{ "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 = 'Fe_C_Hepburn_Ackland_eam'\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": [ { "data": { "text/html": [ "
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