notebooks/pipeline.ipynb

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