Data mining using pyiron tables

In this example, the data mining capabilities of pyiron using the PyironTables class is demonstrated by computing and contrasting the ground state properties of fcc-Al using various force fields.

In [1]:
from pyiron import Project
import numpy as np
In [2]:
pr = Project("potential_scan")

## Uncomment the next line if you want to remove all jobs and start again
# pr.remove_jobs(recursive=True)

Creating a dummy job to get list of potentials

In order to get the list of available LAMMPS potentials, a dummy job with an Al bulk structure is created

In [3]:
dummy_job = pr.create_job(pr.job_type.Lammps, "dummy_job")
dummy_job.structure = pr.create_ase_bulk("Al")
# Chosing only select potentials to run (you can play with these valuess)
num_potentials = 5
potential_list = dummy_job.list_potentials()[:num_potentials]

Creating a Murnaghan job for each potential in their respective subprojects

A separate Murnaghan job (to compute equilibrium lattice constant and the bulk modulus) is created and run for every potential

In [4]:
for pot in potential_list:
    pot_str = pot.replace("-", "_")
    # open a subproject within a project
    with pr.open(pot_str) as pr_sub:
        # no need for unique job name if in different subprojects 
        job_name = "murn_Al"
        # Use the subproject to create the jobs
        murn = pr_sub.create_job(pr.job_type.Murnaghan, job_name)
        job_ref = pr_sub.create_job(pr.job_type.Lammps, "Al_ref")
        job_ref.structure = pr.create_ase_bulk("Al", cubic=True)
        job_ref.potential = pot
        job_ref.calc_minimize()
        murn.ref_job = job_ref
        # Some potentials may not work with certain LAMMPS compilations.
        # Therefore, we need to have a little exception handling
        try:
            murn.run()
        except RuntimeError:
            pass
The job murn_Al was saved and received the ID: 1
The job strain_0_9 was saved and received the ID: 2
The job strain_0_92 was saved and received the ID: 3
The job strain_0_94 was saved and received the ID: 4
The job strain_0_96 was saved and received the ID: 5
The job strain_0_98 was saved and received the ID: 6
The job strain_1_0 was saved and received the ID: 7
The job strain_1_02 was saved and received the ID: 8
The job strain_1_04 was saved and received the ID: 9
The job strain_1_06 was saved and received the ID: 10
The job strain_1_08 was saved and received the ID: 11
The job strain_1_1 was saved and received the ID: 12
job_id:  2 finished
job_id:  3 finished
job_id:  4 finished
job_id:  5 finished
job_id:  6 finished
job_id:  7 finished
job_id:  8 finished
job_id:  9 finished
job_id:  10 finished
job_id:  11 finished
job_id:  12 finished
The job murn_Al was saved and received the ID: 13
The job strain_0_9 was saved and received the ID: 14
The job strain_0_92 was saved and received the ID: 15
The job strain_0_94 was saved and received the ID: 16
The job strain_0_96 was saved and received the ID: 17
The job strain_0_98 was saved and received the ID: 18
The job strain_1_0 was saved and received the ID: 19
The job strain_1_02 was saved and received the ID: 20
The job strain_1_04 was saved and received the ID: 21
The job strain_1_06 was saved and received the ID: 22
The job strain_1_08 was saved and received the ID: 23
The job strain_1_1 was saved and received the ID: 24
job_id:  14 finished
job_id:  15 finished
job_id:  16 finished
job_id:  17 finished
job_id:  18 finished
job_id:  19 finished
job_id:  20 finished
job_id:  21 finished
job_id:  22 finished
job_id:  23 finished
job_id:  24 finished
The job murn_Al was saved and received the ID: 25
The job strain_0_9 was saved and received the ID: 26
The job strain_0_92 was saved and received the ID: 27
The job strain_0_94 was saved and received the ID: 28
The job strain_0_96 was saved and received the ID: 29
The job strain_0_98 was saved and received the ID: 30
The job strain_1_0 was saved and received the ID: 31
The job strain_1_02 was saved and received the ID: 32
The job strain_1_04 was saved and received the ID: 33
The job strain_1_06 was saved and received the ID: 34
The job strain_1_08 was saved and received the ID: 35
The job strain_1_1 was saved and received the ID: 36
job_id:  26 finished
job_id:  27 finished
job_id:  28 finished
job_id:  29 finished
job_id:  30 finished
job_id:  31 finished
job_id:  32 finished
job_id:  33 finished
job_id:  34 finished
job_id:  35 finished
job_id:  36 finished
The job murn_Al was saved and received the ID: 37
The job strain_0_9 was saved and received the ID: 38
2020-05-01 14:22:19,979 - pyiron_log - WARNING - Job aborted
2020-05-01 14:22:19,982 - pyiron_log - WARNING - LAMMPS (3 Mar 2020)
Reading data file ...
  orthogonal box = (0 0 0) to (3.91023 3.91023 3.91023)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  4 atoms
  read_data CPU = 0.00191307 secs
ERROR: MEAM library error 3 (src/USER-MEAMC/pair_meamc.cpp:596)
Last command: pair_coeff * * MgAlZn.library.meam Mg Al MgAlZn.parameter.meam Mg Al Zn

