In [1]:
from pyiron import Project
In [2]:
def calc_minimize(job):
    job_mini = job.copy_to(
        new_job_name=job.job_name + '_mini', 
        new_database_entry=False
    )
    job_mini.calc_minimize(pressure=0)
    return job_mini
In [3]:
def calc_murnaghan(job):
    job_murn = job.copy_to(
        new_job_name=job.job_name + '_murn_lmp', 
        new_database_entry=False
    )
    return job_murn.create_job(
        job_type=pr.job_type.Murnaghan, 
        job_name=job.job_name + '_murn'
    )
In [4]:
def calc_phonons_for_each_structure(job):
    job_phono = job.copy_to(
        new_job_name=job.job_name + '_phono_lmp', 
        new_database_entry=False
    )
    phono = job_phono.create_job(
        job_type=pr.job_type.PhonopyJob, 
        job_name=job.job_name + '_phono'
    )
    return phono.create_job(
        job_type=pr.job_type.StructureListMaster, 
        job_name='struct_master'
    )
In [5]:
pr = Project('calculation')
potential = '2008--Hepburn-D-J--Fe-C--LAMMPS--ipr1'
element = 'Fe'
In [6]:
structure = pr.create_ase_bulk(element, cubic=True)
In [7]:
job = pr.create_job(pr.job_type.Lammps, 'lmp')
job.structure = structure
job.potential = potential
# job.server.run_mode.interactive = True
In [8]:
job_lst_master = job.create_pipeline(
    step_lst=[
        calc_minimize,
        calc_murnaghan,
        calc_phonons_for_each_structure,
    ]
)
In [9]:
job_lst_master.run()
The job lstmaster was saved and received the ID: 77
The job lmp_mini was saved and received the ID: 78
The job lmp_murn was saved and received the ID: 79
The job lmp_murn_lmp_murn_lmp was saved and received the ID: 80
/Users/jan/PycharmProjects/pyiron_mpie/pyiron/pyiron/lammps/interactive.py:349: UserWarning: Warning: setting upper trangular matrix might slow down the calculation
  "Warning: setting upper trangular matrix might slow down the calculation"
/Users/jan/PycharmProjects/pyiron_mpie/pyiron/pyiron/lammps/interactive.py:108: UserWarning: Warning: setting upper trangular matrix might slow down the calculation
  "Warning: setting upper trangular matrix might slow down the calculation"
The job struct_master was saved and received the ID: 81
The job struct_0 was saved and received the ID: 82
The job struct_0_lmp_phono_lmp was saved and received the ID: 83
The job struct_1 was saved and received the ID: 84
The job struct_1_lmp_phono_lmp was saved and received the ID: 85
The job struct_2 was saved and received the ID: 86
The job struct_2_lmp_phono_lmp was saved and received the ID: 87
The job struct_3 was saved and received the ID: 88
The job struct_3_lmp_phono_lmp was saved and received the ID: 89
The job struct_4 was saved and received the ID: 90
The job struct_4_lmp_phono_lmp was saved and received the ID: 91
The job struct_5 was saved and received the ID: 92
The job struct_5_lmp_phono_lmp was saved and received the ID: 93
The job struct_6 was saved and received the ID: 94
The job struct_6_lmp_phono_lmp was saved and received the ID: 95
The job struct_7 was saved and received the ID: 96
The job struct_7_lmp_phono_lmp was saved and received the ID: 97
The job struct_8 was saved and received the ID: 98
The job struct_8_lmp_phono_lmp was saved and received the ID: 99
The job struct_9 was saved and received the ID: 100
The job struct_9_lmp_phono_lmp was saved and received the ID: 101
The job struct_10 was saved and received the ID: 102
The job struct_10_lmp_phono_lmp was saved and received the ID: 103
In [10]:
pr.job_table()
Out[10]:
id status chemicalformula job subjob projectpath project timestart timestop totalcputime computer hamilton hamversion parentid masterid
0 77 finished None lstmaster /lstmaster /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/ 2020-06-14 12:11:14.436169 2020-06-14 12:12:13.970148 59.0 [email protected]#1 FlexibleMaster 0.1 NaN NaN
1 78 finished Fe2 lmp_mini /lmp_mini /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/ 2020-06-14 12:11:14.594122 2020-06-14 12:11:17.222444 2.0 [email protected]#1 Lammps 0.1 NaN 77.0
2 79 finished Fe2 lmp_murn /lmp_murn /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/ 2020-06-14 12:11:18.066551 2020-06-14 12:11:22.704741 4.0 [email protected]#1#0 Murnaghan 0.3.0 78.0 77.0
3 80 finished Fe2 lmp_murn_lmp_murn_lmp /lmp_murn_lmp_murn_lmp /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/ 2020-06-14 12:11:18.314042 2020-06-14 12:11:22.579578 4.0 [email protected]#1 Lammps 0.1 NaN 79.0
