Difference between revisions of "Appendix E: experiment parameters"
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Latest revision as of 17:14, 18 June 2026
This section summarises the subfields of the parameters data structure encountered in tracked Spinach MATLAB source files. This data structure must be passed to context (e.g. powder.m) and pulse sequence (e.g. noesy.m) functions. Individual functions may also have their own case-specific parameters; always check the manual page for the function that you use.
| Subfield | Data type | Notes | functions using this subfield |
|---|---|---|---|
| parameters.addshift | a real scalar | shift to center the field profile | noveldnp_steady.m, topdnp_steady.m, xixdnp_steady.m |
| parameters.angle | a vector of reals | pulse flip angles for those experiments that require them | cosy.m, crazed.m, ct_cosy.m, and others |
| parameters.apodize | a character string | apodisation window name applied before DOSY-COSY fitting | ufdosycosy_2spin.m |
| parameters.assumptions | a character string | Hamiltonian generation assumptions, use 'deer' to keep two- electron flip-flop terms and 'deer-zz' to drop them | deer_3p_soft_diag.m, deer_4p_soft_diag.m |
| parameters.axis | three-element real vector | rotor axis for single rotation solid state NMR experiments | masdnp.m |
| parameters.axis_inner | three-element real vector | inner rotor axis for double rotation solid state NMR experiments | doublerot.m |
| parameters.axis_outer | three-element real vector | outer rotor axis for double rotation solid state NMR experiments | doublerot.m |
| parameters.axis_units | a character string | a character string with the units in which the axis ticks should be returned: 'ppm', 'Gauss', 'mT', 'Hz', 'kHz', 'MHz','MHz-labframe', 'GHz', 'GHz-labframe', 'gtensor', 'points' | axis_1d.m, int_2d.m, plot_1d.m, and others |
| parameters.b_axis | a finite real vector | a vector of magnetic field values, Tesla | fieldsweep.m |
| parameters.bandwidth | a positive real scalar | saltire chirp sweep width, Hz | psyche.m |
| parameters.beta | a finite real scalar | the angle used in the selection pulse, radians | dept.m, deptq.m, psyche.m |
| parameters.box_cent | a real vector with three elements | centre of the PCS inverse-problem solution box, Angstrom | ipcs.m |
| parameters.box_size | a real vector with three elements | oscillator box size, m | ipcs.m |
| parameters.BW | a positive real scalar | chirp or WURST pulse bandwidth, Hz | spencosy.m, spendosy.m, spendosycosy.m, and others |
| parameters.calc_type | a character string | calculation mode: 'time_dependence', 'steady_state', or 'trajectory' | solid_effect.m |
| parameters.centre | a character string | diamond defect centre identifier used to select tabulated spin Hamiltonian data | diamond_co.m, diamond_n_inter.m, diamond_ni.m, and others |
| parameters.chi | a real symmetric 3x3 matrix | electron magnetic susceptibility tensor used in PCS back-calculation, Angstrom^3 | ipcs.m |
| parameters.chirptype | a supported chirp pulse type | can be 'wurst' or 'smoothed' | psyche.m, spendosy.m, spendosycosy.m, and others |
| parameters.coil | A state vector or a density matrix. | Detection state for the simulation. | acquire.m, beamdnp.m, cn2d_dq.m, and others |
| parameters.coil_ph | a cell array of real arrays | spatial detection-sensitivity phantoms paired with coil_st to build the Fokker-Planck detection state | imaging.m, meshflow.m |
| parameters.coil_prob | a spin-space state vector | detection state on the DEER probe spin | deer_3p_hard_deer.m |
| parameters.coil_pump | a spin-space state vector | detection state on the DEER pump spin | deer_3p_hard_deer.m |
| parameters.coil_st | a cell array | spin-space detection state projected out of the final Fokker-Planck density | cpmg_dec.m, udd_dec.m |
| parameters.confine | a real vector with two non-negative elements | inner exclusion and outer inclusion radii for the PCS source volume, Angstrom | ipcs.m |
| parameters.contact_dur | a non-negative real scalar | contact time, seconds | noveldnp_steady.m |
| parameters.cp_dur | a positive real scalar | duration of the contact time, s | cp_acquire_soft.m, fslghetcor.m, wise.m |
| parameters.cp_npt | a positive integer scalar or vector | number of integration steps in each cross-polarisation transfer period | frydman_pump_a.m, frydman_pump_b.m |
| parameters.cp_pwr | a two-element vector of real numbers | nutation frequencies on the two channels during the CP contact time, a two-element vector, Hz | cp_acquire_soft.m, cp_contact_soft.m, fslghetcor.m, and others |
| parameters.d_ambig | a cell array of integer vectors | groups of diamagnetic assignments allowed to permute during PCS combination fitting | pcs_combi_fit.m |
| parameters.d_shifts | a real vector | unique diamagnetic chemical shifts used in PCS combination fitting, ppm | pcs_combi_fit.m |
| parameters.d_sign | a real scalar | sign multiplier for the R2 diamond centre zero-field splitting parameter | diamond_r2.m |
| parameters.dead_time | a non-negative real scalar | the system will be evolved for this time (seconds) before the signal acquisition begins | acquire.m |
| parameters.dec_time | a positive real number | total duration of the CPMG or UDD decoupling sequence, seconds | cpmg_dec.m, udd_dec.m |
| parameters.decouple | A cell array of spin specifications, e.g. {'13C','15N'}. | Spins that must be decoupled analytically during the simulation. | acquire.m, dante.m, hetcor.m, and others |
