Update documentation

kthpanor · Mar 20, 2024 · 754c722 · 754c722
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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/_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/linear_polarization.gif b/_images/linear_polarization.gif
diff --git a/_sources/docs/elec_struct/integrals.ipynb b/_sources/docs/elec_struct/integrals.ipynb
@@ -15,6 +15,25 @@
     "# Integrals"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "d9340b31-456a-41e2-af70-58370029cabb",
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "remove-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import veloxchem as vlx"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "c1077121-bf36-4afb-9758-721d8042d070",
@@ -40,7 +59,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 5,
    "id": "04324370-f96f-4c52-b294-1c992a76ae2b",
    "metadata": {
     "editable": true,
@@ -59,91 +78,6 @@
     "\"\"\""
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "id": "dd1ae7e0-643d-47d6-aaaa-910720d52620",
-   "metadata": {
-    "editable": true,
-    "slideshow": {
-     "slide_type": ""
-    },
-    "tags": [
-     "remove-input"
-    ]
-   },
-   "outputs": [
-    {
-     "data": {
-      "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_1707897534873106\"  style=\"position: relative; width: 300px; height: 200px;\">\n        <p id=\"3dmolwarning_1707897534873106\" 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>\n        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n        </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n  return new Promise((resolve, reject) => {\n    //this is to ignore the existence of requirejs amd\n    var savedexports, savedmodule;\n    if (typeof exports !== 'undefined') savedexports = exports;\n    else exports = {}\n    if (typeof module !== 'undefined') savedmodule = module;\n    else module = {}\n\n    var tag = document.createElement('script');\n    tag.src = uri;\n    tag.async = true;\n    tag.onload = () => {\n        exports = savedexports;\n        module = savedmodule;\n        resolve();\n    };\n  var firstScriptTag = document.getElementsByTagName('script')[0];\n  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n  $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.4/3Dmol-min.js');\n}\n\nvar viewer_1707897534873106 = null;\nvar warn = document.getElementById(\"3dmolwarning_1707897534873106\");\nif(warn) {\n    warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_1707897534873106 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_1707897534873106\"),{backgroundColor:\"white\"});\nviewer_1707897534873106.zoomTo();\n\tviewer_1707897534873106.addModel(\"3\\n\\nO    0.000000000000        0.000000000000        0.000000000000\\nH    0.000000000000        0.740848095288        0.582094932012\\nH    0.000000000000       -0.740848095288        0.582094932012\\n\",\"xyz\");\n\tviewer_1707897534873106.setViewStyle({\"style\": \"outline\", \"width\": 0.05});\n\tviewer_1707897534873106.setStyle({\"stick\": {}, \"sphere\": {\"scale\": 0.25}});\n\tviewer_1707897534873106.rotate(90,\"y\");\n\tviewer_1707897534873106.rotate(-90,\"x\");\nviewer_1707897534873106.render();\n});\n</script>",
-      "text/html": [
-       "<div id=\"3dmolviewer_1707897534873106\"  style=\"position: relative; width: 300px; height: 200px;\">\n",
-       "        <p id=\"3dmolwarning_1707897534873106\" 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>\n",
-       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
-       "        </div>\n",
-       "<script>\n",
-       "\n",
-       "var loadScriptAsync = function(uri){\n",
-       "  return new Promise((resolve, reject) => {\n",
-       "    //this is to ignore the existence of requirejs amd\n",
-       "    var savedexports, savedmodule;\n",
-       "    if (typeof exports !== 'undefined') savedexports = exports;\n",
-       "    else exports = {}\n",
-       "    if (typeof module !== 'undefined') savedmodule = module;\n",
-       "    else module = {}\n",
-       "\n",
-       "    var tag = document.createElement('script');\n",
-       "    tag.src = uri;\n",
-       "    tag.async = true;\n",
-       "    tag.onload = () => {\n",
-       "        exports = savedexports;\n",
-       "        module = savedmodule;\n",
-       "        resolve();\n",
-       "    };\n",
-       "  var firstScriptTag = document.getElementsByTagName('script')[0];\n",
-       "  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n",
-       "});\n",
-       "};\n",
-       "\n",
-       "if(typeof $3Dmolpromise === 'undefined') {\n",
-       "$3Dmolpromise = null;\n",
-       "  $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.4/3Dmol-min.js');\n",
-       "}\n",
-       "\n",
-       "var viewer_1707897534873106 = null;\n",
-       "var warn = document.getElementById(\"3dmolwarning_1707897534873106\");\n",
-       "if(warn) {\n",
-       "    warn.parentNode.removeChild(warn);\n",
-       "}\n",
-       "$3Dmolpromise.then(function() {\n",
-       "viewer_1707897534873106 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_1707897534873106\"),{backgroundColor:\"white\"});\n",
-       "viewer_1707897534873106.zoomTo();\n",
-       "\tviewer_1707897534873106.addModel(\"3\\n\\nO    0.000000000000        0.000000000000        0.000000000000\\nH    0.000000000000        0.740848095288        0.582094932012\\nH    0.000000000000       -0.740848095288        0.582094932012\\n\",\"xyz\");\n",
-       "\tviewer_1707897534873106.setViewStyle({\"style\": \"outline\", \"width\": 0.05});\n",
-       "\tviewer_1707897534873106.setStyle({\"stick\": {}, \"sphere\": {\"scale\": 0.25}});\n",
-       "\tviewer_1707897534873106.rotate(90,\"y\");\n",
-       "\tviewer_1707897534873106.rotate(-90,\"x\");\n",
-       "viewer_1707897534873106.render();\n",
-       "});\n",
-       "</script>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "import py3Dmol as p3d\n",
-    "\n",
-    "viewer = p3d.view(width=300, height=200)\n",
-    "viewer.addModel(h2o_xyz, \"xyz\")\n",
-    "viewer.setViewStyle({\"style\": \"outline\", \"width\": 0.05})\n",
-    "viewer.setStyle({\"stick\": {}, \"sphere\": {\"scale\": 0.25}})\n",
-    "viewer.rotate(90, \"y\")\n",
-    "viewer.rotate(-90, \"x\")\n",
-    "viewer.show()"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "cd559d46-a78b-4fb4-b220-fc0a32108aa1",
@@ -160,8 +94,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
-   "id": "c31f1230-9cc2-47ed-b42a-985d52279ead",
+   "execution_count": 6,
+   "id": "a22f0f63-a344-4ea1-b39f-6f0414c1b24f",
    "metadata": {
     "editable": true,
     "slideshow": {
@@ -171,27 +105,15 @@
      "remove-output"
     ]
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "* Warning * Environment variable OMP_NUM_THREADS not set.\n",
-      "* Warning * Setting OMP_NUM_THREADS to 6.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "import numpy as np\n",
-    "import veloxchem as vlx\n",
-    "\n",
     "molecule = vlx.Molecule.read_xyz_string(h2o_xyz)\n",
     "basis = vlx.MolecularBasis.read(molecule, \"cc-pVDZ\", ostream=None)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 7,
    "id": "e8dfc499-94cb-4995-9d1b-7db39519104e",
    "metadata": {
     "editable": true,