The job murn_Al was saved and received the ID: 39
The job strain_0_9 was saved and received the ID: 40
The job strain_0_92 was saved and received the ID: 41
The job strain_0_94 was saved and received the ID: 42
The job strain_0_96 was saved and received the ID: 43
The job strain_0_98 was saved and received the ID: 44
The job strain_1_0 was saved and received the ID: 45
The job strain_1_02 was saved and received the ID: 46
The job strain_1_04 was saved and received the ID: 47
The job strain_1_06 was saved and received the ID: 48
The job strain_1_08 was saved and received the ID: 49
The job strain_1_1 was saved and received the ID: 50
job_id:  40 finished
job_id:  41 finished
job_id:  42 finished
job_id:  43 finished
job_id:  44 finished
job_id:  45 finished
job_id:  46 finished
job_id:  47 finished
job_id:  48 finished
job_id:  49 finished
job_id:  50 finished

If you inspect the job table, you would find that each Murnaghan job generates various small LAMMPS jobs (see column hamilton). Some of these jobs might have failed with status aborted.

In [5]:
pr.job_table()
Out[5]:
id status chemicalformula job subjob projectpath project timestart timestop totalcputime computer hamilton hamversion parentid masterid
0 1 finished Al4 murn_Al /murn_Al /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_Mg_Mendelev_eam/ 2020-05-01 14:20:15.185926 2020-05-01 14:20:52.212726 37.0 [email protected]#1#11/11 Murnaghan 0.3.0 None NaN
1 2 finished Al4 strain_0_9 /strain_0_9 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_Mg_Mendelev_eam/murn_Al_hdf5/ 2020-05-01 14:20:16.872239 2020-05-01 14:20:18.199291 1.0 [email protected]#1 Lammps 0.1 None 1.0
2 3 finished Al4 strain_0_92 /strain_0_92 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_Mg_Mendelev_eam/murn_Al_hdf5/ 2020-05-01 14:20:20.376998 2020-05-01 14:20:21.474685 1.0 [email protected]#1 Lammps 0.1 None 1.0
3 4 finished Al4 strain_0_94 /strain_0_94 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_Mg_Mendelev_eam/murn_Al_hdf5/ 2020-05-01 14:20:23.410323 2020-05-01 14:20:24.454505 1.0 [email protected]#1 Lammps 0.1 None 1.0
4 5 finished Al4 strain_0_96 /strain_0_96 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_Mg_Mendelev_eam/murn_Al_hdf5/ 2020-05-01 14:20:26.407384 2020-05-01 14:20:27.448024 1.0 [email protected]#1 Lammps 0.1 None 1.0
5 6 finished Al4 strain_0_98 /strain_0_98 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_Mg_Mendelev_eam/murn_Al_hdf5/ 2020-05-01 14:20:29.389853 2020-05-01 14:20:30.457648 1.0 [email protected]#1 Lammps 0.1 None 1.0
6 7 finished Al4 strain_1_0 /strain_1_0 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_Mg_Mendelev_eam/murn_Al_hdf5/ 2020-05-01 14:20:32.440577 2020-05-01 14:20:33.587692 1.0 [email protected]#1 Lammps 0.1 None 1.0
7 8 finished Al4 strain_1_02 /strain_1_02 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_Mg_Mendelev_eam/murn_Al_hdf5/ 2020-05-01 14:20:35.659606 2020-05-01 14:20:36.717203 1.0 [email protected]#1 Lammps 0.1 None 1.0
8 9 finished Al4 strain_1_04 /strain_1_04 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_Mg_Mendelev_eam/murn_Al_hdf5/ 2020-05-01 14:20:39.247825 2020-05-01 14:20:40.631913 1.0 [email protected]#1 Lammps 0.1 None 1.0