| parameters.decouple_f1 | a cell array | nuclei that receive midpoint 180-degree refocusing pulses in F1, e.g. {'1H'} | hmqc.m, hmqcetgp.m, hmqcetgpsi.m, and others |
| parameters.decouple_f2 | a cell array | nuclei to decouple in F2, e.g {'15N','13C'} | ct_hsqc.m, hmqc.m, hmqcetgp.m, and others |
| parameters.decouple_f3 | a cell array of strings | list of spins to be decoupled during the detection period, typically {'13C'} | hcch_cosy.m |
| parameters.del | a positive real scalar | diffusion delay, seconds | dosy_oneshot.m |
| parameters.delay | a non-negative real scalar | J-coupling evolution delay, seconds | mqs.m, ufmq.m |
| parameters.delay_1 | a non-negative real scalar | first evolution delay, seconds | mqs_refocus.m |
| parameters.delay_2 | a non-negative real scalar | second evolution delay, seconds | mqs_refocus.m |
| parameters.delay_dur | a non-negative real scalar | delay_duration, seconds | topdnp.m, topdnp_steady.m |
| parameters.delta | a positive real scalar | evolution delay, see the pulse sequence diagram, typically 1.1e-3 seconds | hcch_cosy.m, idosyzs.m, psyche.m, and others |
| parameters.delta1 | a non-negative real scalar | optional COLOC delta1 delay, seconds; must be at least half of maximum t1 | coloc.m |
| parameters.delta2 | a positive real scalar | COLOC delta2 (see the paper), typically 40e-3 seconds | coloc.m, hncaco.m |
| parameters.delta_b | a positive real scalar | delta_2 delay from the paper cited above; the authors recommend 60e-3 seconds | hmbc.m |
| parameters.delta_big | a positive real scalar | diffusion delay in stimulated-echo and diffusion-ordered SPEN sequences, seconds | idosyzs.m, st_ideal.m |
| parameters.delta_sml | a positive real scalar | gradient pulse duration in diffusion-encoding blocks, seconds | idosyzs.m, st_ideal.m |
| parameters.deltat | a positive real scalar | time step used during gradient readout acquisition, seconds | spencosy.m, spendosy.m, spendosycosy.m, and others |
| parameters.deriv | a cell array with one or two elements | {'fourier'} uses Fourier differentiation matrices; {'period',n} requests n-point central finitedifference matrices with periodic boundary conditions | imaging.m, hydrodynamics.m, v2fplanck.m |
| parameters.derivative | a scalar flag | flag requesting first-derivative plotting of a one-dimensional spectrum | plot_1d.m |
| parameters.detection | a character string | ZULF detection mode, either 'uniaxial' or 'quadrature' | zerofield.m, zulf_abrupt.m |
| parameters.diff | a non-negative real scalar | diffusion constant (m^2/s) | idosyzs.m, psyche.m |
| parameters.diff_g_amp | a vector with two real numbers | [optional] a vector of diffusion gra- dient pair amplitudes in X,Y (T/m) to be active during the echo time | epi_2d.m, epi_3d.m, phase_enc_2d.m |
| parameters.diff_g_dur | a positive real scalar | duration of the diffusion-weighting gradient pulse, seconds | epi_2d.m |
| parameters.dims | a vector with three finite positive real numbers | size of the sample (m) | dosy_oneshot.m, epi_3d.m, idosyzs.m, and others |
| parameters.drop_field | a non-negative real scalar | final magnetic field after the exponential field drop, Tesla | zulf_abrupt.m |
| parameters.drop_npoints | a positive integer | number of time points used to discretise the field drop | zulf_abrupt.m |
| parameters.drop_rate | a positive real scalar | exponential field-drop rate constant, Hz | zulf_abrupt.m |
| parameters.drop_time | a positive real scalar | duration of the field-drop interval, seconds | zulf_abrupt.m |
| parameters.dscale | a positive real scalar | diffusion-coefficient scaling used by the DOSY-COSY fitting model | ufdosycosy_2spin.m |
| parameters.dt | a positive real scalar | time step, seconds | dnp_time_dep.m, simple_flow.m |
| parameters.duration | a positive real scalar | saltire chirp pulse duration, seconds | psyche.m |
| parameters.dxx | a real array matching the spatial grid | XX component of the spatially varying diffusion tensor, m^2/s | imaging.m, v2fplanck.m |
| parameters.dxy | a real array matching the spatial grid | XY component of the spatially varying diffusion tensor, m^2/s | imaging.m, v2fplanck.m |
| parameters.dxz | a real array matching the spatial grid | XZ component of the spatially varying diffusion tensor, m^2/s | v2fplanck.m |
| parameters.dyx | a real array matching the spatial grid | YX component of the spatially varying diffusion tensor, m^2/s | v2fplanck.m |
| parameters.dyy | a real array matching the spatial grid | YY component of the spatially varying diffusion tensor, m^2/s | v2fplanck.m |
| parameters.dyz | a real array matching the spatial grid | YZ component of the spatially varying diffusion tensor, m^2/s | v2fplanck.m |
| parameters.dzx | a real array matching the spatial grid | ZX component of the spatially varying diffusion tensor, m^2/s | v2fplanck.m |
| parameters.dzy | a real array matching the spatial grid | ZY component of the spatially varying diffusion tensor, m^2/s | v2fplanck.m |
| parameters.dzz | a real array matching the spatial grid | ZZ component of the spatially varying diffusion tensor, m^2/s | imaging.m, v2fplanck.m |
| parameters.e_dur | a positive real scalar | duration of the electron pulse, s | endor_davies.m |
| parameters.e_frq | a real scalar | frequency of the electron pulse, Hz | endor_davies.m |
