diff --git a/day_3/ex_01_validation.ipynb b/day_3/ex_01_validation.ipynb index fe459e28264b6fd98164df3302b45ea913d5d276..1a55c5f0e24e0705078a2caad2cb07e204f2360e 100644 --- a/day_3/ex_01_validation.ipynb +++ b/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": []