Crystal.m

Static single crystal simulation context. This function positions the spin system at a particular angle in the laboratory frame of reference, generates Hamiltonian, relaxation superoperator, kinetics superoperator, applies the necessary offsets and rotating frame transformations, updates the parameter set, and passes all of that to the pulse sequence.

Syntax

    answer=crystal(spin_system,@pulse_sequence,parameters,assumptions)

The pulse sequence should have the following input syntax:

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

Arguments

  @pulse_sequence     - pulse sequence function handle

  parameters.spins    - a cell array giving the spins that 
                        the pulse sequence involves, e.g. 
                        {'1H','13C'}

  parameters.offset   - a cell array giving transmitter off-
                        sets in Hz on each of the spins listed
                        in parameters.spins array

  parameters.orientation - a row vector of the three Euler angles
                          (in radians) giving the orientation of
                           the system relative to the input orien-
                           tation.

  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.needs   - a cell array of strings specifying additional
                      information required by the sequence:

                      'zeeman_op' - Zeeman part of the Hamiltonian
                      in the laboratory frame, to be placed into
                      parameters.hseeman and sent to pulse sequence

                      'aniso_eq' - thermal equilibrium is recomputed 
                      using the full anisotropic Hamiltonian at the
                      current orientation, and sent to the pulse 
                      sequence in parameters.aniso_eq subfield
 
  parameters.*        - additional subfields may be required
                        by your pulse sequence - check its 
                        documentation page 

  assumptions         - a character string setting the simulation 
                        assumptions, e.g. 'nmr' - see assume.m
                        for further details.

Outputs

This function returns whatever the pulse sequence returns. 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

Examples

The following example files in the Spinach example set make use of this context function:

dnp_solids/cross_effect_freq_scan_1,2,3.m - cross effect DNP with microwave frequency scan in three different systems

dnp_solids/solid_effect_freq_scan_1.m - solid effect DNP with microwave frequency scan

esr_solids/eseem_methyl_crystal.m - single crystal ESEEM, methyl radical

esr_solids/eseem_phenyl_crystal.m - single crystal ESEEM, phenyl radical

esr_solids/eseem_nitroxide_crystal.m - single crystal ESEEM, nitroxide radical

nmr_solids/cp_crystal_static_1,2,3.m - NMR cross-polarisation in three different systems

Notes

Arbitrary order rotating frame transformation is supported, including infinite order. See rotframe.m for further information.

See also

powder.m, liquid.m, roadmap.m, singlerot.m, doublerot.m, imaging.m, gridfree.m, floquet.m

Version 2.1, authors: Ilya Kuprov