Difference between revisions of "Doublerot.m"

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(sync with Spinach main f053e432: Hilbert-space operation described; grid guidance (two-angle Liouville, three-angle Hilbert); rframes lab-frame assumption note)
 
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{{DISPLAYTITLE:doublerot.m}}
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{{DISPLAYTITLE:doublerot.m}} __NOTOC__
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Fokker-Planck double angle spinning context. Generates a Liouvillian superoperator and passes it on to the pulse sequence function, which
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Double angle spinning context. In Liouville space, this wrapper builds the Fokker-Planck evolution generator and passes it on to the pulse sequence function, which should be supplied as a handle. In Hilbert space, this wrapper builds the stack of spin Hamiltonians, one for each pair of rotor phases on the two-rotor phase grid, and hands that stack to the pulse sequence.
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should be supplied as a handle.
 
  
 
==Syntax==
 
==Syntax==
  
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    answer=doublerot(spin_system,pulse_sequence,parameters,assumptions)
 
  
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==Arguments==
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    [answer,sph_grid]=doublerot(spin_system,pulse_sequence,...
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                                  parameters,assumptions)
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==Parameters==
  
 
     pulse_sequence  - function handle to a pulse sequence, which must have  
 
     pulse_sequence  - function handle to a pulse sequence, which must have  
 
                       the following call syntax:
 
                       the following call syntax:
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                       answer=pulse_sequence(spin_system,parameters,H,R,K)
 
                       answer=pulse_sequence(spin_system,parameters,H,R,K)
 
   
 
   
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                             with respect to carbon-13 and third
 
                             with respect to carbon-13 and third
 
                             order rotating frame transformation
 
                             order rotating frame transformation
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                             with respect to nitrogen-14
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                             with respect to nitrogen-14. When
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                            this option is used, the assumptions
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                            on the respective spins should be
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                            laboratory frame.
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    parameters.grid      - [[Appendix I: powder grids|powder averaging grid]];
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                            two-angle grids should be used in
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                            Liouville space and three-angle
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                            grids in Hilbert space
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    parameters.needs      - a cell array of character strings spe-
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                            cifying additional requirements that
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                            the sequence has:
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                              'iso_eq' - thermal equilibrium state
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                              of the isotropic Hamiltonian will be
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                              placed into parameters.rho0
 
   
 
   
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     parameters.grid      - [[Appendix I: powder grids|powder averaging grid]]
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     parameters.serial    - if set to true, disables automatic pa-
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                            rallelisation
 
   
 
   
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     parameters.sum_up   - when set to 1 (default), returns the
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     parameters.sum_up     - when set to 1 (default), returns the
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                          powder average. When set to 0, returns
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                            powder average. When set to 0, returns
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                          individual answers for each point in  
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                            individual answers for each point in  
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                          the powder as a cell array.
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                            the powder as a cell array.
 
   
 
   
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     parameters.*       - additional subfields may be required by your
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     parameters.*         - additional subfields may be required by your
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                          pulse sequence - check its documentation page  
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                            pulse sequence - check its documentation page  
  
 
The parameters structure is passed to the pulse sequence with the following additional parameters set:
 
The parameters structure is passed to the pulse sequence with the following additional parameters set:
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==Outputs==
 
==Outputs==
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This function returns the powder average of whatever it is that the pulse sequence returns.
 
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==Examples==
 
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The following example files in the ''Spinach'' example set make use of this context function:
 
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'''nmr_soilds/dor_powder_nav_fplanck_freq.m''' - 14N DOR NMR spectrum of N-acetylvaline, frequency domain simulation
 
  
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'''nmr_soilds/dor_powder_nav_fplanck_time.m''' - 14N DOR NMR spectrum of N-acetylvaline, time domain simulation
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answer  - powder average, or a cell array, of whatever the pulse sequence returns
  
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'''nmr_overtone/dor_glycine.m''' - 14N overtone DOR NMR spectrum of glycine, frequency domain simulation
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sph_grid - spherical grid used in the calculation
  
