This is a Jupyter notebook that was composed to run most of the examples distributed with SpinEvolution. It gives a visual overview of the examples and shows how to use SpinEvolution from Jupyter notebooks.
If you are viewing this content in a web browser, then this is just an HTML export (a Web version) of the original notebook. While the notebook format allows making all figures fully interactive, only some of the 2D spectra were made interactive in the Web version.
The whole gallery (~40 simulations) can be fully computed in about 10 minutes on a 4-core CPU. About 95% of this time is spent on five relatively large calculations.
Only about one third of these problems can be simulated with SIMPSON. Except for the most basic ones, however, they will be quite difficult to program for that software and will typically take at least an order of magnitude longer to compute.
#%matplotlib widget
%matplotlib inline
from plot import spinev, plot, setup_ipynb
setup_ipynb()
%cd '~/spinev/examples/'
opts = '-v0 -vf0 -vsf0 --verb'
/Users/mvesh/spinev/examples
spinev('csa/csa', opts)
****** The System ******* spectrometer(MHz) 500 spinning_freq(kHz) * channels C13 nuclei C13 atomic_coords * cs_isotropic * csa_parameters 1 1 0.5 0 0 0 j_coupling * quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) (200)512 power(kHz) 0 phase(deg) 0 freq_offs(kHz) 0 ******* Variables *********************************** fig_title="CSA Powder Pattern" ******* Options ************************************* rho0 I1x observables I1p EulerAngles asgind100o n_gamma * line_broaden(Hz) * zerofill * FFT_dimensions 1 options -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb ****************************************************** -- Note the orientation of the CSA tensor. So that powder averaging over one octant could be used, it has to be alligned with the crystallite frame. -- See also the analytic mode version of this simulation, csa-am
spinev('redor/redor-full', opts)
****** The System *********************************** spectrometer(MHz) 500 spinning_freq(kHz) 10.0 channels C13 N15 nuclei C13 N15 atomic_coords 1.367 cs_isotropic 2 0 csa_parameters * j_coupling * quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) (100)60D1B (95 5 100)1D1A (100)60D1B power(kHz) 0 0 100 0 0 phase(deg) 0 0 0 0 0 freq_offs(kHz) 0 0 0 0 0 CHN 2 timing(usec) (redor.pp) 45 5 50 redor.pp (redor.pp) power(kHz) * 0 100 0 * * phase(deg) * 0 0 0 * * freq_offs(kHz) * 0 0 0 * * ******* Variables ************************************ fig_title="REDOR" ******* Options ************************************** rho0 I1x observables I1p EulerAngles ^asgind30h n_gamma * line_broaden(Hz) * zerofill * FFT_dimensions * options -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
It is sometimes desireable to simulate a pulse sequence, in which some of the RF field parameters are varied continuously rather than in steps, as is usually the case. The simulation below illustrates, on the simplest possible example, how this can be done is SpinEvolution. In the input file, the RF frequency offset is specified as an analytic function of time: xfreq_1_1=0.025*(t_-tp)/tp.
This example also demonstrates that one can use alternative design styles for the output figures.
spinev('cw-nmr/cw-xfreq --style seaborn-dark', opts)
****** The System *********************************** spectrometer(MHz) * spinning_freq(kHz) * channels H1 nuclei H1 atomic_coords * cs_isotropic * csa_parameters * j_coupling * quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) [100000]5001 power(kHz) [0.0001]5001 phase(deg) [90]5001 freq_offs(kHz) [0]5001 ******* Variables *********************************** T1SQ_1_1=2000 T2SQ_1_1=2000 tp=500100000/2 xfreq_1_1=0.025*(t_-tp)/tp dim_1_units="s" fig_title="CW NMR: Continuous Linear Frequency Sweep" ******* Options ************************************* rho0 I1z observables I1p EulerAngles * n_gamma * line_broaden(Hz) * zerofill * FFT_dimensions * options -re -oes -py options_cmd_line --style seaborn-dark -px -py0 -vm -v0 -vf0 -vsf0 --verb
spinev('adiabatic-inversion/adiab', opts)
****** The System *********************************** spectrometer(MHz) * spinning_freq(kHz) * channels C13 nuclei C13 atomic_coords * cs_isotropic * csa_parameters * j_coupling * quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) [200]5001 power(kHz) [0.1]5001 phase(deg) [90]5001 freq_offs(kHz) [0]5001 ******* Variables *********************************** T1SQ_1_1=2000 T2SQ_1_1=2000 freq_1_1=-1:0.0004:1 fig_title="Adiabatic Inversion by Linear Frequency Sweep at Constant Power" dim_2_labels = "$I_x$, $I_y$, $I_z$" ******* Options ************************************* rho0 0.25I1z observables I1p iI1m I1z EulerAngles * n_gamma * line_broaden(Hz) * zerofill * FFT_dimensions * options -oes -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
spinev('cpmg-echo/echo', opts)
****** The System ******* spectrometer(MHz) * spinning_freq(kHz) * channels C13 nuclei C13 atomic_coords * cs_isotropic * csa_parameters * j_coupling * quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) 0.5 [1000]2900 power(kHz) 500 [0]2900 phase(deg) 90 [0]2900 freq_offs(kHz) 0 [0]2900 ******* Variables *********************************** T2SQ_1_1=1000 sigma=0.006 pulse_1_1_[100:200:2900]=1.0 power_1_1_[100:200:2900]=500 ** Chemical shifts inhomogeneity ave_par x/-0.02:0.0025:0.02/ cs_iso_1=0.1+x W=sum(exp(-0.5*(x.mx/sigma).^2)) ave_wht=exp(-0.5*(x/sigma)^2)/W fig_title="Carr-Purcell-Meiboom-Gill Echo Train" ** use thinner lines for the plot fig_options="--widths 0.6" ******* Options ************************************** rho0 I1z observables I1p EulerAngles * n_gamma * line_broaden(Hz) * zerofill * FFT_dimensions * options -oes -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
spinev('tppm/tppm', opts)
****** The System ******* spectrometer(MHz) 500 spinning_freq(kHz) 15.625 channels C13 H1 nuclei C13 H1 H1 H1 H1 atomic_coords ch4.cor cs_isotropic 0.0 -0.3 0.5 0.5 0.2 csa_parameters ch4.csa j_coupling * quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) (8)256x200 power(kHz) 0 phase(deg) 0 freq_offs(kHz) 0 CHN 2 timing(usec) (4 4) power(kHz) 125 125 phase(deg) 0 15 freq_offs(kHz) 0 0 ****** Variables ************************************ spinning_freq=15.625 DW=40*(1000/spinning_freq) scan_par R/4.5:0.25:5.25/ tc=(1000/spinning_freq)/R pulse_1_1_1=tc pulse_2_1_[1:2]=0.5*tc power_2_1_[1:2]=1000/tc gsize_1=round(DW/tc) ****************************************************** fig_title="TPPM Lineshape Dependence on RF Field Strength" dim_2_name="$\omega_1/2\pi$" dim_2_labels=R.mx*spinning_freq dim_2_units="kHz" ******* Options ************************************** rho0 I1x observables F1p EulerAngles rep168 n_gamma 16 line_broaden(Hz) 6 zerofill * FFT_dimensions 1 Hz options -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
The following shows the Linear Ramp Cross-Polarization pulse sequence, which consists of 30 elementary pulse sequences. The diagram shows each sequence repeated just once, but the $D_1$ symbols over the sequences says that the number of repeats grows in dimension 1.
spinev('ramped-cp/rampcp1 -pseq')
spinev('ramped-cp/rampcp1', opts)
****** The System *********************************** spectrometer(MHz) 400 spinning_freq(kHz) 10 channels C13 H1 nuclei C13 H1 H1 H1 atomic_coords * cs_isotropic * csa_parameters * j_coupling * quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) [(0)64]30 power(kHz) [0]30 phase(deg) [0]30 freq_offs(kHz) [0]30 CHN 2 timing(usec) [(0)]30 power(kHz) [0]30 phase(deg) [0]30 freq_offs(kHz) [0]30 ******* Variables *********************************** power_1_[1:30]_1=50+[0:29]*6/29 power_2_[1:30]_1=63 pulse_1_[1:30]_1=1 pulse_2_[1:30]_1=1 sys2ext_map=["1 3 4 5"] fig_title="Linear-Ramp Cross-Polarization in C$_1$H$_3$ Spin System" ******* Options ************************************* rho0 F2x observables I1x EulerAngles rep376 n_gamma 5 line_broaden(Hz) * zerofill * FFT_dimensions * options -zxmatrampcp.zxmat -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
The following simulation computes a histogram demonstrating that even ramped CP may result in the $^{13}$C polarization, which is extremely non-uniform over the crystallite orientations.
