Commit 6514080a authored by Sudarsan Surendralal's avatar Sudarsan Surendralal
Browse files

Fixing notebook

parent d718b9d1
......@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "markdown",
"id": "starting-newfoundland",
"id": "greek-medicare",
"metadata": {},
"source": [
"# [**Workflows for atomistic simulations**](http://potentials.rub.de/) "
......@@ -10,7 +10,7 @@
},
{
"cell_type": "markdown",
"id": "ecological-produce",
"id": "champion-twins",
"metadata": {},
"source": [
"## **Day 1 - Atomistic simulations with [pyiron](https://pyiron.org)**\n",
......@@ -30,7 +30,7 @@
{
"cell_type": "code",
"execution_count": 1,
"id": "english-alias",
"id": "seeing-application",
"metadata": {},
"outputs": [],
"source": [
......@@ -42,7 +42,7 @@
{
"cell_type": "code",
"execution_count": 2,
"id": "defined-ethernet",
"id": "general-sensitivity",
"metadata": {},
"outputs": [],
"source": [
......@@ -53,7 +53,7 @@
{
"cell_type": "code",
"execution_count": 3,
"id": "blessed-batch",
"id": "corresponding-asset",
"metadata": {},
"outputs": [],
"source": [
......@@ -63,7 +63,7 @@
{
"cell_type": "code",
"execution_count": 4,
"id": "impressive-guest",
"id": "adequate-treasury",
"metadata": {},
"outputs": [],
"source": [
......@@ -73,7 +73,7 @@
{
"cell_type": "code",
"execution_count": 5,
"id": "standing-practitioner",
"id": "usual-characterization",
"metadata": {},
"outputs": [],
"source": [
......@@ -82,7 +82,7 @@
},
{
"cell_type": "markdown",
"id": "metric-deputy",
"id": "roman-possible",
"metadata": {},
"source": [
"## **Add structures from the E-V curves**"
......@@ -91,7 +91,7 @@
{
"cell_type": "code",
"execution_count": 6,
"id": "competitive-implementation",
"id": "above-sunrise",
"metadata": {},
"outputs": [],
"source": [
......@@ -103,7 +103,7 @@
{
"cell_type": "code",
"execution_count": 7,
"id": "southern-sharing",
"id": "revolutionary-response",
"metadata": {},
"outputs": [
{
......@@ -768,12 +768,12 @@
}
],
"source": [
"datasetainer.to_pandas()"
"container.to_pandas()"
]
},
{
"cell_type": "markdown",
"id": "derived-contributor",
"id": "still-western",
"metadata": {},
"source": [
"## **Add structures from the MD**\n",
......@@ -784,7 +784,7 @@
{
"cell_type": "code",
"execution_count": 8,
"id": "entertaining-gates",
"id": "accomplished-heart",
"metadata": {},
"outputs": [],
"source": [
......@@ -794,7 +794,7 @@
{
"cell_type": "code",
"execution_count": 9,
"id": "olympic-bottle",
"id": "finite-improvement",
"metadata": {},
"outputs": [],
"source": [
......@@ -807,7 +807,7 @@
},
{
"cell_type": "markdown",
"id": "correct-domain",
"id": "informational-helen",
"metadata": {},
"source": [
"## **Add some wierd structures (vacancies, surfaces, etc)**"
......@@ -816,14 +816,14 @@
{
"cell_type": "code",
"execution_count": 10,
"id": "weekly-reviewer",
"id": "fabulous-upset",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2021-03-05 11:22:33,348 - pyiron_log - WARNING - The job lammps_job_vac is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
"2021-03-06 08:30:54,890 - pyiron_log - WARNING - The job lammps_job_vac is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
]
}
],
......@@ -839,14 +839,14 @@
{
"cell_type": "code",
"execution_count": 11,
"id": "spanish-philippines",
"id": "smart-evanescence",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2021-03-05 11:22:37,456 - pyiron_log - WARNING - The job lammps_job_surf is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
"2021-03-06 08:30:56,197 - pyiron_log - WARNING - The job lammps_job_surf is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
]
}
],
......@@ -861,7 +861,7 @@
{
"cell_type": "code",
"execution_count": 12,
"id": "rotary-delay",
"id": "future-louis",
"metadata": {},
"outputs": [
{
......@@ -882,7 +882,7 @@
{
"cell_type": "code",
"execution_count": 13,
"id": "mysterious-kazakhstan",
"id": "former-marriage",
"metadata": {},
"outputs": [],
"source": [
......@@ -899,14 +899,14 @@
{
"cell_type": "code",
"execution_count": 14,
"id": "thermal-vegetarian",
"id": "genuine-booth",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2021-03-05 11:23:07,054 - pyiron_log - WARNING - The job dataset_example is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
"2021-03-06 08:31:06,560 - pyiron_log - WARNING - The job dataset_example is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
]
}
],
......@@ -917,7 +917,7 @@
{
"cell_type": "code",
"execution_count": 15,
"id": "incredible-broadcasting",
"id": "warming-intake",
"metadata": {},
"outputs": [
{
......@@ -1051,7 +1051,7 @@
{
"cell_type": "code",
"execution_count": 16,
"id": "resident-magnet",
"id": "physical-liverpool",
"metadata": {},
"outputs": [
{
......@@ -1631,8 +1631,8 @@
},
{
"cell_type": "code",
"execution_count": 19,
"id": "impaired-cycling",
"execution_count": 17,
"id": "female-thumb",
"metadata": {},
"outputs": [],
"source": [
......@@ -1641,8 +1641,8 @@
},
{
"cell_type": "code",
"execution_count": 21,
"id": "stock-sewing",
"execution_count": 18,
"id": "standard-whale",
"metadata": {},
"outputs": [],
"source": [
......@@ -1652,7 +1652,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "tracked-halifax",
"id": "worldwide-freight",
"metadata": {},
"outputs": [],
"source": []
......
