# 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.*        - 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.