spinev('ramped-cp/rampcp-hist', opts)
****** The System ***********************************
spectrometer(MHz) 400
spinning_freq(kHz) 10
channels C13 H1
nuclei C13 H1 H1 H1
atomic_coords *
cs_isotropic *
csa_parameters *
j_coupling *
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei *
******* Pulse Sequence ******************************
CHN 1
timing(usec) [0]30
power(kHz) [0]30
phase(deg) [0]30
freq_offs(kHz) [0]30
CHN 2
timing(usec) [0]30
power(kHz) [0]30
phase(deg) [0]30
freq_offs(kHz) [0]30
******* Variables ***********************************
*save(euler_CR',"rep376.dat")
sys2ext_map=["1 3 4 5"]
power_1_1=50+(0:29)*6/29
power_2_1=63
time=2
pulse_[1:2]_1=1000*time/30
rep2000=(load("rep2000.dat"))'
scan_par i/1:2000/
euler_CR(1:2,1)=rep2000(1:2,i)
fig_options ="--hist 25 --colorsx navy"
x_label = "$^{13}$C polarization after CP"
fig_title="Histogram of ramped CP efficiency for a set of 2000 crystallite orientations"
******* Options *************************************
rho0 F2x
observables I1x
EulerAngles *
n_gamma *
line_broaden(Hz) *
zerofill *
FFT_dimensions *
options -zxmatrampcp.zxmat -re -py
options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
The following two simulations compute the R$^2$ magnetization exchange curves between CO and C$_\beta$ in alanine using two model spin systems: C2 (without protons) and C2H7. The normal plotting of the results of the first simulation is suppressed with the -px0 option. Instead, these results are plotted as a reference curve by the second simulation. The -macroX=3 option selects C$_\beta$ as the second $^{13}$C nucleus. Using -macroX=2 instead would select C$_\alpha$.
This illustrates that even at 80 kHz CW decoupling and with both CH3 and NH3 groups in the fast exchange regime, the presence of protons leads to ZQ relaxation and to apparent attenuation of the C-C coupling.
spinev('rotational-resonance/r2-C2 -px0 -macroX=3', opts)
spinev('rotational-resonance/r2-C2H7-hot -macroX=3', opts)
****** The System *******************************************************
spectrometer(MHz) 500
spinning_freq(kHz) 10
channels C13 H1
nuclei *
atomic_coords *
cs_isotropic 176.8 50.9 19.8 0 0 0 0 0 0 0 ppm
csa_parameters 1 -71 0.84 0 0 0 ppm 1
csa_parameters 2 -20 0.44 -20 0 0 ppm 2
csa_parameters 3 -12 0.76 0 -90 0 ppm 3
j_coupling *
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei (8 9 10) (11 12 13)
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei (2 1 4) (7 2 3) (2 3 8)
******* Pulse Sequence ***************************************************
CHN 1
timing(usec) (100)512
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
CHN 2
timing(usec) 100
power(kHz) 80
phase(deg) 0
freq_offs(kHz) 0
******* Variables *********************************************************
sys2ext_map=["1 X 7 8 9 10 11 12 13"]
spinning_freq=cs_iso_X-cs_iso_1
freq_1_1_1=(cs_iso_X+cs_iso_1)/2
pulse_[1:2]_1_1=1000/spinning_freq
** Figure setup ***********************************************************
q = (X==2)? "alpha" : "beta"
fig_title=f"C$'$-C$_\[q]$ Rotational Resonance in Ala: C$_2$H$_7$ vs. C$_2$ spin systems"
y_label="${\langle}I_{1z}-I_{2z}{\rangle}$"
legend_labels="C$_2$H$_7$, C$_2$"
fig_options = f"--text 0.3,0.9,'80 kHz $^1$H CW Decoupling[nl]CH3 and NH3 groups in fast exchange',8.5"
x_lim=["0 10"]
******* Options ************************************************************
rho0 0.5*I1z-0.5*I2z
observables I1z-I2z
EulerAngles rep700
n_gamma 12
line_broaden(Hz) *
zerofill *
FFT_dimensions *
options -zxmatala.zxmat -re -sysc2h7 -nr2-C1CX-H7-hot -refr2-C1CX -py
options_cmd_line -macroX=3 -px -py0 -vm -v0 -vf0 -vsf0 --verb
**************************************************************************
-- Either -macroX=2 or -macroX=3 must be specified at the command line
-- The spinning frequencies used for X=2 and X=3 cases are different. So the total observation times (512 points) will also different. To plot the output results on the same scale, we simply set the same x-axis limits for both cases.
-- CO-CA oscillations after ~10ms are due to incomplete powder averaging. They can be seen if one uses a higher upper limit in x_lim, e.g., x_lim=["0 21"]
These effects become much more pronounced when the fast hopping of both CH3 and NH3 groups is frozen.
The --ref option requests to show the difference in the input files.
spinev('rotational-resonance/r2-C2H7-frozen -macroX=3 --ref rotational-resonance/r2-C2H7-hot', opts)
****** The System *******************************************************
spectrometer(MHz) 500
spinning_freq(kHz) 10
channels C13 H1
nuclei *
atomic_coords *
cs_isotropic 176.8 50.9 19.8 0 0 0 0 0 0 0 ppm
csa_parameters 1 -71 0.84 0 0 0 ppm 1
csa_parameters 2 -20 0.44 -20 0 0 ppm 2
csa_parameters 3 -12 0.76 0 -90 0 ppm 3
j_coupling *
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei (2 1 4) (7 2 3) (2 3 8)
******* Pulse Sequence ***************************************************
CHN 1
timing(usec) (100)512
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
CHN 2
timing(usec) 100
power(kHz) 80
phase(deg) 0
freq_offs(kHz) 0
******* Variables *********************************************************
sys2ext_map=["1 X 7 8 9 10 11 12 13"]
spinning_freq=cs_iso_X-cs_iso_1
freq_1_1_1=(cs_iso_X+cs_iso_1)/2
pulse_[1:2]_1_1=1000/spinning_freq
** Figure setup ***********************************************************
q = (X==2)? "alpha" : "beta"
fig_title=f"C$'$-C$_\[q]$ Rotational Resonance in Ala: C$_2$H$_7$ vs. C$_2$ spin systems"
y_label="${\langle}I_{1z}-I_{2z}{\rangle}$"
legend_labels="C$_2$H$_7$, C$_2$"
fig_options = f"--text 0.3,0.9,'80 kHz $^1$H CW Decoupling[nl]Both CH3 and NH3 groups are frozen',8.5"
x_lim=["0 10"]
******* Options ************************************************************
rho0 0.5*I1z-0.5*I2z
observables I1z-I2z
EulerAngles rep700
n_gamma 12
line_broaden(Hz) *
zerofill *
FFT_dimensions *
options -zxmatala.zxmat -re -sysc2h7 -nr2-C1CX-H7-frozen -refr2-C1CX -py
options_cmd_line -macroX=3 --ref rotational-resonance/r2-C2H7-hot -px -py0 -vm -v0 -vf0 -vsf0 --verb
**************************************************************************
-- Either -macroX=2 or -macroX=3 must be specified at the command line
-- The spinning frequencies used for X=2 and X=3 cases are different. So the total observation times (512 points) will also different. To plot the output results on the same scale, we simply set the same x-axis limits for both cases.