%% Cell type:markdown id:starting-newfoundland tags:
%% Cell type:markdown id:greek-medicare tags:
# [**Workflows for atomistic simulations**](http://potentials.rub.de/)
%% Cell type:markdown id:ecological-produce tags:
%% Cell type:markdown id:champion-twins tags:
## **Day 1 - Atomistic simulations with [pyiron](https://pyiron.org)**
### **Exercise 2: Creating and working with structure databases**
Before the excercise, you should:
* Finish exercises 1 and 2
The aim of this exercise is to make you familiar with:
* Creating structure databases and working with them for potential fitting (day 2)
%% Cell type:code id:english-alias tags:
%% Cell type:code id:seeing-application tags:
``` python
import numpy as np
%matplotlib inline
import matplotlib.pylab as plt
```
%% Cell type:code id:defined-ethernet tags:
%% Cell type:code id:general-sensitivity tags:
``` python
from pyiron import Project
import pyiron_contrib
```
%% Cell type:code id:blessed-batch tags:
%% Cell type:code id:corresponding-asset tags:
``` python
pr = Project("creating_datasets")
```
%% Cell type:code id:impressive-guest tags:
%% Cell type:code id:adequate-treasury tags:
``` python
pr_fs = pr["../first_steps"]
```
%% Cell type:code id:standing-practitioner tags:
%% Cell type:code id:usual-characterization tags:
``` python
container = pr.create.job.TrainingContainer('dataset_example')
```
%% Cell type:markdown id:metric-deputy tags:
%% Cell type:markdown id:roman-possible tags:
## **Add structures from the E-V curves**
%% Cell type:code id:competitive-implementation tags:
%% Cell type:code id:above-sunrise tags:
``` python
for job in pr_fs["E_V_curve"].iter_jobs(status="finished"):
container.include_job(job, iteration_step=-1)
```
%% Cell type:code id:southern-sharing tags:
%% Cell type:code id:revolutionary-response tags:
``` python
datasetainer.to_pandas()
container.to_pandas()
```
%%%% Output: execute_result
name \
0 None
1 None
2 None
3 None
4 None
5 None
6 None
7 None
8 None
9 None
10 None
11 None
12 None
13 None
14 None
15 None
16 None
17 None
18 None
19 None
20 None
21 None
22 None
23 None
24 None
25 None
26 None
27 None
28 None
29 None
30 None
31 None
32 None
33 None
34 None
35 None
36 None
37 None
38 None
39 None
40 job_a_3_4
41 job_a_3_5
42 job_a_3_6
43 job_a_3_7
44 job_a_3_8
45 job_a_3_9
46 job_a_4_0
atoms \
0 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
1 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
2 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
3 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
4 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
5 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
6 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
7 (Atom('Cu', [0.0, 0.0, 0.0], index=0), Atom('Cu', [0.0, 1.8049999999995918, 1.804999999999592], index=1), Atom('Cu', [1.8049999999995918, 1.1052437362302365e-16, 1.804999999999592], index=2), Atom...
8 (Atom('Cu', [0.140426153531212, 11.00934611760493, 10.968207696001379], index=0), Atom('Cu', [10.983357200359302, 1.779939365335074, 1.7146804782560905], index=1), Atom('Cu', [2.1228644677344763, ...
9 (Atom('Cu', [0.1407579358923329, 11.020287239626356, 10.855878337455094], index=0), Atom('Cu', [0.29542104007972325, 1.6514729828183248, 1.7760939949715002], index=1), Atom('Cu', [1.99578258187561...
10 (Atom('Cu', [0.04675277832683521, 10.951786003502875, 0.20014601215416555], index=0), Atom('Cu', [0.08453269827616121, 1.807218974303731, 1.7664733621606055], index=1), Atom('Cu', [1.9597357123378...
11 (Atom('Cu', [10.991332780892245, 11.027168829788469, 0.17044757336885022], index=0), Atom('Cu', [10.869778028731718, 1.9053524080340238, 1.7569642307109068], index=1), Atom('Cu', [1.89027128290555...
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22 (Atom('Cu', [10.827044041159013, 1.814885520198166, 2.1241909251750846], index=0), Atom('Cu', [1.6679142700199647, 0.1106240807045643, 1.629401459425781], index=1), Atom('Cu', [1.29418686613977, 2...
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46 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
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forces \
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1 [[-1.92404082484227e-16, 4.231084758750405e-17, 3.6193775346684653e-17]]
2 [[-2.9113397169423695e-17, 7.54965057835309e-17, -3.624419431643654e-17]]
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4 [[-2.0545362501508919e-16, -3.5486130576273854e-17, 3.5486130576273854e-17]]
5 [[1.6101257219667079e-16, -4.2948421129906387e-17, 4.2948421129906387e-17]]
6 [[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]]
7 [[-1.2656542480726799e-14, -1.46965772884755e-14, -1.61017033040167e-14], [-1.3905543383430098e-14, 4.5310977192514186e-15, 4.8333732849403796e-15], [4.9682480351975795e-15, -1.4072076837123899e-1...
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10 [[-0.32237334386615796, 0.43406651671724894, -0.5886238546572939], [-0.6295919499998729, 0.07530471384300086, -0.12687342568230403], [-0.06506588733991228, 0.8782024477953109, -0.12243680387297393...
