######################################## Welcome to the Mrsimulator documentation ######################################## .. .. image:: _static/mrsimulator_cover_light.png .. :align: center .. only:: html .. cssclass:: table-bordered table-striped centered .. list-table:: :widths: 25 75 :header-rows: 0 * - Deployment - .. image:: https://img.shields.io/pypi/v/mrsimulator.svg?style=flat&logo=pypi&logoColor=white :target: https://pypi.python.org/pypi/mrsimulator :alt: PyPI version .. image:: https://img.shields.io/pypi/pyversions/mrsimulator :target: # :alt: PyPI - Python Version * - Build Status - .. image:: https://img.shields.io/github/workflow/status/deepanshs/mrsimulator/CI?logo=GitHub :target: https://github.com/deepanshs/mrsimulator/actions :alt: GitHub Workflow Status .. image:: https://readthedocs.org/projects/mrsimulator/badge/?version=stable :target: https://mrsimulator.readthedocs.io/en/stable/ :alt: Documentation Status * - License - .. image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg :target: https://opensource.org/licenses/BSD-3-Clause :alt: License * - Metrics - .. image:: https://img.shields.io/lgtm/grade/python/g/deepanshs/mrsimulator.svg?logo=lgtm :target: https://lgtm.com/projects/g/deepanshs/mrsimulator/context:python :alt: Language grade: Python .. image:: https://codecov.io/gh/deepanshs/mrsimulator/branch/master/graph/badge.svg :target: https://codecov.io/gh/deepanshs/mrsimulator .. image:: https://img.shields.io/lgtm/alerts/g/deepanshs/mrsimulator.svg?logo=lgtm :target: https://lgtm.com/projects/g/deepanshs/mrsimulator/alerts/ :alt: Total alerts .. image:: https://www.codefactor.io/repository/github/deepanshs/mrsimulator/badge :target: https://www.codefactor.io/repository/github/deepanshs/mrsimulator :alt: CodeFactor * - Social - .. image:: https://img.shields.io/github/contributors/deepanshs/mrsimulator?style=social&logo=github :target: https://github.com/deepanshs/mrsimulator/graphs/contributors :alt: GitHub contributors .. image:: https://img.shields.io/github/issues/deepanshs/mrsimulator?style=social&logo=github :target: https://github.com/deepanshs/mrsimulator/issues :alt: GitHub issues .. image:: https://img.shields.io/github/stars/deepanshs/mrsimulator?style=social :target: https://github.com/deepanshs/mrsimulator/stargazers :alt: GitHub stars .. image:: https://img.shields.io/github/forks/deepanshs/mrsimulator?style=social :target: https://github.com/deepanshs/mrsimulator/network/members :alt: GitHub forks .. .. image:: https://img.shields.io/github/commits-since/deepanshs/mrsimulator/v0.2.1?logo=github .. :alt: GitHub commits since tagged version .. .. image:: https://img.shields.io/pypi/dm/mrsimulator.svg?style=flat&logo=pypi .. :target: https://img.shields.io/pypi/dm/mrsimulator .. :alt: PyPI - Downloads **About** ``mrsimulator`` is an open-source python package for fast simulation and analysis of multi-dimensional solid-state magnetic resonance (NMR) spectra of crystalline and amorphous materials. ---- .. only:: html .. raw:: html

See our example gallery

Gallery

Simulation
Gallery

Fitting
---- **Why use mrsimulator?** - It is open-source and free. - It is a fast and versatile multi-dimensional solid-state NMR spectra simulator including, MAS and VAS spectra of nuclei experiencing chemical shift (nuclear shielding) and quadrupolar coupling interactions. - It includes simulation of weakly coupled nuclei experiencing J and dipolar couplings. - It is fully documented with a stable and simple API and is easily incorporated into your python scripts and web apps. - It is compatible with modern python packages, such as scikit-learn, Keras, etc. - Packages using mrsimulator - - `mrinversion `_ ---- **A brief example** .. skip: next .. plot:: :caption: An example simulating solid-state NMR spectrums of static and MAS experiments from mrsimulator import Simulator, SpinSystem, Site from mrsimulator.method.lib import BlochDecaySpectrum import matplotlib.pyplot as plt # Make Site and SpinSystem objects H_site = Site(isotope="1H", shielding_symmetric={"zeta": 13.89, "eta": 0.25}) spin_system = SpinSystem(sites=[H_site]) # Make static and MAS one-pulse acquire Method objects static = BlochDecaySpectrum(channels=["1H"]) mas = BlochDecaySpectrum(channels=["1H"], rotor_frequency=1000) # in Hz # Setup and run the Simulation object sim = Simulator(spin_systems=[spin_system], methods=[static, mas]) sim.run() # Plot the spectra fig, ax = plt.subplots(1, 2, figsize=(6, 3), subplot_kw={"projection": "csdm"}) ax[0].plot(sim.methods[0].simulation.real, color="black", linewidth=1) ax[0].set_title("Static") ax[1].plot(sim.methods[1].simulation.real, color="black", linewidth=1) ax[1].set_title("MAS") plt.tight_layout() plt.show() ---- **Features** The ``mrsimulator`` package offers the following - **Fast simulation** of one and two-dimensional solid-state NMR spectra. - Simulation of **coupled and uncoupled spin system** - for spin :math:`I=\frac{1}{2}`, and quadrupole :math:`I \ge \frac{1}{2}` nuclei - at arbitrary macroscopic magnetic flux density - at arbitrary rotor angles - at arbitrary spinning frequency - A library of **NMR methods**, - 1D Bloch decay spectrum - 1D Bloch decay central transition spectrum - 2D Multi-quantum Variable Angle Spinning (MQ-VAS) - 2D Satellite-transition Variable Angle Spinning (ST-VAS) - 2D Dynamic Angle Spinning (DAS) - 2D isotropic/anisotropic sideband correlation spectrum (e.g. PASS and MAT) - 2D Magic Angle Flipping (MAF) - Custom user-defined 1D and 2D methods (Method) - **Models** for tensor parameter distribution in amorphous materials. - Czjzek - Extended Czjzek - Custom user-defined models ---- .. Contribution .. ------------ .. ``Mrsimulator`` is a open source NMR simulation package. We are a small team .. working on developing the package for the NMR community. Any contribution and .. suggestion is greatly appreciated. ---- Introduction ------------ .. toctree:: :maxdepth: 2 :caption: Introduction installation/installation introduction/getting_started introduction/ethanol_example User Guide ---------- .. toctree:: :maxdepth: 2 :caption: User Documentation user_guide/spin_system/spin_system user_guide/spin_system_distributions/spin_system_distributions user_guide/methods_library/methods_library user_guide/method/method_advanced_user user_guide/method/query_objects user_guide/simulator/simulator user_guide/signal_processing/signal_processing user_guide/io/mrsim_IO Examples -------- .. toctree:: :maxdepth: 2 :caption: Galleries examples/index fitting/index signal_processing/index Theory ------ .. toctree:: :maxdepth: 2 :caption: Theory theory/components theory/models API and references ------------------ .. toctree:: :maxdepth: 2 :caption: API and references api_py/py-simulator api_py/py-signal-processing api_py/py-model api_py/py-fitting api_c/c_api Project details --------------- .. toctree:: :maxdepth: 1 :caption: Project details changelog credits/contributors credits/license credits/acknowledgment .. .. only:: html .. .. toctree:: .. :maxdepth: 2 .. :caption: Table of Contents: .. about .. installation .. requirements .. understanding-spin_systems .. getting_started .. using_mrsimulator_objects .. load_sample .. configuring_simulator .. benchmark .. examples/index .. theory/components .. api_py/py_api .. api_c/c_api .. understanding_system .. objects .. spectrum_object .. theory/wigner_rotations .. examples Reporting Bugs -------------- Submit bug reports or feature requests on the `Github issue tracker `_. Discussions are welcome on the `Github discussion `_ page. How to cite ----------- If you use mrsimulator in your publication, please consider citing the following. - Deepansh J. Srivastava, Matthew Giammar, Maxwell C. Venetos, Shyam Dwaraknath, Philip J. Grandinetti, & Alexis McCarthy. (2021). mrsimulator: v0.6.1. Zenodo. https://doi.org/10.5281/zenodo.5559730 - Srivastava DJ, Vosegaard T, Massiot D, Grandinetti PJ (2020) Core Scientific Dataset Model: A lightweight and portable model and file format for multi-dimensional scientific data. PLOS ONE 15(1): e0225953. https://doi.org/10.1371/journal.pone.0225953 *Additionally, if you use lmfit for least-squares fitting, consider citing the lmfit package.* - Matt Newville; Renee Otten; Andrew Nelson; Antonino Ingargiola; Till Stensitzki; Dan Allan; Austin Fox; Faustin Carter; Michał; Dima Pustakhod; lneuhaus; Sebastian Weigand; Ray Osborn; Glenn; Christoph Deil; Mark; Allan L. R. Hansen; Gustavo Pasquevich; Leon Foks; Nicholas Zobrist; Oliver Frost; Alexandre Beelen; Stuermer; kwertyops; Anthony Polloreno; Shane Caldwell; Anthony Almarza; Arun Persaud; Ben Gamari; Benjamin F. Maier. (2021, February 7). lmfit/lmfit-py 1.0.2 (Version 1.0.2). Zenodo. https://doi.org/10.5281/zenodo.4516651 .. only:: html Index ----- * :ref:`genindex` * :ref:`modindex` * :ref:`search`