Welcome to the Mrsimulator documentation

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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.

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See our example gallery

Gallery

Simulation Examples

Gallery

Fitting Examples

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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

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Features

The mrsimulator package offers the following

• Fast simulation of one/two-dimensional solid-state NMR spectra. See our Performance benchmark results.

• Simulation of coupled and uncoupled spin system

  • for spin \(I=\frac{1}{2}\), and quadrupole \(I \ge \frac{1}{2}\) nuclei,

  • at arbitrary macroscopic magnetic flux density,

  • at arbitrary rotor angles, and

  • 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).

• Models for tensor parameter distribution in amorphous materials.

  • Czjzek

  • Extended Czjzek

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Warning

The package is currently under development. We advice using with caution. Bug report are greatly appreciated.

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Getting Started

Getting Started

• Installations
  • Package dependencies
  • For the users
  • For developers and contributors
• Introduction to Spin Systems
  • Site
  • Coupling
  • SpinSystem
• The Basics
  • Setting up the SpinSystem objects
  • Setting up the Method objects
  • Running simulation
  • Visualizing the dataset
• Uncoupled Spin System: Using objects
  • Site object
  • SpinSystem object
  • Method object
  • Simulator object
  • Running simulation
• Coupled Spin System: Using objects
  • Setting up coupled SpinSystem objects
  • Setting up the Method objects
  • Running simulation
  • Visualizing the dataset
• Configuring Simulator object
  • Number of sidebands
  • Integration volume
  • Integration density
  • Decompose spectrum
• mrsimulator I/O
  • Simulator object
  • Spin systems objects from Simulator class
  • Method objects from Simulator class
  • Serialize simulation object from Method class as CSDM compliant file
  • Serialize Simulator, SignalProcessor object to file

Signal Processing (mrsimulator.SignalProcessor)

Signal Processing

• Signal Processing
  • Introduction
  • SignalProcessor class
  • Convolution
  • Serializing the operations list

Models

Models

• Czjzek distribution
  • Czjzek distribution of symmetric shielding tensors
  • Czjzek distribution of symmetric quadrupolar tensors
  • Mini-gallery using the Czjzek distributions
• Extended Czjzek distribution
  • Extended Czjzek distribution of symmetric shielding tensors
  • Extended Czjzek distribution of symmetric quadrupolar tensors
  • Mini-gallery using the extended Czjzek distributions

Examples and Benchmarks

Examples and Benchmarks

• Simulation Examples
  • 1D NMR simulation (small molecules/crystalline solids)
  • 1D NMR simulation (macromolecules/amorphous solids)
  • 2D NMR simulation (Crystalline solids)
  • 2D NMR simulation (Disordered/Amorphous solids)
• Fitting Examples (Least Squares)
  • 1D Data Fitting
  • 2D Data Fitting
• Performance benchmark
  • Benchmark for the previous versions

Theory

Theory

• How does mrsimulator work?
  • Introduction to NMR frequency components
  • Scaled spatial orientation tensor (sSOT) components in PAS, \(\mathbf{\varsigma}_{L,n}^{(k)}\)
  • Spin transition functions, \(\xi_L^{(k)}(i,j)\)
  • Frequency tensor components (FT) in PAS, \(\varpi_{L, n}^{(k)}\)
• Models
  • Czjzek distribution
  • Extended Czjzek distribution

API and references

API and references

• Simulation API
  • Simulator
  • ConfigSimulator
  • SpinSystem
  • Site
  • Coupling
  • Method
  • Methods
  • Other Objects
  • Utility functions
  • Mrsimulator IO
• Signal-processing API
  • Signal Processing
  • Operations
• Models API
  • Czjzek distribution Model
  • Extended Czjzek distribution Model
• Fitting Utility API
  • LMFIT supplement functions
• C-API References
  • Spin transition functions (STF), \(\xi_L^{(k)}(i,j)\)
  • Scaled spatial orientation tensors (sSOT), \(\varsigma_{L,n}^{(k)}\)
  • Frequency Tensors (FT), \(\Lambda_{L, n}^{(k)}(i,j)\)

Project details

Project details

• Changelog
• Authors and Credits
• License
• Acknowledgment

Reporting Bugs

The preferred location for submitting feature requests and bug reports is the Github issue tracker. Reports are also welcomed by directly contacting Deepansh Srivastava.

Discussions are welcome on Github discussion

Index

• Index

• Module Index

• Search Page