11 [[0.45078377546738896, -0.7167806257867769, -0.320969733282763], [0.5707773027838049, -0.5494069530705199, 0.510256621543289], [-0.36439749359274193, 0.17709586752044496, 0.23127352998569298], [0....
12 [[-0.38409855462219894, 0.12077975249818296, 0.024465771201292483], [-0.6560764999451358, -1.05845756801878, -0.658182913095082], [-0.5103420261962529, -0.35656271154938, 0.7090309519821769], [-0....
13 [[0.22044015995668098, -0.2607278388818459, -0.3855032322190499], [0.7754186544660099, -0.04652340102386694, -0.26232164996063695], [0.43147792874898694, -0.9840256256911009, 0.34987911571105595],...
14 [[-0.5020206209676749, 0.007307596544171969, 0.24586848661916993], [-1.1645196400331899, 0.1476285180684419, 0.6168850904586589], [0.7183114431792579, -0.5420093171036479, -0.06687387962480258], [...
15 [[0.04806202889719739, 0.48969724353819394, 1.29371057615331], [0.5538169933185199, -0.7855310261714289, -0.033081946412792815], [0.34832740609982993, 0.9937361742308158, 0.30650548838004904], [-0...
16 [[0.24033044872062098, 1.5305792677179897, -0.6791236163119347], [0.05903491332573559, 0.148151392595253, 0.542468964409148], [0.07921843405670739, 0.145966157214324, 0.7342269238916159], [0.77503...
17 [[-0.13926025211222698, -0.0920021629424733, 0.21001691285267599], [0.6767944835284789, -1.1148612203782198, 1.7165284718417098], [-0.7950973845960859, 0.2356681337270629, 0.13328556064538893], [0...
18 [[-1.3933298959045699e-14, -0.10827842091784899, -0.108278420917849], [-0.10827842091784899, -1.3877479054990188e-14, -0.108278420917849], [-0.10827842091784899, -0.108278420917849, -1.38424758326...
19 [[-0.45079778130218695, 0.19236747741170795, 0.23614131969524693], [1.2984317307784499, 0.04751568933291938, 0.005443425577977482], [0.48875760189522893, -0.5765163470127929, -0.5531364786691719],...
20 [[-0.6920262907044069, 0.3986975029533409, 0.10738641941643497], [-1.2097205794553298, -2.21423543020926, -0.8363385508172672], [-0.36839592956658596, 0.35919893904268096, 0.09738195090664269], [2...
21 [[0.5607305368018309, 0.07454461225822963, 0.17092757180402804], [0.7460358156721709, -0.9693709228665989, -0.357775642488428], [-1.4982109077380097, 1.0695224870660298, 0.17016025464137993], [1.1...
22 [[0.7768634672312369, 0.615614277472231, -0.6520778674544528], [0.5196497874591819, -0.7614150189249069, 0.33452284258026094], [1.0185593798470798, 0.11349094338622906, -1.1138567887728799], [0.39...
23 [[-1.2511641505681497, 0.045660252990561916, 0.39426999337691987], [-0.4923847861277789, -0.676187288680257, -1.3802167704923], [-0.12072100498159098, 0.5666924914439229, -0.8825937576849239], [0....
24 [[0.5080309295986539, -0.4875222169174689, 0.46898176405272696], [0.11031309252296198, -0.7243436014688799, 1.2808414836059598], [0.6855285827079979, 0.576817447055947, 0.31599931473888204], [0.50...
25 [[-0.6923371397061229, 0.9615117892959398, 0.396261839433264], [0.18083100499512797, -0.47103552335731996, 0.5072798013711759], [-0.22735248831930896, 0.37011177620569996, -1.1740345740817597], [0...
26 [[0.46940172398488794, 0.557542533896084, 0.861383405261689], [-0.16043498489103097, -1.0997839627759998, -0.013974118313924476], [-0.13554483762266598, 0.6363641149062679, 0.153788969879775], [1....
27 [[-1.1653987834207897, -0.07515193371140247, -0.13414295102360305], [0.17707911646472896, 0.37588362216028093, 0.10312993516925903], [0.6003632691780849, 0.3869695806628, 0.03431754153949555], [-0...
28 [[0.42819147658911194, -1.3404675072584398, -0.840042992949223], [0.47822853532413195, -0.07949121681390955, -0.36737406099153697], [-0.9172012989939929, 0.3239785862266829, -0.013009375610539234]...
29 [[-8.770761894538741e-15, 1.15657750043852e-09, 0.109956784695642], [-1.0824674490095302e-15, 1.15657515335765e-09, 0.10995678469564], [2.4308896909297503e-15, 1.1565748914144101e-09, 0.1099567846...
30 [[-0.570999988178131, 1.09833300989089, -0.566585257198732], [-0.0492000252908114, 0.597416506778632, 0.966635869516025], [-0.0024866801464792, -0.0674126479000064, 0.2546322145358], [0.2289085885...
31 [[-0.555658749547497, 0.42566314828364993, 0.466167261187443], [-1.39449792316952, -0.5017985009363372, 0.4456531170887249], [1.25410857633035, -0.33111996310077596, -0.24658722383829995], [0.3911...
32 [[0.550884754551829, 0.33865983742272204, 0.12042096866985205], [0.189727589275692, -0.524367356684999, -0.17886090450862402], [-1.6758650723099, -0.31030261483377614, 0.6946509585213989], [0.4453...
