Difference between revisions of "Overtone pa.m"
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| − | Overtone soft pulse-acquire experiment | + | {{DISPLAYTITLE:overtone_pa.m}} __NOTOC__ |
| + | Overtone soft pulse-acquire experiment that applies a soft pulse followed by frequency-domain acquisition at the overtone frequency; because time-domain overtone spectroscopy is difficult (see http://dx.doi.org/10.1039/C4CP03994G), this acquisition mode is preferable in practice, and simulations [[assume.m|assumptions]] should be set to 'qnmr'. | ||
==Syntax== | ==Syntax== | ||
| − | spectrum= | + | spectrum=overtone_pa(spin_system,parameters,H,R,K) |
| − | == | + | ==Parameters== |
| − | |||
| − | |||
| − | |||
parameters.sweep - vector with two elements giving the spectrum frequency extents | parameters.sweep - vector with two elements giving the spectrum frequency extents | ||
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parameters.npoints - number of points in the spectrum | parameters.npoints - number of points in the spectrum | ||
| + | |||
| + | parameters.spins - overtone-active nucleus, specified as a | ||
| + | single-element cell array | ||
| + | |||
| + | parameters.spc_dim - Fokker-Planck spatial dimension | ||
parameters.rho0 - initial state | parameters.rho0 - initial state | ||
parameters.coil - detection state | parameters.coil - detection state | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
parameters.Lx - X Zeeman operator on the quadrupolar nucleus | parameters.Lx - X Zeeman operator on the quadrupolar nucleus | ||
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parameters.rf_frq - pulse frequency offset from the overtone frequency on the quadrupolar nucleus, Hz | parameters.rf_frq - pulse frequency offset from the overtone frequency on the quadrupolar nucleus, Hz | ||
| − | parameters.rf_pwr - pulse power on the quadrupolar nucleus, | + | parameters.rf_pwr - pulse power on the quadrupolar nucleus, rad/s |
parameters.rf_dur - pulse duration, seconds | parameters.rf_dur - pulse duration, seconds | ||
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parameters.method - 'average' uses the average Hamiltonian theory, 'fplanck' uses Fokker-Planck formalism | parameters.method - 'average' uses the average Hamiltonian theory, 'fplanck' uses Fokker-Planck formalism | ||
for the calculation of the pulse evolution. | for the calculation of the pulse evolution. | ||
| + | |||
| + | H - Hamiltonian commutation superoperator | ||
| + | |||
| + | R - unthermalised relaxation superoperator | ||
| + | |||
| + | K - chemical kinetics superoperator | ||
==Returns== | ==Returns== | ||
| − | The function returns the | + | The function returns the spectrum of the system with the specified starting state detected on the specified coil state within the frequency interval requested. |
==Examples== | ==Examples== | ||
| − | The following 15N overtone spectrum is produced by examples/nmr_overtone/ | + | The following 15N overtone spectrum is produced by examples/nmr_overtone/mas_valine_2.m example file: |
[[File:ot_example_2.png]] | [[File:ot_example_2.png]] | ||
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==Notes== | ==Notes== | ||
# Relaxation must be present in the system dynamics, or the matrix inverse-times-vector operation performed by the frequency domain detection module would fail to converge. The relaxation superoperator should ''not'' be thermalised. | # Relaxation must be present in the system dynamics, or the matrix inverse-times-vector operation performed by the frequency domain detection module would fail to converge. The relaxation superoperator should ''not'' be thermalised. | ||
| − | |||
# Relaxation theory is not applied during the pulse. | # Relaxation theory is not applied during the pulse. | ||
| − | + | # Average Hamiltonian and Fokker-Planck pulses produce signals in different phases. We are trying to figure out why, but it looks non-trivial. The average Hamiltonian theory option is faster. | |
| − | # Average Hamiltonian and Fokker- | ||
| − | |||
# Irrespectively of the pulse algorithm option selection, the magic angle spinning is always handled with the Fokker-Planck formalism. | # Irrespectively of the pulse algorithm option selection, the magic angle spinning is always handled with the Fokker-Planck formalism. | ||
==See also== | ==See also== | ||
| − | [[overtone_cp.m]], [[overtone_dante.m]], [[ | + | [[overtone_cp.m]], [[overtone_dante.m]], [[overtone_a.m]], [[slowpass.m]], [[assume.m]], [[Built-in_experiments]] |
| − | |||
| − | '' | + | ''Version 2.9, authors: [[Ilya Kuprov]]'' |
Latest revision as of 19:39, 6 June 2026
Overtone soft pulse-acquire experiment that applies a soft pulse followed by frequency-domain acquisition at the overtone frequency; because time-domain overtone spectroscopy is difficult (see http://dx.doi.org/10.1039/C4CP03994G), this acquisition mode is preferable in practice, and simulations assumptions should be set to 'qnmr'.
Syntax
spectrum=overtone_pa(spin_system,parameters,H,R,K)
Parameters
parameters.sweep - vector with two elements giving the spectrum frequency extents
in Hz around the overtone frequency
parameters.npoints - number of points in the spectrum
parameters.spins - overtone-active nucleus, specified as a
single-element cell array
parameters.spc_dim - Fokker-Planck spatial dimension
parameters.rho0 - initial state
parameters.coil - detection state
parameters.Lx - X Zeeman operator on the quadrupolar nucleus
parameters.rf_frq - pulse frequency offset from the overtone frequency on the quadrupolar nucleus, Hz
parameters.rf_pwr - pulse power on the quadrupolar nucleus, rad/s
parameters.rf_dur - pulse duration, seconds
parameters.method - 'average' uses the average Hamiltonian theory, 'fplanck' uses Fokker-Planck formalism
for the calculation of the pulse evolution.
H - Hamiltonian commutation superoperator
R - unthermalised relaxation superoperator
K - chemical kinetics superoperator
Returns
The function returns the spectrum of the system with the specified starting state detected on the specified coil state within the frequency interval requested.
Examples
The following 15N overtone spectrum is produced by examples/nmr_overtone/mas_valine_2.m example file:
Notes
- Relaxation must be present in the system dynamics, or the matrix inverse-times-vector operation performed by the frequency domain detection module would fail to converge. The relaxation superoperator should not be thermalised.
- Relaxation theory is not applied during the pulse.
- Average Hamiltonian and Fokker-Planck pulses produce signals in different phases. We are trying to figure out why, but it looks non-trivial. The average Hamiltonian theory option is faster.
- Irrespectively of the pulse algorithm option selection, the magic angle spinning is always handled with the Fokker-Planck formalism.
See also
overtone_cp.m, overtone_dante.m, overtone_a.m, slowpass.m, assume.m, Built-in_experiments
Version 2.9, authors: Ilya Kuprov