-- CO-CA oscillations after ~10ms are due to incomplete powder averaging. They can be seen if one uses a higher upper limit in x_lim, e.g., x_lim=["0 21"]
- exchange_nuclei (8 9 10) (11 12 13) + exchange_nuclei * - fig_options = f"--text 0.3,0.9,'80 kHz $^1$H CW Decoupling[nl]CH3 and NH3 groups in fast exchange',8.5" + fig_options = f"--text 0.3,0.9,'80 kHz $^1$H CW Decoupling[nl]Both CH3 and NH3 groups are frozen',8.5" - options -zxmatala.zxmat -re -sysc2h7 -nr2-C1CX-H7-hot -refr2-C1CX -py + options -zxmatala.zxmat -re -sysc2h7 -nr2-C1CX-H7-frozen -refr2-C1CX -py
We can model these effects by supplementing the two-spin model with a ZQ relaxation time constant and with a dipolar coupling scaling factor. These two parameters can then be fit using SpinEvolution data fitting feature to "explain" the behavior observed in the C2H7 systems:
spinev('rotational-resonance/r2-C2-T2ZQ -macroX=3 -macroTEMP=hot', opts)
****** The System *******************************************************
spectrometer(MHz) 500
spinning_freq(kHz) 10
channels C13
nuclei C13 C13
atomic_coords *
cs_isotropic 176.8 50.9 19.8 0 0 0 0 0 0 0 ppm
csa_parameters 1 -71 0.84 0 0 0 ppm 1
csa_parameters 2 -20 0.44 -20 0 0 ppm 2
csa_parameters 3 -12 0.76 0 -90 0 ppm 3
j_coupling *
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei (2 1 4) (7 2 3) (2 3 8)
******* Pulse Sequence ***************************************************
CHN 1
timing(usec) (100)512
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
******* Variables *********************************************************
sys2ext_map=["1 X"]
spinning_freq=cs_iso_X-cs_iso_1
freq_1_1_1=(cs_iso_X+cs_iso_1)/2
pulse_1_1_1=1000/spinning_freq
T2ZQ_1_2=10
fit_re=(load("r2-C1CX-H7-TEMP_re.dat"))(:,2)
wht_re(range(["10 100"],"ms"))=0
fit_par T2ZQ_1_2_1 dip_swb_1_2_1
** Figure setup ***********************************************************
q = (X==2)? "alpha" : "beta"
fig_title=f"C$'$-C$_\[q]$ Rotational Resonance in Ala: T2ZQ vs H7"
y_label="${\langle}I_{1z}-I_{2z}{\rangle}$"
x_lim=["0 10"]
T2 = str(T2ZQ_1_2_1,3), x_
SF = str(dip_swb_1_2_1,3), x_
fig_options = f"--text 0.2,0.8,'$\mathrm{T2ZQ}=[T2]$ ms [nl]$\mathrm{SF}=[SF]$'"
******* Options ************************************************************
rho0 0.5*I1z-0.5*I2z
observables I1z-I2z
EulerAngles rep700
n_gamma 12
line_broaden(Hz) *
zerofill *
FFT_dimensions *
options -zxmatala.zxmat -re -nr2-C1CX-T2ZQ-TEMP -py
options_cmd_line -macroX=3 -macroTEMP=hot -px -py0 -vm -v0 -vf0 -vsf0 --verb
*****************************************************************************
-- Either -macroX=2 or -macroX=3 must be specified at the command line
-- Also, -macroTEMP=hot, -macroTEMP=cold, or -macroTEMP=frozen must be specified
-- The spinning frequencies used for X=2 and X=3 cases are different. So the total observation times (512 points) will also different. To plot the output results on the same scale, we simply set the same x-axis limits for both cases.
-- CO-CA oscillations after ~10ms are due to incomplete powder averaging. They can be seen if one uses a higher upper limit in x_lim, e.g., x_lim=["0 21"]
The following shows the SPC-5 dipolar recoupling pulse sequence
spinev('spc5/spc5 -pseq')
spinev('spc5/spc5', opts)
****** The System *******
spectrometer(MHz) 400
spinning_freq(kHz) 10.0
channels C13
nuclei C13 C13
atomic_coords 4
cs_isotropic *
csa_parameters 1 70 0.8 0 60 0 ppm
csa_parameters 2 70 0.8 30 90 0 ppm
j_coupling *
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei *
******* Pulse Sequence ******************************
CHN 1
timing(usec) (spc5.pp)41 (spc5.pp)41 0.5
power(kHz) * * 500
phase(deg) * * 90
freq_offs(kHz) * * 0
phase_cycling * 1234 * 3131(RCV)
******* Variables **********************************
spinning_freq=9
psf_1_[1 2]=0.1*spinning_freq
tsf_[1 2]=1/psf_1_1
** Turn on/off the CSA
scan_par csa/0 1/
csa_swb_[1 2]_1 = csa
csa_swb_[1 2]_2 = csa
** Set up the Figure
legend_labels = "'SPC-5 no CSA', 'SPC-5 70 ppm CSA'"
y_label = "DQ filtering efficiency"
fig_title = "SPC-5"
fig_options = f"--text 0.6,0.4,'$^1$H 400 MHz $\omega_R/2\pi=9$ kHz[nl]$^{13}$C$-^{13}$C pair $r=4$ Å',8"
******* Options *************************************
rho0 F1z
observables I1p
EulerAngles rep168
n_gamma 20
line_broaden(Hz) *
zerofill *
FFT_dimensions *
options -re -dw1 -py
options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
spinev('hccn/hccn', opts)
****** The System ***********************************
spectrometer(MHz) 500
spinning_freq(kHz) 10
channels C13 H1 N15
nuclei H1 C13 C13 N15
atomic_coords hccn.cor
cs_isotropic *
csa_parameters *
j_coupling *
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei (1 2 3 4)
groups_nuclei *
******* Pulse Sequence *****************************************
CHN 1
timing(usec) (100)21 100 1 100 (100)21 (100)x7 (12.5)21
power(kHz) 0 0 500 0 0 5.0 70.0
phase(deg) 0 0 0 0 0 0 0
freq_offs(kHz) 0 0 0 0 0 0 0
CHN 2
timing(usec) (100) 200 (100) 100 (12.5)
power(kHz) 100 100 100 100 65.574
phase(deg) 0 0 0 0 0
freq_offs(kHz) 0 0 0 0 45.826
CHN 3
timing(usec) (redor1.pp) 200 (redor2.pp) 100 (12.5)
power(kHz) * 0 * 0 0
phase(deg) * 0 * 0 0
freq_offs(kHz) * 0 * 0 0
******* Variables **********************************************
scan_par phi_1/-130:-10:-180/
spinning_freq=12.9
tsf_[1:5]=10/spinning_freq
psf_1_[1:4]=spinning_freq/10
psf_3_[1:4]=spinning_freq/10
power_1_5_1=80-spinning_freq
****************************************************************
fig_title="HCCN Correlation Experiment"
y_label="C$'\to\mathrm{C}_\alpha$"
******* Options ************************************************
rho0 -I3x
observables I2p
EulerAngles rep168
n_gamma 16
line_broaden(Hz) *
zerofill *
FFT_dimensions *
options -dw13 -re -py
options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
spinev('noesy/noesy', opts)
******************************************************************* ** NOESY with axial peak suppression, hypercomplex-detected ** ****** The System ************************************************* spectrometer(MHz) 500 spinning_freq(kHz) * channels H1 nuclei H1 H1 atomic_coords * cs_isotropic -2 2 ppm csa_parameters * j_coupling * quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) 0.5 (250)256D1 0.5 (200000) 0.5 (250)256D2 power(kHz) 500 0 500 0 500 0 phase(deg) 90 0 -90 0 90 0 freq_offs(kHz) 0 0 0 0 0 0 phase_cycling_cos 11113333 * * * 12341234 * 12343412(RCV) phase_cycling_sin 44442222 * * * 12341234 * 12343412(RCV) ******* Variables ************************************************ W0= 5e-4 W1a=5e-4 W1b=5e-4 W2= 2.5e-4 T1ZQ_1_2_4=0.5/W0 T1DQ_1_2_4=0.5/W2 T1SQ_1_4=0.5/W1a T1SQ_2_4=0.5/W1b ** Alternatively, one can use RZ/RR variables to define spin-lattice relaxation: *R1=-(W0+2*W1a+W2) *R2=-(W0+2*W1b+W2) *Rc=W0-W2 *RZ_1_4="I1z" *RZ_2_4="I2z" *RR_4=["R1 Rc; Rc R2"] fig_title="NOESY with axial peak suppression" ******* Options ************************************************** rho0 F1z observables F1p EulerAngles * n_gamma * line_broaden(Hz) 0 0 100 100 zerofill * FFT_dimensions 1 2 ppm options -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
Note that Gaussian line broadening is used in the NOESY spectrum above, while Lorentzian line broadening is used in the HMQC spectrum below. The peak shapes reflect which type of line broadening was applied to them.