9 10 finished Al4 strain_1_06 /strain_1_06 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_Mg_Mendelev_eam/murn_Al_hdf5/ 2020-05-01 14:20:43.093369 2020-05-01 14:20:44.365442 1.0 [email protected]#1 Lammps 0.1 None 1.0
10 11 finished Al4 strain_1_08 /strain_1_08 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_Mg_Mendelev_eam/murn_Al_hdf5/ 2020-05-01 14:20:46.700972 2020-05-01 14:20:47.809129 1.0 [email protected]#1 Lammps 0.1 None 1.0
11 12 finished Al4 strain_1_1 /strain_1_1 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_Mg_Mendelev_eam/murn_Al_hdf5/ 2020-05-01 14:20:49.872971 2020-05-01 14:20:51.002065 1.0 [email protected]#1 Lammps 0.1 None 1.0
12 13 finished Al4 murn_Al /murn_Al /home/surendralal/ programs/pyiron/notebooks/potential_scan/Zope_Ti_Al_2003_eam/ 2020-05-01 14:20:52.854206 2020-05-01 14:21:40.211332 47.0 [email protected]#1#11/11 Murnaghan 0.3.0 None NaN
13 14 finished Al4 strain_0_9 /strain_0_9 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Zope_Ti_Al_2003_eam/murn_Al_hdf5/ 2020-05-01 14:20:54.595238 2020-05-01 14:20:55.863602 1.0 [email protected]#1 Lammps 0.1 None 13.0
14 15 finished Al4 strain_0_92 /strain_0_92 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Zope_Ti_Al_2003_eam/murn_Al_hdf5/ 2020-05-01 14:20:58.465134 2020-05-01 14:20:59.616677 1.0 [email protected]#1 Lammps 0.1 None 13.0
15 16 finished Al4 strain_0_94 /strain_0_94 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Zope_Ti_Al_2003_eam/murn_Al_hdf5/ 2020-05-01 14:21:02.323952 2020-05-01 14:21:03.842627 1.0 [email protected]#1 Lammps 0.1 None 13.0
16 17 finished Al4 strain_0_96 /strain_0_96 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Zope_Ti_Al_2003_eam/murn_Al_hdf5/ 2020-05-01 14:21:07.120770 2020-05-01 14:21:08.247122 1.0 [email protected]#1 Lammps 0.1 None 13.0
17 18 finished Al4 strain_0_98 /strain_0_98 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Zope_Ti_Al_2003_eam/murn_Al_hdf5/ 2020-05-01 14:21:10.867935 2020-05-01 14:21:12.084671 1.0 [email protected]#1 Lammps 0.1 None 13.0
18 19 finished Al4 strain_1_0 /strain_1_0 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Zope_Ti_Al_2003_eam/murn_Al_hdf5/ 2020-05-01 14:21:14.859515 2020-05-01 14:21:15.890379 1.0 [email protected]#1 Lammps 0.1 None 13.0
19 20 finished Al4 strain_1_02 /strain_1_02 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Zope_Ti_Al_2003_eam/murn_Al_hdf5/ 2020-05-01 14:21:18.333658 2020-05-01 14:21:19.773168 1.0 [email protected]#1 Lammps 0.1 None 13.0
20 21 finished Al4 strain_1_04 /strain_1_04 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Zope_Ti_Al_2003_eam/murn_Al_hdf5/ 2020-05-01 14:21:23.134672 2020-05-01 14:21:24.701105 1.0 [email protected]#1 Lammps 0.1 None 13.0
21 22 finished Al4 strain_1_06 /strain_1_06 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Zope_Ti_Al_2003_eam/murn_Al_hdf5/ 2020-05-01 14:21:28.160753 2020-05-01 14:21:29.635477 1.0 [email protected]#1 Lammps 0.1 None 13.0
22 23 finished Al4 strain_1_08 /strain_1_08 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Zope_Ti_Al_2003_eam/murn_Al_hdf5/ 2020-05-01 14:21:32.177125 2020-05-01 14:21:33.407034 1.0 [email protected]#1 Lammps 0.1 None 13.0
