Fix problem with notebook

day_3/ex_01_validation.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "weekly-printer",
+   "id": "modified-armor",
    "metadata": {},
    "source": [
     "# [**Workflows for atomistic simulations**](http://potentials.rub.de/) "
@@ -10,7 +10,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "medical-crazy",
+   "id": "immediate-glass",
    "metadata": {},
    "source": [
     "## **Day 3 - Validation of various potentials**\n",
@@ -30,7 +30,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ecological-affairs",
+   "id": "arbitrary-performance",
    "metadata": {},
    "source": [
     "## **Importing the modules and creating the project**"
@@ -39,7 +39,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "indie-synthesis",
+   "id": "peripheral-anime",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -52,7 +52,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "id": "lesser-match",
+   "id": "considered-width",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -62,7 +62,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "id": "regular-matthew",
+   "id": "tutorial-oklahoma",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -72,7 +72,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "convertible-purchase",
+   "id": "sixth-england",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -87,7 +87,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "id": "attractive-commodity",
+   "id": "charged-typing",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -109,7 +109,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "metropolitan-single",
+   "id": "proved-extent",
    "metadata": {},
    "source": [
     "## **Step 1: Get the equilibrium Cu lattice constant determined by the potentials**\n",
@@ -120,7 +120,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "reported-observer",
+   "id": "negative-motel",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -132,7 +132,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "id": "initial-reach",
+   "id": "variable-bidder",
    "metadata": {},
    "outputs": [
     {
@@ -279,7 +279,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "designing-tours",
+   "id": "domestic-reminder",
    "metadata": {},
    "outputs": [
     {
@@ -300,7 +300,7 @@
   {
    "cell_type": "code",
    "execution_count": 9,
-   "id": "turkish-librarian",
+   "id": "swedish-vertical",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -332,7 +332,7 @@
   {
    "cell_type": "code",
    "execution_count": 10,
-   "id": "systematic-tunnel",
+   "id": "parliamentary-bronze",
    "metadata": {},
    "outputs": [
     {
@@ -492,7 +492,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "chicken-roots",
+   "id": "brutal-smell",
    "metadata": {},
    "source": [
     "## **Compute elastic constants**\n",
@@ -503,7 +503,7 @@
   {
    "cell_type": "code",
    "execution_count": 11,
-   "id": "available-sapphire",
+   "id": "intimate-mouse",
    "metadata": {},
    "outputs": [
     {
@@ -621,7 +621,7 @@
   {
    "cell_type": "code",
    "execution_count": 12,
-   "id": "attached-textbook",
+   "id": "abstract-treasure",
    "metadata": {},
    "outputs": [
     {
@@ -645,7 +645,7 @@
   {
    "cell_type": "code",
    "execution_count": 13,
-   "id": "sticky-break",
+   "id": "juvenile-secondary",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -669,7 +669,7 @@
   {
    "cell_type": "code",
    "execution_count": 14,
-   "id": "architectural-composition",
+   "id": "silent-queensland",
    "metadata": {},
    "outputs": [
     {
@@ -805,7 +805,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "greater-brain",
+   "id": "genuine-princess",
    "metadata": {},
    "source": [
     "## **Compare computed elastic constants with that from DFT calculations**\n",
@@ -816,7 +816,7 @@
   {
    "cell_type": "code",
    "execution_count": 15,
-   "id": "third-combining",
+   "id": "positive-exclusion",
    "metadata": {},
    "outputs": [
     {
@@ -856,7 +856,7 @@
   {
    "cell_type": "code",
    "execution_count": 16,
-   "id": "knowing-despite",
+   "id": "asian-employment",
    "metadata": {},
    "outputs": [
     {
@@ -878,7 +878,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "heated-cleaning",
+   "id": "rubber-estate",
    "metadata": {},
    "source": [
     "## **Calculation of surface energies**\n",
