Merge remote-tracking branch 'origin/master' into update-dataset-intro

# Conflicts:
#	day_2/00-IntroductionDay2.ipynb

day_1/ex_02_creating_structure_databases.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "previous-lotus",
+   "id": "expired-green",
    "metadata": {},
    "source": [
     "# [**Workflows for atomistic simulations**](http://potentials.rub.de/) "
@@ -10,7 +10,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "solid-explosion",
+   "id": "brutal-healing",
    "metadata": {},
    "source": [
     "## **Day 1 - Atomistic simulations with [pyiron](https://pyiron.org)**\n",
@@ -29,7 +29,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "apparent-assembly",
+   "id": "cheap-chick",
    "metadata": {},
    "source": [
     "## **Importing necessary modules and creating a project**\n",
@@ -40,7 +40,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "fitting-testing",
+   "id": "married-kidney",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -52,7 +52,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "id": "mature-bearing",
+   "id": "academic-print",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -62,7 +62,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "id": "considered-karma",
+   "id": "comparable-creation",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -71,7 +71,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "controlled-david",
+   "id": "focal-percentage",
    "metadata": {},
    "source": [
     "## Creating a structure \"container\" from the data\n",
@@ -84,7 +84,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "wrong-pickup",
+   "id": "contrary-spider",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -95,7 +95,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "id": "current-vanilla",
+   "id": "superior-prospect",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -105,7 +105,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "dominican-northwest",
+   "id": "verified-lancaster",
    "metadata": {},
    "source": [
     "## **Add structures from the E-V curves**\n",
@@ -116,7 +116,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "concrete-background",
+   "id": "false-flexibility",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -127,7 +127,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "worse-scheduling",
+   "id": "boolean-reply",
    "metadata": {},
    "source": [
     "We can obtain this data as a `pandas` table"
@@ -136,7 +136,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "id": "changed-shame",
+   "id": "introductory-latitude",
    "metadata": {},
    "outputs": [
     {
@@ -268,7 +268,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ultimate-duncan",
+   "id": "indirect-sellers",
    "metadata": {},
    "source": [
     "## **Add structures from the MD**\n",
@@ -279,7 +279,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "disabled-computer",
+   "id": "applied-spank",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -290,7 +290,7 @@
   {
    "cell_type": "code",
    "execution_count": 9,
-   "id": "aggregate-wilderness",
+   "id": "operating-academy",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -305,7 +305,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "welsh-commercial",
+   "id": "consecutive-arbitration",
    "metadata": {},
    "source": [
     "## **Add some defect structures (vacancies, surfaces, etc)**\n",
@@ -316,14 +316,14 @@
   {
    "cell_type": "code",
    "execution_count": 10,
-   "id": "continuing-upset",
+   "id": "certified-eligibility",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "The job lammps_job_vac was saved and received the ID: 303\n"
+      "The job lammps_job_vac was saved and received the ID: 52\n"
      ]
     }
    ],
@@ -340,14 +340,14 @@
   {
    "cell_type": "code",
    "execution_count": 11,
-   "id": "listed-occurrence",
+   "id": "eleven-intermediate",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "The job lammps_job_surf was saved and received the ID: 304\n"
+      "The job lammps_job_surf was saved and received the ID: 53\n"
      ]
     }
    ],
@@ -363,7 +363,7 @@
   {
    "cell_type": "code",
    "execution_count": 12,
-   "id": "sound-bathroom",
+   "id": "accepted-silly",
    "metadata": {},
    "outputs": [
     {
@@ -383,7 +383,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "processed-liability",
+   "id": "diverse-stability",
    "metadata": {},
    "source": [
     "We now add these structures to the dataset"
@@ -391,8 +391,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
-   "id": "trained-target",
+   "execution_count": 13,
+   "id": "single-treasure",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -408,14 +408,14 @@
   {
    "cell_type": "code",
    "execution_count": 14,
-   "id": "attended-drama",
+   "id": "widespread-homework",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "The job dataset_example was saved and received the ID: 306\n"
+      "The job dataset_example was saved and received the ID: 54\n"
      ]
     },
     {
@@ -438,7 +438,7 @@
   {
    "cell_type": "code",
    "execution_count": 15,
-   "id": "signal-establishment",
+   "id": "professional-change",
    "metadata": {},
    "outputs": [
     {
@@ -482,17 +482,17 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>303</td>\n",
+       "      <td>52</td>\n",
        "      <td>finished</td>\n",
        "      <td>Cu107</td>\n",
        "      <td>lammps_job_vac</td>\n",
        "      <td>/lammps_job_vac</td>\n",
        "      <td>/home/pyiron/</td>\n",
        "      <td>day_1/creating_datasets/</td>\n",
-       "      <td>2021-03-09 09:38:28.337496</td>\n",
