Appendix E: experiment parameters
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 | Experiment files 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 | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| 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 | none |
| parameters.axis_outer | three-element real vector | outer rotor axis for double rotation solid state NMR experiments | none |
| 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' | none |
| parameters.b_axis | a finite real vector | a vector of magnetic field values, Tesla | fieldsweep.m |
| parameters.bandwidth | a positive real scalar | Function-specific parameter; see the linked experiment files. | 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 | Function-specific parameter; see the linked experiment files. | ipcs.m |
| parameters.box_size | a real vector with three elements | oscillator box size, m | ipcs.m |
| parameters.BW | Function-specific. | bandwidth of the pulse | spencosy.m, spendosy.m, spendosycosy.m, and others |
| parameters.calc_type | Function-specific. | set to 'time_dependence' to get the time dependence of the longitudinal magnetization and to 'steady_state' to get the asymptotic longitudinal magnetization | solid_effect.m |
| parameters.centre | a character string | Function-specific parameter used outside built-in experiment files. | none |
| parameters.chi | a real symmetric 3x3 matrix | Function-specific parameter; see the linked experiment files. | 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 | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.coil_prob | Function-specific. | detection state on probe spin | deer_3p_hard_deer.m |
| parameters.coil_pump | Function-specific. | detection state on pump spin | deer_3p_hard_deer.m |
| parameters.coil_st | a cell array | Function-specific parameter; see the linked experiment files. | cpmg_dec.m, udd_dec.m |
| parameters.confine | a real vector with two non-negative elements | Function-specific parameter; see the linked experiment files. | 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 | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| 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 | Function-specific. | a cell array of integer vectors spe- cifying the spins for which the dia- magnetic assignment can potentially be swapped around | pcs_combi_fit.m |
| parameters.d_shifts | Function-specific. | a vector of unique diamagnetic che- mical shifts, in ppm | pcs_combi_fit.m |
| parameters.d_sign | a real scalar | Function-specific parameter used outside built-in experiment files. | none |
| 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 | Function-specific parameter; see the linked experiment files. | 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 | Function-specific. | Function-specific parameter; see the linked experiment files. | idosyzs.m, st_ideal.m |
| parameters.delta_sml | Function-specific. | Function-specific parameter; see the linked experiment files. | idosyzs.m, st_ideal.m |
| parameters.deltat | Function-specific. | timestep for acquisition | 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 | none |
| parameters.derivative | Function-specific. | if set to 1, the spectrum is differentiated before plotting | none |
| parameters.detection | Function-specific. | 'uniaxial' to emulate common ZULF hardware, 'quadrature' for proper frequency sign discrimination | 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 | Function-specific parameter; see the linked experiment files. | 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 | Function-specific parameter; see the linked experiment files. | zulf_abrupt.m |
| parameters.drop_npoints | a positive integer | Function-specific parameter; see the linked experiment files. | zulf_abrupt.m |
| parameters.drop_rate | a positive real scalar | Function-specific parameter; see the linked experiment files. | zulf_abrupt.m |
| parameters.drop_time | a positive real scalar | Function-specific parameter; see the linked experiment files. | zulf_abrupt.m |
| parameters.dscale | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.dt | a positive real scalar | time step, seconds | dnp_time_dep.m, simple_flow.m |
| parameters.duration | a positive real scalar | Function-specific parameter; see the linked experiment files. | psyche.m |
| parameters.dxx | Function-specific. | Cartesian components of the diffusion | none |
| parameters.dxy | Function-specific. | tensor for each voxel of the sample | none |
| parameters.dxz | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.dyx | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.dyy | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.dyz | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.dzx | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.dzy | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.dzz | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| 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 | Function-specific. | optional pulse operator for echo detection | 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 | Function-specific. | Function-specific parameter; see the linked experiment files. | ipcs.m |
| parameters.ex_hard | Function-specific. | hard pulse excitation operator | deer_3p_hard_deer.m |
| parameters.ex_prob | Function-specific. | excitation operators to be used for | deer_3p_hard_deer.m, deer_3p_hard_echo.m |
| parameters.ex_pump | Function-specific. | the probe and pump electron respectively | 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 | Function-specific parameter; see the linked experiment files. | ipcs.m |
