{ "cells": [ { "cell_type": "markdown", "id": "48cb61ff", "metadata": {}, "source": [ "## Initial imports" ] }, { "cell_type": "code", "execution_count": 1, "id": "9c004d5a", "metadata": {}, "outputs": [], "source": [ "from scm.base import ChemicalSystem\n", "from scm.plams import AMSJob, Settings, view" ] }, { "cell_type": "markdown", "id": "3513432c", "metadata": {}, "source": [ "## System" ] }, { "cell_type": "code", "execution_count": 2, "id": "1f5b7c70", "metadata": {}, "outputs": [], "source": [ "cs = ChemicalSystem(\n", " \"\"\"\n", "System\n", " Atoms\n", " O 1.48603879 -1.49561627 0.0 \n", " C 1.29751002 -0.30552432 0.0 \n", " O 0.07403584000000001 0.25228979 0.0 \n", " C -1.02449892 -0.67494471 0.0 \n", " C -2.30056502 0.12358769 0.0 \n", " C 2.36905363 0.74347075 0.0 \n", " H -0.9418758699999999 -1.31519741 0.88039373 \n", " H -0.9418758699999999 -1.31519741 -0.88039373 \n", " H -2.36617127 0.7582087199999999 0.88525259 \n", " H -3.15628689 -0.55419212 0.0 \n", " H -2.36617127 0.7582087199999999 -0.88525259 \n", " H 3.34355252 0.26293272 0.0 \n", " H 2.26362714 1.38098693 0.87932777 \n", " H 2.26362714 1.38098693 -0.87932777 \n", " End\n", "End\n", "\"\"\"\n", ")" ] }, { "cell_type": "code", "execution_count": 3, "id": "e45b5230", "metadata": {}, "outputs": [ { "data": { "image/png": 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\n", "text/plain": [ "" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "view(cs, guess_bonds=True, height=200, width=200)" ] }, { "cell_type": "markdown", "id": "59832642", "metadata": {}, "source": [ "## Job settings: DFT and NMR\n", "\n", "There are three calculations:\n", "\n", "1. A DFT calculation with a main results file ``adf.rkf``. We must set the ``Save TAPE10`` input option. The ``TAPE10`` file is later used by the ``$AMSBIN/nmr`` program.\n", "\n", "2. An ``$AMSBIN/cpl`` calculation. This program *modifies* ``adf.rkf``\n", "\n", "3. An ``$AMSBIN/nmr`` calculation. This program reads ``TAPE10`` and *modifies* ``adf.rkf``.\n", "\n", "In the end, all results are stored on ``adf.rkf``.\n", "\n", "There is no PLAMS job for the ``$AMSBIN/cpl`` and ``$AMSBIN/nmr`` programs. Instead, we set up the calculation explicitly in the ``settings.runscript.postamble_lines`` option." ] }, { "cell_type": "code", "execution_count": 4, "id": "16e5bac8", "metadata": {}, "outputs": [], "source": [ "# DFT Settings\n", "s = Settings()\n", "s.input.ams.Task = \"SinglePoint\"\n", "s.input.adf.Basis.Type = \"TZ2P-J\"\n", "s.input.adf.Basis.Core = \"None\"\n", "s.input.adf.Save = \"TAPE10\"\n", "s.input.adf.xc.GGA = \"OPBE\"\n", "s.input.adf.Symmetry = \"NOSYM\"\n", "s.input.adf.NumericalQuality = \"Good\"" ] }, { "cell_type": "code", "execution_count": 5, "id": "b62f92d9", "metadata": {}, "outputs": [], "source": [ "from typing import Mapping, List\n", "\n", "\n", "def get_cpl_script(s: Mapping) -> List[str]:\n", " ret = (\n", " ['\"$AMSBIN/cpl\" < List[str]:\n", " ret = (\n", " ['\"$AMSBIN/nmr\" <" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "import numpy as np\n", "import matplotlib.pyplot as plt\n", "from scm.plams.tools.postprocess_results import broaden_results\n", "\n", "sigma_ref_h = 31.7\n", "shieldings = np.array(props[\"NMR Shieldings InputOrder\"])\n", "\n", "chemical_shifts = sigma_ref_h - np.array(shieldings)\n", "\n", "x, y = broaden_results(\n", " chemical_shifts,\n", " areas=np.ones(chemical_shifts.shape), # weigh all peaks equally\n", " broadening_width=0.01,\n", " broadening_type=\"lorentzian\",\n", " x_data=(0, 5, 0.01), # x range and resolution\n", ")\n", "\n", "fig, ax = plt.subplots()\n", "ax.set_title(\"1H-NMR (no coupling)\")\n", "ax.set_xlabel(\"Chemical shift (ppm)\")\n", "ax.set_ylabel(\"Intensity (arbitrary)\")\n", "ax.plot(x, y)\n", "ax;" ] }, { "cell_type": "markdown", "id": "3830ceea", "metadata": {}, "source": [ "## Conclusion\n", "\n", "In this Python example you learned how to set up and run the NMR calculation.\n", "\n", "For more detailed analysis, including multiplet splitting (coupling), see the GUI tutorial.\n", "\n", "**Recommendation**: Use AMSspectra for further analysis." ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.8.16" } }, "nbformat": 4, "nbformat_minor": 5 }