spinev('hmqc/hmqc', opts)
****** The System ****************************************************************** spectrometer(MHz) 400 spinning_freq(kHz) * channels H1 C13 nuclei H1 C13 atomic_coords * cs_isotropic 2 1 csa_parameters * j_coupling 1 2 10 quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ************************************************************* CHN 1 timing(usec) 2 (50e3) 2 (100)1024D1 4 (100)1024D1 2 (50e3) (100)1024D2 power(kHz) 125 0 0 0 125 0 0 0 0 phase(deg) 90 0 0 0 180 0 0 0 0 freq_offs(kHz) 0 0 0 0 0 0 0 0 0 CHN 2 timing(usec) 2 (50e3) 2 (100) 4 (100) 2 (50e3) (100) power(kHz) 0 0 125 0 0 0 125 0 0 phase(deg) 0 0 0 0 0 0 0 0 0 freq_offs(kHz) 0 0 0 0 0 0 0 0 0 phase_cycling_cos * * 24 * * * 44 * * 13(RCV) phase_cycling_sin * * 24 * * * 11 * * 13(RCV) ******* Variables ****************************************************************** fig_title="HMQC" fig_options="--size 6.4,3.6" ******* Options ******************************************************************** rho0 I1z observables I1p EulerAngles * n_gamma * line_broaden(Hz) 100 100 zerofill * FFT_dimensions 1 2 options -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb ************************************************************************************ - Coherence transfer pathway foe the first step of the phase cycle: 'cos': I1z->I1x->I1yI2z->I1yI2x->-I1yI2x*cos(w*t1)->-I1yI2z*cos(w*t1)->I1x 'sin': I1z->I1x->I1yI2z->I1yI2x->-I1yI2y*sin(w*t1)->-I1yI2z*sin(w*t1)->I1x - The two-step phase cycle selects I1yI2z->±I1yI2x during the first 90-degree pulse on the second channel, while killing the I1x and I1y coherences
spinev('cosy/cosy-2QF-ABX', opts, HTML=True)
**************************************************************** ** 2Q-filtered COSY in ABX system, hypercomplex detection ** ****** The System ********************************************** spectrometer(MHz) 500 spinning_freq(kHz) * channels H1 nuclei H1 H1 H1 atomic_coords * cs_isotropic 4.1 4.14 5.0 ppm csa_parameters * j_coupling 1 3 3 j_coupling 2 3 9 j_coupling 1 2 -14 quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ***************************************** CHN 1 timing(usec) 0.5 (1600)1024D1 0.5 (0.5) (1600)1024D2 power(kHz) 500 0 500 500 0 phase(deg) 0 0 0 0 0 freq_offs(kHz) 0 0 0 0 0 phase_cycling_cos 4444 * * 2341 * 2143(RCV) phase_cycling_sin 3333 * * 2341 * 2143(RCV) ******* Variables ********************************************** ppm_center_1=4.56 fig_title="2Q-filtered COSY in ABX system" ******* Options ************************************************ rho0 F1z observables F1p EulerAngles * n_gamma * line_broaden(Hz) 0 0 3 3 zerofill * FFT_dimensions 1 2 ppm options -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb **************************************************************** -- Accompanying pdf figure was obtained with the additional option --widths 0.25
Now, we will plot the same simulation output (option -plot), but as a filled contour plot, and with a zoom on the peaks.
spinev('cosy/cosy-2QF-ABX -plot -contf --zlog --xlim=4.97,5.03 --ylim=4.06,4.18', opts)
**************************************************************** ** 2Q-filtered COSY in ABX system, hypercomplex detection ** ****** The System ********************************************** spectrometer(MHz) 500 spinning_freq(kHz) * channels H1 nuclei H1 H1 H1 atomic_coords * cs_isotropic 4.1 4.14 5.0 ppm csa_parameters * j_coupling 1 3 3 j_coupling 2 3 9 j_coupling 1 2 -14 quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ***************************************** CHN 1 timing(usec) 0.5 (1600)1024D1 0.5 (0.5) (1600)1024D2 power(kHz) 500 0 500 500 0 phase(deg) 0 0 0 0 0 freq_offs(kHz) 0 0 0 0 0 phase_cycling_cos 4444 * * 2341 * 2143(RCV) phase_cycling_sin 3333 * * 2341 * 2143(RCV) ******* Variables ********************************************** ppm_center_1=4.56 fig_title="2Q-filtered COSY in ABX system" ******* Options ************************************************ rho0 F1z observables F1p EulerAngles * n_gamma * line_broaden(Hz) 0 0 3 3 zerofill * FFT_dimensions 1 2 ppm options -re -py options_cmd_line -plot -contf --zlog --xlim=4.97,5.03 --ylim=4.06,4.18 -px -py0 -vm -v0 -vf0 -vsf0 --verb **************************************************************** -- Accompanying pdf figure was obtained with the additional option --widths 0.25
Interactive Plot: The 2D spectrum above is interactive even in the Web version of this notebook. Hover with a mouse over the figure, and the Zoom/Pan/Home menu will appear.
Now, let's plot the same data again, but as a regular (non-filled) contour plot, using the linear scale instead of logarithmic for the peak height, and using a different (Red-Blue) color map.
spinev('cosy/cosy-2QF-ABX -plot -cont --cmap RdBu --xlim=4.97,5.03 --ylim=4.06,4.18', opts)
**************************************************************** ** 2Q-filtered COSY in ABX system, hypercomplex detection ** ****** The System ********************************************** spectrometer(MHz) 500 spinning_freq(kHz) * channels H1 nuclei H1 H1 H1 atomic_coords * cs_isotropic 4.1 4.14 5.0 ppm csa_parameters * j_coupling 1 3 3 j_coupling 2 3 9 j_coupling 1 2 -14 quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ***************************************** CHN 1 timing(usec) 0.5 (1600)1024D1 0.5 (0.5) (1600)1024D2 power(kHz) 500 0 500 500 0 phase(deg) 0 0 0 0 0 freq_offs(kHz) 0 0 0 0 0 phase_cycling_cos 4444 * * 2341 * 2143(RCV) phase_cycling_sin 3333 * * 2341 * 2143(RCV) ******* Variables ********************************************** ppm_center_1=4.56 fig_title="2Q-filtered COSY in ABX system" ******* Options ************************************************ rho0 F1z observables F1p EulerAngles * n_gamma * line_broaden(Hz) 0 0 3 3 zerofill * FFT_dimensions 1 2 ppm options -re -py options_cmd_line -plot -cont --cmap RdBu --xlim=4.97,5.03 --ylim=4.06,4.18 -px -py0 -vm -v0 -vf0 -vsf0 --verb **************************************************************** -- Accompanying pdf figure was obtained with the additional option --widths 0.25
The following is a full-scale simulation of a 2D spectrum in a 6-spin system under MAS. The computation time is about 5 minutes. Zoom on the peaks to see more detail.
spinev('rfdr/rfdr', opts, HTML=True)
****** The System **************************************************
spectrometer(MHz) 400
spinning_freq(kHz) 8.0
channels C13
nuclei C13 C13 C13 C13 C13 C13
atomic_coords leu.cor
cs_isotropic leu.cs
csa_parameters *
j_coupling leu.j
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei *
******* Pulse Sequence **********************************************
CHN 1
timing(usec) (0)2048D1 0.5 (0) (rfdr8.pp)x2 (0) 0.5 (0)1024D2
power(kHz) 0 500 0 * 0 500 0
phase(deg) 0 270 0 * 0 90 0
freq_offs(kHz) 0 0 0 * 0 0 0
******* Variables ***************************************************
spinning_freq=8
taur=1000/spinning_freq
pulse_1_1_1=taur/6
pulse_1_7_1=taur/3
tsf_4=taur/64
psf_1_4=1/tsf_4
zfilter_[3 5]=1
frs_1_[1 4 7]=[-16 -4 -16]
fig_title="2D RFDF $^{13}$C$-^{13}$C correlation"
******* Options *****************************************************
rho0 F1x
observables F1p
EulerAngles rep100
n_gamma 12
line_broaden(Hz) 0 0 60 60
zerofill *
FFT_dimensions 1c 2
options -re -py
options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
Interactive Plot: The 2D spectrum above is interactive even in the Web version of this notebook. Hover with a mouse over the figure, and the Zoom/Pan/Home menu will appear.
