{ "cells": [ { "cell_type": "markdown", "source": [ "# Generation and use of an orbital-based grid" ], "metadata": { "collapsed": false } }, { "cell_type": "code", "execution_count": 1, "outputs": [], "source": [ "import pymolpro\n", "p = pymolpro.Project(\"orbital\")\n", "p.write_input(\"symmetry,nosym;geometry={o;h,o,r;h,o,r,h,theta};r=1 angstrom, theta=104 degree; rhf;locali,pipek,thrpip=1e-10;put,xml\")\n", "p.run(wait=True)" ], "metadata": { "collapsed": false, "pycharm": { "name": "#%%\n" } } }, { "cell_type": "code", "execution_count": 2, "outputs": [], "source": [ "orbitals = p.orbitals(minocc=1.0)" ], "metadata": { "collapsed": false, "pycharm": { "name": "#%%\n" } } }, { "cell_type": "code", "execution_count": 3, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1.1 [4.36189315945102e-17, -5.65839184589554e-18, -0.129953086882215] [0.01772806 0.01772858 0.01772861]\n", " 0 1 2 3 4 5 6 \\\n", "0 -0.079239 -0.023853 0.023853 0.079239 -0.079239 -0.023853 0.023853 \n", "1 -0.079238 -0.079238 -0.079238 -0.079238 -0.079238 -0.079238 -0.079238 \n", "2 -0.209192 -0.209192 -0.209192 -0.209192 -0.153806 -0.153806 -0.153806 \n", "\n", " 7 8 9 ... 54 55 56 57 \\\n", "0 0.079239 -0.079239 -0.023853 ... 0.023853 0.079239 -0.079239 -0.023853 \n", "1 -0.079238 -0.079238 -0.079238 ... 0.079238 0.079238 0.079238 0.079238 \n", "2 -0.153806 -0.106100 -0.106100 ... -0.153806 -0.153806 -0.106100 -0.106100 \n", "\n", " 58 59 60 61 62 63 \n", "0 0.023853 0.079239 -0.079239 -0.023853 0.023853 0.079239 \n", "1 0.079238 0.079238 0.079238 0.079238 0.079238 0.079238 \n", "2 -0.106100 -0.106100 -0.050714 -0.050714 -0.050714 -0.050714 \n", "\n", "[3 rows x 64 columns]\n", " 0 1 2 3 4 5 6 \\\n", "0 4.148478 4.946147 4.946147 4.148478 4.942366 6.16284 6.16284 \n", "\n", " 7 8 9 ... 54 55 56 57 \\\n", "0 4.942366 4.939117 6.157132 ... 6.16284 4.942366 4.939117 6.157132 \n", "\n", " 58 59 60 61 62 63 \n", "0 6.157132 4.939117 4.141304 4.935353 4.935353 4.141304 \n", "\n", "[1 rows x 64 columns]\n", "2.1 [-2.23133341860535e-12, -0.78317178943009, 0.524537657987677] [0.44530382 0.45564982 0.9098715 ]\n", " 0 1 2 3 4 5 6 \\\n", "0 -0.397127 -0.397127 -0.397127 -0.397127 -0.397127 -0.397127 -0.397127 \n", "1 -0.543217 -0.870101 -1.151653 -1.478537 -0.384056 -0.710940 -0.992493 \n", "2 -0.128179 0.096732 0.290453 0.515364 0.103144 0.328055 0.521776 \n", "\n", " 7 8 9 ... 54 55 56 57 \\\n", "0 -0.397127 -0.397127 -0.397127 ... 0.397127 0.397127 0.397127 0.397127 \n", "1 -1.319376 -0.246967 -0.573851 ... -0.992493 -1.319376 -0.246967 -0.573851 \n", "2 0.746687 0.302388 0.527299 ... 0.521776 0.746687 0.302388 0.527299 \n", "\n", " 58 59 60 61 62 63 \n", "0 0.397127 0.397127 0.397127 0.397127 0.397127 0.397127 \n", "1 -0.855404 -1.182288 -0.087806 -0.414690 -0.696243 -1.023127 \n", "2 0.721020 0.945931 0.533711 0.758622 0.952343 1.177254 \n", "\n", "[3 rows x 64 columns]\n", " 0 1 2 3 4 5 6 \\\n", "0 0.399322 0.38697 0.338028 0.291293 0.478133 0.440586 0.378372 \n", "\n", " 7 8 9 ... 54 55 56 57 \\\n", "0 0.33094 0.4647 0.433285 ... 0.378372 0.33094 0.4647 0.433285 \n", "\n", " 58 59 60 61 62 63 \n", "0 0.376373 0.332005 0.371588 0.37075 0.332924 0.293541 \n", "\n", "[1 rows x 64 columns]\n", "3.1 [8.26672974408137e-13, 9.77485020009494e-13, -0.732716827889661] [0.46977397 0.49098249 0.50177496]\n", " 0 1 2 3 4 5 6 \\\n", "0 -0.416999 -0.416999 -0.416999 -0.416999 -0.125526 -0.125526 -0.125526 \n", "1 0.421557 0.126898 -0.126898 -0.421557 0.421557 0.126898 -0.126898 \n", "2 -1.140610 -1.140610 -1.140610 -1.140610 -1.140610 -1.140610 -1.140610 \n", "\n", " 7 8 9 ... 54 55 56 57 \\\n", "0 -0.125526 0.125526 0.125526 ... -0.125526 -0.125526 0.125526 0.125526 \n", "1 -0.421557 0.421557 0.126898 ... -0.126898 -0.421557 0.421557 0.126898 \n", "2 -1.140610 -1.140610 -1.140610 ... -0.324824 -0.324824 -0.324824 -0.324824 \n", "\n", " 58 59 60 61 62 63 \n", "0 0.125526 0.125526 0.416999 0.416999 0.416999 0.416999 \n", "1 -0.126898 -0.421557 0.421557 0.126898 -0.126898 -0.421557 \n", "2 -0.324824 -0.324824 -0.324824 -0.324824 -0.324824 -0.324824 \n", "\n", "[3 rows x 64 columns]\n", " 0 1 2 3 4 5 6 \\\n", "0 0.33011 0.372633 0.372633 0.33011 0.371277 0.422702 0.422702 \n", "\n", " 7 8 9 ... 54 55 56 57 \\\n", "0 0.371277 0.371277 0.422702 ... 0.272424 0.439186 0.439186 0.272424 \n", "\n", " 58 59 60 61 62 63 \n", "0 0.272424 0.439186 0.413244 0.439966 0.439966 0.413244 \n", "\n", "[1 rows x 64 columns]\n", "4.1 [1.64073810474965e-12, -5.72458747072346e-17, -0.0876418809415855] [0.43603925 0.45045416 1.25108042]\n", " 0 1 2 3 4 5 6 \\\n", "0 0.665647 0.200375 -0.200375 -0.665647 0.665647 0.200375 -0.200375 \n", "1 -0.399417 -0.399417 -0.399417 -0.399417 -0.120234 -0.120234 -0.120234 \n", "2 0.305333 0.305333 0.305333 0.305333 0.305333 0.305333 0.305333 \n", "\n", " 7 8 9 ... 54 55 56 57 \\\n", "0 -0.665647 0.665647 0.200375 ... -0.200375 -0.665647 0.665647 0.200375 \n", "1 -0.120234 0.120234 0.120234 ... -0.120234 -0.120234 0.120234 0.120234 \n", "2 0.305333 0.305333 0.305333 ... -0.480616 -0.480616 -0.480616 -0.480616 \n", "\n", " 58 59 60 61 62 63 \n", "0 -0.200375 -0.665647 0.665647 0.200375 -0.200375 -0.665647 \n", "1 0.120234 0.120234 0.399417 0.399417 0.399417 0.399417 \n", "2 -0.480616 -0.480616 -0.480616 -0.480616 -0.480616 -0.480616 \n", "\n", "[3 rows x 64 columns]\n", " 0 1 2 3 4 5 6 \\\n", "0 0.344496 0.198343 -0.198343 -0.344496 0.420137 0.274622 -0.274622 \n", "\n", " 7 8 9 ... 54 55 56 57 \\\n", "0 -0.420137 0.420137 0.274622 ... -0.323382 -0.445447 0.445447 0.323382 \n", "\n", " 58 59 60 61 62 63 \n", "0 -0.323382 -0.445447 0.358141 0.219639 -0.219639 -0.358141 \n", "\n", "[1 rows x 64 columns]\n", "5.1 [-2.37023848286065e-13, 0.783171789429109, 0.524537657987883] [0.44530382 0.45564982 0.9098715 ]\n", " 0 1 2 3 4 5 6 \\\n", "0 -0.397127 -0.397127 -0.397127 -0.397127 -0.397127 -0.397127 -0.397127 \n", "1 0.087806 0.414690 0.696243 1.023127 0.246967 0.573851 0.855404 \n", "2 0.533711 0.758622 0.952343 1.177254 0.302388 0.527299 0.721020 \n", "\n", " 7 8 9 ... 54 55 56 57 \\\n", "0 -0.397127 -0.397127 -0.397127 ... 0.397127 0.397127 0.397127 0.397127 \n", "1 1.182288 0.384056 0.710940 ... 0.855404 1.182288 0.384056 0.710940 \n", "2 0.945931 0.103144 0.328055 ... 0.721020 0.945931 0.103144 0.328055 \n", "\n", " 58 59 60 61 62 63 \n", "0 0.397127 0.397127 0.397127 0.397127 0.397127 0.397127 \n", "1 0.992493 1.319376 0.543217 0.870101 1.151653 1.478537 \n", "2 0.521776 0.746687 -0.128179 0.096732 0.290453 0.515364 \n", "\n", "[3 rows x 64 columns]\n", " 0 1 2 3 4 5 6 \\\n", "0 0.371588 0.37075 0.332924 0.293541 0.4647 0.433285 0.376373 \n", "\n", " 7 8 9 ... 54 55 56 57 \\\n", "0 0.332005 0.478133 0.440586 ... 0.376373 0.332005 0.478133 0.440586 \n", "\n", " 58 59 60 61 62 63 \n", "0 0.378372 0.33094 0.399322 0.38697 0.338028 0.291293 \n", "\n", "[1 rows x 64 columns]\n" ] } ], "source": [ "import pandas\n", "for orbital in orbitals:\n", " points = orbital.grid(4)\n", " # values = p.evaluateOrbitals(points, ID=orbital.ID, values=True)\n", " # values = p.evaluateOrbitals(points, ID=orbital.ID)['values']\n", " values = orbital.evaluate(points, values=True)\n", " print(orbital.ID, orbital.centroid, orbital.second_moment_eigenvalues)\n", " print(pandas.DataFrame(points).transpose())\n", " print(pandas.DataFrame(values).transpose())" ], "metadata": { "collapsed": false, "pycharm": { "name": "#%%\n" } } } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.6" } }, "nbformat": 4, "nbformat_minor": 0 }