33 [[0.235449441284142, 0.601163461325591, 0.04737458109310825], [0.337344266123105, 0.66485729403382, 0.37768738132523805], [-0.171831038530166, -0.11286098093109101, -0.07415135874528352], [-0.1966...
34 [[1.15453322332565, 0.04603660924771737, -1.21282260887155], [-0.403390913673288, -0.18969536874868004, 0.030526533198225264], [-0.683024325114862, -0.967333273082708, 0.4114320467737619], [-0.867...
35 [[0.742004122721361, 0.22577315893502206, 0.12298868177971806], [0.771069504028052, -0.90014541931557, -0.660403448738781], [-0.462456173466872, 1.24796716628589, -0.4192010350460109], [0.08219110...
36 [[0.552749731038993, -0.46087407707755496, 0.177277816519943], [0.340079509783844, 0.23574679643440802, 0.26784307872713603], [0.388298578408562, 0.331969932822417, 0.34399524632239104], [-0.59826...
37 [[0.570532228156976, 0.17193739345012202, 0.796311675035985], [0.67297011060888, -0.81773224395498, 0.207420342553107], [0.391385096561351, -0.862073619446019, 0.597813478897486], [-0.270452726779...
38 [[-1.11093024791963, -0.6986058376048401, 0.44674121624886787], [0.0416051560041239, -0.0424634970331458, -0.0874515615419252], [-0.135122617155289, -0.778975629913174, -1.04402814519501], [0.8442...
39 [[-0.645092069902244, 0.04920122139904896, 0.21081031345366397], [1.14893686034324, -0.6114894792387109, -0.40665475671972495], [-0.287092609914331, 0.292443458702414, -0.801010316546939], [-0.184...
40 [[1.1869253621046177e-16, -1.7429070520896771e-16, -1.397277865277868e-16]]
41 [[-1.92404082484227e-16, 4.231084758750405e-17, 3.6193775346684653e-17]]
42 [[-2.9113397169423695e-17, 7.54965057835309e-17, -3.624419431643654e-17]]
43 [[3.771496125435321e-17, 3.412312546579927e-17, -2.4310047599025677e-17]]
44 [[-2.0545362501508919e-16, -3.5486130576273854e-17, 3.5486130576273854e-17]]
45 [[1.6101257219667079e-16, -4.2948421129906387e-17, 4.2948421129906387e-17]]
46 [[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]]
number_of_atoms
0 1.0
1 1.0
2 1.0
3 1.0
4 1.0
5 1.0
6 1.0
7 108.0
8 108.0
9 108.0
10 108.0
11 108.0
12 108.0
13 108.0
14 108.0
15 108.0
16 108.0
17 108.0
18 107.0
19 107.0
20 107.0
21 107.0
22 107.0
23 107.0
24 107.0
25 107.0
26 107.0
27 107.0
28 107.0
29 128.0
30 128.0
31 128.0
32 128.0
33 128.0
34 128.0
35 128.0
36 128.0
37 128.0
38 128.0
39 128.0
40 1.0
41 1.0
42 1.0
43 1.0
44 1.0
45 1.0
46 1.0
%% Cell type:markdown id:derived-contributor tags:
%% Cell type:markdown id:still-western tags:
## **Add structures from the MD**
Structures sampled every 10 snapshots (we may need to minimize the structures from the MD)
%% Cell type:code id:entertaining-gates tags:
%% Cell type:code id:accomplished-heart tags:
``` python
job_md = pr_fs["lammps_job"]
```
%% Cell type:code id:olympic-bottle tags:
%% Cell type:code id:finite-improvement tags:
``` python
traj_length = len(job_md["output/generic/positions"])
stride = 10
for i in range(0, traj_length, stride):
container.include_job(job_md, iteration_step=i)
```
%% Cell type:markdown id:correct-domain tags:
%% Cell type:markdown id:informational-helen tags:
## **Add some wierd structures (vacancies, surfaces, etc)**
%% Cell type:code id:weekly-reviewer tags:
%% Cell type:code id:fabulous-upset tags:
``` python
job_lammps = pr.create.job.Lammps("lammps_job_vac")
job_lammps.structure = pr.create_ase_bulk('Cu', cubic=True, a=3.61).repeat([3, 3, 3])
del job_lammps.structure[0]
job_lammps.potential = '2012--Mendelev-M-I--Cu--LAMMPS--ipr1'
job_lammps.calc_md(temperature=800, pressure=0, n_ionic_steps=10000)
job_lammps.run()
```
%%%% Output: stream
2021-03-05 11:22:33,348 - pyiron_log - WARNING - The job lammps_job_vac is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'
2021-03-06 08:30:54,890 - pyiron_log - WARNING - The job lammps_job_vac is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'
%% Cell type:code id:spanish-philippines tags:
%% Cell type:code id:smart-evanescence tags:
``` python
job_lammps = pr.create.job.Lammps("lammps_job_surf")
job_lammps.structure = pr.create_surface("Cu", surface_type="fcc111", size=(4, 4, 8), vacuum=12, orthogonal=True)
job_lammps.potential = '2012--Mendelev-M-I--Cu--LAMMPS--ipr1'
job_lammps.calc_md(temperature=800, pressure=0, n_ionic_steps=10000)
job_lammps.run()
```
%%%% Output: stream
2021-03-05 11:22:37,456 - pyiron_log - WARNING - The job lammps_job_surf is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'
2021-03-06 08:30:56,197 - pyiron_log - WARNING - The job lammps_job_surf is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'
%% Cell type:code id:rotary-delay tags:
%% Cell type:code id:future-louis tags:
``` python
pr
```
%%%% Output: execute_result
{'groups': ['tc'], 'nodes': ['lammps_job_vac', 'lammps_job_surf', 'dataset_example']}