spinev('chem-exchange/exch', opts)
****** The System ******* spectrometer(MHz) 400 spinning_freq(kHz) * channels H1 nuclei H1 H1 atomic_coords * cs_isotropic 1 -1 csa_parameters * j_coupling * quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei (1 2) bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) (100)1024 power(kHz) 0 phase(deg) 0 freq_offs(kHz) 0 ******* Variables *********************************** scan_par k_1/0.7 1.5 3 4.4 6 16/ pdata_re=pdata_re/pdata_re(512,6) fig_title="Chemical Exchange in a Two-Spin System" ******* Options ************************************* rho0 F1x observables F1p EulerAngles * n_gamma * line_broaden(Hz) * zerofill * FFT_dimensions 1 options -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb ****************************************************** -- 4.4 ≈ π√2 -- The signal is normalized by the height of the last peak
Now, we will perform essentially the same simulation as above, but with more points for the exchange rate constant, and visualizing the output as a filled contour plot.
spinev('chem-exchange/exch2D', opts)
****** The System ******* spectrometer(MHz) 400 spinning_freq(kHz) * channels H1 nuclei H1 H1 atomic_coords * cs_isotropic 1 -1 csa_parameters * j_coupling * quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei (1 2) bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) (100)1024 power(kHz) 0 phase(deg) 0 freq_offs(kHz) 0 ******* Variables *********************************** scan_par k_1/1:50/ k_1.mx = 10^linspace(log10(0.2), log10(50), 50) fig_title="Chemical Exchange in a Two-Spin System" ******* Options ************************************* rho0 F1x observables F1p EulerAngles * n_gamma * line_broaden(Hz) * zerofill * FFT_dimensions 1 options -re -py -contf --ylog --contn=41 --cmap plasma options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
spinev('quad-echo-dynamics/quad-echo', opts)
********************************************************************************* ** This example implements the dynamical model described in ** Kolokolov, D., Stepanov, A.G., & Jobic, H. (2015). ** Mobility of the 2-Methylimidazolate Linkers in ZIF-8 Probed by 2H NMR: ** Saloon Doors for the Guests. Journal of Physical Chemistry C, 119, 27512-27520. ****** The System **************************************************************** spectrometer(MHz) 400 spinning_freq(kHz) * channels H2 nuclei H2 atomic_coords * cs_isotropic * csa_parameters * j_coupling * quadrupole 1 175 0 0 109.5 0 quadrupole 2 203 0 0 36 90 dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei (1) (1 2) ******* Pulse Sequence ****************************** CHN 1 timing(usec) (2) (20) (2) (21) (3)8k power(kHz) 125 0 125 0 0 phase(deg) 0 0 0 0 0 freq_offs(kHz) 0 0 0 0 0 phase_cycling 11 * 24 * * 44(RCV) ******* Variables *********************************** ** CD3 group hopping group_1_R=["0 0 0; 0 0 120; 0 0 -120"]' ** Two-site flip of a ring bearing the CD3 group and two CD groups group_2_R=["0 17 0; 0 -17 0"]' ** The signal is a sum of one CD3 and two CD groups ave_par1d sys2ext_map/1 2/ ave_par1d ave_wht/3 2/ fig_title="Quadrupole Echo: Mobility of ZIF-8 2-mIM-d$_6$ linker" ******* Options ************************************* rho0 F1z observables F1p EulerAngles asgind50h n_gamma * line_broaden(Hz) 100 2000 zerofill * FFT_dimensions 1 options -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
spinev('quad-echo-dynamics/quad-echo-k', opts)
****** The System **************************************************************** spectrometer(MHz) 600 spinning_freq(kHz) * channels H2 nuclei H2 atomic_coords * cs_isotropic * csa_parameters * j_coupling * quadrupole 1 177 0.03 0 0 90 dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei (1) ******* Pulse Sequence ****************************** CHN 1 timing(usec) (2) (0) (20) (2) (21) (2.3)256 power(kHz) 125 0 0 125 0 0 phase(deg) 90 0 0 0 0 0 freq_offs(kHz) 0 0 0 0 0 0 ******* Variables *********************************** ** Quad Echo Pulse Sequence p90=2 tau=20 pulse_1_[1 4]_1=p90 power_1_[1 4]_1=1000/(4*p90) p90a=(power_1_1_1>499)?0:p90 // actual p90 is zero for ideal pulses pulse_1_3_1=tau-p90a pulse_1_5_1=tau-p90a/2 ** Select -1 and +1 coherences (instead of phase cycling) select_2=["-1 1"] ** 180° flip AND ±10° fast librations: group_1_R_$1=["10 60 0; -10 60 0"]' group_1_R_$2=["10 -60 0; -10 -60 0"]' ** Pure 2-site 180° flip: *group_1_R_$1=["0; 60; 0"] *group_1_R_$2=["0;-60; 0"] scan_par k_exch(1,2)/10 50 250 1250 6250/ dim_2_units="1/s" // units to use for the legend ** Equilibrium populations pe_exch=["1; 1"] ** Make a stack plot by shifting the data pdata_re=pdata_re+ones(2048,1)*["0 1 2 3 4"]*2 ** To also normalize by the max intensity, use this instead: *pdata_re=pdata_re.*(ones(2048,1)*(1./max(pdata_re)))+ones(2048,1)*["0 1 2 3 4 5"] fig_title="$^2$H spectra of a librating phenylene group undergoing 180° flip" ** Add Cq and eta to the figure and place the legend under the axes box ani = str(quad_ani_1_$1,3) asy = str(quad_asy_1_$1,1) text=f"'$C_Q=[ani]$ kHz [nl]$\eta_Q=[asy]$'" fig_options = f"--size 6.4,6.4 --legloc 'upper center' --leganch 0.5,-0.15 --legncol 3 --text 0.05,0.9,[text]" ******* Options ************************************* rho0 F1z observables F1p EulerAngles asgind100h n_gamma * line_broaden(Hz) 100 2000 zerofill 2048 FFT_dimensions 1 options -xn2 -re -py -lv options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
spinev('cest/cest', opts)
****** The System *********************************** spectrometer(MHz) 500 spinning_freq(kHz) * channels H1 nuclei H1 atomic_coords * cs_isotropic * csa_parameters * j_coupling * quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) 10e+6 power(kHz) 0.2 phase(deg) 0 freq_offs(kHz) 0 ******* Variables *************************************** ** state 1 is H2O; state 2 is NH ********************************************** ** user input ********************************************** ** chemical shifts, kHz cs_iso_1_$1=0 // H2O cs_iso_1_$2=-1.75 // NH ** Relaxation rates, Hz R1$H20=0.2 R2$H20=0.6 R1$NH=2.0 R2$NH=3.0 ** NH -> H2O exchange rate, kHz k_exch(1,2)=0.4 ** Molar ratio of H2O to NH protons M=2000 ** saturation pulse frequency sweep scan_par1d freq_1_1_1/-2.5:0.01:2.5/ ** saturation pulse power scan_par2d power_1_1_1/0.2 0.1 0.05/ *********************************************** ** T1 and T2 relaxation times, ms T1SQ_1_$1=1000/R1$H20 T2SQ_1_$1=1000/R2$H20 T1SQ_1_$2=1000/R1$NH T2SQ_1_$2=1000/R2$NH ** exchange parameters p0_exch=["M; 1"] pe_exch=p0_exch ** average over RF inhomogeneity ave_par x/-1:0.025:0/ psf_1_1=1+0.05*x W=sum(cos(pi*x.mx)+1) ave_wht_1=(cos(pi*x)+1)/W fig_title = "Chemical Exchange Saturation Transfer (CEST)" ******* Options etc ************************************* rho0 Ieq observables I1z EulerAngles * n_gamma * line_broaden(Hz) * zerofill * FFT_dimensions * options -xn2 -re -dp -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
The following calculation fits the CSA parameters to an experimental CSA sideband spectrum
spinev('csa-fitting/SnC2O4', opts)
****** The System ****************************************************************
spectrometer(MHz) 500
spinning_freq(kHz) 3.8
channels Sn(74.56 -1/2)
nuclei Sn
atomic_coords *
cs_isotropic *
csa_parameters 1 -600 0.1 0 0 0 ppm
j_coupling *
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei *
******* Pulse Sequence ***********************************************************
CHN 1
timing(usec) (0)32
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
******* Variables ****************************************************************
pulse_1_1_1=1000/spinning_freq/32
signal_sf=40
fit_par cs_ani_1 cs_asy_1 signal_sf
** Figure options ****************************************************************
x_label="$^{119}$Sn frequency, kHz"
ani = str(cs_ppm_ani_1,3), x_
asy = str(cs_asy_1,2), x_
text = f"'$\delta_{\mathrm{ani}}=[ani]$ ppm [nl]$\eta_{\delta}=[asy]$'"
fig_options = f"--xinv --markers *b --lines '' --colors ky --text 0.08,0.8,[text]"
fig_title = "CSA sideband fitting in $^{119}$SnC$_2$O$_4$"
******* Options ******************************************************************
rho0 I1x
observables I1p
EulerAngles lebind29o
n_gamma 10
line_broaden(Hz) *
zerofill *
FFT_dimensions 1
options -re -fft0 -ws -py
options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
**********************************************************************************
-- See comments in the quad1_full example to understand how sideband inteinsities are simulated here
-- Experimental data are taken from Fig. 2(d) in P. Amornsakchai, D.C. Apperley, R.K. Harris, P. Hodgkinson, P.C. Waterfield, Solid-state NMR studies of some tin(II) compounds, Solid State Nucl. Magn. Reson 26 (2004) 160-171
The following calculation is a simplified version of using SpinEvolution to design high-quality selective excitation pulses, as described in detail in M. Veshtort, R.G. Griffin (2004). High-Performance Selective Excitation Pulses for Solid- and Liquid-State NMR Spectroscopy, ChemPhysChem, 5, 834-850.
The pulse shape that this optimization produces (in a fraction of a second!) is the e100A member of the E-Family.
spinev('selective-pulse-design/selpul', opts)
****** The System **********************************************************************
spectrometer(MHz) *
spinning_freq(kHz) *
channels H1
nuclei H1
atomic_coords *
cs_isotropic *
csa_parameters *
j_coupling *
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei *
******* Pulse Sequence *****************************************************************
CHN 1
timing(usec) t100.tm
power(kHz) 0
phase(deg) 90
freq_offs(kHz) 0
******* Variables **********************************************************************
scan_par cs_iso_1/0:0.025:5/
*** Compute the pulse shape
A=zeros(15,1)
B=zeros(15,1)
n=1:15
t=(50:100:9950)'
C=cos((2*pi/10000)*t*n)
S=sin((2*pi/10000)*t*n)
power_1_1=0.1*(A0+C*A+S*B)
*** Optimization routine options
RFC_TOL=0.001
RDX_FDJ=0.001
fit_par A0 A([1:15]) B([1:15])
*** Show the results *******************************************************************
** Plot the pulse shape
opts1 = "--title='Selective Pulse Optimization: Pulse Shape (e100A)' --xlabel='time, ms' --ylabel '$\omega_1/2\pi$, kHz'"
plot(t, 0.1*(A0+C*A+S*B), opts1), x_
** Recompute the excitation profile using different scan_par steps & range **
** Results will be saved in e100A_re.dat and e100A_im.dat
system("spinev profile -macro{name}=e100A"), x_
** Plot the results
files = "e100A_re.dat e100A_im.dat"
opts2 = " --title='Selective Pulse Optimization: Excitation Profile (e100A)' --xlabel='Frequency Offset, kHz'"
plot(files & opts2), x_
******* Options etc ********************************************************************
rho0 I1z
observables I1p
EulerAngles *
n_gamma *
line_broaden(Hz) *
zerofill *
FFT_dimensions *
options -varselpul0.par -ne100A -fne100 -o0
options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
****************************************************************************************
-- The initial conditions for the optimizarion are loaded from selpul0.par
-- The optimized pulse shape parameters are saved as e100A.par
-- The target excitation profile is specified by the e100_re/im.fit/wht files
-- The profile has has a 100 Hz pure excitation band and 150 Hz transition regions
In the following spectral fitting calculation, chemical shifts and J-couplings are extracted from an 1H spectrum without any prior knowledge about their values. The figure shows the results of the fitting: the calculated (best-fit) and the experimental (target) spectra are identical, indicating that the spectral fitting was successful.
spinev('spectral-fitting/sfit -fnsfit1', opts)
****** The System ******* spectrometer(MHz) 300 spinning_freq(kHz) * channels H1 nuclei * atomic_coords * cs_isotropic * csa_parameters * j_coupling * quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) (10000)8192 power(kHz) 0 phase(deg) 0 freq_offs(kHz) 0 ******* Variables *********************************** fig_title="Extraction of Chem. Shifts and J-couplings from ABCD-System Spectrum" ******* Options ************************************* rho0 F1x observables F1p EulerAngles * n_gamma * line_broaden(Hz) 0.5 zerofill * FFT_dimensions 1 options -re -sysh4 -decprec4g -sfit -py options_cmd_line -fnsfit1 -px -py0 -vm -v0 -vf0 -vsf0 --verb ********************************************************** -- Use this file to fit any of the following *.fit files contained in this directory: sfit1_re.fit, sfit2_re.fit, sfit3_re.fit, sfit4_re.fit. These *.fit files have been generated using parameters saved in sfit1.par, sfit2.par, sfit3.par, and sfit4.par files, accordingly. -- For example, for spectral fitting of the sfit1_re.fit data, run spinev sfit -fnsfit1 -- The best-fit parameters will be saved in sfit.par file, which can be compared with the parameter file used to generate the "experimental" data in the sfit1_re.fit file.
spinev('mrs-press/press -pseq')
spinev('mrs-press/press', opts)
******************************************************************************* ** PRESS localization: 1H spectrum averaged over 3D voxel ** Reference: Kaiser, L. G., Young, K., Matson, G. B. (2008) ** Numerical simulations of localized high field 1H MR spectroscopy. ** Journal of Magnetic Resonance, 195(1), 67–75. ****** The System ************************************************************* spectrometer(MHz) 125 spinning_freq(kHz) * channels H1 nuclei * atomic_coords * cs_isotropic MOL.cs ppm csa_parameters * j_coupling MOL.j quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ******************************************************* CHN 1 timing(usec) (t128.tm) 0 (0) (t200.tm) 0 (0 0) (t200.tm) 0 (4000)8k power(kHz) slr90.pwr 0 0 s180.pwr 0 0 0 s180.pwr 0 0 phase(deg) 90 0 0 0 0 0 0 0 0 0 freq_offs(kHz) 0 0 0 0 0 0 0 0 0 0 CHN G timing(usec) (t128.tm) 0 (0) (t200.tm) 0 (0 0) (t200.tm) 0 (4000) grad_offs(kHz) 0 0 0 0 0 0 0 0 0 0 ******* Variables ************************************************************ ** slr90.pwr is the selective excitation pulse powers, kHz, for a 10 ms pulse ** s180.pwr is the selective refocusing pulse powers, kHz, for a 10 ms pulse ** See examples/selective-pulses to investigate how these pulses work ** Specify selective pulses lengths, usec T90 = 4000 T180 = 5000 ** Specify (refocusing time)/(pulse length) ratio for the excitation pulse ** The refocusing time for the excitation pulse is given as a comment in slr90.pwr r90 = 0.5050 // slr90 ** Set up the selective excitation pulse pulse_[1 2]_1=T90/128 psf_1_1=10000/T90 ** Set up the selective refocusing pulses pulse_[1 2]_4=T180/200 pulse_[1 2]_7=T180/200 psf_1_[4 7]=10000/T180 ** Coherence pathway selected with the crusher gradinents select_[2 5]=[-1 1] ** Localization: 3D average over the voxel volume ** ** G1, G2, G3 are offsets, kHz, generated by PFGs along X, Y, and Z ave_par1d G1/-2.5:0.1:2.5/ ave_par2d G2/-1:0.05:1/ ave_par3d G3/-1:0.05:1/ *G[1 2 3]=[0 0 0] // for a single point inside the voxel grad_offs_[1 4 7]=G[1 2 3] ** Refocus the linear phase generated by the selective excitation pulse pulse_[1 2]_6_1=T90*r90 grad_offs_6_1=G1 ** Additional interpulse delays (due to crusher gradients etc.) t1=1000 t2=1000 pulse_[1 2]_3_1=t1 pulse_[1 2]_6_2=t1+t2 pulse_[1 2]_8_1=t2 fig_options="--text 0.07,0.90,Myo-inositol" fig_title="PRESS localization: 1H spectrum averaged over 3D voxel" ******* Options *************************************************************** rho0 F1z observables F1p EulerAngles * n_gamma * line_broaden(Hz) 1 zerofill * FFT_dimensions 1 ppm options -re -macroMOL=myo-inositol -sysh6 -varppm_center_1=3.6 -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb ******************************************************************************* -- A different molecule can be easily chosen by using different values for the command line options -macroMOL=... -sysh... -varppm_center_1=...
