{ "cells": [ { "cell_type": "markdown", "id": "brutal-healing", "metadata": {}, "source": [ "# Exercise 2: Creating and working with structure databases\n", "\n", "Before the excercise, you should:\n", "\n", "* Finish exercise 1\n", "\n", "The aim of this exercise is to make you familiar with:\n", "\n", "* Creating structure databases and working with them for potential fitting (day 2)" ] }, { "cell_type": "markdown", "id": "cheap-chick", "metadata": {}, "source": [ "## Importing necessary modules and creating a project\n", "\n", "This is done the same way as shown in the first exercise" ] }, { "cell_type": "code", "execution_count": 1, "id": "2ef1e9e7-492a-4208-9d3b-3444f4d81ad2", "metadata": {}, "outputs": [], "source": [ "import numpy as np\n", "%matplotlib inline\n", "import matplotlib.pylab as plt\n", "import os" ] }, { "cell_type": "code", "execution_count": 2, "id": "academic-print", "metadata": {}, "outputs": [], "source": [ "from pyiron import Project" ] }, { "cell_type": "code", "execution_count": 3, "id": "comparable-creation", "metadata": {}, "outputs": [], "source": [ "pr = Project(\"creating_datasets\")" ] }, { "cell_type": "markdown", "id": "focal-percentage", "metadata": {}, "source": [ "## Creating a structure \"container\" from the data\n", "\n", "We now go over the jobs generated in the first notebook to store structures, energies, and forces into a structure container which will later be used for potential fitting\n", "\n", "**Note**: Usually these datasets are created using highly accurate DFT calculations. But for practical reasons, we only demonstrate how to do this using data from LAMMPS calculations (the workflow remain the same)" ] }, { "cell_type": "markdown", "id": "7c95a6c4-9332-41b4-a3fe-d87194d1bc2e", "metadata": {}, "source": [ "Access the project created in exercise 1. `..` means go up one folder in the directory tree as usual in linux." ] }, { "cell_type": "code", "execution_count": 4, "id": "contrary-spider", "metadata": {}, "outputs": [], "source": [ "pr_fs = pr[\"../first_steps\"]" ] }, { "cell_type": "markdown", "id": "1497263c-38c3-4c0f-9015-4dcdb6b2f3f1", "metadata": {}, "source": [ "Create a TrainingContainer job (to store structures and databases)." ] }, { "cell_type": "code", "execution_count": 5, "id": "superior-prospect", "metadata": {}, "outputs": [], "source": [ "container = pr.create.job.TrainingContainer('dataset_example')" ] }, { "cell_type": "markdown", "id": "verified-lancaster", "metadata": {}, "source": [ "## Add structures from the E-V curves\n", "\n", "For starters, we append structures from the energy volume curves we calculated earlier" ] }, { "cell_type": "code", "execution_count": 6, "id": "false-flexibility", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "b1848ff9b9ae4cad9b8c0bb14ce6a858", "version_major": 2, "version_minor": 0 }, "text/plain": [ " 0%| | 0/7 [00:00\n", "\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
nameatomsenergyforcesstressnumber_of_atoms
0job_a_3_8[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.192897[[1.6276043110675176e-16, 1.0529105848988851e-16, 5.1718187378489473e-17]][25.037460606087844, 25.03746060546885, 25.03746060312137, 1.2058153515681625e-10, -5.4886913858354095e-11, 5.489273462444544e-11]1
1job_a_3_9[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.319542[[7.639186604470375e-18, 1.2897999183801789e-17, 6.560662375038692e-17]][11.783580963401858, 11.783580963641624, 11.783580962525912, -9.081682946998626e-10, -5.281239282339811e-10, 5.281079211272299e-10]1
2job_a_4_0[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.367063[[-3.5024524628727396e-17, -1.320930466294525e-17, 5.849496262865057e-18]][2.177486595771194, 2.1774865945028847, 2.1774865945028834, -1.07506321000983e-09, 1.2040691217407586e-09, 7.657961759832688e-10]1
3job_a_4_1[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.360600[[-2.237762269513316e-17, -4.0689075283847526e-17, 2.1062919550300275e-17]][-3.3265634524504444, -3.3265634530820014, -3.3265634530820085, -6.528356607304887e-10, 1.6521880752407014e-12, 6.566095180460252e-10]1