%% Cell type:code id:mysterious-kazakhstan tags:
%% Cell type:code id:former-marriage tags:
``` python
for job_md in pr.iter_jobs(convert_to_object=True, status="finished"):
# only check Lammps jobs
pos = job_md["output/generic/positions"]
if pos is not None:
traj_length = len(pos)
stride = 10
for i in range(0, traj_length, stride):
container.include_job(job_md, iteration_step=i)
```
%% Cell type:code id:thermal-vegetarian tags:
%% Cell type:code id:genuine-booth tags:
``` python
container.run()
```
%%%% Output: stream
2021-03-05 11:23:07,054 - pyiron_log - WARNING - The job dataset_example is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'
2021-03-06 08:31:06,560 - pyiron_log - WARNING - The job dataset_example is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'
%% Cell type:code id:incredible-broadcasting tags:
%% Cell type:code id:warming-intake tags:
``` python
pr.job_table()
```
%%%% Output: execute_result
id status chemicalformula job subjob \
0 4332 finished Cu107 lammps_job_vac /lammps_job_vac
1 4333 finished Cu128 lammps_job_surf /lammps_job_surf
2 4334 finished None dataset_example /dataset_example
projectpath project \
0 /home/surendralal/ notebooks/pyiron_potentialfit/day_1/creating_datasets/
1 /home/surendralal/ notebooks/pyiron_potentialfit/day_1/creating_datasets/
2 /home/surendralal/ notebooks/pyiron_potentialfit/day_1/creating_datasets/
timestart timestop totalcputime \
0 2021-03-04 15:54:10.622737 2021-03-04 15:54:15.859551 5.0
1 2021-03-04 15:54:16.720902 2021-03-04 15:54:21.579389 4.0
2 2021-03-04 15:54:23.919785 NaT NaN
computer hamilton hamversion parentid masterid
0 pyiron@cmdell17#1 Lammps 0.1 None None
1 pyiron@cmdell17#1 Lammps 0.1 None None
2 pyiron@cmdell17#1 TrainingContainer 0.4 None None
%% Cell type:code id:resident-magnet tags:
%% Cell type:code id:physical-liverpool tags:
``` python
dataset = pr["dataset_example"]
dataset.to_pandas()
```
%%%% Output: execute_result
name \
0 None
1 None
2 None
3 None
4 None
5 None
6 None
7 None
8 None
9 None
10 None
11 None
12 None
13 None
14 None
15 None
16 None
17 None
18 None
19 None
20 None
21 None
22 None
23 None
24 None
25 None
26 None
27 None
28 None
29 None
30 None
31 None
32 None
33 None
34 None
35 None
36 None
37 None
38 None
39 None
atoms \
0 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
1 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
2 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
3 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
4 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
5 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
6 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
7 (Atom('Cu', [0.0, 0.0, 0.0], index=0), Atom('Cu', [0.0, 1.8049999999995918, 1.804999999999592], index=1), Atom('Cu', [1.8049999999995918, 1.1052437362302365e-16, 1.804999999999592], index=2), Atom...
8 (Atom('Cu', [0.140426153531212, 11.00934611760493, 10.968207696001379], index=0), Atom('Cu', [10.983357200359302, 1.779939365335074, 1.7146804782560905], index=1), Atom('Cu', [2.1228644677344763, ...
9 (Atom('Cu', [0.1407579358923329, 11.020287239626356, 10.855878337455094], index=0), Atom('Cu', [0.29542104007972325, 1.6514729828183248, 1.7760939949715002], index=1), Atom('Cu', [1.99578258187561...
10 (Atom('Cu', [0.04675277832683521, 10.951786003502875, 0.20014601215416555], index=0), Atom('Cu', [0.08453269827616121, 1.807218974303731, 1.7664733621606055], index=1), Atom('Cu', [1.9597357123378...
11 (Atom('Cu', [10.991332780892245, 11.027168829788469, 0.17044757336885022], index=0), Atom('Cu', [10.869778028731718, 1.9053524080340238, 1.7569642307109068], index=1), Atom('Cu', [1.89027128290555...
12 (Atom('Cu', [10.958070767872973, 0.05270018288525903, 11.015795828313184], index=0), Atom('Cu', [0.04540970504125744, 2.0780519854689388, 1.8353871076994486], index=1), Atom('Cu', [1.8285627799497...
13 (Atom('Cu', [10.903697402270481, 10.843249424147054, 0.09574490333935876], index=0), Atom('Cu', [10.594918916668115, 1.7187193807013557, 1.957301113531466], index=1), Atom('Cu', [1.676074002401865...
14 (Atom('Cu', [0.25841198959969514, 0.07063449316617948, 10.912283030401635], index=0), Atom('Cu', [0.19649020014428978, 1.7891621064498946, 1.803181486480956], index=1), Atom('Cu', [1.7493171890008...
15 (Atom('Cu', [0.004994793789590358, 10.985055637636528, 10.904222762438215], index=0), Atom('Cu', [10.941729664004177, 1.8868614122932958, 1.8147512571785023], index=1), Atom('Cu', [1.8438031255437...
16 (Atom('Cu', [0.03645923830333788, 10.856010693932728, 10.970572990196315], index=0), Atom('Cu', [10.913522535008392, 1.8161914381204696, 1.5447581077411967], index=1), Atom('Cu', [1.77583933019795...