| parameters.e_phi | a real scalar | phase of the electron pulse, rad | endor_davies.m |
| parameters.e_pwr | a positive real scalar | power of the electron pulse, rad/s | endor_davies.m |
| parameters.e_rnk | a positive real integer | Fokker-Planck cut-off rank for the electron pulse | endor_davies.m |
| parameters.echo_angle | a real scalar | optional pulse angle for echo detection | hp_acquire.m |
| parameters.echo_npts | a positive real integer | number of points in the echo discretization | deer_3p_soft_deer.m, deer_3p_soft_diag.m, deer_4p_soft_deer.m, and others |
| parameters.echo_oper | a spin operator matrix | optional echo pulse operator applied during hyperpolarised acquisition | hp_acquire.m |
| parameters.echo_time | a positive real scalar | time to sample around the ex- pected echo position | deer_3p_soft_deer.m, deer_3p_soft_diag.m, deer_4p_soft_deer.m, and others |
| parameters.edit_time | a positive real scalar | multiplicity editing delay, s | hsqcedetgp.m |
| parameters.el_offs | an array of real numbers | microwave resonance offsets | noveldnp_steady.m, topdnp_steady.m, xixdnp_steady.m |
| parameters.electrons | a row vector of positive integers | a vector of integers specifying which spins in sys.isotopes are electrons | endor_mims_echo.m, endor_mims_ideal.m, rydmr_exp.m |
| parameters.equation | a character string | PCS inverse-problem equation: 'kuprov' for probability density or 'poisson' for source term | ipcs.m |
| parameters.ex_hard | a spin operator matrix | broadband hard-pulse excitation operator used for DEER diagnostic output | deer_3p_hard_deer.m |
| parameters.ex_prob | a spin operator matrix | selective excitation operator applied to the DEER probe spin | deer_3p_hard_deer.m, deer_3p_hard_echo.m |
| parameters.ex_pump | a spin operator matrix | selective excitation operator applied to the DEER pump spin | deer_3p_hard_deer.m, deer_3p_hard_echo.m |
| parameters.exc_opers | a non-empty cell array of matrices | a cell array of spin operators for the ideal pi/2 excitation pulse (same flip angle on all channels) | cp_contact_hard.m |
| parameters.expt_pcs | a real column vector | experimental pseudocontact shifts at the PCS-active nuclei, ppm | ipcs.m |
| parameters.ez_oper | a spin operator matrix | electron Lz operator used for microwave offset or field scanning | dnp_field_scan.m, dnp_freq_scan.m, dnp_time_dep.m |
| parameters.f1_decouple | set to 1 or 0 | logical switch controlling proton de- coupling during the T1 period | hnco.m |
| parameters.fields | a row vector with two elements in ascending order | two-element vector in Tesla, ordered as [from to] | dnp_field_scan.m, fieldscan_enlev.m, fieldscan_magn.m, and others |
| parameters.filename | a character string | waveform file read for the selective pulse | idosyzs.m |
| parameters.flip_angle | a real scalar | pulse flip angle in radians for protons; for other nuclei, this will be scaled by the gamma ratio | zerofield.m, zulf_abrupt.m |
| parameters.flipback | an integer scalar equal to 0 or 1 | NOVEL flag selecting whether a flipback pulse is applied | noveldnp_steady.m |
| parameters.flippulse | an integer scalar equal to 0 or 1 | DNP sequence flag selecting solid-effect or NOVEL pulse treatment | noveldnp.m, noveldnp_steady.m |
| parameters.fovmax | a real scalar | upper field-of-view bound for the DOSY-COSY spatial model, metres | ufdosycosy_2spin.m |
| parameters.fovmin | a real scalar | lower field-of-view bound for the DOSY-COSY spatial model, metres | ufdosycosy_2spin.m |
| parameters.frc_cnst | a positive real number | force constant, N/m | oscillator.m |
| parameters.fwhm | a positive real scalar | Lorentzian line FWHM, Tesla | fieldsweep.m |
| parameters.g_amp | a vector with two real numbers | amplitudes of the two gradients, T/m | dosy_oneshot.m, dpfgse_select.m, dpfgse_suppress.m, and others |
| parameters.g_dur | a positive real number | gradient duration, seconds | dosy_oneshot.m, dpfgse_select.m, dpfgse_suppress.m, and others |
| parameters.g_n_steps | a positive real integer | number of time steps | grad_echo.m, spin_echo.m |
| parameters.g_ref | a real scalar | reference g-factor around which frequency offsets are specified | dnp_freq_scan.m |
| parameters.g_stab_del | a non-negative real scalar | post-gradient stabilisation delay in seconds, defaults to 2e-4 | dosy_oneshot.m, gcosy.m |
| parameters.g_step_dur | a positive real scalar | time step duration | grad_echo.m, spin_echo.m |
| parameters.g_trityl | a real scalar | mean trityl electron g factor used to convert field to microwave frequency | fig_1_exch_and_field_scan.m, fig_2_tau_and_field_traject.m, fig_3_time_dep_bot_row.m, and others |
| parameters.Ga | a real scalar | acquisition gradient amplitude, T/m | spencosy.m, spendosy.m, spendosycosy.m, and others |
| parameters.gamp | a finite real scalar | gradient amplitude, T/m | psycosy.m |
| parameters.Ge | a real scalar | encoding gradient amplitude, T/m | spencosy.m, spendosy.m, spendosycosy.m, and others |
| parameters.germanium | a character string | germanium isotope specification for the GeV0 diamond defect model | diamond_gev0.m |
| parameters.Gp | a real scalar | coherence-selection gradient amplitude, T/m | spencosy.m |
| parameters.gpu | a logical scalar | logical flag enabling GPU arrays in PCS inversion | ipcs.m |
| parameters.grad_amp | a finite real scalar | gradient amplitude at the end of the spiral, T/m | spiral.m |
