {
     margin-bottom: 0;
 }
 
+/* Docutils 0.17 and older (footnotes & citations) */
+dl.footnote > dt,
+dl.citation > dt {
+    float: left;
+    margin-right: 0.5em;
+}
+
+dl.footnote > dd,
+dl.citation > dd {
+    margin-bottom: 0em;
+}
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
+    content: "";
+    clear: both;
+}
+
+/* Docutils 0.18+ (footnotes & citations) */
 aside.footnote > span,
 div.citation > span {
     float: left;
@@ -637,6 +652,8 @@ div.citation > p:last-of-type:after {
     clear: both;
 }
 
+/* Footnotes & citations ends */
+
 dl.field-list {
     display: grid;
     grid-template-columns: fit-content(30%) auto;
@@ -649,6 +666,10 @@ dl.field-list > dt {
     padding-right: 5px;
 }
 
+dl.field-list > dt:after {
+    content: ":";
+}
+
 dl.field-list > dd {
     padding-left: 0.5em;
     margin-top: 0em;
@@ -674,16 +695,6 @@ dd {
     margin-left: 30px;
 }
 
-.sig dd {
-    margin-top: 0px;
-    margin-bottom: 0px;
-}
-
-.sig dl {
-    margin-top: 0px;
-    margin-bottom: 0px;
-}
-
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -752,14 +763,6 @@ abbr, acronym {
     cursor: help;
 }
 
-.translated {
-    background-color: rgba(207, 255, 207, 0.2)
-}
-
-.untranslated {
-    background-color: rgba(255, 207, 207, 0.2)
-}
-
 /* -- code displays --------------------------------------------------------- */
 
 pre {

diff --git a/_static/design-style.4045f2051d55cab465a707391d5b2007.min.css b/_static/design-style.4045f2051d55cab465a707391d5b2007.min.css
-Original file line number
+Diff line change
@@ Expand Up / @@ -30,7 +30,7 @@ @@
         "\n",
         "This serve as a convenient alternative if you just wish to try things out. Note, however, that session startup times will be in the order of minutes as software needs to be installed on the cloud resource made available to you (one typically gets two CPU cores). \n",
         "\n",
-        "If you are new to Colab, there is an abundance of introductory material such as the YouTube video below."
+        "If you are new to Colab, there is an abundance of introductory material on the internet such as the YouTube video below."
        ]
       },
       {
@@ Expand Down @@