17 (Atom('Cu', [0.009767181825404037, 0.0071865231528328395, 11.0089023992238], index=0), Atom('Cu', [10.89374596605574, 1.9969194212313586, 1.595578837066423], index=1), Atom('Cu', [2.05442192913884...
18 (Atom('Cu', [0.0, 1.8049999999995918, 1.804999999999592], index=0), Atom('Cu', [1.8049999999995918, 1.1052437362302365e-16, 1.804999999999592], index=1), Atom('Cu', [1.8049999999995918, 1.80499999...
19 (Atom('Cu', [0.10390109091492504, 1.9580560553035629, 1.779188560767685], index=0), Atom('Cu', [1.3868099266682106, 10.93717630776342, 1.601790948781396], index=1), Atom('Cu', [1.7183987889409966,...
20 (Atom('Cu', [0.2223234793002756, 1.6999920633404135, 1.7623980235259114], index=0), Atom('Cu', [2.122882660879041, 0.18624238423025943, 2.030808683988878], index=1), Atom('Cu', [1.7334689484700414...
21 (Atom('Cu', [10.839434974930338, 1.9008464900018593, 1.6867963294684278], index=0), Atom('Cu', [1.5876598581358559, 0.15447557118789498, 1.715299994817798], index=1), Atom('Cu', [2.148606011735498...
22 (Atom('Cu', [10.827044041159013, 1.814885520198166, 2.1241909251750846], index=0), Atom('Cu', [1.6679142700199647, 0.1106240807045643, 1.629401459425781], index=1), Atom('Cu', [1.29418686613977, 2...
23 (Atom('Cu', [0.18579648605077317, 1.6025971043596021, 1.8725196193757527], index=0), Atom('Cu', [2.0480835165906024, 0.055238510607153124, 2.258841094259334], index=1), Atom('Cu', [1.8423446841272...
24 (Atom('Cu', [10.902653792490328, 1.9016481867720487, 1.712386801004505], index=0), Atom('Cu', [1.6843656295425262, 0.20454959542790652, 1.4940727709027473], index=1), Atom('Cu', [1.628967729295861...
25 (Atom('Cu', [0.2202511036922136, 1.5872348575607442, 1.7623998700282655], index=0), Atom('Cu', [1.8386689358546338, 10.988833155546024, 1.8571406735818983], index=1), Atom('Cu', [1.976390891645592...
26 (Atom('Cu', [10.746144724861097, 1.6561216261540705, 1.6676063346982197], index=0), Atom('Cu', [1.8697696006277247, 0.29566102043388925, 1.9071090181664805], index=1), Atom('Cu', [1.82013088394316...
27 (Atom('Cu', [0.17063059290766686, 1.8534187978406447, 1.7423748775395635], index=0), Atom('Cu', [1.8595651370150335, 10.90572322929213, 1.810598025463111], index=1), Atom('Cu', [1.934651223968069,...
28 (Atom('Cu', [10.866365842640102, 1.8491297818376022, 2.093244182315977], index=0), Atom('Cu', [1.7536272335648937, 10.898985481755824, 1.8241252890179567], index=1), Atom('Cu', [1.994555230114336,...
29 (Atom('Cu', [0.0, 1.4737763285740602, 9.024277317236803e-17], index=0), Atom('Cu', [2.5526554800834376, 1.4737763285740604, 2.4654784132287465e-16], index=1), Atom('Cu', [5.105310960166875, 1.4737...
30 (Atom('Cu', [0.4126496185424086, 0.9553642998076769, 0.12158924761653131], index=0), Atom('Cu', [2.831118842513476, 1.0700158216349893, 25.916922304272767], index=1), Atom('Cu', [5.314789299948389...
31 (Atom('Cu', [10.151562776611806, 1.6587733567107183, 26.43035938894712], index=0), Atom('Cu', [2.5212828819853748, 1.9070842851152785, 26.36203940098048], index=1), Atom('Cu', [4.715098279443367, ...
32 (Atom('Cu', [0.19573901040697333, 1.051460534941847, 26.530022925039237], index=0), Atom('Cu', [2.995726956631421, 1.1546751485293076, 26.840478692293868], index=1), Atom('Cu', [5.923947432763936,...
33 (Atom('Cu', [9.888379625890167, 1.4968159202602271, 26.58551059472236], index=0), Atom('Cu', [2.207544057015841, 1.290074245861123, 26.685466830386254], index=1), Atom('Cu', [4.939145903748478, 1....
34 (Atom('Cu', [0.3429326290376805, 1.5170285327525175, 0.14896315086845416], index=0), Atom('Cu', [3.129345868860857, 1.495102964861245, 0.01607848650845961], index=1), Atom('Cu', [5.714332108258016...
35 (Atom('Cu', [9.95801241508363, 1.4359511579313753, 26.639342243648862], index=0), Atom('Cu', [2.2681416259098204, 1.7861270127574713, 0.0041936446239185], index=1), Atom('Cu', [5.074253116948648, ...
36 (Atom('Cu', [10.225027496779227, 1.7848555655274232, 26.42388292769549], index=0), Atom('Cu', [2.4914869938632442, 1.861119175102061, 26.64826771541495], index=1), Atom('Cu', [4.968442272624181, 1...
37 (Atom('Cu', [10.188116701703345, 1.3482529143763475, 26.353847647582224], index=0), Atom('Cu', [2.4559442807081986, 1.4757747059762696, 26.57379282025388], index=1), Atom('Cu', [5.077086561123585,...
