Unverified Commit dc1cac58 authored by Sudarsan Surendralal's avatar Sudarsan Surendralal Committed by GitHub
Browse files

Fix problem with notebook

parent 4d81b0fb
......@@ -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": []
......
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