| parameters.grad_angles | a real vector | rotation angles for Fokker-Planck gradient operators, radians | g2fplanck.m |
| parameters.grid | character string with a file name | spherical averaging grid for solid state experiments | eqmag.m, fieldsweep.m, masdnp.m |
| parameters.grv_cnst | a real number | gravitational acceleration. m/s^2 | oscillator.m |
| parameters.guess | a real three-dimensional array | initial probability-density guess for PCS inversion | ipcs.m |
| parameters.H_op | a cell array of Hamiltonian matrices | Hamiltonian operator matrices paired with H_ph in meshflow | meshflow.m |
| parameters.H_ph | a cell array of real arrays | spatial Hamiltonian phantoms paired with H_op in meshflow | meshflow.m |
| parameters.hfcs | a cell array of 3x3 real matrices | hyperfine coupling tensors used for PCS tensor fitting, Gauss | pcs_combi_fit.m |
| parameters.hi_pwr | a positive real scalar | nutation frequency of the excitation pulse on the high-gamma channel, Hz | cp_acquire_soft.m, cp_contact_soft.m, fslghetcor.m, and others |
| parameters.homodec_oper | a numeric matrix | operator to add to the Liouvillian at the detection stage | acquire.m |
| parameters.homodec_pwr | a real scalar | power coefficient for the operator, Hz | acquire.m |
| parameters.Hx | a spin operator matrix | X pulse operator on the spin-1/2 nucleus in overtone cross-polarisation | overtone_cp.m |
| parameters.hzeeman | a Zeeman operator matrix | separate Zeeman operator used to sweep the magnetic field in RYDMR | rydmr_exp.m |
| parameters.image_size | a vector of two integers greater than one | number of points in each dimension of the resulting image | epi_2d.m, epi_3d.m, fse.m, and others |
| parameters.include_13c | a logical scalar | logical flag adding nearest-neighbour 13C nuclei to supported diamond defect models | diamond_n2vm.m, diamond_p.m |
| parameters.int_tol | a positive real scalar | powder integration tolerance, a balance between speed and integration accuracy | fieldsweep.m |
| parameters.invert_axis | a scalar flag | flag reversing the plotted frequency axis | plot_1d.m |
| parameters.irr_opers | a non-empty cell array of matrices | a cell array of spin operators corresponding to the spin-lock on each channel | cp_contact_hard.m |
| parameters.irr_powers | a non-empty real matrix | a matrix containing the values of the spin-lock nutation fre- quency on each channel (rows) at each time slice (cols), Hz | beamdnp.m, cp_contact_hard.m, noveldnp.m, and others |
| parameters.isotopes | a cell array of character strings | isotope labels corresponding to the hyperfine tensors | pcs_combi_fit.m |
| parameters.J | A vector of reals. | The values of J-couplings that should be used for coherence transfer stages of NMR pulse sequences. | clip_hsqc.m, ct_hsqc.m, dept.m, and others |
| parameters.J_cc | a positive real scalar | 13C-13C J-coupling to be used for mag- netisation transfer, typically 35 Hz | hcch_cosy.m |
| parameters.J_ch | a positive real scalar | 1H-13C J-coupling to be used for mag- netisation transfer, typically 140 Hz | hcch_cosy.m |
| parameters.J_nh | a positive real scalar | 1H-15N J-coupling in Hz to be used for magnetisation transfer | hncaco.m |
| parameters.K_op | a cell array of kinetics matrices | kinetics operator matrices paired with K_ph in meshflow | meshflow.m |
| parameters.K_ph | a cell array of real arrays | spatial kinetics phantoms paired with K_op in meshflow | meshflow.m |
| parameters.kappa | a real scalar | bipolar-gradient unbalancing factor in the one-shot DOSY sequence | dosy_oneshot.m |
| parameters.lamp | a positive real scalar | spin-lock power, Hz | tocsy.m |
| parameters.Lx | a numeric matrix | Lx and Ly operators that go into | nqr_pa.m, overtone_dante.m, overtone_pa.m |
| parameters.Ly | a numeric matrix | the RF Hamiltonian | nqr_pa.m |
| parameters.margins | a real vector with six elements | six Cartesian margins added around the nuclear-coordinate bounding box, Angstrom | ipcs.m |
| parameters.marker | a logical scalar | regression-test marker forwarded through drifts.m to the test context | drifts.m |
| parameters.masframe | a character string | the frame in which the rotations are applied. The possibilities are: | rotor_stack.m |
| parameters.max_delay | a positive real number | longest relaxation delay | inv_rec.m, sat_rec.m |
| parameters.max_rank | a positive real integer | rotor discretization grid rank | dpfgse_select.m, dpfgse_suppress.m, masdnp.m, and others |
| parameters.method | a character string | soft puse propagation method, 'expv' for Krylov propagation, 'expm' for exponential propagation, 'evolution' for Spin- ach evolution function | deer_3p_soft_deer.m, deer_3p_soft_diag.m, deer_3p_soft_hole.m, and others |
| parameters.model | a character string | DOSY-COSY fitting model name, such as keeler_corr | ufdosycosy_2spin.m |
| parameters.mq_order | an integer | MQMAS coherence order | mqmas.m |
| parameters.mqorder | an integer scalar | coherence order to select | mqs.m, mqs_refocus.m, ufmq.m |
| parameters.mw_dur | a vector of real numbers | microwave irradiation durations on each channel | fig_1_exch_and_field_scan.m |
| parameters.mw_freq | a real scalar | microwave frequency, Hz | fieldsweep.m |
| parameters.mw_frq | a vector of real numbers | microwave irradiation frequencies on each channel | dnp_field_scan.m, dnp_freq_scan.m, masdnp.m |
| parameters.mw_off | a real scalar | microwave frequency offset from free electron,rad/s | dnp_time_dep.m |
| parameters.mw_oper | a spin operator matrix | microwave irradiation operator used in DNP field or frequency scans | dnp_field_scan.m, dnp_freq_scan.m, dnp_time_dep.m |
| parameters.mw_pwr | a vector of real numbers | microwave irradiation powers on each channel | dnp_field_scan.m, dnp_freq_scan.m, dnp_time_dep.m, and others |
| parameters.mw_time | a non-negative real scalar | microwave irradiation duration before the average magnetistion is computed, seconds | masdnp.m |
| parameters.n_13c | an integer scalar | number of explicit nearest-neighbour 13C nuclei included in a diamond defect model | diamond_ni.m, diamond_siv0.m, diamond_ti.m |
| parameters.n_delays | a positive integer | number of relaxation delays to run | inv_rec.m, sat_rec.m |
| parameters.n_dur | a positive real scalar | duration of the nuclei pulse, s | endor_davies.m, endor_mims_echo.m, endor_mims_ideal.m |
| parameters.n_frq | an array of real numbers | vector of frequencies for the nuclei pulse, in Hz. The answer is returned as a vector of the same dimension | endor_davies.m, endor_mims_ideal.m |
| parameters.n_periods | a positive integer | number of rotor periods that the sequence is active for | dante.m, overtone_dante.m |
| parameters.n_phi | a real scalar | phase of the nuclei pulse, rad | endor_davies.m |
| parameters.n_points | a positive real integer | number of discretization points | oscillator.m |
| parameters.n_pwr | a positive real scalar | power of the nuclei pulse, rad/s | endor_davies.m |
| parameters.n_rnk | a positive real integer | Fokker-Planck cut-off rank for the nuclei pulse | endor_davies.m, endor_mims_ideal.m |
| parameters.n_steps | a finite positive real integer | if 'time_dependence' is set in the calc_type parameter, sets the num- ber of time steps | solid_effect.m |
| parameters.nblocks | a positive integer | number of FSLG blocks per indirect-dimension point | fslghetcor.m |
| parameters.ncycles | a row vector of non-negative integers | row vector with numbers of rotor cycles in the REDOR evolution time | redor.m |
| parameters.needs | specified | should be set to {'rho_eq'}, this sequence needs the thermal equilibrium state | rydmr_exp.m |
| parameters.nel | a finite positive real integer | number of unpaired electrons involved | pcs_combi_fit.m |
| parameters.nickel | a character string | nickel isotope specification for the W8 diamond defect model | diamond_ni.m |
| parameters.nitrogen | a character string | nitrogen isotope specification, normally '14N' or '15N' | diamond_nvm_gs.m, diamond_p1.m |
| parameters.nloops | a positive integer | number of CPMG loops | beamdnp.m, cpmg.m, respiration.m, and others |
| parameters.nphases | a positive real integer | number of microwave phase grid points for the Fokker-Planck path | dnp_freq_scan.m |
| parameters.npoints | A vector of integers. | Number of points in each dimension of the output data array. | acquire.m, basic_1d_hard.m, clip_hsqc.m, and others |
| parameters.npoints1 | a positive integer scalar | acquired point count in the SPENDOSYCOSY gradient-readout dimension | spendosycosy.m |
| parameters.npoints2 | a positive integer scalar | acquired point count in the SPENDOSYCOSY COSY evolution dimension | spendosycosy.m |
| parameters.npts | a positive integer | number of discretization points in the grid | basic_1d_hard.m, cpmg_dec.m, dosy_oneshot.m, and others |
| parameters.npulses | a positive real integer | number of refocusing pulses after the initial pi/2 pulse | cpmg_dec.m, udd_dec.m |
| parameters.nstates | a positive real integer | number of lowest energy states to solve for | fieldscan_enlev.m, fieldscan_magn.m |
| parameters.nsteps | a positive integer | number of time steps to take during the CP contact time | cp_contact_soft.m, deer_3p_hard_deer.m, deer_3p_hard_echo.m, and others |
| parameters.nuclear_frq | a real scalar | nuclear Zeeman angular frequency used in solid-effect DNP, rad/s | solid_effect.m |
| parameters.nuclei | a row vector of positive integers | a vector of integers specifying which spins in sys.isotopes are nuclei to irradiate | endor_mims_ideal.m |
| parameters.nWURST | a positive real scalar | WURST pulse smoothing factor | spencosy.m, ufmq.m |
| parameters.Nx | a spin operator matrix | X pulse operator on the quadrupolar nucleus in overtone cross-polarisation | overtone_cp.m |
| parameters.offset | a finite real scalar | receiver offset for the time domain detection, Hz | deer_3p_soft_deer.m, deer_3p_soft_diag.m, deer_3p_soft_hole.m, and others |
| parameters.offset_uf_cov | a real scalar | offset between conventional and ultrafast multiple-quantum F1 axes | plot_uf.m |
| parameters.oldschool | a logical scalar | set to 1 to disable homospoil gradient before the mixing time | noesy.m |
| parameters.orientation | a character string | system orientation, threeelement vector containing Euler angles in radians, ordered as [alp bet gam] | fieldscan_enlev.m, fieldscan_magn.m |
| parameters.output | a character string | 'brief' returns just the DEER trace, 'detailed' also returns excitation profiles and the EPR spectrum | deer_3p_hard_deer.m |
| parameters.p1_p2_gap | a finite positive real scalar | time between the end of the first and the start of the second pulse, seconds | deer_4p_soft_deer.m, deer_4p_soft_diag.m |
