{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/prehner/.conda/envs/feos/lib/python3.9/site-packages/pymatgen/core/__init__.py:49: UserWarning: Error loading .pmgrc.yaml: [Errno 2] No such file or directory: '/home/prehner/.pmgrc.yaml'. You may need to reconfigure your yaml file.\n", " warnings.warn(f\"Error loading .pmgrc.yaml: {ex}. You may need to reconfigure your yaml file.\")\n" ] } ], "source": [ "from feos.si import *\n", "from feos.dft import Pore3D, Adsorption3D, DFTSolver, FMTVersion, HelmholtzEnergyFunctional\n", "from feos.pcsaft import PcSaftParameters\n", "\n", "import pandas as pd\n", "import numpy as np\n", "\n", "from pymatgen.core import Structure\n", "from pymatgen.analysis import structure_matcher\n", "\n", "import matplotlib.pyplot as plt" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "formula: Zn12 H120 C96 N48\n", "num_sites: 276\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/home/prehner/.conda/envs/feos/lib/python3.9/site-packages/pymatgen/io/cif.py:669: UserWarning: A 1-line symmetry op P1 CIF is detected!\n", " warnings.warn(msg)\n", "/home/prehner/.conda/envs/feos/lib/python3.9/site-packages/pymatgen/io/cif.py:1160: UserWarning: Issues encountered while parsing CIF: A 1-line symmetry op P1 CIF is detected!\n", " warnings.warn(\"Issues encountered while parsing CIF: %s\" % \"\\n\".join(self.warnings))\n" ] } ], "source": [ "structure = Structure.from_file('structure_parameters/ZIF-8.cif')\n", "print('formula: ', structure.formula)\n", "print('num_sites:', structure.num_sites)" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "coordinates = structure.cart_coords.T * ANGSTROM\n", "system_size = [l * ANGSTROM for l in structure.lattice.lengths]" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | type | \n", "sigma | \n", "epsilon | \n", "mass | \n", "
---|---|---|---|---|
0 | \n", "O | \n", "3.03300 | \n", "48.1581 | \n", "15.99900 | \n", "
1 | \n", "C | \n", "3.47299 | \n", "47.8562 | \n", "12.01070 | \n", "
2 | \n", "H | \n", "2.84600 | \n", "7.6489 | \n", "1.00784 | \n", "
3 | \n", "N | \n", "3.26250 | \n", "38.9492 | \n", "14.00670 | \n", "
4 | \n", "B | \n", "3.58100 | \n", "47.8059 | \n", "10.81100 | \n", "
5 | \n", "Zn | \n", "1.33000 | \n", "109.4710 | \n", "65.38000 | \n", "