Kernel contexts - Revision history

Kuprov: Index the new Spinach 2.12 spin-boson functions and tutorial (PR 195)

2026-08-06T04:42:23Z

Index the new Spinach 2.12 spin-boson functions and tutorial (PR 195)

2026-04-25T11:49:16Z

‎Available contexts

2026-04-25T11:26:44Z

Normalise sequential blank lines

2023-07-28T09:03:53Z

‎Call syntax for imaging and microfluidics contexts

2023-07-28T09:03:34Z

‎Call syntax for imaging and microfluidics contexts

2023-07-28T09:03:21Z

‎Call syntax for imaging contexts

2023-07-28T09:02:55Z

‎Available contexts

2018-07-08T14:30:49Z

2018-07-08T14:30:13Z

‎Call syntax for imaging contexts

2018-07-08T14:29:48Z

‎Call syntax for spectroscopy contexts

@@ Line 12: / Line 12: @@
 # [[crystal.m]] - single static orientation simulations.
 # [[doublerot.m]] - double rotation simulations using Fokker-Planck formalism for the rotation part and a spherical grid for the powder average operation.
 # [[floquet.m]] - single rotation simulations using Floquet formalism for the rotation part and a spherical grid for the powder average operation.
@@ Line 46: / Line 47: @@
 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 normalised to 1 Tesla/m, and F is the diffusion and flow superoperator.
 ''Version 2.8, authors: [[Ilya Kuprov]]''

@@ Line 19: / Line 19: @@
 # [[powder.m]] - static powder simulations using a spherical grid for the powder average operation.
 # [[meshflow.m]] - microfluidic simulations where spin dynamics is accompanied by chemical reactions, diffusion, and flow.
 # [[singlerot.m]] - single rotation simulations using Fokker-Planck formalism for the rotation part and a spherical grid for the powder average operation.

← Older revision		Revision as of 11:26, 25 April 2026
Line 47:		Line 47:

	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 normalised to 1 Tesla/m, and F is the diffusion and flow superoperator.		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 normalised to 1 Tesla/m, and F is the diffusion and flow superoperator.
−

	''Version 2.8, authors: [[Ilya Kuprov]]''		''Version 2.8, authors: [[Ilya Kuprov]]''

@@ Line 46: / Line 46: @@
       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.
+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 normalised to 1 Tesla/m, and F is the diffusion and flow superoperator.
 ''Version 2.8, authors: [[Ilya Kuprov]]''

@@ Line 36: / Line 36: @@
 where H is the Hamiltonian commutation superoperator, R is the relaxation superoperator, and K is the kinetics superoperator.
-==Call syntax for imaging contexts==
+==Call syntax for imaging and microfluidics contexts==
 The imaging context has a similar call:

@@ Line 18: / Line 18: @@
 # [[liquid.m]] - liquid state simulations.
 # [[powder.m]] - static powder simulations using a spherical grid for the powder average operation.
 # [[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.
 # [[singlerot.m]] - single rotation simulations using Fokker-Planck formalism for the rotation part and a spherical grid for the powder average operation.

← Older revision		Revision as of 14:30, 8 July 2018
Line 1:		Line 1:
−	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 creating operators (evolution, kinetics, relaxation, diffusion, ''etc.'') and for running miscellaneous housekeeping ~~operations~~ (rotating frame transformations, transmitter offsets, powder averages, magic angle spinning, ''etc.'').	+	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 creating operators (evolution, kinetics, relaxation, diffusion, ''etc.'') and for running miscellaneous housekeeping (rotating frame transformations, transmitter offsets, powder averages, magic angle spinning, ''etc.'').

	Most built-in pulse sequences in Spinach should be called via a context, for example:		Most built-in pulse sequences in Spinach should be called via a context, for example:

@@ Line 41: / Line 41: @@
       answer=imaging(spin_system,pulse_sequence,parameters)
-but the assumptions are set internally to 'nmr' and the pulse sequence must have the following syntax:
+but the assumptions are set internally to 'nmr'. All pulse sequences using the imaging context must have the following syntax:
       answer=pulse_sequence(spin_system,parameters,H,R,K,G,F);

@@ Line 29: / Line 29: @@
 The first argument is the spin system object, the second is a function handle for the pulse sequence, the third is the parameter set expected by the sequence, and the last argument is the [[assume.m|assumption set]].
-All pulse sequences using a context must have the same call syntax:
+All pulse sequences using a spectroscopy context must have the following call syntax:
       answer=pulse_sequence(spin_system,parameters,H,R,K);