spinev('mrs-slaser/slaser2D -pseq -varX3=0.75')
EQ4000A B1max = 24 uT GOIA B1max = 24.9 uT
spinev('mrs-slaser/slaser2D', opts)
EQ4000A B1max = 24 uT GOIA B1max = 24.9 uT
******************************************************************************************
** EQ4000A/GOIA-W(16,4) semi-LASER slice map in N-acetylaspartate (NAA)
** The spin system: one NH proton and one CH3 proton
** Reference:
** Kaiser et al., Broadband selective excitation radiofrequency pulses for optimized localization in vivo, Magnetic Resonance in Medicine (2022)
** https://doi.org/10.1002/mrm.29119
****** The System ************************************************************************
spectrometer(MHz) 125
spinning_freq(kHz) *
channels H1
nuclei H1 H1
atomic_coords *
cs_isotropic 7.84 2 ppm
csa_parameters *
j_coupling *
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei *
******* Pulse Sequence *******************************************************************
CHN 1
timing(usec) (tNs.tm) 0 (0) (t256.tm) 0 (0 0) (<4>) 0 (0) (<4>) 0 (0) (<4>) 0
power(kHz) SHAPE.pwr 0 0 goia.pwr 0 0 0 * 0 0 * 0 0 * 0
phase(deg) SHAPE.phs 0 0 goia.phs 0 0 0 * 0 0 * 0 0 * 0
freq_offs(kHz) 0 0 0 0 0 0 0 * 0 0 * 0 0 * 0
CHN G
timing(usec) (tNs.tm) 0 (0) (t256.tm) 0 (0 0) (<4>) 0 (0) (<4>) 0 (0) (<4>) 0
grad_offs(kHz) 0 0 0 0 0 0 0 * 0 0 * 0 0 * 0
******* Variables ************************************************************************
** <4> at the timing(usec) line above means "the same as pulse sequence 4"
** SHAPE and Ns are macros set at the options line
** SHAPE.pwr/phs are the excitation pulse powers, kHz, and phases, deg, for a 10 ms pulse
** goia.pwr/phs are the refocusing pulse powers, kHz, and phases, deg, for a 10 ms pulse
** See slaser1D and examples/selective-pulses to investigate how these pulses work
** Specify the location of the spectrum center (zero frequecy in kHz) in ppm
ppm_center_1=4.9
** Specify selective excitation pulse length, usec
** EQ4000A: 5000, EB2000A: 4000, P10: 1600
T90 = ("SHAPE"=="EQ4000A")? 5000 : (("SHAPE"=="EB2000A")? 4000 : 1600)
** Specify selective refocusing GOIA-W(16,4) pulse length, usec
T180 = 2700
** Specify (refocusing time)/(pulse length) ratio for the excitation pulse
** The refocusing time for the excitation pulse is given as a comment in SHAPE.pwr
r90 = ("SHAPE"=="EQ4000A")? 0.43823 : (("SHAPE"=="EB2000A")? 0.29997 : 0.188)
*r90 = 0.43823 // EQ4000A
*r90 = 0.29997 // EB2000A
*r90 = 0.188 // P10
** Specify the pulse bandwidths, kHz
BW90 = ("SHAPE"=="EQ4000A")? 8.4 : (("SHAPE"=="EB2000A")? 5.6 : 4.0)
BW180 = 20*3500/T180 // The original pulse is 20 kHz for 3.5 ms pulse length
** Set up the selective excitation pulse
pulse_[1 2]_1=T90/Ns
psf_1_1=10000/T90
phase_1_1=phase_1_1+90 // to observe as Ix
** Print B1max, uT, for the excitation pulse
disp("SHAPE B1max = "&str(1000*max(abs(power_1_1*psf_1_1))/42.5773,3)&" uT")
** Set up the selective refocusing pulses
pulse_1_[4 7 10 13]=T180/256
pulse_2_[4 7 10 13]=T180/256
psf_1_[4 7 10 13]=10000/T180
** Print B1max, uT, for the refocusing pulse
disp("GOIA B1max = "&str(1000*max(abs(power_1_4*psf_1_4))/42.5773,3)&" uT")
** Coherence pathway selected with the crusher gradinents
select_[2 5 8 11]=[-1 1 -1 1]
** Localization **
** Gradient strengths, kHz/cm required to localize a 1cm x 1cm x 1cm voxel
G1 = BW90 // X axis
G2 = BW180 // Y axis
G3 = BW180 // Z axis
** X1, X2 and X3 are the spacial offsets, cm, from the gradients center
X3 = 0 // fixed offest along Z
scan_par1d X2/0.75:-0.01:-0.75/
scan_par2d X1/0.75:-0.01:-0.75/
grad_offs_1=X1*G1
g=load("goia.pfg")
grad_offs_[4 7 10 13]=g*X[2 2 3 3]*G[2 2 3 3]