38 (Atom('Cu', [10.165259029706933, 1.7122531598094173, 26.335638965295193], index=0), Atom('Cu', [2.3513330869200098, 1.5487334168655387, 26.34258116233103], index=1), Atom('Cu', [4.95573138146394, ...
39 (Atom('Cu', [0.36893784059756035, 1.481831927531004, 26.53504700964859], index=0), Atom('Cu', [2.6965712181950883, 1.488812429574298, 26.730123522873537], index=1), Atom('Cu', [5.668661292604278, ...
energy \
0 -3.142019
1 -3.338596
2 -3.416929
3 -3.409602
4 -3.330215
5 -3.195118
6 -3.035358
7 -347.182406
8 -348.253665
9 -345.424528
10 -346.758349
11 -344.603627
12 -346.849801
13 -345.015235
14 -346.569097
15 -344.892954
16 -347.628843
17 -345.776979
18 -342.906251
19 -343.569002
20 -343.317892
21 -341.057270
22 -342.067006
23 -342.528496
24 -342.900954
25 -340.983380
26 -342.479965
27 -340.174298
28 -343.805462
29 -400.111422
30 -399.591699
31 -398.422617
32 -395.110340
33 -396.833326
34 -400.444368
35 -397.843043
36 -399.776798
37 -399.168074
38 -396.984690
39 -399.581912
forces \
0 [[1.1869253621046177e-16, -1.7429070520896771e-16, -1.397277865277868e-16]]
1 [[-1.92404082484227e-16, 4.231084758750405e-17, 3.6193775346684653e-17]]
2 [[-2.9113397169423695e-17, 7.54965057835309e-17, -3.624419431643654e-17]]
3 [[3.771496125435321e-17, 3.412312546579927e-17, -2.4310047599025677e-17]]
4 [[-2.0545362501508919e-16, -3.5486130576273854e-17, 3.5486130576273854e-17]]
5 [[1.6101257219667079e-16, -4.2948421129906387e-17, 4.2948421129906387e-17]]
6 [[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]]
7 [[-1.2656542480726799e-14, -1.46965772884755e-14, -1.61017033040167e-14], [-1.3905543383430098e-14, 4.5310977192514186e-15, 4.8333732849403796e-15], [4.9682480351975795e-15, -1.4072076837123899e-1...
8 [[-0.21910202935187897, -0.37573419410584397, 0.43392575377979187], [0.16208168404695897, -0.00671505675904709, 1.03458554920361], [-1.2001630139266497, -0.40207322348963503, -0.45620473735655703]...
9 [[-0.023031834879881696, 0.042841438691562095, 0.5899774836434479], [-0.5418151518759569, 0.6754733604036028, -0.5582999589284809], [-0.6011411771360858, -0.355590065329821, -0.0035901986306415582...
10 [[-0.32237334386615796, 0.43406651671724894, -0.5886238546572939], [-0.6295919499998729, 0.07530471384300086, -0.12687342568230403], [-0.06506588733991228, 0.8782024477953109, -0.12243680387297393...
11 [[0.45078377546738896, -0.7167806257867769, -0.320969733282763], [0.5707773027838049, -0.5494069530705199, 0.510256621543289], [-0.36439749359274193, 0.17709586752044496, 0.23127352998569298], [0....
12 [[-0.38409855462219894, 0.12077975249818296, 0.024465771201292483], [-0.6560764999451358, -1.05845756801878, -0.658182913095082], [-0.5103420261962529, -0.35656271154938, 0.7090309519821769], [-0....
13 [[0.22044015995668098, -0.2607278388818459, -0.3855032322190499], [0.7754186544660099, -0.04652340102386694, -0.26232164996063695], [0.43147792874898694, -0.9840256256911009, 0.34987911571105595],...
14 [[-0.5020206209676749, 0.007307596544171969, 0.24586848661916993], [-1.1645196400331899, 0.1476285180684419, 0.6168850904586589], [0.7183114431792579, -0.5420093171036479, -0.06687387962480258], [...
15 [[0.04806202889719739, 0.48969724353819394, 1.29371057615331], [0.5538169933185199, -0.7855310261714289, -0.033081946412792815], [0.34832740609982993, 0.9937361742308158, 0.30650548838004904], [-0...
16 [[0.24033044872062098, 1.5305792677179897, -0.6791236163119347], [0.05903491332573559, 0.148151392595253, 0.542468964409148], [0.07921843405670739, 0.145966157214324, 0.7342269238916159], [0.77503...
17 [[-0.13926025211222698, -0.0920021629424733, 0.21001691285267599], [0.6767944835284789, -1.1148612203782198, 1.7165284718417098], [-0.7950973845960859, 0.2356681337270629, 0.13328556064538893], [0...
18 [[-1.3933298959045699e-14, -0.10827842091784899, -0.108278420917849], [-0.10827842091784899, -1.3877479054990188e-14, -0.108278420917849], [-0.10827842091784899, -0.108278420917849, -1.38424758326...
19 [[-0.45079778130218695, 0.19236747741170795, 0.23614131969524693], [1.2984317307784499, 0.04751568933291938, 0.005443425577977482], [0.48875760189522893, -0.5765163470127929, -0.5531364786691719],...
20 [[-0.6920262907044069, 0.3986975029533409, 0.10738641941643497], [-1.2097205794553298, -2.21423543020926, -0.8363385508172672], [-0.36839592956658596, 0.35919893904268096, 0.09738195090664269], [2...
21 [[0.5607305368018309, 0.07454461225822963, 0.17092757180402804], [0.7460358156721709, -0.9693709228665989, -0.357775642488428], [-1.4982109077380097, 1.0695224870660298, 0.17016025464137993], [1.1...