 
==Notes==
 
==Notes==
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==See also==
 
==See also==
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[[powder.m]], [[liquid.m]], [[roadmap.m]], [[singlerot.m]], [[crystal.m]], [[imaging.m]], [[gridfree.m]], [[floquet.m]]
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[[assume.m]], [[rotframe.m]], [[crystal.m]], [[floquet.m]], [[gridfree.m]], [[imaging.m]], [[liquid.m]], [[meshflow.m]], [[powder.m]], [[singlerot.m]], [[Kernel contexts]], [[Built-in_experiments]]
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''Version 2.2, authors: [[Ilya Kuprov]]''
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''Version 2.8, authors: [[Ilya Kuprov]]''

Latest revision as of 06:40, 30 August 2026

Double angle spinning context. In Liouville space, this wrapper builds the Fokker-Planck evolution generator and passes it on to the pulse sequence function, which should be supplied as a handle. In Hilbert space, this wrapper builds the stack of spin Hamiltonians, one for each pair of rotor phases on the two-rotor phase grid, and hands that stack to the pulse sequence.

Syntax

    [answer,sph_grid]=doublerot(spin_system,pulse_sequence,...
                                  parameters,assumptions)

Parameters

    pulse_sequence  - function handle to a pulse sequence, which must have 
                      the following call syntax:

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

                      where parameters is a structure described below, H is
                      the Hamiltonian, R is relaxation superoperator, and K
                      is the kinetics superoperator

    assumptions     - the string that will be passed to assume.m when 
                      the Hamiltonian is built

    parameters.rate_outer - outer rotor spinning rate in Hz

    parameters.rate_inner - inner rotor spinning rate in Hz

    parameters.axis_outer - spinning axis of the outer rotor,
                            given as a normalized 3-element
                            vector

    parameters.axis_inner - spinning axis of the inner rotor,
                            given as a normalized 3-element
                            vector

    parameters.rank_outer - maximum harmonic rank to retain in
                            the solution (increase till conver-
                            gence is achieved, approximately
                            equal to the number of spinning si-
                            debands in the spectrum) for the
                            outer rotor

    parameters.rank_inner - maximum harmonic rank to retain in
                            the solution (increase till conver-
                            gence is achieved, approximately
                            equal to the number of spinning si-
                            debands in the spectrum) for the
                            inner rotor

    parameters.rframes    - rotating frame specification, e.g.
                            {{'13C',2},{'14N,3}} requests second
                            order rotating frame transformation
                            with respect to carbon-13 and third
                            order rotating frame transformation
                            with respect to nitrogen-14. When
                            this option is used, the assumptions
                            on the respective spins should be
                            laboratory frame.

    parameters.grid       - powder averaging grid;
                            two-angle grids should be used in
                            Liouville space and three-angle
                            grids in Hilbert space

    parameters.needs      - a cell array of character strings spe-
                            cifying additional requirements that
                            the sequence has:

                             'iso_eq' - thermal equilibrium state
                             of the isotropic Hamiltonian will be
                             placed into parameters.rho0

    parameters.serial     - if set to true, disables automatic pa-
                            rallelisation

    parameters.sum_up     - when set to 1 (default), returns the
                            powder average. When set to 0, returns
                            individual answers for each point in 
                            the powder as a cell array.

    parameters.*          - additional subfields may be required by your
                            pulse sequence - check its documentation page

The parameters structure is passed to the pulse sequence with the following additional parameters set: 

    parameters.spc_dim  - matrix dimension for the spatial
                          dynamics subspace

    parameters.spn_dim  - matrix dimension for the spin 
                          dynamics subspace

Outputs

answer - powder average, or a cell array, of whatever the pulse sequence returns

sph_grid - spherical grid used in the calculation

Notes

  1. Arbitrary order rotating frame transformation is supported, including infinite order. See rotframe.m for further information.
  2. The state projector assumes a powder - single crystal DOR is not currently supported.
  3. The function supports parallel processing via Matlab's Distributed Computing Toolbox - different system orientations are evaluated on different labs.

See also

assume.m, rotframe.m, crystal.m, floquet.m, gridfree.m, imaging.m, liquid.m, meshflow.m, powder.m, singlerot.m, Kernel contexts, Built-in_experiments

Version 2.8, authors: Ilya Kuprov

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