| parameters.p1_p3_gap | a positive real scalar | time between the first and the third pulses, seconds | deer_3p_soft_deer.m, deer_3p_soft_diag.m |
| parameters.p2_nsteps | a positive real integer | number of second pulse positions in the interval between the first and the third pulse | deer_3p_soft_deer.m, deer_3p_soft_diag.m |
| parameters.p2_p4_gap | a finite positive real scalar | time between the end of the second the start of the third pulse, seconds | deer_4p_soft_deer.m, deer_4p_soft_diag.m |
| parameters.p3_nsteps | a positive real integer | number of third pulse positions in the interval between the first echo and the fourth pulse | deer_4p_soft_deer.m, deer_4p_soft_diag.m |
| parameters.p_ambig | a cell array of integer vectors | groups of paramagnetic assignments allowed to permute during PCS combination fitting | pcs_combi_fit.m |
| parameters.p_shifts | a real vector | unique paramagnetic chemical shifts used in PCS combination fitting, ppm | pcs_combi_fit.m |
| parameters.par_mass | a positive real number | particle mass, kg | oscillator.m |
| parameters.pathway | a character string | coherence-transfer pathway selector: 'P', 'N', or 'P+N' | gcosy.m |
| parameters.pe_grad_amp | a real scalar | phase encoding gradient amplitude, T/m | epi_2d.m, epi_3d.m, fse.m, and others |
| parameters.pe_grad_dur | a positive real scalar | the duration of the phase encoding gradient, seconds | epi_2d.m, epi_3d.m, fse.m, and others |
| parameters.phase | a real scalar | phase of the second pulse | xixdnp.m, xixdnp_steady.m |
| parameters.plot | a cell array of character strings | PCS inversion diagnostic plot selectors | ipcs.m |
| parameters.pp_tol | a real scalar | peak position tolerance in Tesla, this should be much smaller than the typical line width | fieldsweep.m |
| parameters.probe_spin | a positive real integer | number of the spin on which the sequence operates | ridme.m |
| parameters.pulse_amp | a real number | amplitude of each pulse, Hz | dante.m, mqmas.m, overtone_dante.m |
| parameters.pulse_angle | a real number | pulse angle, radians | hp_acquire.m |
| parameters.pulse_dur | an array of reals | durations for the three pulses, seconds | beamdnp.m, dante.m, deer_3p_soft_deer.m, and others |
| parameters.pulse_frq | an array of reals | frequencies for the three pulses, Hz | deer_3p_soft_deer.m, deer_3p_soft_diag.m, deer_3p_soft_hole.m, and others |
| parameters.pulse_npoints | a positive integer scalar | number of time points in the selective pulse waveform | idosyzs.m |
| parameters.pulse_num | a positive integer | number of pulses within rotor period | dante.m, overtone_dante.m |
| parameters.pulse_op | a spin operator matrix | hard-pulse operator used by the pulse sequence | cpmg.m, eseem.m, hp_acquire.m, and others |
| parameters.pulse_opx | a spin operator matrix | X-phase pulse operator used by SIFTER | sifter.m |
| parameters.pulse_opy | a spin operator matrix | Y-phase pulse operator used by SIFTER | sifter.m |
| parameters.pulse_phase | a non-empty row vector of real numbers | phases of the dephasing-channel pi pulses, radians; the vector is cycled through the pulse train, and defaults to [0 pi/2] | redor.m |
| parameters.pulse_phi | a real scalar | initial phases for the three pulses, radians | deer_3p_soft_deer.m, deer_3p_soft_diag.m, deer_3p_soft_hole.m, and others |
| parameters.pulse_pwr | an array of reals | power levels for the three pulses, rad/s | deer_3p_soft_deer.m, deer_3p_soft_diag.m, deer_3p_soft_hole.m, and others |
| parameters.pulse_rnk | a real integer | Fokker-Planck ranks for the three pulses | deer_3p_soft_deer.m, deer_3p_soft_diag.m, deer_3p_soft_hole.m, and others |
| parameters.pulsenpoints | a positive integer scalar | number of points in the pulse shape | psyche.m, spencosy.m, spendosy.m, and others |
| parameters.R_op | a cell array of relaxation matrices | relaxation superoperator matrices paired with R_ph in meshflow | meshflow.m |
| parameters.R_ph | a cell array of real arrays | spatial relaxation phantoms paired with R_op in meshflow | meshflow.m |
| parameters.rank_inner | positive integer | Floquet or Fokker-Planck rank for the inner rotor in double rotation solid state NMR experiments | doublerot.m |
| parameters.rank_outer | positive integer | Floquet or Fokker-Planck rank for the outer rotor in double rotation solid state NMR experiments | doublerot.m |
| parameters.rate | real numbers | spinning rate for single rotation solid state NMR experiments | dante.m, masdnp.m, mqmas.m, and others |
| parameters.rate_inner | real number | inner rotor spinning rate for double rotation solid state NMR experiments | doublerot.m |
| parameters.rate_outer | real number | outer rotor spinning rate for double rotation solid state NMR experiments | doublerot.m |
| parameters.rates | a vector of positive real numbers | row vector of singlet recombination rate constants, Hz | rydmr_exp.m |
| parameters.ref_frame | a character string | rotating frame used for the MAS Floquet example, such as rotor | mas_powder_dip_floquet.m |
| parameters.refocus_phase | a real scalar | phase of the observed-channel pi refocusing pulses, radians; defaults to 0 | redor.m |
| parameters.rf_amp_list | a real vector | be passed to shaped_pulse_af | dpfgse_select.m, dpfgse_suppress.m, epi_3d.m, and others |
| parameters.rf_b1_field | a real scalar | RF B1 field strength | endor_mims_ideal.m |