23 24 finished Al4 strain_1_1 /strain_1_1 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Zope_Ti_Al_2003_eam/murn_Al_hdf5/ 2020-05-01 14:21:36.544373 2020-05-01 14:21:38.079025 1.0 [email protected]#1 Lammps 0.1 None 13.0
24 25 finished Al4 murn_Al /murn_Al /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_H_Ni_Angelo_eam/ 2020-05-01 14:21:41.112811 2020-05-01 14:22:14.935040 33.0 [email protected]#1#11/11 Murnaghan 0.3.0 None NaN
25 26 finished Al4 strain_0_9 /strain_0_9 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_H_Ni_Angelo_eam/murn_Al_hdf5/ 2020-05-01 14:21:43.292578 2020-05-01 14:21:44.486249 1.0 [email protected]#1 Lammps 0.1 None 25.0
26 27 finished Al4 strain_0_92 /strain_0_92 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_H_Ni_Angelo_eam/murn_Al_hdf5/ 2020-05-01 14:21:46.220651 2020-05-01 14:21:47.239424 1.0 [email protected]#1 Lammps 0.1 None 25.0
27 28 finished Al4 strain_0_94 /strain_0_94 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_H_Ni_Angelo_eam/murn_Al_hdf5/ 2020-05-01 14:21:49.064622 2020-05-01 14:21:50.027115 0.0 [email protected]#1 Lammps 0.1 None 25.0
28 29 finished Al4 strain_0_96 /strain_0_96 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_H_Ni_Angelo_eam/murn_Al_hdf5/ 2020-05-01 14:21:51.711371 2020-05-01 14:21:52.700248 0.0 [email protected]#1 Lammps 0.1 None 25.0
29 30 finished Al4 strain_0_98 /strain_0_98 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_H_Ni_Angelo_eam/murn_Al_hdf5/ 2020-05-01 14:21:54.391263 2020-05-01 14:21:55.421046 1.0 [email protected]#1 Lammps 0.1 None 25.0
30 31 finished Al4 strain_1_0 /strain_1_0 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_H_Ni_Angelo_eam/murn_Al_hdf5/ 2020-05-01 14:21:57.127116 2020-05-01 14:21:58.177664 1.0 [email protected]#1 Lammps 0.1 None 25.0
31 32 finished Al4 strain_1_02 /strain_1_02 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_H_Ni_Angelo_eam/murn_Al_hdf5/ 2020-05-01 14:21:59.836684 2020-05-01 14:22:00.908548 1.0 [email protected]#1 Lammps 0.1 None 25.0
32 33 finished Al4 strain_1_04 /strain_1_04 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_H_Ni_Angelo_eam/murn_Al_hdf5/ 2020-05-01 14:22:02.637902 2020-05-01 14:22:03.654759 1.0 [email protected]#1 Lammps 0.1 None 25.0
33 34 finished Al4 strain_1_06 /strain_1_06 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_H_Ni_Angelo_eam/murn_Al_hdf5/ 2020-05-01 14:22:05.431956 2020-05-01 14:22:06.592121 1.0 [email protected]#1 Lammps 0.1 None 25.0
34 35 finished Al4 strain_1_08 /strain_1_08 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_H_Ni_Angelo_eam/murn_Al_hdf5/ 2020-05-01 14:22:09.286335 2020-05-01 14:22:10.252819 0.0 [email protected]#1 Lammps 0.1 None 25.0
35 36 finished Al4 strain_1_1 /strain_1_1 /home/surendralal/ programs/pyiron/notebooks/potential_scan/Al_H_Ni_Angelo_eam/murn_Al_hdf5/ 2020-05-01 14:22:12.026812 2020-05-01 14:22:13.233506 1.0 [email protected]#1 Lammps 0.1 None 25.0
36 37 aborted Al4 murn_Al /murn_Al /home/surendralal/ programs/pyiron/notebooks/potential_scan/2018__Dickel_D_E__Mg_Al_Zn__LAMMPS__ipr1/ 2020-05-01 14:22:16.205392 NaT NaN [email protected]#1#1/11 Murnaghan 0.3.0 None NaN
