Update documentation

kthpanor · Mar 22, 2024 · e3be17c · e3be17c
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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: 6e2531388bad5c7431eb69dd2a4c263e
+config: 1730e940bd0f5a51009b164991c631c2
 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
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diff --git a/_sources/docs/mol_struct/coordinates.ipynb b/_sources/docs/mol_struct/coordinates.ipynb
@@ -7,7 +7,7 @@
     "tags": []
    },
    "source": [
-    "(coord)=\n",
+    "(sec:coord)=\n",
     "\n",
     "# Choice of coordinates\n",
     "\n",
@@ -175,7 +175,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

diff --git a/_sources/docs/mol_struct/molstruct_gen.ipynb b/_sources/docs/mol_struct/molstruct_gen.ipynb
@@ -7,7 +7,12 @@
    "source": [
     "# General aspects\n",
     "\n",
-    "This section deals with general aspects of concern for explorations of potential energy surfaces, focusing on various types of [molecular coordinates](coord)."
+    "This section deals with general aspects of concern for explorations of potential energy surfaces. \n",
+    "- **[Choice of coordinates](sec:coord)**\n",
+    "  contains an introduction to various types of molecular coordinates, from Cartesian coordinates to different internal coordinates.\n",
+    "- **[Molecular symmetry](sec:molsymm)** contains an introduction to molecular symmetry operations and point symmetry groups.\n",
+    "- **[Transition-state theory](sec:tst)** introduces the basic ideas related to transitions states and their role in chemical reactions, as well as the steps required to identify a transition state on the global potential energy surface.\n",
+    "- **[Optimization methods](sec:structopt-methods)** illustrates the basic algorithms for performing structure optimizations and how they compare to each other. "
    ]
   },
   {
@@ -35,7 +40,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

diff --git a/_sources/docs/mol_struct/opt_struct.ipynb b/_sources/docs/mol_struct/opt_struct.ipynb
diff --git a/_sources/docs/mol_struct/symmetry.ipynb b/_sources/docs/mol_struct/symmetry.ipynb
@@ -11,6 +11,7 @@
     "tags": []
    },
    "source": [
+    "(sec:molsymm)=\n",
     "# Molecular symmetry\n",
     "\n",
     "Molecular symmetry operations are given by rotations, reflections, and inversions of the molecule which leaves the molecule unchanged. For further details about symmetry see [this section](https://kthpanor.github.io/echem/docs/elec_struct/group_theory.html)."
@@ -41,7 +42,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

diff --git a/_sources/docs/mol_struct/tst.ipynb b/_sources/docs/mol_struct/tst.ipynb
@@ -34,7 +34,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

diff --git a/_sources/docs/mol_struct/tst_gen.ipynb b/_sources/docs/mol_struct/tst_gen.ipynb
@@ -984,7 +984,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,