{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Interoperability with Other Simulation Software\n", "The python programming language is great for hooking together software. We include interoperability with a few useful programs to help expand the types of workflows that can be done." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## ASE Interoperability\n", "The [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase/) provides access to a whole host of quantum chemistry codes. With this in mind, we provide a conversion routine to use ASE calculators with BigDFT systems. First we create a system." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "from BigDFT.Systems import System\n", "from BigDFT.Fragments import Fragment\n", "from BigDFT.IO import XYZReader\n", "from copy import deepcopy\n", "\n", "sys = System()\n", "reader = XYZReader(\"H2O\")\n", "sys[\"FRA:1\"] = Fragment(xyzfile=reader)\n", "sys[\"FRA:2\"] = deepcopy(sys[\"FRA:1\"])\n", "sys[\"FRA:2\"].translate([-5, 0, 0])" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "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
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
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