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pyiron
Potentials Workshop 2021
Commits
dc1cac58
Unverified
Commit
dc1cac58
authored
Mar 09, 2021
by
Sudarsan Surendralal
Committed by
GitHub
Mar 09, 2021
Browse files
Fix problem with notebook
parent
4d81b0fb
Changes
1
Hide whitespace changes
Inline
Side-by-side
day_3/ex_01_validation.ipynb
View file @
dc1cac58
...
...
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "markdown",
"id": "
weekly-printe
r",
"id": "
modified-armo
r",
"metadata": {},
"source": [
"# [**Workflows for atomistic simulations**](http://potentials.rub.de/) "
...
...
@@ -10,7 +10,7 @@
},
{
"cell_type": "markdown",
"id": "medi
cal-crazy
",
"id": "
im
medi
ate-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-matc
h",
"id": "
considered-widt
h",
"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": "d
esigning-tours
",
"id": "d
omestic-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-sapphir
e",
"id": "
intimate-mous
e",
"metadata": {},
"outputs": [
{
...
...
@@ -621,7 +621,7 @@
{
"cell_type": "code",
"execution_count": 12,
"id": "a
ttached-textbook
",
"id": "a
bstract-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": "g
reater-brain
",
"id": "g
enuine-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": "
no
te
d
-m
atter
",
"id": "
prosta
te-m
istress
",
"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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