Search found 106 matches

by kuprov
Wed Jun 15, 2022 8:54 am
Forum: Spinach support
Topic: Formalisms and approximations
Replies: 1
Views: 180

Re: Formalisms and approximations

Different formalisms (zeeman-liouv, sphten-liouv) would of course produce the same answer, but different assumptions would not. Assumptions refer to "what Spinach can assume it can ignore or approximate". For example in high-field NMR, weak coupling is a common assumption. It would of cour...
by kuprov
Tue Jun 07, 2022 9:32 am
Forum: Spinach support
Topic: Problem with Spin polarization graphs
Replies: 4
Views: 248

Re: Problem with Spin polarization graphs

That depends on what your dynamics is. The safe choice is always 'labframe', although the calculation might be very slow and require very short time step because you are explicitly digitising very high frequencies. You can use 'nmr' when the rotating frame is a good approximation. That is roughly wh...
by kuprov
Tue Jun 07, 2022 8:14 am
Forum: Spinach support
Topic: Problem with Spin polarization graphs
Replies: 4
Views: 248

Re: Problem with Spin polarization graphs

Simple - the 'nmr' assumptions (in the Hamitonian function call) are essentially high-field secular approximation. That does of course break down at zero field. Use 'labframe' assumptions instead, further details here:

https://spindynamics.org/wiki/index.php?title=Assume.m
by kuprov
Mon Jun 06, 2022 2:14 pm
Forum: Spinach support
Topic: Pseudocontact shift calculation from spin density
Replies: 5
Views: 317

Re: Pseudocontact shift calculation from spin density

Yes, the PDE essentially treats the problem as multiple tiny susceptibility centres at each voxel - a distributed susceptibility density. To make the problem tractable, we assume the same tensor everywhere, and only the amplitude is variable. Of course, the amplitude has to stay positive.
by kuprov
Wed Jun 01, 2022 12:40 pm
Forum: Spinach support
Topic: Coherence
Replies: 3
Views: 263

Re: Coherence

Well, sure - choose Hilbert space as formalism, get the Hamiltonian, diagonalise it, transform your density matrix into its eigenframe, and just use Matlab indexing to extract the elements of the matrix.
by kuprov
Wed Jun 01, 2022 12:17 pm
Forum: Spinach support
Topic: Coherence
Replies: 3
Views: 263

Re: Coherence

Well, yes, coherence() and correlation() filter specific coherence and correlation orders. https://spindynamics.org/wiki/index.php?title=Coherence.m https://spindynamics.org/wiki/index.php?title=Correlation.m The difference is that coherence order is an eigenstate of the total Lz operator with a par...
by kuprov
Fri May 27, 2022 10:57 am
Forum: Spinach support
Topic: Spin polarization graph
Replies: 1
Views: 184

Re: Spin polarization graph

Call create() and basis() to set things up, then request a Hamiltonian by calling assume() and hamiltonian(), then get your initial condition from state() or equilibrium() calls, then choose a time step and calculate the propagator by calling propagator(), then apply that propagator to the initial c...
by kuprov
Thu May 26, 2022 3:03 pm
Forum: Spinach support
Topic: Pseudocontact shift calculation from spin density
Replies: 5
Views: 317

Re: Pseudocontact shift calculation from spin density

Finally on physics. The partial differential equation that is being solved was derived for a classical probability density of a classical magnetic susceptibility centre. In quantum mechanical calculations, we assume that one or more unpaired electrons can be treated in that way. So the density does ...
by kuprov
Thu May 26, 2022 2:59 pm
Forum: Spinach support
Topic: Pseudocontact shift calculation from spin density
Replies: 5
Views: 317

Re: Pseudocontact shift calculation from spin density

Also correct for the XYZ order - that would teach me not to use highly symmetric examples for testing... :)
by kuprov
Thu May 26, 2022 2:19 pm
Forum: Spinach support
Topic: Pseudocontact shift calculation from spin density
Replies: 5
Views: 317

Re: Pseudocontact shift calculation from spin density

OK, looking at the extents matter... you are right of course, thanks for spotting that bug! Indeed, the example file has symmetric extents and therefore works by pure accident. I'll update the extent handling.