4job_a_4_2[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.317017[[2.140556230444804e-17, 9.465137265930533e-17, -1.6146749725116617e-17]][-7.344005402848352, -7.344005402593722, -7.344005404806233, -4.6368149924092e-10, -7.669372280361131e-10, 7.669350452488288e-10]1
5job_a_4_3[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.241535[[-5.0018187940959333e-17, -7.753256254350387e-17, -7.947668332487412e-17]][-10.206225126673713, -10.206225127480902, -10.2062251274809, -6.120026228018106e-11, 5.826092092320323e-10, 7.850612746551634e-11]1
6job_a_4_4[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.145751[[-7.31320096256601e-17, 2.773206044106321e-16, -1.2031135854225408e-16]][-11.04382992252993, -11.043829922467113, -11.043829922415048, -1.632215571589768e-11, 6.058689905330539e-12, -6.060145096853376e-12]1
\n", "" ], "text/plain": [ " name \\\n", "0 job_a_3_8 \n", "1 job_a_3_9 \n", "2 job_a_4_0 \n", "3 job_a_4_1 \n", "4 job_a_4_2 \n", "5 job_a_4_3 \n", "6 job_a_4_4 \n", "\n", " atoms \\\n", "0 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "1 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "2 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "3 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "4 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "5 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "6 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "\n", " energy \\\n", "0 -3.192897 \n", "1 -3.319542 \n", "2 -3.367063 \n", "3 -3.360600 \n", "4 -3.317017 \n", "5 -3.241535 \n", "6 -3.145751 \n", "\n", " forces \\\n", "0 [[1.6276043110675176e-16, 1.0529105848988851e-16, 5.1718187378489473e-17]] \n", "1 [[7.639186604470375e-18, 1.2897999183801789e-17, 6.560662375038692e-17]] \n", "2 [[-3.5024524628727396e-17, -1.320930466294525e-17, 5.849496262865057e-18]] \n", "3 [[-2.237762269513316e-17, -4.0689075283847526e-17, 2.1062919550300275e-17]] \n", "4 [[2.140556230444804e-17, 9.465137265930533e-17, -1.6146749725116617e-17]] \n", "5 [[-5.0018187940959333e-17, -7.753256254350387e-17, -7.947668332487412e-17]] \n", "6 [[-7.31320096256601e-17, 2.773206044106321e-16, -1.2031135854225408e-16]] \n", "\n", " stress \\\n", "0 [25.037460606087844, 25.03746060546885, 25.03746060312137, 1.2058153515681625e-10, -5.4886913858354095e-11, 5.489273462444544e-11] \n", "1 [11.783580963401858, 11.783580963641624, 11.783580962525912, -9.081682946998626e-10, -5.281239282339811e-10, 5.281079211272299e-10] \n", "2 [2.177486595771194, 2.1774865945028847, 2.1774865945028834, -1.07506321000983e-09, 1.2040691217407586e-09, 7.657961759832688e-10] \n", "3 [-3.3265634524504444, -3.3265634530820014, -3.3265634530820085, -6.528356607304887e-10, 1.6521880752407014e-12, 6.566095180460252e-10] \n", "4 [-7.344005402848352, -7.344005402593722, -7.344005404806233, -4.6368149924092e-10, -7.669372280361131e-10, 7.669350452488288e-10] \n", "5 [-10.206225126673713, -10.206225127480902, -10.2062251274809, -6.120026228018106e-11, 5.826092092320323e-10, 7.850612746551634e-11] \n", "6 [-11.04382992252993, -11.043829922467113, -11.043829922415048, -1.632215571589768e-11, 6.058689905330539e-12, -6.060145096853376e-12] \n", "\n", " number_of_atoms \n", "0 1 \n", "1 1 \n", "2 1 \n", "3 1 \n", "4 1 \n", "5 1 \n", "6 1 " ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "container.to_pandas()" ] }, { "cell_type": "markdown", "id": "indirect-sellers", "metadata": {}, "source": [ "## Add structures from the MD\n", "\n", "We also add some structures obtained from the MD simulations" ] }, { "cell_type": "markdown", "id": "4e67fde4-6c7e-41d4-90b1-f86996cb8119", "metadata": {}, "source": [ "Reloading the MD job. Indexing a project loads jobs within." ] }, { "cell_type": "code", "execution_count": 8, "id": "applied-spank", "metadata": {}, "outputs": [], "source": [ "job_md = pr_fs[\"lammps_job\"]" ] }, { "cell_type": "markdown", "id": "28ed1a2c-dbf9-4bc9-80fa-ec38cfb51ef5", "metadata": {}, "source": [ "We can now iterate over the structures within and add each of them to the container." ] }, { "cell_type": "code", "execution_count": 9, "id": "972b14db-1ce6-4379-86a9-e93e14bdd07a", "metadata": {}, "outputs": [], "source": [ "traj_length = job_md.number_of_structures\n", "stride = 10" ] }, { "cell_type": "markdown", "id": "f944de10-37d8-466a-8a63-66225debf2ea", "metadata": {}, "source": [ "By default include_job will fetch the last computation step from the given job\n", "for other steps you have to explicitly pass which step you want." ] }, { "cell_type": "code", "execution_count": 10, "id": "56883632-a394-46fe-955c-57652a6181ee", "metadata": {}, "outputs": [], "source": [ "for i in range(0, traj_length, stride):\n", " container.include_job(job_md, iteration_step=i)" ] }, { "cell_type": "markdown", "id": "consecutive-arbitration", "metadata": {}, "source": [ "## Add some defect structures (vacancies, surfaces, etc)\n", "\n", "It's necessary to also include some defect structures, and surfaces to the training dataset.\n", "\n", "Setup a MD calculation for a structure with a vacancy." ] }, { "cell_type": "code", "execution_count": 11, "id": "a02096a1-fb7e-4a8b-99ce-4ce56f99dd2f", "metadata": {}, "outputs": [], "source": [ "job_lammps = pr.create.job.Lammps(\"lammps_job_vac\")\n", "job_lammps.structure = pr.create.structure.bulk(\"Al\", cubic=True, a=3.61).repeat([3, 3, 3])" ] }, { "cell_type": "markdown", "id": "f791fdfc-0ed8-4bd7-9002-230a9b2cc327", "metadata": {}, "source": [ "remove the first atom of the structure to create the vacancy" ] }, { "cell_type": "code", "execution_count": 12, "id": "3bb72ef5-77c2-443f-b9fc-ffedf3fe2a3d", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "The job lammps_job_vac was saved and received the ID: 94\n" ] } ], "source": [ "del job_lammps.structure[0]\n", "job_lammps.potential = \"2005--Mendelev-M-I--Al-Fe--LAMMPS--ipr1\"\n", "job_lammps.calc_md(temperature=800, pressure=0, n_ionic_steps=10000)\n", "job_lammps.run()" ] }, { "cell_type": "markdown", "id": "b3b44c05-493d-45b1-ad7d-556ae6c3aab4", "metadata": {}, "source": [ "Setup a MD calculation for a surface structure" ] }, { "cell_type": "code", "execution_count": 13, "id": "7299eb34-2b12-4730-b2eb-02991c78f8c7", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "The job lammps_job_surf was saved and received the ID: 95\n" ] } ], "source": [ "job_lammps = pr.create.job.Lammps(\"lammps_job_surf\")\n", "job_lammps.structure = pr.create.structure.surface(\"Al\", surface_type=\"fcc111\", size=(4, 4, 8), vacuum=12, orthogonal=True)\n", "job_lammps.potential = \"2005--Mendelev-M-I--Al-Fe--LAMMPS--ipr1\"\n", "job_lammps.calc_md(temperature=800, pressure=0, n_ionic_steps=10000)\n", "job_lammps.run()" ] }, { "cell_type": "code", "execution_count": 14, "id": "accepted-silly", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "{'groups': [], 'nodes': ['lammps_job_vac', 'lammps_job_surf']}" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "pr" ] }, { "cell_type": "markdown", "id": "diverse-stability", "metadata": {}, "source": [ "We now add these structures to the dataset like we did before." ] }, { "cell_type": "code", "execution_count": 15, "id": "single-treasure", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "31bc8ca78c8342b99dd8870a3d673da9", "version_major": 2, "version_minor": 0 }, "text/plain": [ " 0%| | 0/2 [00:00\n", "\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
idstatuschemicalformulajobsubjobprojectpathprojecttimestarttimestoptotalcputimecomputerhamiltonhamversionparentidmasterid
094finishedAl107lammps_job_vac/lammps_job_vac/home/jovyan/potentials/introduction/creating_datasets/2022-06-07 16:37:46.7207562022-06-07 16:37:49.8238563.0pyiron@jupyter-m-2epoul#1Lammps0.1NoneNone
195finishedAl128lammps_job_surf/lammps_job_surf/home/jovyan/potentials/introduction/creating_datasets/2022-06-07 16:37:51.2148532022-06-07 16:37:53.8329372.0pyiron@jupyter-m-2epoul#1Lammps0.1NoneNone