| parameters.rf_dur | a vector of real numbers | radiofrequency irradiation durations on each channel | cn2d_dq.m, cn2d_sq.m, idosyzs.m, and others |
| parameters.rf_dur_list | a positive real vector | function | dpfgse_select.m, dpfgse_suppress.m, epi_3d.m, and others |
| parameters.rf_frq | a vector of real numbers | radiofrequency irradiation frequencies on each channel | nqr_pa.m, overtone_cp.m, overtone_dante.m, and others |
| parameters.rf_frq_list | a real vector | soft pulse parameters that will | dpfgse_select.m, dpfgse_suppress.m, epi_3d.m, and others |
| parameters.rf_phi | a vector of real numbers | radiofrequency irradiation initial phases on each channel | dpfgse_select.m, dpfgse_suppress.m, epi_3d.m, and others |
| parameters.rf_pwr | a vector of real numbers | radiofrequency irradiation powers on each channel | cn2d_dq.m, cn2d_sq.m, nqr_pa.m, and others |
| parameters.rframes | a cell array of the following shape: {{'E',2},{'1H',1}} with the first element indicating the spins and the second the order of the rotating frame transformation | numerical rotating frame transformation specification | crystal.m, doublerot.m, liquid.m, and others |
| parameters.rho0 | A state vector or a density matrix. | Initial state for the simulation. | acquire.m, basic_1d_hard.m, beamdnp.m, and others |
| parameters.rho0_ph | a cell array of real arrays | initial-state spatial phantoms paired with rho0_st | imaging.m, meshflow.m |
| parameters.rho0_st | cell arrays | spin-space initial states paired with rho0_ph | imaging.m, meshflow.m |
| parameters.rho_eq | a state vector or a denisty matrix | equilibrium state for the experiments that require it | inv_rec_2.m |
| parameters.rlx_op | cell arrays | relaxation superoperators paired with rlx_ph | imaging.m |
| parameters.rlx_ph | a cell array of real arrays | spatial relaxation phantoms paired with rlx_op | imaging.m |
| parameters.ro_grad_amp | a real scalar | readout gradient amplitude, T/m | basic_1d_hard.m, epi_2d.m, epi_3d.m, and others |
| parameters.ro_grad_dur | a positive real scalar | the duration of the readout gradient, seconds | epi_2d.m, epi_3d.m, fse.m, and others |
| parameters.rspt_order | a non-negative integer or Inf | perturbation theory order for eigenfields calculation, 2 is a good start; specify Inf for exact diagonalisation | fieldsweep.m |
| parameters.s_len | a positive real scalar | active sample length in cm, defaults to 1.5 | gcosy.m |
| parameters.sal_ang | a finite real scalar | flip angle of the saltire chirp (degrees) | psycosy.m |
| parameters.sal_del | a real scalar greater than twice parameters | chirp pulse gradient duration (s) | psycosy.m |
| parameters.sal_dur | a positive real scalar | pulse width of saltire chirp (s) | psycosy.m |
| parameters.sal_npt | a positive integer scalar | number of points in the saltire chirp | psycosy.m |
| parameters.sal_smf | a real scalar between 0 and 50 | saltire chirp smoothing factor | psycosy.m |
| parameters.sal_swp | a positive real scalar | sweep width of saltire chirp (Hz) | psycosy.m |
| parameters.screen | a spin-space state vector | optional screening state used during ESEEM trajectory propagation | eseem.m, oopeseem.m |
| parameters.sel_g_amp | a real scalar | gradient amplitude during the selective 180-degree pulse, T/m | idosyzs.m |
| parameters.serial | a logical scalar | logical flag disabling automatic orientation parallelisation | doublerot.m, floquet.m, powder.m, and others |
| parameters.sharpen | a real scalar | contrast penalty weight used to sharpen the PCS source distribution | ipcs.m |
| parameters.shot_spacing | a non-negative real scalar | delay between microwave irradiation periods | noveldnp_steady.m, topdnp_steady.m, xixdnp_steady.m |
| parameters.si_time | a positive real scalar | sensitivity improvement delay, s | hsqcetgpsi.m |
| parameters.silicon | a character string | silicon isotope specification for the SiV0 diamond defect model | diamond_siv0.m |
| parameters.smfactor | a finite real scalar | smoothing factor for the pulse | psyche.m, spendosy.m, spendosycosy.m |
| parameters.sp_grad_amp | a real scalar | crusher gradient amplitude, T/m | press_2d.m |
| parameters.sp_grad_dur | a positive real scalar | crusher gradient duration, seconds | press_2d.m |
| parameters.spc_dim | integer number | The dimension of the spatial sub-problem in a Fokker-Planck space. This parameter sould normally be set by the kernel context function and passed on to the pulse sequence. | acquire.m, cn2d_dq.m, cn2d_sq.m, and others |
| parameters.spectrum_nsteps | a positive real integer | number of time steps in the FID | deer_3p_hard_deer.m |
| parameters.spectrum_sweep | a positive real number | sweep width of the EPR spectrum, Hz | deer_3p_hard_deer.m |
| parameters.spin_groups | a cell array of integer vectors | spin-index groups sharing each chemical shift in PCS combination fitting | pcs_combi_fit.m |
| parameters.spins | A cell array of spin specifications, e.g. {'13C','15N'}. | Spins that are to be assigned to each instrument channel during the simulation. | basic_1d_hard.m, clip_hsqc.m, cn2d_dq.m, and others |
| parameters.spiral_dur | a finite positive real scalar | duration of the spiral, seconds | spiral.m |
| parameters.spiral_frq | a finite real scalar | frequency of the spiral, Hz | spiral.m |
| parameters.spiral_npts | a finite positive real integer | number of time points in the spiral k-space trajectory | spiral.m |