-       "      <td>2021-03-09 09:38:33.222851</td>\n",
+       "      <td>2021-03-09 09:56:52.116789</td>\n",
+       "      <td>2021-03-09 09:56:56.507766</td>\n",
        "      <td>4.0</td>\n",
-       "      <td>pyiron@jupyter-sudarsan#1</td>\n",
+       "      <td>pyiron@jupyter-janssen#1</td>\n",
        "      <td>Lammps</td>\n",
        "      <td>0.1</td>\n",
        "      <td>None</td>\n",
@@ -500,17 +500,17 @@
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
-       "      <td>304</td>\n",
+       "      <td>53</td>\n",
        "      <td>finished</td>\n",
        "      <td>Cu128</td>\n",
        "      <td>lammps_job_surf</td>\n",
        "      <td>/lammps_job_surf</td>\n",
        "      <td>/home/pyiron/</td>\n",
        "      <td>day_1/creating_datasets/</td>\n",
-       "      <td>2021-03-09 09:38:34.181033</td>\n",
-       "      <td>2021-03-09 09:38:39.609826</td>\n",
-       "      <td>5.0</td>\n",
-       "      <td>pyiron@jupyter-sudarsan#1</td>\n",
+       "      <td>2021-03-09 09:56:57.326228</td>\n",
+       "      <td>2021-03-09 09:57:02.004791</td>\n",
+       "      <td>4.0</td>\n",
+       "      <td>pyiron@jupyter-janssen#1</td>\n",
        "      <td>Lammps</td>\n",
        "      <td>0.1</td>\n",
        "      <td>None</td>\n",
@@ -518,17 +518,17 @@
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
-       "      <td>306</td>\n",
+       "      <td>54</td>\n",
        "      <td>finished</td>\n",
        "      <td>None</td>\n",
        "      <td>dataset_example</td>\n",
        "      <td>/dataset_example</td>\n",
        "      <td>/home/pyiron/</td>\n",
        "      <td>day_1/creating_datasets/</td>\n",
-       "      <td>2021-03-09 09:38:48.660175</td>\n",
+       "      <td>2021-03-09 09:57:10.376230</td>\n",
        "      <td>NaT</td>\n",
        "      <td>NaN</td>\n",
-       "      <td>pyiron@jupyter-sudarsan#1</td>\n",
+       "      <td>pyiron@jupyter-janssen#1</td>\n",
        "      <td>TrainingContainer</td>\n",
        "      <td>0.4</td>\n",
        "      <td>None</td>\n",
@@ -539,20 +539,20 @@
        "</div>"
       ],
       "text/plain": [
-       "    id    status chemicalformula              job            subjob  \\\n",
-       "0  303  finished           Cu107   lammps_job_vac   /lammps_job_vac   \n",
-       "1  304  finished           Cu128  lammps_job_surf  /lammps_job_surf   \n",
-       "2  306  finished            None  dataset_example  /dataset_example   \n",
+       "   id    status chemicalformula              job            subjob  \\\n",
+       "0  52  finished           Cu107   lammps_job_vac   /lammps_job_vac   \n",
+       "1  53  finished           Cu128  lammps_job_surf  /lammps_job_surf   \n",
+       "2  54  finished            None  dataset_example  /dataset_example   \n",
        "\n",
        "     projectpath                   project                  timestart  \\\n",
-       "0  /home/pyiron/  day_1/creating_datasets/ 2021-03-09 09:38:28.337496   \n",
-       "1  /home/pyiron/  day_1/creating_datasets/ 2021-03-09 09:38:34.181033   \n",
-       "2  /home/pyiron/  day_1/creating_datasets/ 2021-03-09 09:38:48.660175   \n",
+       "0  /home/pyiron/  day_1/creating_datasets/ 2021-03-09 09:56:52.116789   \n",
+       "1  /home/pyiron/  day_1/creating_datasets/ 2021-03-09 09:56:57.326228   \n",
+       "2  /home/pyiron/  day_1/creating_datasets/ 2021-03-09 09:57:10.376230   \n",
        "\n",
-       "                    timestop  totalcputime                   computer  \\\n",
-       "0 2021-03-09 09:38:33.222851           4.0  pyiron@jupyter-sudarsan#1   \n",
-       "1 2021-03-09 09:38:39.609826           5.0  pyiron@jupyter-sudarsan#1   \n",
-       "2                        NaT           NaN  pyiron@jupyter-sudarsan#1   \n",
+       "                    timestop  totalcputime                  computer  \\\n",
+       "0 2021-03-09 09:56:56.507766           4.0  pyiron@jupyter-janssen#1   \n",
+       "1 2021-03-09 09:57:02.004791           4.0  pyiron@jupyter-janssen#1   \n",
+       "2                        NaT           NaN  pyiron@jupyter-janssen#1   \n",
        "\n",
        "            hamilton hamversion parentid masterid  \n",
        "0             Lammps        0.1     None     None  \n",
@@ -571,7 +571,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "lyric-blair",
+   "id": "technological-partner",
    "metadata": {},
    "source": [
     "## **Reloading the dataset**\n",
@@ -582,7 +582,7 @@
   {
    "cell_type": "code",
    "execution_count": 16,
-   "id": "swiss-catering",
+   "id": "processed-samuel",
    "metadata": {},
    "outputs": [
     {
@@ -1162,7 +1162,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "premier-least",
+   "id": "julian-helena",
    "metadata": {},
    "source": [
     "We can now inspect the data in this dataset quite easily"
@@ -1171,7 +1171,7 @@
   {
    "cell_type": "code",
    "execution_count": 17,
-   "id": "difficult-cartoon",
+   "id": "starting-dress",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1181,7 +1181,7 @@
   {
    "cell_type": "code",
    "execution_count": 18,
-   "id": "analyzed-bargain",
+   "id": "massive-wheat",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1190,7 +1190,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "serious-carry",
+   "id": "suited-blank",
    "metadata": {},
    "source": [
     "The datasets used in the potential fitting procedure for day 2 (obtained from accurate DFT calculations) will be accessed in the same way"
@@ -1199,7 +1199,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "simple-packet",
+   "id": "standard-organic",
    "metadata": {},
    "outputs": [],
    "source": []