22 [[0.7768634672312369, 0.615614277472231, -0.6520778674544528], [0.5196497874591819, -0.7614150189249069, 0.33452284258026094], [1.0185593798470798, 0.11349094338622906, -1.1138567887728799], [0.39...
23 [[-1.2511641505681497, 0.045660252990561916, 0.39426999337691987], [-0.4923847861277789, -0.676187288680257, -1.3802167704923], [-0.12072100498159098, 0.5666924914439229, -0.8825937576849239], [0....
24 [[0.5080309295986539, -0.4875222169174689, 0.46898176405272696], [0.11031309252296198, -0.7243436014688799, 1.2808414836059598], [0.6855285827079979, 0.576817447055947, 0.31599931473888204], [0.50...
25 [[-0.6923371397061229, 0.9615117892959398, 0.396261839433264], [0.18083100499512797, -0.47103552335731996, 0.5072798013711759], [-0.22735248831930896, 0.37011177620569996, -1.1740345740817597], [0...
26 [[0.46940172398488794, 0.557542533896084, 0.861383405261689], [-0.16043498489103097, -1.0997839627759998, -0.013974118313924476], [-0.13554483762266598, 0.6363641149062679, 0.153788969879775], [1....
27 [[-1.1653987834207897, -0.07515193371140247, -0.13414295102360305], [0.17707911646472896, 0.37588362216028093, 0.10312993516925903], [0.6003632691780849, 0.3869695806628, 0.03431754153949555], [-0...
28 [[0.42819147658911194, -1.3404675072584398, -0.840042992949223], [0.47822853532413195, -0.07949121681390955, -0.36737406099153697], [-0.9172012989939929, 0.3239785862266829, -0.013009375610539234]...
29 [[-8.770761894538741e-15, 1.15657750043852e-09, 0.109956784695642], [-1.0824674490095302e-15, 1.15657515335765e-09, 0.10995678469564], [2.4308896909297503e-15, 1.1565748914144101e-09, 0.1099567846...
30 [[-0.570999988178131, 1.09833300989089, -0.566585257198732], [-0.0492000252908114, 0.597416506778632, 0.966635869516025], [-0.0024866801464792, -0.0674126479000064, 0.2546322145358], [0.2289085885...
31 [[-0.555658749547497, 0.42566314828364993, 0.466167261187443], [-1.39449792316952, -0.5017985009363372, 0.4456531170887249], [1.25410857633035, -0.33111996310077596, -0.24658722383829995], [0.3911...
32 [[0.550884754551829, 0.33865983742272204, 0.12042096866985205], [0.189727589275692, -0.524367356684999, -0.17886090450862402], [-1.6758650723099, -0.31030261483377614, 0.6946509585213989], [0.4453...
33 [[0.235449441284142, 0.601163461325591, 0.04737458109310825], [0.337344266123105, 0.66485729403382, 0.37768738132523805], [-0.171831038530166, -0.11286098093109101, -0.07415135874528352], [-0.1966...
34 [[1.15453322332565, 0.04603660924771737, -1.21282260887155], [-0.403390913673288, -0.18969536874868004, 0.030526533198225264], [-0.683024325114862, -0.967333273082708, 0.4114320467737619], [-0.867...
35 [[0.742004122721361, 0.22577315893502206, 0.12298868177971806], [0.771069504028052, -0.90014541931557, -0.660403448738781], [-0.462456173466872, 1.24796716628589, -0.4192010350460109], [0.08219110...
36 [[0.552749731038993, -0.46087407707755496, 0.177277816519943], [0.340079509783844, 0.23574679643440802, 0.26784307872713603], [0.388298578408562, 0.331969932822417, 0.34399524632239104], [-0.59826...
37 [[0.570532228156976, 0.17193739345012202, 0.796311675035985], [0.67297011060888, -0.81773224395498, 0.207420342553107], [0.391385096561351, -0.862073619446019, 0.597813478897486], [-0.270452726779...
38 [[-1.11093024791963, -0.6986058376048401, 0.44674121624886787], [0.0416051560041239, -0.0424634970331458, -0.0874515615419252], [-0.135122617155289, -0.778975629913174, -1.04402814519501], [0.8442...
39 [[-0.645092069902244, 0.04920122139904896, 0.21081031345366397], [1.14893686034324, -0.6114894792387109, -0.40665475671972495], [-0.287092609914331, 0.292443458702414, -0.801010316546939], [-0.184...
number_of_atoms
0 1.0
1 1.0
2 1.0
3 1.0
4 1.0
5 1.0
6 1.0
7 108.0
8 108.0
9 108.0
10 108.0
11 108.0
12 108.0
13 108.0
14 108.0
15 108.0
16 108.0
17 108.0
18 107.0
19 107.0
20 107.0
21 107.0
22 107.0
23 107.0
24 107.0
25 107.0
26 107.0
27 107.0
28 107.0
29 128.0
30 128.0
31 128.0
32 128.0
33 128.0
34 128.0
35 128.0
36 128.0
37 128.0
38 128.0
39 128.0
%% Cell type:code id:impaired-cycling tags:
%% Cell type:code id:female-thumb tags:
``` python
struct = dataset.get_structure(30)
```
%% Cell type:code id:stock-sewing tags:
%% Cell type:code id:standard-whale tags:
``` python
structures, energies, forces, num_atoms = dataset.to_list()
```
%% Cell type:code id:tracked-halifax tags:
%% Cell type:code id:worldwide-freight tags:
``` python
```
......
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