| parameters.ez_oper | Function-specific. | Lz operator on the electrons | 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 | Function-specific parameter; see the linked experiment files. | 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 | Function-specific. | 0: NOVEL without flipback pulse 1: NOVEL with flipback pulse | noveldnp_steady.m |
| parameters.flippulse | Function-specific. | 0: Solid Effect (no flip pulse) 1: NOVEL (90-degree flip pulse) | noveldnp.m, noveldnp_steady.m |
| parameters.fovmax | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.fovmin | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.frc_cnst | a positive real number | force constant, N/m | none |
| 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 | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.Ga | Function-specific. | acquisition gradient in T/m | spencosy.m, spendosy.m, spendosycosy.m, and others |
| parameters.gamp | a finite real scalar | gradient amplitude, T/m | psycosy.m |
| parameters.Ge | Function-specific. | encoding gradient in T/m | spencosy.m, spendosy.m, spendosycosy.m, and others |
| parameters.germanium | a character string | Function-specific parameter used outside built-in experiment files. | none |
| parameters.Gp | Function-specific. | coherence selection gradient in T/m | spencosy.m |
| parameters.gpu | a logical scalar | Function-specific parameter; see the linked experiment files. | ipcs.m |
| parameters.grad_amp | a finite real scalar | gradient amplitude at the end of the spiral, T/m | spiral.m |
| parameters.grad_angles | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| 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 | none |
| parameters.guess | Function-specific. | Function-specific parameter; see the linked experiment files. | ipcs.m |
| parameters.H_op | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.H_ph | Function-specific. | , parameters.H_op | none |
| parameters.hfcs | Function-specific. | cell array of 3x3 hyperfine tensors, in Gauss, usually out of gparse() or something similar | 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 | Function-specific. | X Zeeman operator on the spin-1/2 nucleus | overtone_cp.m |
| parameters.hzeeman | Function-specific. | and sent to pulse sequence | 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 | Function-specific parameter used outside built-in experiment files. | none |
| parameters.int_tol | a positive real scalar | powder integration tolerance, a balance between speed and integration accuracy | fieldsweep.m |
| parameters.invert_axis | Function-specific. | if set to 1, the frequency axis is inverted before plotting | none |
| 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 | Function-specific. | cell array of isotope specificati- ons, e.g. {'1H','1H'} | 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 | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.K_ph | Function-specific. | , parameters.K_op | none |
| parameters.kappa | Function-specific. | unbalancing factor to unbalance the bipolar gradients in the ratio (1+kappa):(1-kappa) | 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 | Function-specific parameter; see the linked experiment files. | ipcs.m |
| parameters.marker | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.masframe | a character string | the frame in which the rotations are applied. The possibilities are: | none |
| 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 | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| 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 | none |
| 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 | Function-specific. | microwave irradiation operator | 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 | Function-specific parameter used outside built-in experiment files. | none |
| 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 | none |
| 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 | Function-specific parameter used outside built-in experiment files. | none |
| parameters.nitrogen | a character string | Function-specific parameter used outside built-in experiment files. | none |
| 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 | Function-specific. | Function-specific parameter; see the linked experiment files. | spendosycosy.m |
| parameters.npoints2 | Function-specific. | Function-specific parameter; see the linked experiment files. | 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 | Function-specific parameter; see the linked experiment files. | 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 | Function-specific. | nuclear Zeeman frequency in 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 | Function-specific. | smoothing factor for the pulse | spencosy.m, ufmq.m |
| parameters.Nx | Function-specific. | X Zeeman operator on the quadrupolar nucleus | 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 | Function-specific. | offset between chemical shifts of a MQ along the F1 dimension of a conventional and an UF spectra ('ppm' or 'Hz') | none |
| 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 | Function-specific. | a cell array of integer vectors spe- cifying the spins for which the paramagnetic assignment can potentially be swapped around | pcs_combi_fit.m |
| parameters.p_shifts | Function-specific. | a vector of unique paramagnetic chemical shifts, in ppm | pcs_combi_fit.m |
| parameters.par_mass | a positive real number | particle mass, kg | none |
