Changelog

v0.7.0

What’s new

General

  • Support for complex amplitude simulation.

  • Add isotropic_interpolation as a sim.config parameter. The interpolation schemes are linear and Gaussian.

Method

  • Removed Method1D and Method2D classes. Use the generic mrsimulator.method.Method object for custom1D and 2D methods.

  • New Event classes—SpectralEvent and MixingEvent. The MixingEvent controls the mixing of transitions in a multi-event method.

  • A TransitionPathway object now includes a weight attribute, which holds the probability of the transition pathway based on the mixing events defined within the method.

  • New class method, plot(), which will create a visual representation of the events, transition pathways, rotor angle, etc. a method object defines.

SpinSystem

  • Add a new function simplify() to the spin system object, which reduces a spin system to a list of irreducible spin systems.

  • Add a new function site_generator() to the utility collection sub-module, which simplify the process of creating Site objects in bulk.

  • Added gyromagnetic ratio and quadrupole moment data for all isotopes, including unstable isotopes.

Documentation

  • Restructured documentation layout

  • Added instillation troubleshooting section

  • Added section User Guide detailing use and attributes of most objects.

  • Condensed simulation/fitting gallery by removing redundant examples

  • New gallery demonstrating signal processing functions.

Changes

  • reduced_dict function is deprecated, use json(units=False) instead.

Bug fixes

  • Fixed bug where spectral interpolation resulted in segmentation fault.

  • Fixed memory leak issue in the C code.

v0.6.0

What’s new

  • ⭐ Improved simulation performance. ⭐ See our Performance benchmark.

  • Simulation of one-dimensional spectra of coupled spin systems. The frequency contributions from the coupled sites include weak J-couplings and weak dipolar couplings.

  • New Coupling class.

  • Added a new Sites class that holds a list of Site objects. The Sites class method, to_pd(), exports the sites as a pandas data frame.

  • A new method, sites(), is added to the Simulator object, which returns a list of unique Sites objects within the Simulator object across multiple spin systems.

  • Added three new arguments to the single_site_system_generator() method, ‘site_labels’, ‘site_names’, and ‘site_descriptions’.

Changes

  • The get_isotopes() method from the SpinSystem object, will now return Isotope objects by default. Use the symbol=True argument of the method to get a list of string isotopes.

  • The to_freq_dict() function is deprecated.

  • The D symmetry of transition_query attribute from Method2D method is now None by default.

  • BlochDecayCTSpectrum is an alias for BlochDecayCentralTransitionSpectrum class.

Bug fixes

  • Fixed a bug related to get_spectral_dimensions() utility method in cases when CSDM dimension objects have negative increment.

  • Fixed a bug resulting in the non-conserved spectral area after a Gaussian apodization.

  • Fixed a bug in Gaussian apodization, which raised an error when the FWHM argument is a scalar.

  • Fixed bug causing multi-dataset fit to fail.

v0.5.1

Bug fixes

  • Fixed a bug that was causing incorrect spectral binning when the frequency contribution is pure isotropic.

Other changes

  • The to_dict_with_units() method is deprecated and is replaced with json()

  • The json() function returns a python dictionary object with minimal required keywords, where the event keys are globally serialized at the root method object. In the case where the event key value is different from the global value, the respective key is serialized within the event object.

  • The json() function will no longer serialize the transition_query objects for the named objects.

v0.5.0

What’s new

The update introduces various two-dimensional methods for simulating NMR spectrum.

  • Introduces a generic one-dimensional method, Method1D.

  • Introduces a generic two-dimensional method, Method2D.

  • Specialized two-dimensional methods for multi-quantum variable-angle spinning with build-in affine transformations.

  • Specialized two-dimensional methods for satellite-transition variable-angle spinning with build-in affine transformations.

  • Specialized two-dimensional isotropic/anisotropic sideband correlation method, SSB2D.

Other changes

  • The get_transition_pathways() method no longer return a numpy array, instead a python list.

  • Renamed mrsimulator.methods module to mrsimulator.method.lib.

v0.4.0

What’s new!

v0.3.0

What’s new!

  • ⭐ Improved simulation performance. ⭐ See our Performance benchmark.

  • Removed the Dimension class and added a new Method class instead.

  • New methods for simulating the NMR spectrum:

    • BlochDecaySpectrum and

    • BlochDecayCentralTransitionSpectrum.

    The Bloch decay spectrum method simulates all p=Δm=-1 transition pathways, while the Bloch decay central transition selective spectrum method simulates all transition pathways with p=Δm=-1 and d=0.

  • New Isotope, Transition, and ZeemanState classes.

  • Every class now includes a reduced_dict() method. The reduced_dict method returns a dictionary with minimal key-value pairs required to simulate the spectrum. Note, this may cause metadata loss, if any.

  • Added a label and description attributes to the Site class.

  • Added a new label attribute to the SpinSystem class.

  • New SignalProcessor class for post-simulation signal processing.

  • Improved usage of least-squares minimization using python LMFIT package.

  • Added a new get_spectral_dimensions utility function to extract the spectral dimensions information from the CSDM object.

Bug fixes

  • Fixed bug resulting from the rotation of the fourth rank tensor with non-zero euler angles.

  • Fixed bug causing a change in the spectral area as the sampling points change. Now the area is constant.

  • Fixed bug resulting in an incorrect spectrum when non-coincidental quad and shielding tensors are given.

  • Fixed bug causing incorrect generation of transition pathways when multiple events are present.

Other changes

  • Renamed the decompose attribute from the ConfigSimulator class to decompose_spectrum. The attribute is an enumeration with the following literals:

    • none: Computes a spectrum which is an integration of the spectra from all spin systems.

    • spin_system: Computes a series of spectra each corresponding to a single spin system.

  • Renamed Isotopomer class to SpinSystem.

  • Renamed isotopomers attribute from Simulator class to spin_systems.

  • Renamed dimensions attribute from Simulator class to methods.

  • Changed the default value of name and description attribute from the SpinSystem class from "" to None.

v0.2.x

What’s new!

Bug fixes

  • Fixed amplitude normalization. The spectral amplitude no longer change when the integration_density, integration_volume`, or the number_of_sidebands attributes change.

Other changes

  • Removed plotly-dash app to its own repository.

  • Renamed the class Spectrum to Dimension

v0.1.3

  • Fixed missing files from source tar.

v0.1.2

  • Initial release on pypi.

v0.1.1

  • Added solid state quadrupolar spectrum simulation.

  • Added mrsimulator plotly-dash app.

v0.1.0

  • Solid state chemical shift anisotropy spectrum simulation.