Kernel contexts

A context is an intermediate layer between the kernel (which runs the mathematics) and the experiment (which is programmed as it would be on a spectrometer). Context functions are responsible for setting up rotating frame transformations, transmitter offsets, powder averages, magic angle spinning and other such matters. The following contexts are available:

1. crystal.m - single static orientation simulations.
2. doublerot.m - double rotation simulations using Fokker-Planck formalism for the rotation part and a spherical grid for the powder average operation.
3. floquet.m - single rotation simulations using Floquet formalism for the rotation part and a spherical grid for the powder average operation.
4. gridfree.m - single rotation simulations using Fokker-Planck formalism for both the rotation part and the powder average operation. This module also supports stochastic Liouville equation formalism for spin relaxation theory.
5. imaging.m - imaging and spatial encoding simulations.
6. liquid.m - liquid state simulations.
7. powder.m - static powder simulations using a spherical grid for the powder average operation.
8. roadmap.m - static powder simulations using a spherical grid. Simulation results are returned as an array with an answer reported at each orientation found in the spherical grid.
9. singlerot.m - single rotation simulations using Fokker-Planck formalism for the rotation part and a spherical grid for the powder average operation.

Call syntax for spectroscopy contexts

All context functions, except for imaging.m have the same call syntax, e.g.:

    answer=doublerot(spin_system,pulse_sequence,parameters,assumptions);

and call experiment functions using the same syntax:

    answer=pulse_sequence(spin_system,parameters,H,R,K);

where H is the Hamiltonian commutation superoperator, R is the relaxation superoperator, and K is the kinetics superoperator. The parameter lists of different pulse sequences are broadly similar. This allows rapid switching of the simulation context by simply calling the same experiment from a different context.

Call syntax for imaging contexts

The imaging context has a similar call:

    answer=imaging(spin_system,pulse_sequence,parameters)

but the assumptions are set internally to 'nmr' and the pulse sequence must have the following syntax:

    answer=pulse_sequence(spin_system,parameters,H,R,K,G,F);

where H is the Hamiltonian commutation superoperator, R is the relaxation superoperator, K is the kinetics superoperator, G is a cell array of three gradient operators normalized to 1 Tesla/m, and F is the diffusion and flow superoperator.