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Merge pull request #295 from pyiron/interactive_units
Interactive units
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,162 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "This notebooks compares the outputs from two static LAMMPS jobs one of which is an interactive job. This is to ensure that the outputs from interactive and non-interactive jobs are consistent." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from pyiron import Project\n", | ||
| "import numpy as np" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 2, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "pr = Project(\"water_interactive\")\n", | ||
| "pr.remove_jobs_silently()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 3, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "dx = 0.7\n", | ||
| "cell = np.eye(3) * 10\n", | ||
| "r_O = [0, 0, 0]\n", | ||
| "r_H1 = [dx, dx, 0]\n", | ||
| "r_H2 = [-dx, dx, 0]\n", | ||
| "water = pr.create_atoms(elements=['H', 'H', 'O'],\n", | ||
| " positions=[r_H1, r_H2, r_O],\n", | ||
| " cell=cell, pbc=True)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 4, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stderr", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "/cmmc/u/chandu/programs/pyiron_mpie/pyiron_atomistics/pyiron_atomistics/lammps/base.py:210: UserWarning: WARNING: Non-'metal' units are not fully supported. Your calculation should run OK, but results may not be saved in pyiron units.\n", | ||
| " \"WARNING: Non-'metal' units are not fully supported. Your calculation should run OK, but \"\n", | ||
| "/cmmc/u/chandu/programs/pyiron_mpie/pyiron_atomistics/pyiron_atomistics/lammps/base.py:262: UserWarning: No potential set via job.potential - use default potential, H2O_tip3p\n", | ||
| " warnings.warn(\"No potential set via job.potential - use default potential, \" + lst_of_potentials[0])\n" | ||
| ] | ||
| }, | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "The job test was saved and received the ID: 15458456\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# Interactive job\n", | ||
| "job_int = pr.create.job.Lammps(\"test\", delete_existing_job=True)\n", | ||
| "job_int.structure = water\n", | ||
| "job_int.interactive_open()\n", | ||
| "job_int.calc_static()\n", | ||
| "job_int.run()\n", | ||
| "job_int.interactive_close()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 5, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "The job test_ni was saved and received the ID: 15458457\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# Non-interactive job\n", | ||
| "job = pr.create.job.Lammps(\"test_ni\", delete_existing_job=True)\n", | ||
| "job.structure = water\n", | ||
| "job.calc_static()\n", | ||
| "job.run()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 6, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "cells\n", | ||
| "energy_pot\n", | ||
| "energy_tot\n", | ||
| "forces\n", | ||
| "indices\n", | ||
| "positions\n", | ||
| "pressures\n", | ||
| "steps\n", | ||
| "temperature\n", | ||
| "volume\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# Assert that the unit converstions work even in the interactive mode\n", | ||
| "\n", | ||
| "int_nodes = job_int[\"output/generic\"].list_nodes()\n", | ||
| "usual_nodes = job[\"output/generic\"].list_nodes()\n", | ||
| "for node in int_nodes:\n", | ||
| " if node in usual_nodes:\n", | ||
| " print(node)\n", | ||
| " assert np.allclose(job_int[\"output/generic/\" + node], job[\"output/generic/\" + node])" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.7.9" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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