296finishedNonedataset_example/dataset_example/home/jovyan/potentials/introduction/creating_datasets/2022-06-07 16:37:56.081557NaTNaNpyiron@jupyter-m-2epoul#1TrainingContainer0.4NoneNone
\n", "" ], "text/plain": [ " id status chemicalformula job subjob \\\n", "0 94 finished Al107 lammps_job_vac /lammps_job_vac \n", "1 95 finished Al128 lammps_job_surf /lammps_job_surf \n", "2 96 finished None dataset_example /dataset_example \n", "\n", " projectpath project \\\n", "0 /home/jovyan/ potentials/introduction/creating_datasets/ \n", "1 /home/jovyan/ potentials/introduction/creating_datasets/ \n", "2 /home/jovyan/ potentials/introduction/creating_datasets/ \n", "\n", " timestart timestop totalcputime \\\n", "0 2022-06-07 16:37:46.720756 2022-06-07 16:37:49.823856 3.0 \n", "1 2022-06-07 16:37:51.214853 2022-06-07 16:37:53.832937 2.0 \n", "2 2022-06-07 16:37:56.081557 NaT NaN \n", "\n", " computer hamilton hamversion parentid masterid \n", "0 pyiron@jupyter-m-2epoul#1 Lammps 0.1 None None \n", "1 pyiron@jupyter-m-2epoul#1 Lammps 0.1 None None \n", "2 pyiron@jupyter-m-2epoul#1 TrainingContainer 0.4 None None " ] }, "execution_count": 17, "metadata": {}, "output_type": "execute_result" } ], "source": [ "pr.job_table()" ] }, { "cell_type": "markdown", "id": "technological-partner", "metadata": {}, "source": [ "## Reloading the dataset\n", "\n", "This dataset can now be reloaded anywhere to use in the potential fitting procedures" ] }, { "cell_type": "code", "execution_count": 18, "id": "processed-samuel", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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nameatomsenergyforcesstressnumber_of_atoms
0job_a_3_8[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.192897[[1.6276043110675176e-16, 1.0529105848988851e-16, 5.1718187378489473e-17]][25.037460606087844, 25.03746060546885, 25.03746060312137, 1.2058153515681625e-10, -5.4886913858354095e-11, 5.489273462444544e-11]1
1job_a_3_9[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.319542[[7.639186604470375e-18, 1.2897999183801789e-17, 6.560662375038692e-17]][11.783580963401858, 11.783580963641624, 11.783580962525912, -9.081682946998626e-10, -5.281239282339811e-10, 5.281079211272299e-10]1
2job_a_4_0[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.367063[[-3.5024524628727396e-17, -1.320930466294525e-17, 5.849496262865057e-18]][2.177486595771194, 2.1774865945028847, 2.1774865945028834, -1.07506321000983e-09, 1.2040691217407586e-09, 7.657961759832688e-10]1
3job_a_4_1[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.360600[[-2.237762269513316e-17, -4.0689075283847526e-17, 2.1062919550300275e-17]][-3.3265634524504444, -3.3265634530820014, -3.3265634530820085, -6.528356607304887e-10, 1.6521880752407014e-12, 6.566095180460252e-10]1
4job_a_4_2[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.317017[[2.140556230444804e-17, 9.465137265930533e-17, -1.6146749725116617e-17]][-7.344005402848352, -7.344005402593722, -7.344005404806233, -4.6368149924092e-10, -7.669372280361131e-10, 7.669350452488288e-10]1
5job_a_4_3[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.241535[[-5.0018187940959333e-17, -7.753256254350387e-17, -7.947668332487412e-17]][-10.206225126673713, -10.206225127480902, -10.2062251274809, -6.120026228018106e-11, 5.826092092320323e-10, 7.850612746551634e-11]1
6job_a_4_4[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-3.145751[[-7.31320096256601e-17, 2.773206044106321e-16, -1.2031135854225408e-16]][-11.04382992252993, -11.043829922467113, -11.043829922415048, -1.632215571589768e-11, 6.058689905330539e-12, -6.060145096853376e-12]1
7lammps_job[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-363.917370[[5.8841820305133305e-15, 3.7990444123892135e-16, 2.740863092043364e-16], [5.02375918642883e-15, -1.5751289161869397e-15, -1.3274971399912499e-15], [1.02695629777827e-15, 8.812395257962181e-16, -8...[0.999556665124294, 0.9904736758167861, 0.824951894171107, -0.0179550181978282, 0.0636336051961363, -0.042563616603965106]108
8lammps_job[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-352.327898[[-0.75036385499113, 0.4598380918639449, 0.725200216845603], [-0.271732166045788, 0.302073802280348, 0.257384300490495], [0.448407157614891, -0.296549448310268, 0.241166662468148], [-0.00933123696...[-0.20333593198685002, -0.0514950077978542, -0.380336649881006, -0.192008378726288, -0.000849147802610262, -0.021247590027086802]108
9lammps_job[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-349.888834[[-0.380822550162949, 0.795020858927261, 0.552227922138795], [-0.815959874301847, -0.02386117799239805, -0.47623155209815404], [-0.286795110662345, 0.30418979949872, 0.970569998348215], [-0.550088...[-0.636237386917572, -1.22215332293502, -0.718802458515107, 0.0334113551032086, -0.467781756142989, -0.15083572558775]108
10lammps_job[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-350.830057[[-0.420012726158848, -0.266177748010431, -0.10061532349639205], [0.127384145208824, -0.248152628480852, -0.154576243850877], [-0.968537642185758, -0.39199433409687007, 0.11778481825176891], [-0.5...[-0.5131786603043991, 0.0857860295485518, -0.487658631946179, -0.00960577613028209, -0.194135185700395, -0.21118720406901198]108
11lammps_job[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-350.702007[[0.9153781717748, -0.5196757756775509, 0.498517073710415], [-0.667528324894004, -0.21672146416275304, -0.31211194811421505], [0.120312800491091, -0.043411302241849095, -0.406043538747074], [0.235...[-0.51351056300053, -0.20205565562462502, -0.349611569619353, 0.0656675082015293, -0.549794514544474, -0.0898565835636916]108
12lammps_job[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-350.283347[[0.235132393610786, -0.92320491047853, 0.23010090806109595], [0.4464059221284, 0.599380126332439, -0.47014243704993197], [-0.0750267922586507, 0.262245923203885, 0.479967633267096], [-0.694735048...[-0.578429638769351, -0.434046865104863, -0.168847000423391, 0.144047568705863, -0.10672866413529901, -0.318309629189494]108
13lammps_job[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-351.595189[[-0.10082749580572, 0.523484145402097, -1.0350343625323], [0.354729759304219, 0.701653159364364, 0.7878115361205081], [-0.0367556462367837, -0.495902791299659, 1.00115978036795], [-0.010109163992...[-0.48245036720220597, -0.6429619358987481, -0.45615891646821305, 0.12156601043839001, 0.028722694543442204, -0.138869603615178]108
14lammps_job[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-351.355429[[-0.53033805263242, 0.30151077109769797, 0.48889617311781], [0.365332073308618, 0.257204756311451, 0.46421415718266706], [-0.55795462205606, -0.528920209655739, -1.01193560142206], [-0.8349912505...[0.13501098545634, 0.8436525885969681, 0.633953784861439, -0.09832009167866321, -0.0583454827760237, -0.148099371736581]108
15lammps_job[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-349.861266[[-0.735834944299172, 0.16983472103263894, 0.30896574018502293], [-0.56617377829579, -0.06252047071209063, -0.18361928260349702], [-0.326718424112994, -0.721001479459434, 0.09705913082936173], [0....[0.446586866327166, 0.13068019034171802, -0.0693758990272317, -0.263866851749946, 0.10925215678469699, 0.13607792544806202]108
16lammps_job[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-352.007585[[0.301178602933076, 0.258002276944641, -0.27143156569769294], [-0.298930228924858, -0.03075712133705462, -0.364812391605405], [-0.797427142712701, -0.74286906074633, -0.4273785140338071], [0.0727...[-0.757934402614806, -0.614667264232027, -0.667927922027262, -0.20235825539995303, -0.188727963861254, 0.38752048478086604]108
17lammps_job[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-350.590328[[0.224009094047, -0.839607604551706, 0.777637424807001], [0.694708728593008, -0.01978842244270086, -0.563089538819962], [-0.0726046276015651, 0.180208519203361, 0.157259401253289], [0.11284631102...[-0.57750724810661, -0.330705291904955, -0.24897277922262204, 0.0035474383929712198, 0.217652379540492, -0.372803571664775]108
18lammps_job_vac[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-290.793066[[-3.1974423109204496e-14, -0.5904705706758219, -0.590470570675822], [-0.5904705706758229, -3.325957990662624e-14, -0.590470570675822], [-0.5904705706758219, -0.590470570675821, -3.642777903722078...[58.87969078759508, 58.65874845858828, 58.50796880315438, -0.047554178778302515, -0.33314286846391333, 0.07410497611298358]107
19lammps_job_surf[element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ...-428.609075[[2.44249065417534e-15, 4.56905929757667e-10, 0.314474097336679], [-9.29811783123569e-16, 4.56905354696835e-10, 0.314474097336678], [2.7611647777231502e-15, 4.56905929757667e-10, 0.314474097336678...[-0.693731819636784, -0.575956660364361, -0.802656043307567, -0.0667956150106202, -0.145663378134875, -0.0209963500927039]128
\n", "
" ], "text/plain": [ " name \\\n", "0 job_a_3_8 \n", "1 job_a_3_9 \n", "2 job_a_4_0 \n", "3 job_a_4_1 \n", "4 job_a_4_2 \n", "5 job_a_4_3 \n", "6 job_a_4_4 \n", "7 lammps_job \n", "8 lammps_job \n", "9 lammps_job \n", "10 lammps_job \n", "11 lammps_job \n", "12 lammps_job \n", "13 lammps_job \n", "14 lammps_job \n", "15 lammps_job \n", "16 lammps_job \n", "17 lammps_job \n", "18 lammps_job_vac \n", "19 lammps_job_surf \n", "\n", " atoms \\\n", "0 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "1 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "2 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "3 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "4 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "5 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "6 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "7 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "8 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "9 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "10 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "11 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "12 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "13 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "14 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "15 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "16 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "17 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "18 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "19 [element: [None, AtomicNumber 13\\nAtomicRadius 118.0\\nAtomicMass 26.981539\\nColor Silver\\nCovalentRadius ... \n", "\n", " energy \\\n", "0 -3.192897 \n", "1 -3.319542 \n", "2 -3.367063 \n", "3 -3.360600 \n", "4 -3.317017 \n", "5 -3.241535 \n", "6 -3.145751 \n", "7 -363.917370 \n", "8 -352.327898 \n", "9 -349.888834 \n", "10 -350.830057 \n", "11 -350.702007 \n", "12 -350.283347 \n", "13 -351.595189 \n", "14 -351.355429 \n", "15 -349.861266 \n", "16 -352.007585 \n", "17 -350.590328 \n", "18 -290.793066 \n", "19 -428.609075 \n", "\n", " forces \\\n", "0 [[1.6276043110675176e-16, 1.0529105848988851e-16, 5.1718187378489473e-17]] \n", "1 [[7.639186604470375e-18, 1.2897999183801789e-17, 6.560662375038692e-17]] \n", "2 [[-3.5024524628727396e-17, -1.320930466294525e-17, 5.849496262865057e-18]] \n", "3 [[-2.237762269513316e-17, -4.0689075283847526e-17, 2.1062919550300275e-17]] \n", "4 [[2.140556230444804e-17, 9.465137265930533e-17, -1.6146749725116617e-17]] \n", "5 [[-5.0018187940959333e-17, -7.753256254350387e-17, -7.947668332487412e-17]] \n", "6 [[-7.31320096256601e-17, 2.773206044106321e-16, -1.2031135854225408e-16]] \n", "7 [[5.8841820305133305e-15, 3.7990444123892135e-16, 2.740863092043364e-16], [5.02375918642883e-15, -1.5751289161869397e-15, -1.3274971399912499e-15], [1.02695629777827e-15, 8.812395257962181e-16, -8... \n", "8 [[-0.75036385499113, 0.4598380918639449, 0.725200216845603], [-0.271732166045788, 0.302073802280348, 0.257384300490495], [0.448407157614891, -0.296549448310268, 0.241166662468148], [-0.00933123696... \n", "9 [[-0.380822550162949, 0.795020858927261, 0.552227922138795], [-0.815959874301847, -0.02386117799239805, -0.47623155209815404], [-0.286795110662345, 0.30418979949872, 0.970569998348215], [-0.550088... \n", "10 [[-0.420012726158848, -0.266177748010431, -0.10061532349639205], [0.127384145208824, -0.248152628480852, -0.154576243850877], [-0.968537642185758, -0.39199433409687007, 0.11778481825176891], [-0.5... \n", "11 [[0.9153781717748, -0.5196757756775509, 0.498517073710415], [-0.667528324894004, -0.21672146416275304, -0.31211194811421505], [0.120312800491091, -0.043411302241849095, -0.406043538747074], [0.235... \n", "12 [[0.235132393610786, -0.92320491047853, 0.23010090806109595], [0.4464059221284, 0.599380126332439, -0.47014243704993197], [-0.0750267922586507, 0.262245923203885, 0.479967633267096], [-0.694735048... \n", "13 [[-0.10082749580572, 0.523484145402097, -1.0350343625323], [0.354729759304219, 0.701653159364364, 0.7878115361205081], [-0.0367556462367837, -0.495902791299659, 1.00115978036795], [-0.010109163992... \n", "14 [[-0.53033805263242, 0.30151077109769797, 0.48889617311781], [0.365332073308618, 0.257204756311451, 0.46421415718266706], [-0.55795462205606, -0.528920209655739, -1.01193560142206], [-0.8349912505... \n", "15 [[-0.735834944299172, 0.16983472103263894, 0.30896574018502293], [-0.56617377829579, -0.06252047071209063, -0.18361928260349702], [-0.326718424112994, -0.721001479459434, 0.09705913082936173], [0.... \n", "16 [[0.301178602933076, 0.258002276944641, -0.27143156569769294], [-0.298930228924858, -0.03075712133705462, -0.364812391605405], [-0.797427142712701, -0.74286906074633, -0.4273785140338071], [0.0727... \n", "17 [[0.224009094047, -0.839607604551706, 0.777637424807001], [0.694708728593008, -0.01978842244270086, -0.563089538819962], [-0.0726046276015651, 0.180208519203361, 0.157259401253289], [0.11284631102... \n", "18 [[-3.1974423109204496e-14, -0.5904705706758219, -0.590470570675822], [-0.5904705706758229, -3.325957990662624e-14, -0.590470570675822], [-0.5904705706758219, -0.590470570675821, -3.642777903722078... \n", "19 [[2.44249065417534e-15, 4.56905929757667e-10, 0.314474097336679], [-9.29811783123569e-16, 4.56905354696835e-10, 0.314474097336678], [2.7611647777231502e-15, 4.56905929757667e-10, 0.314474097336678... \n", "\n", " stress \\\n", "0 [25.037460606087844, 25.03746060546885, 25.03746060312137, 1.2058153515681625e-10, -5.4886913858354095e-11, 5.489273462444544e-11] \n", "1 [11.783580963401858, 11.783580963641624, 11.783580962525912, -9.081682946998626e-10, -5.281239282339811e-10, 5.281079211272299e-10] \n", "2 [2.177486595771194, 2.1774865945028847, 2.1774865945028834, -1.07506321000983e-09, 1.2040691217407586e-09, 7.657961759832688e-10] \n", "3 [-3.3265634524504444, -3.3265634530820014, -3.3265634530820085, -6.528356607304887e-10, 1.6521880752407014e-12, 6.566095180460252e-10] \n", "4 [-7.344005402848352, -7.344005402593722, -7.344005404806233, -4.6368149924092e-10, -7.669372280361131e-10, 7.669350452488288e-10] \n", "5 [-10.206225126673713, -10.206225127480902, -10.2062251274809, -6.120026228018106e-11, 5.826092092320323e-10, 7.850612746551634e-11] \n", "6 [-11.04382992252993, -11.043829922467113, -11.043829922415048, -1.632215571589768e-11, 6.058689905330539e-12, -6.060145096853376e-12] \n", "7 [0.999556665124294, 0.9904736758167861, 0.824951894171107, -0.0179550181978282, 0.0636336051961363, -0.042563616603965106] \n", "8 [-0.20333593198685002, -0.0514950077978542, -0.380336649881006, -0.192008378726288, -0.000849147802610262, -0.021247590027086802] \n", "9 [-0.636237386917572, -1.22215332293502, -0.718802458515107, 0.0334113551032086, -0.467781756142989, -0.15083572558775] \n", "10 [-0.5131786603043991, 0.0857860295485518, -0.487658631946179, -0.00960577613028209, -0.194135185700395, -0.21118720406901198] \n", "11 [-0.51351056300053, -0.20205565562462502, -0.349611569619353, 0.0656675082015293, -0.549794514544474, -0.0898565835636916] \n", "12 [-0.578429638769351, -0.434046865104863, -0.168847000423391, 0.144047568705863, -0.10672866413529901, -0.318309629189494] \n", "13 [-0.48245036720220597, -0.6429619358987481, -0.45615891646821305, 0.12156601043839001, 0.028722694543442204, -0.138869603615178] \n", "14 [0.13501098545634, 0.8436525885969681, 0.633953784861439, -0.09832009167866321, -0.0583454827760237, -0.148099371736581] \n", "15 [0.446586866327166, 0.13068019034171802, -0.0693758990272317, -0.263866851749946, 0.10925215678469699, 0.13607792544806202] \n", "16 [-0.757934402614806, -0.614667264232027, -0.667927922027262, -0.20235825539995303, -0.188727963861254, 0.38752048478086604] \n", "17 [-0.57750724810661, -0.330705291904955, -0.24897277922262204, 0.0035474383929712198, 0.217652379540492, -0.372803571664775] \n", "18 [58.87969078759508, 58.65874845858828, 58.50796880315438, -0.047554178778302515, -0.33314286846391333, 0.07410497611298358] \n", "19 [-0.693731819636784, -0.575956660364361, -0.802656043307567, -0.0667956150106202, -0.145663378134875, -0.0209963500927039] \n", "\n", " number_of_atoms \n", "0 1 \n", "1 1 \n", "2 1 \n", "3 1 \n", "4 1 \n", "5 1 \n", "6 1 \n", "7 108 \n", "8 108 \n", "9 108 \n", "10 108 \n", "11 108 \n", "12 108 \n", "13 108 \n", "14 108 \n", "15 108 \n", "16 108 \n", "17 108 \n", "18 107 \n", "19 128 " ] }, "execution_count": 18, "metadata": {}, "output_type": "execute_result" } ], "source": [ "dataset = pr[\"dataset_example\"]\n", "dataset.to_pandas()" ] }, { "cell_type": "markdown", "id": "julian-helena", "metadata": {}, "source": [ "We can now inspect the data in this dataset quite easily" ] }, { "cell_type": "code", "execution_count": 19, "id": "starting-dress", "metadata": {}, "outputs": [], "source": [ "struct = dataset.get_structure(10)" ] }, { "cell_type": "code", "execution_count": 20, "id": "17e6c3dc-9434-4423-86e6-50c014ce34e6", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "be32df4aeb1540f48e05dfc3ffe9b651", "version_major": 2, "version_minor": 0 }, "text/plain": [] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "7b5ac841e06742c99f8085b15a5ebdb4", "version_major": 2, "version_minor": 0 }, "text/plain": [ "NGLWidget()" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "struct.plot3d()" ] }, { "cell_type": "code", "execution_count": 21, "id": "8ee351f5-d547-4270-b4b4-3bec1af7eed1", "metadata": {}, "outputs": [ { "data": { "image/png": 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\n", 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" ] }, "metadata": { "needs_background": "light" }, "output_type": "display_data" } ], "source": [ "dataset.plot.energy_volume();" ] }, { "cell_type": "code", "execution_count": 22, "id": "ccd8a646-7767-4a85-9cfa-fb4fccd5b574", "metadata": {}, "outputs": [ { "data": { "image/png": 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\n", 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" ] }, "metadata": { "needs_background": "light" }, "output_type": "display_data" } ], "source": [ "dataset.plot.forces()" ] }, { "cell_type": "markdown", "id": "suited-blank", "metadata": {}, "source": [ "The datasets used in the potential fitting procedure for day 2 (obtained from accurate DFT calculations) will be accessed in the same way." ] }, { "cell_type": "markdown", "id": "82610317-50e7-4ebe-9344-6418e8c01715", "metadata": {}, "source": [ "## Extra Credit\n", "\n", "1. Add more interesting structures. Ideas:\n", " - Dimer, trimers\n", " - Cleaving of a bulk structure, i.e. create a super cell and separate the atoms along a chosen plane\n", " - high or low pressure MD\n", " - Different crystal structures\n", " - ..." ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "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": "3.10.5" }, "widgets": { "application/vnd.jupyter.widget-state+json": { "state": {}, "version_major": 2, "version_minor": 0 } } }, "nbformat": 4, "nbformat_minor": 5 }