diff --git a/_sources/docs/spec_prop/hf_param_energy.ipynb b/_sources/docs/spec_prop/hf_param_energy.ipynb
@@ -0,0 +1,41 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "20fb2dab-c6f5-4e68-a79e-113381e903b0",
+   "metadata": {},
+   "source": [
+    "# Energy determination of parameters"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dfaf8341-01c1-4b78-9d93-26ffd0477c19",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/_sources/docs/spec_prop/orb_rot.ipynb b/_sources/docs/spec_prop/orb_rot.ipynb
@@ -44,10 +44,10 @@
     "    \\Big]\n",
     "$$\n",
     "\n",
-    "It is convenient to organize the electron transfer amplitudes into the virtual–occupied (vo) and occupied–virtual (ov) blocks of a molecular orbital (MO) matrix. In the vo- and ov-blocks, we put amplitudes $\\kappa_{ai}$ and $\\kappa_{ia} = \\kappa_{ai}^\\ast$, respectively.\n",
+    "It is convenient to organize the electron transfer amplitudes into the virtual–occupied (vo) and occupied–virtual (ov) blocks of a molecular orbital (MO) matrix. In the vo- and ov-blocks, we put amplitudes $\\kappa_{ai}$ and $\\kappa_{ai}^\\ast \\equiv \\kappa_{ia}$, respectively.\n",
     "\n",
     "$$\n",
-    "\\kappa = \n",
+    "\\boldsymbol{\\kappa} = \n",
     "\\begin{bmatrix}\n",
     "0 & \\kappa_{ia} \\\\\n",
     "\\kappa_{ai} & 0 \\\\\n",
@@ -118,7 +118,7 @@
     "where we have introduced the unitary matrix\n",
     "\n",
     "$$\n",
-    "U = e^{-i\\kappa}\n",
+    "\\mathbf{U} = e^{-i\\boldsymbol{\\kappa}}\n",
     "$$\n",
     "\n",
     "Following the determinant property of linearity, this transformation of creation operators translates directly into a transformation of orbitals in the wave function\n",
@@ -300,7 +300,7 @@
     "We reach the doubly excited determinant with\n",
     "\n",
     "$$\n",
-    "\\kappa = \n",
+    "\\boldsymbol{\\kappa} = \n",
     "\\begin{bmatrix}\n",
     "0 & 0 & -i\\pi/2 & 0 \\\\\n",
     "0 & 0 & 0 & -i\\pi/2 \\\\\n",
@@ -356,7 +356,7 @@
     "Let us create a random generator of orbital rotations on the form\n",
     "\n",
     "$$\n",
-    "\\kappa = \n",
+    "\\boldsymbol{\\kappa} = \n",
     "\\begin{bmatrix}\n",
     "0 & \\kappa_{ia} \\\\\n",
     "\\kappa_{ai} & 0 \\\\\n",
@@ -448,7 +448,7 @@
     "As an example, let us consider\n",
     "\n",
     "$$\n",
-    "\\kappa = \n",
+    "\\boldsymbol{\\kappa} = \n",
     "\\begin{bmatrix}\n",
     "0 & 0 & -i\\pi/4 & 0 \\\\\n",
     "0 & 0 & 0 & -i\\pi/4 \\\\\n",
@@ -526,7 +526,7 @@
     "Finally, let us consider a somewhat larger system with four electrons in six MOs (or 12 spin orbitals). In the spin-orbital basis, it is convenient to organize parameters in spin blocks.\n",
     "\n",
     "$$\n",
-    "\\kappa =\n",
+    "\\boldsymbol{\\kappa} =\n",
     "\\begin{bmatrix}\n",
     "0 & 0 & \\kappa_{ia} & \\kappa_{i\\bar{a}} \\\\\n",
     "0 & 0 & \\kappa_{\\bar{i}a} & \\kappa_{\\bar{i}\\bar{a}} \\\\\n",

diff --git a/_sources/docs/visualize/opt_vib_vis.ipynb b/_sources/docs/visualize/opt_vib_vis.ipynb