Appendix E: experiment parameters

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This section summarises the common sibfields of the parameters data structure used by Spinach kernel contexts and experiment simulations. This data structure must be passed to context (e.g. powder.m) and pulse sequence (e.g. noesy.m) functions. Individual functions may also have their own case-specific parameters, always check the manual page for the function that you use.

Subfield Data type Notes
parameters.sweep A vector of reals. Sweep width in each dimension of the spectrum (Hz).
parameters.npoints A vector of integers. Number of points in each dimension of the output data array.
parameters.rho0 A state vector or a density matrix. Initial state for the simulation.
parameters.coil A state vector or a density matrix. Detection state for the simulation.
parameters.decouple A cell array of spin specifications, e.g. {'13C','15N'}. Spins that must be decoupled analytically during the simulation.
parameters.spins A cell array of spin specifications, e.g. {'13C','15N'}. Spins that are to be assigned to each instrument channel during the simulation.
parameters.J A vector of reals. The values of J-couplings that should be used for coherence transfer stages of NMR pulse sequences.
parameters.spc_dim integer number The dimension of the spatial sub-problem in a Fokker-Planck space. This parameter sould normally be set by the kernel context function and passed on to the pulse sequence.
parameters.spn_dim integer number The dimension of the spin sub-problem in a Fokker-Planck space. This parameter sould normally be set by the kernel context function and passed on to the pulse sequence.
parameters.rf_pwr a vector of real numbers radiofrequency irradiation powers on each channel
parameters.rf_dur a vector of real numbers radiofrequency irradiation durations on each channel
parameters.rf_frq a vector of real numbers radiofrequency irradiation frequencies on each channel
parameters.rf_phi a vector of real numbers radiofrequency irradiation initial phases on each channel
parameters.rf_rnk a vector of real numbers radiofrequency irradiation Floquet or Fokker-Planck rank on each channel
parameters.rf_opr a cell array of sparse matrices radiofrequency irradiation operators on each channel
parameters.angle a vector of reals pulse flip angles for those experiments that require them
parameters.mw_pwr a vector of real numbers microwave irradiation powers on each channel
parameters.mw_dur a vector of real numbers microwave irradiation durations on each channel
parameters.mw_frq a vector of real numbers microwave irradiation frequencies on each channel
parameters.mw_phi a vector of real numbers microwave irradiation initial phases on each channel
parameters.mw_rnk a vector of real numbers microwave irradiation Floquet or Fokker-Planck rank on each channel
parameters.mw_opr a cell array of sparse matrices microwave irradiation operators on each channel
parameters.rho_eq a state vector or a denisty matrix equilibrium state for the experiments that require it
parameters.rlx a sparse matrix relaxation superoperator for the experiments that require it separately
parameters.rframes a cell array of the following shape: {{'E',2},{'1H',1}} with the first element indicating the spins and the second the order of the rotating frame transformation numerical rotating frame transformation specification
parameters.theory a character string theory specification for experiments that can be computed using several methods
parameters.rate real numbers spinning rate for single rotation solid state NMR experiments
parameters.axis three-element real vector rotor axis for single rotation solid state NMR experiments
parameters.grid character string with a file name spherical averaging grid for solid state experiments
parameters.rank positive integer Floquet or Fokker-Planck rank for single rotation solid state NMR experiments
parameters.rate_inner real number inner rotor spinning rate for double rotation solid state NMR experiments
parameters.rate_outer real number outer rotor spinning rate for double rotation solid state NMR experiments
parameters.axis_inner three-element real vector inner rotor axis for double rotation solid state NMR experiments
parameters.axis_outer three-element real vector outer rotor axis for double rotation solid state NMR experiments
parameters.rank_inner positive integer Floquet or Fokker-Planck rank for the inner rotor in double rotation solid state NMR experiments
parameters.rank_outer positive integer Floquet or Fokker-Planck rank for the outer rotor in double rotation solid state NMR experiments