import os
import pyiron
from ase.io import read
import pyscal.core as pc
import matplotlib.pyplot as plt
import numpy as np
pr = pyiron.Project('ADIS')
pr.job_table()
id | status | chemicalformula | job | subjob | projectpath | project | timestart | timestop | totalcputime | computer | hamilton | hamversion | parentid | masterid | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | 2 | finished | H8192 | Nucleus | /Nucleus | /home/jovyan/ | ADIS/ | 2020-11-05 21:11:34.985406 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
1 | 4 | finished | H3980 | Si_1400_20 | /Si_1400_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:11:40.585864 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
2 | 5 | finished | H1529 | S5_s00_n130_r1024_720_5 | /S5_s00_n130_r1024_720_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:11:43.147042 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
3 | 6 | finished | H1980 | Fe_1050_20 | /Fe_1050_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:11:47.255863 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
4 | 7 | finished | H1980 | Fe_1350_20 | /Fe_1350_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:11:53.247038 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
5 | 8 | finished | H3995 | Si_1000_5 | /Si_1000_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:11:59.993315 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
6 | 9 | finished | H1980 | Cu_720_20 | /Cu_720_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:12:06.132659 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
7 | 10 | finished | H2000 | Cu_400_0 | /Cu_400_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:12:11.172906 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
8 | 11 | finished | H4000 | Mg_900_0 | /Mg_900_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:12:18.633493 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
9 | 12 | finished | H4000 | Mg_500_0 | /Mg_500_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:12:24.458570 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
10 | 13 | finished | H1534 | S5_s00_n130_r1024_720_0 | /S5_s00_n130_r1024_720_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:12:26.942533 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
11 | 15 | finished | H3995 | Mg_700_5 | /Mg_700_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:12:33.466119 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
12 | 16 | finished | H3980 | Si_1000_20 | /Si_1000_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:12:40.492150 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
13 | 17 | finished | H1554 | S5_s00_n130_r1024_560_5 | /S5_s00_n130_r1024_560_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:12:43.054725 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
14 | 18 | finished | H1584 | S5_s00_n130_r1024_400_0 | /S5_s00_n130_r1024_400_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:12:44.725043 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
15 | 19 | finished | H1980 | Cu_400_20 | /Cu_400_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:12:49.268366 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
16 | 20 | finished | H1995 | Fe_1350_5 | /Fe_1350_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:12:54.623718 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
17 | 21 | finished | H3995 | Mg_1000_5 | /Mg_1000_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:13:01.055022 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
18 | 22 | finished | H4000 | Si_1400_0 | /Si_1400_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:13:09.023513 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
19 | 23 | finished | H2000 | Fe_1350_0 | /Fe_1350_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:13:14.466088 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
20 | 24 | finished | H4000 | Mg_700_0 | /Mg_700_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:13:21.071463 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
21 | 26 | finished | H1995 | Fe_1050_5 | /Fe_1050_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:13:26.326193 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
22 | 27 | finished | H3980 | Mg_1000_20 | /Mg_1000_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:13:34.325798 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
23 | 28 | finished | H2000 | Cu_560_0 | /Cu_560_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:13:40.855803 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
24 | 29 | finished | H2000 | Fe_750_0 | /Fe_750_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:13:48.369252 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
25 | 30 | finished | H1995 | Cu_400_5 | /Cu_400_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:13:55.268210 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
26 | 31 | finished | H1579 | S5_s00_n130_r1024_400_5 | /S5_s00_n130_r1024_400_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:13:57.530915 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
27 | 32 | finished | H1980 | Fe_750_20 | /Fe_750_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:14:01.649228 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
28 | 33 | finished | H1980 | Cu_560_20 | /Cu_560_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:14:06.227415 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
29 | 34 | finished | H2000 | Cu_720_0 | /Cu_720_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:14:10.660001 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
30 | 35 | finished | H3980 | Mg_500_20 | /Mg_500_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:14:15.234711 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
31 | 36 | finished | H3980 | Mg_700_20 | /Mg_700_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:14:19.744690 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
32 | 38 | finished | H3995 | Mg_500_5 | /Mg_500_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:14:25.832014 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
33 | 39 | finished | H500 | Liquid | /Liquid | /home/jovyan/ | ADIS/ | 2020-11-05 21:14:28.167739 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
34 | 40 | finished | H1995 | Cu_560_5 | /Cu_560_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:14:34.625711 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
35 | 41 | finished | H1510 | S5_s00_n130_r1024_720_20 | /S5_s00_n130_r1024_720_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:14:37.464296 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
36 | 42 | finished | H3980 | Mg_900_20 | /Mg_900_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:14:45.426443 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
37 | 43 | finished | H2000 | Fe_1050_0 | /Fe_1050_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:14:52.439612 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
38 | 44 | finished | H1559 | S5_s00_n130_r1024_560_0 | /S5_s00_n130_r1024_560_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:14:55.155021 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
39 | 45 | finished | H4000 | Mg_1000_0 | /Mg_1000_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:15:02.737287 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
40 | 46 | finished | H1534 | S5_s00_n130_r1024_560_20 | /S5_s00_n130_r1024_560_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:15:06.033125 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
41 | 47 | finished | H3995 | Si_1400_5 | /Si_1400_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:15:13.332531 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
42 | 48 | finished | H1995 | Cu_720_5 | /Cu_720_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:15:21.831887 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
43 | 49 | finished | H1995 | Fe_750_5 | /Fe_750_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:15:29.351879 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
44 | 50 | finished | H4000 | Si_1000_0 | /Si_1000_0 | /home/jovyan/ | ADIS/ | 2020-11-05 21:15:37.769224 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
45 | 51 | finished | H1559 | S5_s00_n130_r1024_400_20 | /S5_s00_n130_r1024_400_20 | /home/jovyan/ | ADIS/ | 2020-11-05 21:15:39.951420 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
46 | 53 | finished | H3995 | Mg_900_5 | /Mg_900_5 | /home/jovyan/ | ADIS/ | 2020-11-05 21:15:46.458817 | NaT | NaN | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | AtomisticGenericJob | 0.2.0 | None | None |
47 | 56 | finished | Cu1995 | Cu_minimization | /Cu_minimization | /home/jovyan/ | ADIS/ | 2020-11-05 21:43:41.296584 | 2020-11-05 21:43:43.276914 | 1.0 | pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 | Lammps | 0.1 | None | None |
We will start with a small configuration in which a small solid cluster is embedded in a liquid.
job = pr.load("Nucleus")
struct = job.get_structure()
One good idea is to get the q6 values.
Pyiron can calculate the q6 values and cluster them. Let's see how that works.
from pyiron.atomistics.structure.pyscal import get_steinhardt_parameter_job
q46, cluster = get_steinhardt_parameter_job(job, clustering=True)
We will switch a bit onto pyscal now. All the features of pyscal are not yet available on pyiron.
sys = pc.System()
sys.read_inputfile(struct, format="ase")
sys.find_neighbors(method="cutoff", cutoff=0)
sys.calculate_q(6, averaged=True)
from the previous example, we saw that the solid structures had average q6 roughly above 0.3
atoms = sys.atoms
for count, atom in enumerate(atoms):
if atom.get_q(6, averaged=True) > 0.3:
atom.solid = 1
else:
atom.solid = 0