4 81 finished None struct_master /struct_master /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/ 2020-06-14 12:11:23.904042 2020-06-14 12:12:13.953624 50.0 [email protected]#1#11/11 StructureListMaster 0.0.1 79.0 77.0
5 82 finished Fe2 struct_0 /struct_0 /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:24.990524 2020-06-14 12:11:28.236264 3.0 [email protected]#1#0 PhonopyJob 0.0.1 NaN 81.0
6 83 finished Fe128 struct_0_lmp_phono_lmp /struct_0_lmp_phono_lmp /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:25.867071 2020-06-14 12:11:26.892291 1.0 [email protected]#1 Lammps 0.1 NaN 82.0
7 84 finished Fe2 struct_1 /struct_1 /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:29.407809 2020-06-14 12:11:32.849175 3.0 [email protected]#1#0 PhonopyJob 0.0.1 NaN 81.0
8 85 finished Fe128 struct_1_lmp_phono_lmp /struct_1_lmp_phono_lmp /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:30.420492 2020-06-14 12:11:31.553013 1.0 [email protected]#1 Lammps 0.1 NaN 84.0
9 86 finished Fe2 struct_2 /struct_2 /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:33.869453 2020-06-14 12:11:37.016653 3.0 [email protected]#1#0 PhonopyJob 0.0.1 NaN 81.0
10 87 finished Fe128 struct_2_lmp_phono_lmp /struct_2_lmp_phono_lmp /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:34.718565 2020-06-14 12:11:35.747398 1.0 [email protected]#1 Lammps 0.1 NaN 86.0
11 88 finished Fe2 struct_3 /struct_3 /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:38.411149 2020-06-14 12:11:41.717434 3.0 [email protected]#1#0 PhonopyJob 0.0.1 NaN 81.0
12 89 finished Fe128 struct_3_lmp_phono_lmp /struct_3_lmp_phono_lmp /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:39.357975 2020-06-14 12:11:40.449788 1.0 [email protected]#1 Lammps 0.1 NaN 88.0
13 90 finished Fe2 struct_4 /struct_4 /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:42.732800 2020-06-14 12:11:46.103109 3.0 [email protected]#1#0 PhonopyJob 0.0.1 NaN 81.0
14 91 finished Fe128 struct_4_lmp_phono_lmp /struct_4_lmp_phono_lmp /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:43.585601 2020-06-14 12:11:44.620598 1.0 [email protected]#1 Lammps 0.1 NaN 90.0
15 92 finished Fe2 struct_5 /struct_5 /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:47.170780 2020-06-14 12:11:50.664073 3.0 [email protected]#1#0 PhonopyJob 0.0.1 NaN 81.0
16 93 finished Fe128 struct_5_lmp_phono_lmp /struct_5_lmp_phono_lmp /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:48.136868 2020-06-14 12:11:49.355210 1.0 [email protected]#1 Lammps 0.1 NaN 92.0
17 94 finished Fe2 struct_6 /struct_6 /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:51.855833 2020-06-14 12:11:55.495523 3.0 [email protected]#1#0 PhonopyJob 0.0.1 NaN 81.0
18 95 finished Fe128 struct_6_lmp_phono_lmp /struct_6_lmp_phono_lmp /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:52.860252 2020-06-14 12:11:54.097916 1.0 [email protected]#1 Lammps 0.1 NaN 94.0
19 96 finished Fe2 struct_7 /struct_7 /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:56.637786 2020-06-14 12:12:00.067366 3.0 [email protected]#1#0 PhonopyJob 0.0.1 NaN 81.0
20 97 finished Fe128 struct_7_lmp_phono_lmp /struct_7_lmp_phono_lmp /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:11:57.492511 2020-06-14 12:11:58.693642 1.0 [email protected]#1 Lammps 0.1 NaN 96.0
21 98 finished Fe2 struct_8 /struct_8 /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:12:01.301509 2020-06-14 12:12:04.890735 3.0 [email protected]#1#0 PhonopyJob 0.0.1 NaN 81.0
22 99 finished Fe128 struct_8_lmp_phono_lmp /struct_8_lmp_phono_lmp /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:12:02.321387 2020-06-14 12:12:03.529445 1.0 [email protected]#1 Lammps 0.1 NaN 98.0
23 100 finished Fe2 struct_9 /struct_9 /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:12:05.923702 2020-06-14 12:12:09.170589 3.0 [email protected]#1#0 PhonopyJob 0.0.1 NaN 81.0
24 101 finished Fe128 struct_9_lmp_phono_lmp /struct_9_lmp_phono_lmp /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:12:06.779443 2020-06-14 12:12:07.874052 1.0 [email protected]#1 Lammps 0.1 NaN 100.0
25 102 finished Fe2 struct_10 /struct_10 /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:12:10.426567 2020-06-14 12:12:13.920485 3.0 [email protected]#1#0 PhonopyJob 0.0.1 NaN 81.0
26 103 finished Fe128 struct_10_lmp_phono_lmp /struct_10_lmp_phono_lmp /Users/jan/pyiron/projects/ 2020/2020-05-27-thesis/calculation/struct_master_hdf5/ 2020-06-14 12:12:11.332099 2020-06-14 12:12:12.574144 1.0 [email protected]#1 Lammps 0.1 NaN 102.0
In [ ]: