{ "cells": [ { "cell_type": "markdown", "id": "a2dcd883", "metadata": { "editable": true, "slideshow": { "slide_type": "" }, "tags": [] }, "source": [ "# Exercises\n", "\n", "In this exercise we will look at how substitution affects the vibrational frequencies, IR, and Raman spectra." ] }, { "cell_type": "code", "execution_count": 1, "id": "50d67d06-0b76-4fa4-af57-f4930deddf34", "metadata": { "editable": true, "slideshow": { "slide_type": "" }, "tags": [ "remove-output" ] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "* Warning * Environment variable OMP_NUM_THREADS not set.\n", "* Warning * Setting OMP_NUM_THREADS to 4.\n" ] } ], "source": [ "# import section\n", "import numpy as np\n", "import py3Dmol as p3d\n", "import veloxchem as vlx\n", "from matplotlib import pyplot as plt\n", "from veloxchem.veloxchemlib import bohr_in_angstroms\n", "\n", "basis_set_label = \"6-31G\"" ] }, { "cell_type": "code", "execution_count": 2, "id": "b57d9a98-7ea2-437c-896b-82b105add8cd", "metadata": { "editable": true, "scrolled": true, "slideshow": { "slide_type": "" }, "tags": [ "remove-output" ] }, "outputs": [], "source": [ "# define molecules and basis sets\n", "ethene_xyz = \"\"\"6\n", " ethene\n", " C 0.000000 -0.663984 0.000000\n", " C 0.000000 0.663984 0.000000\n", " H 0.919796 -1.223061 0.000000\n", " H -0.919796 -1.223061 0.000000\n", " H 0.919796 1.223061 0.000000\n", " H -0.919796 1.223061 0.000000\n", "\"\"\"\n", "ethene = vlx.Molecule.read_xyz_string(ethene_xyz)\n", "ethene_basis = vlx.MolecularBasis.read(ethene, basis_set_label, ostream=None)" ] }, { "cell_type": "code", "execution_count": 3, "id": "4a03887a-dec0-4181-8028-ee4aa350af4e", "metadata": { "editable": true, "scrolled": true, "slideshow": { "slide_type": "" }, "tags": [ "remove-output" ] }, "outputs": [], "source": [ "fluoroethene_xyz = \"\"\"6\n", "fluoroethene\n", " C 0.000000 -0.663984 0.000000\n", " C 0.000000 0.663984 0.000000\n", " F 1.519796 -1.223061 0.000000\n", " H -0.919796 -1.223061 0.000000\n", " H 0.919796 1.223061 0.000000\n", " H -0.919796 1.223061 0.000000\n", " \"\"\"\n", "fluoroethene = vlx.Molecule.read_xyz_string(fluoroethene_xyz)\n", "fluoroethene_basis = vlx.MolecularBasis.read(fluoroethene, basis_set_label, ostream=None)" ] }, { "cell_type": "code", "execution_count": 4, "id": "fc99ed95-c7ac-45d3-a2b0-5ac29a0e6e52", "metadata": { "editable": true, "scrolled": true, "slideshow": { "slide_type": "" }, "tags": [ "remove-output" ] }, "outputs": [], "source": [ "chloroethene_xyz = \"\"\"6\n", "chloroethene\n", " C 0.000000 -0.663984 0.000000\n", " C 0.000000 0.663984 0.000000\n", " Cl 1.519796 -1.223061 0.000000\n", " H -0.919796 -1.223061 0.000000\n", " H 0.919796 1.223061 0.000000\n", " H -0.919796 1.223061 0.000000\n", " \"\"\"\n", "chloroethene = vlx.Molecule.read_xyz_string(chloroethene_xyz)\n", "chloroethene_basis = vlx.MolecularBasis.read(chloroethene, basis_set_label, ostream=None)" ] }, { "cell_type": "code", "execution_count": 5, "id": "51919f03-2853-45bb-89c7-f78f0dac5acf", "metadata": { "editable": true, "slideshow": { "slide_type": "" }, "tags": [] }, "outputs": [ { "data": { "application/3dmoljs_load.v0": "
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n",
" jupyter labextension install jupyterlab_3dmol