{ "cells": [ { "cell_type": "markdown", "id": "aa90814d", "metadata": {}, "source": [ "\n", "# Visualization" ] }, { "cell_type": "code", "execution_count": 1, "id": "13b6fb7e", "metadata": {}, "outputs": [], "source": [ "from eminus import Atoms, read, SCF\n", "from eminus.extras import view, view_atoms, view_contour, view_file" ] }, { "cell_type": "code", "execution_count": 2, "id": "4aa79c38", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "6dfe9cb77bdd4dd8b56e9abf8b6f9056", "version_major": 2, "version_minor": 0 }, "text/plain": [] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "XYZ file comment: \"Experimental geometry from CCCBDB: https://cccbdb.nist.gov/exp2x.asp?casno=74828&charge=0\"\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "d237f79edd99475e9ce53a403e8786db", "version_major": 2, "version_minor": 0 }, "text/plain": [ "NGLWidget()" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# View the initial xyz file\n", "mol = view_file(\"CH4.xyz\")\n", "mol" ] }, { "cell_type": "code", "execution_count": 3, "id": "64b432af", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "0abe36e215904b53854ffa6cd520c8cb", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Image(value=b'', width='400px')" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Render the view as an image, e.g., to download it\n", "# See the options here: https://nglviewer.org/nglview/latest/api.html#nglview.NGLWidget.render_image\n", "mol_img = mol.render_image()\n", "mol_img.width = \"400px\"\n", "mol_img" ] }, { "cell_type": "code", "execution_count": 4, "id": "df9c9c4c", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "XYZ file comment: \"Experimental geometry from CCCBDB: https://cccbdb.nist.gov/exp2x.asp?casno=74828&charge=0\"\n" ] } ], "source": [ "# Create the Atoms object\n", "atoms = Atoms(*read(\"CH4.xyz\"), center=True)\n", "atoms.s = 50" ] }, { "cell_type": "code", "execution_count": 5, "id": "ddcc7001", "metadata": {}, "outputs": [], "source": [ "# The calculations and writing steps have already been done, uncomment them if you want to do them for yourself\n", "# from eminus import USCF, write_cube, write_xyz\n", "# from eminus.extras import get_fods\n", "\n", "# Do the DFT calculation\n", "# scf = USCF(atoms)\n", "# scf.run()\n", "\n", "# Calculate FODs and write them to a xyz file\n", "# fods = get_fods(scf.atoms)\n", "# write_xyz(scf.atoms, \"CH4_fods.xyz\", fods)\n", "\n", "# Write the density to a cube file\n", "# write_cube(scf, \"CH4_density.cube\", scf.n)\n", "\n", "# One can even display FODs or the density without writing them to files\n", "# view_atoms(scf, fods, plot_n=True)" ] }, { "cell_type": "code", "execution_count": 6, "id": "8b5f21fd", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "cc2e69c3c00748c39dd86cc000931cf8", "version_major": 2, "version_minor": 0 }, "text/plain": [ "ThemeManager()" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "XYZ file comment: \"File generated with eminus 2.5.0 on Mon Jul 31 12:23:45 2023\"\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "45b8aa3c256e49269bbd2d87cc85ad3d", "version_major": 2, "version_minor": 0 }, "text/plain": [ "NGLWidget(gui_style='ngl')" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# View molecule with FODs with the GUI enabled\n", "view_file(\"CH4_fods.xyz\", gui=True)" ] }, { "cell_type": "code", "execution_count": 7, "id": "980e5726", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "CUBE file comment: \"File generated with eminus 2.5.0 on Mon Jul 31 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