From 04f618feaa447fb981ee42dfc7ffd7bb0deeae50 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Mon, 11 Jan 2021 19:41:31 -0500
Subject: [PATCH] Change 'all' to 'default' and  add family_auto_generated flag

---
 ipython/kinetics_library_to_training.ipynb | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/ipython/kinetics_library_to_training.ipynb b/ipython/kinetics_library_to_training.ipynb
index ec66a23a29..1bb4ce34d7 100644
--- a/ipython/kinetics_library_to_training.ipynb
+++ b/ipython/kinetics_library_to_training.ipynb
@@ -20,7 +20,7 @@
     "# Set libraries to load reactions from; set to None to load all libraries\n",
     "libraries = ['vinylCPD_H']\n",
     "\n",
-    "# Set families to add training reactions to; either 'all' or a list, e.g. ['R_Addition_MultipleBond']\n",
+    "# Set families to add training reactions to; either 'default' or a list, e.g. ['R_Addition_MultipleBond']\n",
     "families = ['Intra_R_Add_Endocyclic']\n",
     "\n",
     "# Specify whether to plot kinetics comparisons\n",
@@ -73,8 +73,9 @@
     "# If we want accurate kinetics comparison, add existing training reactions and fill tree by averaging\n",
     "if compare_kinetics:\n",
     "    for family in database.kinetics.families.values():\n",
-    "        family.add_rules_from_training(thermo_database=database.thermo)\n",
-    "        family.fill_rules_by_averaging_up(verbose=verbose_comments)"
+    "        if not family.auto_generated:\n",
+    "            family.add_rules_from_training(thermo_database=database.thermo)\n",
+    "            family.fill_rules_by_averaging_up(verbose=verbose_comments)"
    ]
   },
   {
@@ -94,7 +95,7 @@
    "source": [
     "master_dict, multiple_dict = process_reactions(database,\n",
     "                                               libraries,\n",
-    "                                               families,\n",
+    "                                               list(database.kinetics.families.keys()),\n",
     "                                               compare_kinetics=compare_kinetics,\n",
     "                                               show_all=show_all,\n",
     "                                               filter_aromatic=filter_aromatic)"
@@ -213,9 +214,9 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python [conda env:rmg_env]",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "conda-env-rmg_env-py"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -227,7 +228,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.7.7"
   }
  },
  "nbformat": 4,