37 38 aborted Al4 strain_0_9 /strain_0_9 /home/surendralal/ programs/pyiron/notebooks/potential_scan/2018__Dickel_D_E__Mg_Al_Zn__LAMMPS__ipr1/murn_Al_hdf5/ 2020-05-01 14:22:19.500822 NaT NaN [email protected]#1 Lammps 0.1 None 37.0
38 39 finished Al4 murn_Al /murn_Al /home/surendralal/ programs/pyiron/notebooks/potential_scan/2000__Landa_A__Al_Pb__LAMMPS__ipr1/ 2020-05-01 14:22:20.918639 2020-05-01 14:22:56.348776 35.0 [email protected]#1#11/11 Murnaghan 0.3.0 None NaN
39 40 finished Al4 strain_0_9 /strain_0_9 /home/surendralal/ programs/pyiron/notebooks/potential_scan/2000__Landa_A__Al_Pb__LAMMPS__ipr1/murn_Al_hdf5/ 2020-05-01 14:22:23.362886 2020-05-01 14:22:24.543279 1.0 [email protected]#1 Lammps 0.1 None 39.0
40 41 finished Al4 strain_0_92 /strain_0_92 /home/surendralal/ programs/pyiron/notebooks/potential_scan/2000__Landa_A__Al_Pb__LAMMPS__ipr1/murn_Al_hdf5/ 2020-05-01 14:22:26.098609 2020-05-01 14:22:27.456331 1.0 [email protected]#1 Lammps 0.1 None 39.0
41 42 finished Al4 strain_0_94 /strain_0_94 /home/surendralal/ programs/pyiron/notebooks/potential_scan/2000__Landa_A__Al_Pb__LAMMPS__ipr1/murn_Al_hdf5/ 2020-05-01 14:22:29.355607 2020-05-01 14:22:30.418893 1.0 [email protected]#1 Lammps 0.1 None 39.0
42 43 finished Al4 strain_0_96 /strain_0_96 /home/surendralal/ programs/pyiron/notebooks/potential_scan/2000__Landa_A__Al_Pb__LAMMPS__ipr1/murn_Al_hdf5/ 2020-05-01 14:22:32.522105 2020-05-01 14:22:34.234605 1.0 [email protected]#1 Lammps 0.1 None 39.0
43 44 finished Al4 strain_0_98 /strain_0_98 /home/surendralal/ programs/pyiron/notebooks/potential_scan/2000__Landa_A__Al_Pb__LAMMPS__ipr1/murn_Al_hdf5/ 2020-05-01 14:22:36.960119 2020-05-01 14:22:38.166629 1.0 [email protected]#1 Lammps 0.1 None 39.0
44 45 finished Al4 strain_1_0 /strain_1_0 /home/surendralal/ programs/pyiron/notebooks/potential_scan/2000__Landa_A__Al_Pb__LAMMPS__ipr1/murn_Al_hdf5/ 2020-05-01 14:22:39.686173 2020-05-01 14:22:40.836256 1.0 [email protected]#1 Lammps 0.1 None 39.0
45 46 finished Al4 strain_1_02 /strain_1_02 /home/surendralal/ programs/pyiron/notebooks/potential_scan/2000__Landa_A__Al_Pb__LAMMPS__ipr1/murn_Al_hdf5/ 2020-05-01 14:22:42.989847 2020-05-01 14:22:44.268105 1.0 [email protected]#1 Lammps 0.1 None 39.0
46 47 finished Al4 strain_1_04 /strain_1_04 /home/surendralal/ programs/pyiron/notebooks/potential_scan/2000__Landa_A__Al_Pb__LAMMPS__ipr1/murn_Al_hdf5/ 2020-05-01 14:22:46.008623 2020-05-01 14:22:47.372670 1.0 [email protected]#1 Lammps 0.1 None 39.0
47 48 finished Al4 strain_1_06 /strain_1_06 /home/surendralal/ programs/pyiron/notebooks/potential_scan/2000__Landa_A__Al_Pb__LAMMPS__ipr1/murn_Al_hdf5/ 2020-05-01 14:22:49.144214 2020-05-01 14:22:50.153294 1.0 [email protected]#1 Lammps 0.1 None 39.0
48 49 finished Al4 strain_1_08 /strain_1_08 /home/surendralal/ programs/pyiron/notebooks/potential_scan/2000__Landa_A__Al_Pb__LAMMPS__ipr1/murn_Al_hdf5/ 2020-05-01 14:22:51.746560 2020-05-01 14:22:52.772483 1.0 [email protected]#1 Lammps 0.1 None 39.0
49 50 finished Al4 strain_1_1 /strain_1_1 /home/surendralal/ programs/pyiron/notebooks/potential_scan/2000__Landa_A__Al_Pb__LAMMPS__ipr1/murn_Al_hdf5/ 2020-05-01 14:22:54.390591 2020-05-01 14:22:55.348395 0.0 [email protected]#1 Lammps 0.1 None 39.0