@@ -889,7 +889,7 @@
   {
    "cell_type": "code",
    "execution_count": 17,
-   "id": "sapphire-station",
+   "id": "entire-trout",
    "metadata": {},
    "outputs": [
     {
@@ -952,7 +952,7 @@
   {
    "cell_type": "code",
    "execution_count": 18,
-   "id": "capable-calgary",
+   "id": "native-breach",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -976,7 +976,7 @@
   {
    "cell_type": "code",
    "execution_count": 19,
-   "id": "configured-joint",
+   "id": "tracked-renaissance",
    "metadata": {},
    "outputs": [
     {
@@ -1227,7 +1227,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "verbal-smith",
+   "id": "sunset-surface",
    "metadata": {},
    "source": [
     "Compute surface energies using data from the bulk fcc crystal"
@@ -1236,7 +1236,7 @@
   {
    "cell_type": "code",
    "execution_count": 20,
-   "id": "terminal-dream",
+   "id": "suitable-wichita",
    "metadata": {},
    "outputs": [
     {
@@ -1393,7 +1393,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "elementary-special",
+   "id": "important-berkeley",
    "metadata": {},
    "source": [
     "## **Finite temperature thermodynamics (Harmonic approximation)**\n",
@@ -1404,7 +1404,7 @@
   {
    "cell_type": "code",
    "execution_count": 21,
-   "id": "practical-proposal",
+   "id": "cardiac-black",
    "metadata": {},
    "outputs": [
     {
@@ -1447,7 +1447,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "novel-sussex",
+   "id": "comparative-concrete",
    "metadata": {},
    "source": [
     "Plotting the thermodynamic properties using phonopy"
@@ -1456,7 +1456,7 @@
   {
    "cell_type": "code",
    "execution_count": 22,
-   "id": "smaller-lyric",
+   "id": "least-trance",
    "metadata": {},
    "outputs": [
     {
@@ -1507,7 +1507,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "thirty-savings",
+   "id": "impaired-reception",
    "metadata": {},
    "source": [
     "We can also compute the phonon density of states and compare with that from benchmarked DFT calculations"
@@ -1516,7 +1516,7 @@
   {
    "cell_type": "code",
    "execution_count": 23,
-   "id": "rubber-football",
+   "id": "exclusive-prerequisite",
    "metadata": {},
    "outputs": [
     {
@@ -1546,7 +1546,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "royal-austria",
+   "id": "stable-northwest",
    "metadata": {},
    "source": [
     "## **Validating against original dataset**\n",
@@ -1557,19 +1557,19 @@
   {
    "cell_type": "code",
    "execution_count": 24,
-   "id": "documented-begin",
+   "id": "champion-wright",
    "metadata": {},
    "outputs": [],
    "source": [
-    "pr_import = Project("../datasets")\n",
+    "pr_import = Project(\"../datasets\")\n",
     "if len(pr_import.job_table()) == 0:\n",
-    "    pr_import.unpack("Cu_training_archive")"
+    "    pr_import.unpack(\"Cu_training_archive\")"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 25,
-   "id": "fitting-being",
+   "id": "exclusive-trick",
    "metadata": {},
    "outputs": [
     {
@@ -1731,7 +1731,7 @@
   {
    "cell_type": "code",
    "execution_count": 26,
-   "id": "noted-matter",
+   "id": "prostate-mistress",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1741,7 +1741,7 @@
   {
    "cell_type": "code",
    "execution_count": 27,
-   "id": "filled-squad",
+   "id": "shared-great",
    "metadata": {},
    "outputs": [
     {
@@ -1946,7 +1946,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "forty-signal",
+   "id": "explicit-memorabilia",
    "metadata": {},
    "source": [
     "Now we iterate over the structures in the dataset and compute the energies and forces for comparison"
@@ -1955,7 +1955,7 @@
   {
    "cell_type": "code",
    "execution_count": 28,
-   "id": "demanding-firmware",
+   "id": "positive-scanner",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1967,7 +1967,7 @@
   {
    "cell_type": "code",
    "execution_count": 29,
-   "id": "hindu-coordination",
+   "id": "worthy-couple",
    "metadata": {},
    "outputs": [
     {
@@ -2051,7 +2051,7 @@
   {
    "cell_type": "code",
    "execution_count": 30,
-   "id": "permanent-disposition",
+   "id": "wrapped-conference",
    "metadata": {},
    "outputs": [
     {
@@ -2097,7 +2097,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "related-shell",
+   "id": "international-worship",
    "metadata": {},
    "outputs": [],
    "source": []