######################################## 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 :alt: PyPI - Python Version * - Build Status - .. image:: https://img.shields.io/github/workflow/status/deepanshs/mrsimulator/CI%20(pip)?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 * - GitHub - .. image:: https://img.shields.io/github/contributors/DeepanshS/mrsimulator.svg?logo=github :target: https://github.com/DeepanshS/mrsimulator/graphs/contributors :alt: GitHub contributors .. image:: https://img.shields.io/github/issues/deepanshs/mrsimulator?logo=github :target: https://github.com/DeepanshS/mrsimulator/issues :alt: GitHub issues * - Citation - .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3978779.svg :target: https://doi.org/10.5281/zenodo.3978779 .. .. 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 materials, bio macro-molecules, and even amorphous materials. Simulate the NMR spectrum of macro-molecules or amorphous in just a few seconds. ---- .. only:: html .. raw:: html

See our example gallery

Gallery

Simulation Examples
Gallery

Fitting Examples
---- **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. - Future release will include simulations of weakly coupled nuclei experiencing J and dipolar couplings, and multi-dimensional NMR spectra. - 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 `_ ---- **Features** The ``mrsimulator`` package currently offers the following - **Fast simulation** of one-dimensional solid-state NMR spectra. See our :ref:`benchmark` results. - Simulation of **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, and - at arbitrary spinning frequency. - The library includes the following **NMR methods**, - 1D Bloch decay spectrum, and - 1D Bloch decay central transition spectrum. - 2D Multi-quantum Variable Angle Spinning (MQ-VAS), - 2D Satellite-transition Variable Angle Spinning (ST-VAS), and - 2D Dynamic Angle Spinning (DAS), - 2D isotropic/anisotropic sideband correlation spectrum (e.g. PASS and MAT), and - 2D Magic Angle Flipping (MAF). - **Models** for tensor parameter distribution in amorphous materials. - Czjzek - Extended Czjzek ---- **Goals for the near future** Our current objectives are the following - Include spectral simulation of coupled spin systems. .. 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. .. warning:: The package is currently under development. We advice using with caution. Bug report are greatly appreciated. ---- Getting Started --------------- .. toctree:: :maxdepth: 2 :caption: Getting Started installation requirements introduction getting_started getting_started-objects configuring_simulator mrsim_IO .. designing_methods Signal Processing (``mrsimulator.SignalProcessor``) --------------------------------------------------- .. toctree:: :maxdepth: 2 :caption: Signal Processing signal_processing Models ------ .. toctree:: :maxdepth: 2 :caption: Models model/czjzek model/extended_czjzek Examples and Benchmarks ----------------------- .. toctree:: :maxdepth: 2 :caption: Examples and Benchmarks examples/index fitting/index benchmark 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_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 -------------- The preferred location for submitting feature requests and bug reports is the `Github issue tracker `_. Reports are also welcomed on the `mrsimulator mailing list `_ or by directly contacting `Deepansh Srivastava `_. .. only:: html Index ----- * :ref:`genindex` * :ref:`modindex` * :ref:`search`