Analysis using PyironTables

The idea now is to go over all finished Murnaghan jobs and extract the equilibrium lattice parameter and bulk modulus, and classify them based of the potential used.

Defining filter functions

Since a project can have thousands if not millions of jobs, it is necessary to "filter" the data and only apply the functions (some of which can be computationally expensive) to only this data. In this example, we need to filter jobs that are finished and are of type Murnaghan. This can be done in two ways: using the job table i.e. the entries in the database, or using the job itself i.e. using entries in the stored HDF5 file. Below are examples of filter functions acting on the job and the job table respectively.

In [6]:
# Filtering using the database entries (which are obtained as a pandas Dataframe)
def db_filter_function(job_table):
    # Returns a pandas Series of boolean values (True for entries that have status finished 
    # and hamilton type Murnaghan.)
    return (job_table.status == "finished") & (job_table.hamilton == "Murnaghan")

# Filtering based on the job
def job_filter_function(job):
    # returns a boolean value if the status of the job 
    #is finished and if "murn" is in it's job name 
    return (job.status == "finished") & ("murn" in job.job_name)

Obviously, using the database is faster in this case but sometimes it might be necessary to filter based on some data that are stored in the HDF5 file of the job. The database filter is applied first followed by the job based filter.

Defining functions that act on jobs

Now we define a set of functions that will be applied on each job to return a certain value. The filtered jobs will be loaded and these functions will be applied on the loaded jobs. The advantage of such functions is that the jobs do not have to be loaded every time such operations are performed. The filtered jobs are loaded once, and then they are passed to these functions to construct the table.

In [7]:
# Getting equilibrium lattice parameter from Murnaghan jobs
def get_lattice_parameter(job):
    return job["output/equilibrium_volume"] ** (1/3)

# Getting equilibrium bulk modulus from Murnaghan jobs
def get_bm(job):
    return job["output/equilibrium_bulk_modulus"]

# Getting the potential used in each Murnaghan job
def get_pot(job):
    child = job.project.inspect(job["output/id"][0])
    return child["input/potential/Name"]

Creating a pyiron table

Now that all the functions are defined, the pyiron table called "table" is created in the following way. This works like a job and can be reloaded at any time.

In [8]:
%%time
# creating a pyiron table
table = pr.create_table("table")

# assigning a database filter function
table.db_filter_function = db_filter_function

# Alternatively/additionally, a job based filter function can be applied 
# (it does the same thing in this case).

#table.filter_function = job_filter_function

# Adding the functions using the labels you like
table.add["a_eq"] = get_lattice_parameter
table.add["bulk_modulus"] = get_bm
table.add["potential"] = get_pot
# Running the table to generate the data
table.run(run_again=True)
  0%|          | 0/4 [00:00<?, ?it/s]
The job table was saved and received the ID: 51
100%|██████████| 4/4 [00:00<00:00, 20.91it/s]
2020-05-01 14:22:57,257 - pyiron_log - WARNING - The job table is being loaded instead of running. To re-run use the argument 'run_again=True'
CPU times: user 531 ms, sys: 156 ms, total: 688 ms
Wall time: 725 ms

The output can now be obtained as a pandas DataFrame

In [9]:
table.get_dataframe()
Out[9]:
job_id a_eq bulk_modulus potential
0 1 4.045415 89.015487 Al_Mg_Mendelev_eam
1 13 4.049946 80.836779 Zope_Ti_Al_2003_eam
2 25 4.049954 81.040445 Al_H_Ni_Angelo_eam
3 39 4.031246 78.213776 2000--Landa-A--Al-Pb--LAMMPS--ipr1

You can now compare the computed equilibrium lattice constants for each potential to those computed in the NIST database for Al (fcc phase). https://www.ctcms.nist.gov/potentials/system/Al/#Al.

In [ ]: