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{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"name": "pbx_stable_entry.ipynb",
"provenance": [],
"authorship_tag": "ABX9TyMnKVMFA5XbpTq19FcwBSDs",
"include_colab_link": true
},
"kernelspec": {
"name": "python3",
"display_name": "Python 3"
}
},
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
},
"source": [
"<a href=\"https://colab.research.google.com/gist/onepunchdan/4c1054d3d7a396d407d652f79db76b8f/pbx_stable_entry.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"cell_type": "code",
"metadata": {
"id": "NuJwmt4PmRUl",
"colab_type": "code",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 987
},
"outputId": "883141ff-b97b-48af-fe2e-6f18ed7313fe"
},
"source": [
"!pip install pymatgen"
],
"execution_count": 1,
"outputs": [
{
"output_type": "stream",
"text": [
"Collecting pymatgen\n",
"\u001b[?25l Downloading https://files.pythonhosted.org/packages/01/82/5802c2a0014c57e9de11ab46718edf1f3f3d9e449c86f378819ec3dd540f/pymatgen-2020.3.2.tar.gz (2.6MB)\n",
"\u001b[K |████████████████████████████████| 2.6MB 5.0MB/s \n",
"\u001b[?25hRequirement already satisfied: numpy>=1.14.3 in /usr/local/lib/python3.6/dist-packages (from pymatgen) (1.17.5)\n",
"Requirement already satisfied: requests in /usr/local/lib/python3.6/dist-packages (from pymatgen) (2.21.0)\n",
"Collecting ruamel.yaml>=0.15.6\n",
"\u001b[?25l Downloading https://files.pythonhosted.org/packages/a6/92/59af3e38227b9cc14520bf1e59516d99ceca53e3b8448094248171e9432b/ruamel.yaml-0.16.10-py2.py3-none-any.whl (111kB)\n",
"\u001b[K |████████████████████████████████| 112kB 51.8MB/s \n",
"\u001b[?25hCollecting monty>=3.0.2\n",
"\u001b[?25l Downloading https://files.pythonhosted.org/packages/b1/a4/d57b127ad2103ebc1a21a9c6379abc10d5f57f5d92cac86532c15a43818f/monty-3.0.2-py3-none-any.whl (61kB)\n",
"\u001b[K |████████████████████████████████| 61kB 8.8MB/s \n",
"\u001b[?25hRequirement already satisfied: scipy>=1.0.1 in /usr/local/lib/python3.6/dist-packages (from pymatgen) (1.4.1)\n",
"Collecting pydispatcher>=2.0.5\n",
" Downloading https://files.pythonhosted.org/packages/cd/37/39aca520918ce1935bea9c356bcbb7ed7e52ad4e31bff9b943dfc8e7115b/PyDispatcher-2.0.5.tar.gz\n",
"Requirement already satisfied: tabulate in /usr/local/lib/python3.6/dist-packages (from pymatgen) (0.8.6)\n",
"Collecting spglib>=1.9.9.44\n",
"\u001b[?25l Downloading https://files.pythonhosted.org/packages/2c/95/a9da9b1c7f176347cd268c9d618535194d796f0e3d1c5566738bd2fe3dd9/spglib-1.14.1.post0-cp36-cp36m-manylinux2010_x86_64.whl (287kB)\n",
"\u001b[K |████████████████████████████████| 296kB 54.7MB/s \n",
"\u001b[?25hRequirement already satisfied: networkx>=2.2 in /usr/local/lib/python3.6/dist-packages (from pymatgen) (2.4)\n",
"Requirement already satisfied: matplotlib>=1.5 in /usr/local/lib/python3.6/dist-packages (from pymatgen) (3.1.3)\n",
"Requirement already satisfied: palettable>=3.1.1 in /usr/local/lib/python3.6/dist-packages (from pymatgen) (3.3.0)\n",
"Requirement already satisfied: sympy in /usr/local/lib/python3.6/dist-packages (from pymatgen) (1.1.1)\n",
"Requirement already satisfied: pandas<1.0 in /usr/local/lib/python3.6/dist-packages (from pymatgen) (0.25.3)\n",
"Requirement already satisfied: dataclasses>=0.6 in /usr/local/lib/python3.6/dist-packages (from pymatgen) (0.7)\n",
"Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /usr/local/lib/python3.6/dist-packages (from requests->pymatgen) (3.0.4)\n",
"Requirement already satisfied: urllib3<1.25,>=1.21.1 in /usr/local/lib/python3.6/dist-packages (from requests->pymatgen) (1.24.3)\n",
"Requirement already satisfied: idna<2.9,>=2.5 in /usr/local/lib/python3.6/dist-packages (from requests->pymatgen) (2.8)\n",
"Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.6/dist-packages (from requests->pymatgen) (2019.11.28)\n",
"Collecting ruamel.yaml.clib>=0.1.2; platform_python_implementation == \"CPython\" and python_version < \"3.9\"\n",
"\u001b[?25l Downloading https://files.pythonhosted.org/packages/53/77/4bcd63f362bcb6c8f4f06253c11f9772f64189bf08cf3f40c5ccbda9e561/ruamel.yaml.clib-0.2.0-cp36-cp36m-manylinux1_x86_64.whl (548kB)\n",
"\u001b[K |████████████████████████████████| 552kB 44.6MB/s \n",
"\u001b[?25hRequirement already satisfied: decorator>=4.3.0 in /usr/local/lib/python3.6/dist-packages (from networkx>=2.2->pymatgen) (4.4.1)\n",
"Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib>=1.5->pymatgen) (1.1.0)\n",
"Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib>=1.5->pymatgen) (2.6.1)\n",
"Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib>=1.5->pymatgen) (2.4.6)\n",
"Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.6/dist-packages (from matplotlib>=1.5->pymatgen) (0.10.0)\n",
"Requirement already satisfied: mpmath>=0.19 in /usr/local/lib/python3.6/dist-packages (from sympy->pymatgen) (1.1.0)\n",
"Requirement already satisfied: pytz>=2017.2 in /usr/local/lib/python3.6/dist-packages (from pandas<1.0->pymatgen) (2018.9)\n",
"Requirement already satisfied: setuptools in /usr/local/lib/python3.6/dist-packages (from kiwisolver>=1.0.1->matplotlib>=1.5->pymatgen) (45.2.0)\n",
"Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.6/dist-packages (from python-dateutil>=2.1->matplotlib>=1.5->pymatgen) (1.12.0)\n",
"Building wheels for collected packages: pymatgen, pydispatcher\n",
" Building wheel for pymatgen (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
" Created wheel for pymatgen: filename=pymatgen-2020.3.2-cp36-cp36m-linux_x86_64.whl size=3482672 sha256=7ce135377de0f0ffc864686bdf240705d7be32411a9d0adff573fc7dc0cec16b\n",
" Stored in directory: /root/.cache/pip/wheels/ae/bd/ee/fc00e534c39ca4646bb87f17af30388cef5d6f23741f007aaf\n",
" Building wheel for pydispatcher (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
" Created wheel for pydispatcher: filename=PyDispatcher-2.0.5-cp36-none-any.whl size=11515 sha256=473eda18c478214e4d3db10120aadecab891137ce3cc82c9940f2f64ebada56b\n",
" Stored in directory: /root/.cache/pip/wheels/88/99/96/cfef6665f9cb1522ee6757ae5955feedf2fe25f1737f91fa7f\n",
"Successfully built pymatgen pydispatcher\n",
"Installing collected packages: ruamel.yaml.clib, ruamel.yaml, monty, pydispatcher, spglib, pymatgen\n",
"Successfully installed monty-3.0.2 pydispatcher-2.0.5 pymatgen-2020.3.2 ruamel.yaml-0.16.10 ruamel.yaml.clib-0.2.0 spglib-1.14.1.post0\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "RUMqFcmImhso",
"colab_type": "code",
"colab": {}
},
"source": [
"\n",
"from getpass import getpass\n",
"from pymatgen import MPRester, Composition\n",
"from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, PourbaixPlotter, MultiEntry\n",
"import numpy as np\n",
"import pandas as pd\n",
"import matplotlib.pyplot as plt"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "0LOAai9PmiU7",
"colab_type": "code",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 36
},
"outputId": "36d8b68d-f59f-42bf-f7cf-37cc9b8b7d8b"
},
"source": [
"apikey = getpass()"
],
"execution_count": 3,
"outputs": [
{
"output_type": "stream",
"text": [
"··········\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "MIUYPdvUmlYx",
"colab_type": "code",
"colab": {}
},
"source": [
"r = MPRester(api_key=apikey)\n",
"\n",
"ids = [\"mp-504747\"]\n",
"\n",
"features = [\n",
" \"material_id\",\n",
" \"pretty_formula\",\n",
" \"unit_cell_formula\",\n",
" \"energy\",\n",
" \"energy_per_atom\",\n",
" \"nsites\",\n",
" \"elements\",\n",
" \"nelements\",\n",
" \"formation_energy_per_atom\",\n",
" \"e_above_hull\",\n",
" \"band_gap\",\n",
"]\n",
"\n",
"results = r.query(criteria={\"task_ids\": {\"$in\": ids}}, properties=features)"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "FHZEArYcnXIW",
"colab_type": "code",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 226
},
"outputId": "3b5ad780-47ad-4af0-a8e5-96795d055c72"
},
"source": [
"results[0]"
],
"execution_count": 8,
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": [
"{'band_gap': 0.0,\n",
" 'e_above_hull': 0.015648529230769093,\n",
" 'elements': ['Cu', 'O', 'V'],\n",
" 'energy': -82.61259564,\n",
" 'energy_per_atom': -6.354815049230769,\n",
" 'formation_energy_per_atom': -1.669922047692307,\n",
" 'material_id': 'mp-504747',\n",
" 'nelements': 3,\n",
" 'nsites': 13,\n",
" 'pretty_formula': 'V2Cu3O8',\n",
" 'unit_cell_formula': {'Cu': 3.0, 'O': 8.0, 'V': 2.0}}"
]
},
"metadata": {
"tags": []
},
"execution_count": 8
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "w_aY_-tJm1Iw",
"colab_type": "code",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 36
},
"outputId": "1ba5d274-738b-483a-f798-32a867f4868a"
},
"source": [
"comp = Composition(results[0]['pretty_formula'])\n",
"anions = [\n",
" \"H\",\n",
" \"B\",\n",
" \"C\",\n",
" \"Si\",\n",
" \"N\",\n",
" \"P\",\n",
" \"As\",\n",
" \"Sb\",\n",
" \"O\",\n",
" \"S\",\n",
" \"Se\",\n",
" \"Te\",\n",
" \"F\",\n",
" \"Cl\",\n",
" \"Br\",\n",
" \"I\",\n",
"]\n",
"els = [k for k in comp.as_dict().keys() if k not in anions]\n",
"comps_in = (\n",
" np.array([comp.as_dict()[el] for el in els])\n",
" / np.array([comp.as_dict()[el] for el in els]).sum()\n",
")\n",
"chemsys = comp.to_data_dict[\"elements\"]\n",
"compdict = comp.fractional_composition.get_el_amt_dict()\n",
"pbx_entries = r.get_pourbaix_entries(chemsys)\n",
"ref_entries = [entry for entry in pbx_entries if entry.entry_id == results[0][\"material_id\"]]\n",
"ref_mentry = MultiEntry(ref_entries)\n",
"pbx_diagram = PourbaixDiagram(\n",
" pbx_entries,\n",
" comp_dict={k: v for k, v in compdict.items() if k not in [\"H\", \"O\"]},\n",
" filter_solids=True,\n",
")"
],
"execution_count": 9,
"outputs": [
{
"output_type": "stream",
"text": [
"100%|██████████| 139/139 [00:00<00:00, 747.70it/s]\n"
],
"name": "stderr"
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "eCsVQVqNob60",
"colab_type": "code",
"colab": {}
},
"source": [
"rheshe = lambda rhe, ph: rhe - 0.059 * ph"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "uWBUgJKYoeFp",
"colab_type": "code",
"colab": {}
},
"source": [
"stable = pbx_diagram.get_stable_entry(13, rheshe(1.5, 13))"
],
"execution_count": 0,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "QEsmD5MOopFc",
"colab_type": "code",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 36
},
"outputId": "a8c2a7fd-e666-48b2-ef8b-a2492eb76ab9"
},
"source": [
"stable.name"
],
"execution_count": 13,
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": [
"'VO4[-] + VO4[3-]'"
]
},
"metadata": {
"tags": []
},
"execution_count": 13
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "pPiJgBSVoprK",
"colab_type": "code",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 55
},
"outputId": "a68fe3c6-7b30-4990-e46e-b152e56302d9"
},
"source": [
"stable.entry_list"
],
"execution_count": 14,
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": [
"[Pourbaix Entry : V1 O4 with energy = 0.6115, npH = -8.0, nPhi = -7.0, nH2O = 4.0, entry_id = ion-4 ,\n",
" Pourbaix Entry : V1 O4 with energy = 0.1351, npH = -8.0, nPhi = -5.0, nH2O = 4.0, entry_id = ion-3 ]"
]
},
"metadata": {
"tags": []
},
"execution_count": 14
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "AzIgTBDzowGm",
"colab_type": "text"
},
"source": [
"Compare with materialsproject.org [pourbaix diagram](https://materialsproject.org/#apps/pourbaixdiagram/%7B%22chemsys%22%3A%5B%22Cu%22%2C%22V%22%5D%2C%22projel%22%3A%22%22%2C%22mp_id%22%3A%22mp-504747%22%7D) which shows VO4[-] + Cu2O3(s) at these conditions"
]
},
{
"cell_type": "code",
"metadata": {
"id": "CijR8bSMp7ld",
"colab_type": "code",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 36
},
"outputId": "6b0fcba3-9dd0-43e7-dbfa-c1631f363e2d"
},
"source": [
"ref_mentry.entry_list"
],
"execution_count": 15,
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": [
"[Pourbaix Entry : O8 V2 Cu3 with energy = 0.4913, npH = -16.0, nPhi = -16.0, nH2O = 8.0, entry_id = mp-504747 ]"
]
},
"metadata": {
"tags": []
},
"execution_count": 15
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "Isp1t6mBp0QX",
"colab_type": "code",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 36
},
"outputId": "e5fd15cf-e36a-4e08-b7e4-5d77f764cf46"
},
"source": [
"pbx_diagram.get_decomposition_energy(ref_mentry, 13, rheshe(1.5, 13))"
],
"execution_count": 16,
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": [
"2.102000956662368"
]
},
"metadata": {
"tags": []
},
"execution_count": 16
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "Eg1M6nQ2qINx",
"colab_type": "text"
},
"source": [
"delta_Gpbx also ~0.7 eV/atom in this region according to online pourbaix diagram"
]
}
]
}
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