| parameters.pathway | Function-specific. | optional coherence pathway selection, either 'P', 'N', or 'P+N', defaults to 'P' | 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 | Function-specific. | Function-specific parameter; see the linked experiment files. | 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 | Function-specific. | Function-specific parameter; see the linked experiment files. | idosyzs.m |
| parameters.pulse_num | a positive integer | number of pulses within rotor period | dante.m, overtone_dante.m |
| parameters.pulse_op | Function-specific. | pulse operator | cpmg.m, eseem.m, hp_acquire.m, and others |
| parameters.pulse_opx | Function-specific. | pulse operator in X phase | sifter.m |
| parameters.pulse_opy | Function-specific. | pulse operator in Y phase | 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 | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.R_ph | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.rank_inner | positive integer | Floquet or Fokker-Planck rank for the inner rotor in double rotation solid state NMR experiments | none |
| parameters.rank_outer | positive integer | Floquet or Fokker-Planck rank for the outer rotor in double rotation solid state NMR experiments | none |
| 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 | none |
| parameters.rate_outer | real number | outer rotor spinning rate for double rotation solid state NMR experiments | none |
| parameters.rates | a vector of positive real numbers | row vector of singlet recombination rate constants, Hz | rydmr_exp.m |
| parameters.ref_frame | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| 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 | none |
| 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 | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.rho0_st | cell arrays | Function-specific parameter used outside built-in experiment files. | none |
| parameters.rho_eq | a state vector or a denisty matrix | equilibrium state for the experiments that require it | none |
| parameters.rlx_op | cell arrays | Function-specific parameter used outside built-in experiment files. | none |
| parameters.rlx_ph | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| 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 | Function-specific. | optional screen state (must be the Hermitian conjugate of the detection state) | eseem.m, oopeseem.m |
| parameters.sel_g_amp | Function-specific. | Function-specific parameter; see the linked experiment files. | idosyzs.m |
| parameters.serial | Function-specific. | if set to true, disables automatic pa- rallelisation | none |
| parameters.sharpen | a real scalar | Function-specific parameter; see the linked experiment files. | 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 | Function-specific parameter used outside built-in experiment files. | none |
| 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 | Function-specific. | cell array of integer vectors specifying the numbers of spins that have each of the chemical shifts specified, e.g {[28 22 30]; [25 33 81]} | 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 | Function-specific parameter; see the linked experiment files. | 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. | none |
| 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 | Function-specific. | the duration of the slice selection gradient, seconds | none |
| parameters.stepsize | a positive real number | increment time for the pump pulse sandwich | deer_3p_hard_deer.m, ridme.m |
| parameters.sum_up | Function-specific. | if set to false, causes the pulse sequence output at each orientation to be returned instead of the powder average | none |
| 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 | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| parameters.t_step | Function-specific. | Function-specific parameter used outside built-in experiment files. | none |
| 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 | Function-specific. | duration extra dephasing gradient | spendosy.m, spendosycosy.m |
| parameters.tau_c | a scalar or a 3x3 matrix | Function-specific parameter used outside built-in experiment files. | none |
| 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 | Function-specific. | diffusion delay | 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 | Function-specific parameter; see the linked experiment files. | psyche.m |
| parameters.timestep2 | a positive real scalar | Function-specific parameter; see the linked experiment files. | psyche.m |
| parameters.titanium | a character string | Function-specific parameter used outside built-in experiment files. | none |
| 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 | Function-specific parameter; see the linked experiment files. | rydmr.m |
| parameters.Tp | Function-specific. | duration of the coherence selection gradient | 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 | none |
| parameters.v | a real array of dimension | Y components of the velocity vectors for each point in the sample, m/s | none |
| 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 | none |
| parameters.window | Function-specific. | field sweep window in Tesla, as a vector [Bmin Bmax] | fieldsweep.m |
| parameters.xyz | an Nx3 array of atomic coordinates | Function-specific parameter; see the linked experiment files. | ipcs.m |
| parameters.xyz_all | an Nx3 array of atomic coordinates | Function-specific parameter; see the linked experiment files. | 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 2.1, authors: Ilya Kuprov