| parameters.spn_dim | integer number | The dimension of the spin sub-problem in a Fokker-Planck space. This parameter sould normally be set by the kernel context function and passed on to the pulse sequence. | crystal.m, doublerot.m, floquet.m, and others |
| parameters.ss_grad_amp | a finite real scalar | the amplitude of slice selection gradient,T/m | epi_3d.m, phase_enc_3d.m, press_1d.m, and others |
| parameters.ss_grad_dur | a positive real scalar | the duration of the slice selection gradient, seconds | phase_enc_3d.m |
| parameters.stepsize | a positive real number | increment time for the pump pulse sandwich | deer_3p_hard_deer.m, ridme.m |
| parameters.sum_up | a logical scalar | logical flag selecting powder averaging rather than returning individual orientations | doublerot.m, floquet.m, powder.m, and others |
| parameters.sweep | A vector of reals. | Sweep width in each dimension of the spectrum (Hz). | acquire.m, basic_1d_hard.m, clip_hsqc.m, and others |
| parameters.sweep_time | a positive real number | sweep time, seconds | fieldscan_magn.m |
| parameters.T | a positive real scalar | evolution delay in the indirect 15N dimension, in seconds | hncaco.m |
| parameters.t_echo | a finite positive real scalar | echo time, seconds | epi_3d.m, phase_enc_2d.m, phase_enc_3d.m, and others |
| parameters.t_evol | a positive real scalar | DNP evolution time used before spatial-distribution readout, seconds | fig_5_spatial_distribution.m |
| parameters.t_step | a positive real scalar | time step used for liquid-DNP trajectory propagation, seconds | fig_2_tau_and_field_traject.m, fig_3_time_dep_bot_row.m, fig_3_time_dep_top_row.m, and others |
| parameters.ta | a positive number | time between first and third pulse, s | deer_3p_hard_echo.m |
| parameters.tau | a non-negative real scalar | optional spin echo delay, seconds | endor_davies.m, endor_mims.m, endor_mims_echo.m, and others |
| parameters.Tau | a positive real scalar | extra dephasing-gradient duration in ultrafast DOSY, seconds | spendosy.m, spendosycosy.m |
| parameters.tau_c | a scalar or a 3x3 matrix | rotational correlation time or tensor used in stochastic Liouville relaxation | gridfree.m |
| parameters.tb | a positive number | time between first and second pulse, s | deer_3p_hard_echo.m |
| parameters.tc | a positive number | time interval to sample around the echo, s | deer_3p_hard_echo.m |
| parameters.td | a positive real scalar | diffusion delay in ultrafast DOSY, seconds | spendosy.m, spendosycosy.m |
| parameters.Te | a finite positive real scalar | duration of the pulse | spencosy.m, spendosy.m, spendosycosy.m, and others |
| parameters.theory | a character string | theory specification for experiments that can be computed using several methods | solid_effect.m |
| parameters.theta | a real scalar | the angle of the ideal pulse at the end of each loop | respiration.m |
| parameters.time_step | a finite positive real scalar | if 'time_dependence' is set in the calc_type parameter, sets the time step, seconds | solid_effect.m |
| parameters.time_steps | a row vector of positive real numbers | a vector of time slice durati- ons, seconds | cp_contact_hard.m |
| parameters.timestep | a positive real scalar | time step of the CP contact ti- me, seconds | cp_contact_soft.m, cpmg.m, eseem.m, and others |
| parameters.timestep1 | a positive real scalar | indirect-dimension evolution time step before the PSYCHE element, seconds | psyche.m |
| parameters.timestep2 | a positive real scalar | direct-dimension acquisition time step after the PSYCHE element, seconds | psyche.m |
| parameters.titanium | a character string | titanium isotope specification for titanium-related diamond defect models | diamond_ti.m |
| parameters.tm_tol | a non-negative real scalar | relative transition moment to- lerance, 0.01 is a good start | fieldsweep.m |
| parameters.tmix | a positive real scalar | mixing time, seconds | hoesy.m, noesy.m, noesyhsqc.m, and others |
| parameters.tol | a positive real scalar | BICG solver tolerance for spin-chemistry singlet-yield calculation | rydmr.m |
| parameters.Tp | a positive real scalar | coherence-selection gradient duration, seconds | spencosy.m |
| parameters.trim_angle | a finite real scalar | proton trim pulse angle, rad | hsqcedetgp.m, hsqcetgp.m, hsqcetgpsi.m |
| parameters.u | a real column vector | X components of the velocity vectors for each point in the sample, m/s | imaging.m, v2fplanck.m |
| parameters.v | a real array of dimension | Y components of the velocity vectors for each point in the sample, m/s | imaging.m, v2fplanck.m |
| parameters.verbose | a real scalar | set this to 1 to enable diagnostic output | masdnp.m |
| parameters.w | a real array of dimension | Z components of the velocity vectors for each point in the sample, m/s | imaging.m, v2fplanck.m |
| parameters.window | a two-element real vector | field sweep interval as [Bmin Bmax], Tesla | fieldsweep.m |
| parameters.xyz | an Nx3 array of atomic coordinates | coordinates of PCS-active nuclei, Angstrom | ipcs.m |
| parameters.xyz_all | an Nx3 array of atomic coordinates | coordinates of all molecular atoms used for confinement and plotting, Angstrom | ipcs.m |
| parameters.zerofill | an integer not smaller than parameters | length of the zero-filled FFT | deer_3p_soft_diag.m, deer_4p_soft_diag.m |
Version 2.12, authors: Ilya Kuprov