** Refocus the linear phase generated by the selective excitation pulse
pulse_[1 2]_6_1=T90*r90
grad_offs_6_1=X1*G1
** Additional interpulse delays (due to crusher gradients etc.)
t1=1000
t2=1000
pulse_[1 2]_3=t1
pulse_[1 2]_6_2=t1+t2
pulse_[1 2]_9=t1+t2
pulse_[1 2]_12=t1+t2
pulse_[1 2]_14=t2
** Truncate the negative signal
pdata_re = (pdata_re<0)?0:pdata_re
x_label="Y (ref 180°), mm"
y_label="X (exc 90°), mm"
fig_title = f"Localization map of a SHAPE/GOIA-W(16,4) semi-LASER slice [nl] in a two-spin system with signals at 2.0 and 7.8 ppm"
fig_options = "--contn 11 --cmap gray --scaled --colorbar-off"
******* Options **************************************************************************
rho0 0.5*F1z
observables F1p
EulerAngles *
n_gamma *
line_broaden(Hz) *
zerofill *
FFT_dimensions *
options -re -py -contf -macroNs=400 -macroSHAPE=EQ4000A
options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
******************************************************************************************
-- Any of the three available shapes can be chosen by setting SHAPE macro to EQ4000A, EB2000A, or P10
-- The Ns macro (the number of steps in the shape) must be then set to 400 for EQ4000A, and to 256 for EB2000A or P10
SpinEvolution plot command can be used to automatically generate complex publication-ready figures from the simulation results
spinev('figure/figure',opts)
****** The System ******************************************************
spectrometer(MHz) *
spinning_freq(kHz) *
channels H1
nuclei H1
atomic_coords *
cs_isotropic *
csa_parameters *
j_coupling *
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei *
******* Pulse Sequence **************************************************
CHN 1
timing(usec) 0
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
******* Variables *******************************************************
** This input file has been used to generate Figure 2 for the following paper:
** Kaiser et al., Broadband selective excitation radiofrequency pulses for optimized localization in vivo, Magnetic Resonance in Medicine (2022)
** https://doi.org/10.1002/mrm.29119
** There is no need to read the above paper to understand this input file
** Just see the resulting figure (figure.pdf) and follow the notes below
** The figure illustrates the properties of three selective excitation pulses
** Each row of subfigures corresponds to one of these pulses:
** P10, EB2000A, and EQ4000A
** The 1st column of subfigures shows the pulse shape
** The 2nd column shows the excitation profile
** The 3rd column shows a 2D slice simulation as a filled contour plot
** The data files for this figure were generated using
** examples/selective-pulses/sel-exc and examples/mrs-slaser/slaser2D
** Please read the following sections in the Plot Manual:
* Multiple subplots
* (La)TeX-style formatting
* Execution of user-specified Matplotlib code
* Options: --axes, --text
****************************************************************************
** Figure width and height, in
FW=6.90 // full page width
FH=5.65
** Aspect Ratio (W/H) for the subfigures
AR = 4/3
** The placement of the lower left subfigure will be specified as --axes X0,Y0,W,H
X0 = 0.060 // units: fraction of FW
Y0 = 0.060 // units: fraction of FH
H = 0.281 // units: fraction of FH
W = AR*H*FH/FW // units: fraction of FW
** Horizontal and vertical spacing b/w subfigures, fractional units
dx = 0.054
dy = 0.046
** The placement of the filled contour plots (the 3rd column of subfigures)
X3 = X0+2*(W+dx)-0.02 // X0 of the 3rd column of subfigures, fractional units
W3 = H*FH/FW // W of the 3rd column of subfigures (making them square)
** Axes labeling for the filled contour plots
T3 = "--text 0.30,0.03,'ref 180°\, mm',,w --text 0.92,0.30,'exc 90°\, mm',,w,90"
** Subfigure letter location, fractional coordinates
L = "0.07,0.87"
** Options for EQ4000A subfigures (G,H,I)
Q1 = f"EQ4000A_plot1.dat --xlabel 'time, ms' --ylabel '$B_1$ amplitude, $\mu T$' --ylim=-25,25 --xlim=0,5 --text 0.91,0.07,'EQ4000A',9.5,,90 --text [L],$\mathbf{G}$,11 --axes [X0],[Y0],[W],[H] "
Q2 = f"EQ4000A_re.dat --xlabel 'frequency offset, kHz' --ylim=-0.43,1.07 --ynticks 3 --xlim=-8,8 --xnticks 5 --text -1.8,0.35,'8.4 kHz',,,,d --exec ax.hlines(0.5,-4.2,4.2,colors='k',linewidths=0.7) --text [L],$\mathbf{H}$,11 --axes [X0+W+dx],[Y0],[W],[H] "
Q3 = f"EQ4000A_2D_re.dat --contf --axis-off --text [L],'$\mathbf{I}$',11,w [T3] --axes [X3],[Y0],[W3],[H] "
** Options for EB2000A subfigures (D,E,F)
B1 = f"EB2000A_plot1.dat --ylabel '$B_1$ amplitude, $\mu T$' --ylim=-25,25 --xlim=0,4 --text 0.91,0.07,'EB2000A',9.5,,90 --text [L],$\mathbf{D}$,11 --axes [X0],[Y0+H+dy],[W],[H] "
B2 = f"EB2000A_re.dat --ylim=-0.43,1.07 --ynticks 3 --xlim=-8,8 --xnticks 5 --text -1.8,0.35,'5.6 kHz',,,,d --exec ax.hlines(0.5,-2.8,2.8,colors='k',linewidths=0.7) --text [L],$\mathbf{E}$,11 --axes [X0+W+dx],[Y0+H+dy],[W],[H] "
B3 = f"EB2000A_2D_re.dat --contf --axis-off --text [L],'$\mathbf{F}$',11,w [T3] --axes [X3],[Y0+H+dy],[W3],[H] "
** Options for P10 subfigures (A,B,C)
P1 = f"P10_plot1.dat --ylabel '$B_1$ amplitude, $\mu T$' --legend real,imag --legloc 'upper center' --ylim=-25,25 --xlim=0,1.6 --text 0.91,0.14,'P10',9.5,,90 --text [L],$\mathbf{A}$,11 --axes [X0],[Y0+2*(H+dy)],[W],[H] "
P2 = f"P10_re.dat --legend '$M_x$, $M_y$' --ylim=-0.43,1.07 --ynticks 3 --xlim=-8,8 --xnticks 5 --text -1.10,0.33,'4 kHz',,,,d --exec ax.hlines(0.5,-2,2,colors='k',linewidths=0.7) --text [L],$\mathbf{B}$,11 --axes [X0+W+dx],[Y0+2*(H+dy)],[W],[H] "
P3 = f"P10_2D_re.dat --contf --axis-off --text [L],$\mathbf{C}$,11,w [T3] --axes [X3],[Y0+2*(H+dy)],[W3],[H] "
** Plot the Figure
** Options common to all subfigures are given first, followed by the options for each subfigure
plot(f"--lines=-,-- --colors=k --widths=0.9 --font Arial --fontsize 9 --ksize 8 --xpad 4 --ypad 2 --ykpad 2 --ticks-in --size [FW],[FH] --contn 11 --cmap gray --colorbar-off --save figure.pdf " & P1 & P2 & P3 & B1 & B2 & B3 & Q1 & Q2 & Q3)
******* Options etc *****************************************************
rho0 I1z
observables I1z
EulerAngles *
n_gamma *
line_broaden(Hz) *
zerofill *
FFT_dimensions *
options -v0 -o0
options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
**************************************************************************
spinev('epr/e-N14', opts)
************************************************************************************
* TEMPO/Nitroxide EPR powder pattern
* Data from: W. Snipes, J. Cupp, G. Cohn, and A. Keith, Biophys. J. 14 (1974), 20
* See also Fig. 3 in: K.R. Thurber, R. Tycko, J. Chem. Phys., 137, 084508 (2012).
****** The System ******************************************************************
spectrometer(MHz) *
spinning_freq(kHz) *
channels e N14
nuclei e N14
atomic_coords *
cs_isotropic *
csa_parameters *
g-tensor 1 2.0094 2.0061 2.0021 0 0 0
j_coupling *
spin-spin_coupling 1 2 43.1e+3 49.3e+3 0.012 0 0 0
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei *
******* Pulse Sequence ******************************
CHN 1
timing(usec) (0.0004)8192
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
CHN 2
timing(usec) 0.0004
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
******* Variables *************************************************************
B0_field=9.4
** Convert the output data labeling from Frequency offset, kHz to Frequency, GHz
dim_1_labels= ref_freq_1*1e-3 + dim_1_labels*1e-6
x_label = "Frequency, GHz"
fig_title = "TEMPO/Nitroxide EPR powder pattern at 9.4T (e-$^{14}$N spin system)"
******* Options ****************************************************************
rho0 I1x
observables I1p
EulerAngles asgind100o
n_gamma *
line_broaden(Hz) 5e+6
zerofill *
FFT_dimensions 1
options -re -py
options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
*********************************************************************************
-- We use powder averaging over just one octant (the 'o' suffix in asgind100o).
This is legal only because both tensors are alligned with the crystal axes.
In the following figure, the main plot is supplemented with two instes, showing the shape of a single peak, and the "symmetric staircase" shape of the baseline, which is completely unnoticeable on the full-scale spectrum.
spinev('epr/Mn55', opts)
****** The System *******
spectrometer(MHz) 500
spinning_freq(kHz) *
channels e6(329688 -5/2) Mn55
nuclei e6 Mn55
atomic_coords *
cs_isotropic *
csa_parameters *
g-tensor 1 2.0023 2.0023 2.0023 0 0 0
j_coupling *
spin-spin_coupling 1 2 250e+3 0 0 0 0 0
zerofield_coupling 1 1500e+3 0 0 0 0
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei *
******* Pulse Sequence ******************************
CHN 1
timing(usec) (0.00004)64k
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
CHN 2
timing(usec) 0.00004
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
******* Variables ***********************************
** Place the reference frequency at the center of the spectrum
ref_freq_1 = ref_freq_1 + 1e-3*cs_iso_1
** Convert the output data labeling from Frequency offset, kHz to Frequency, GHz
dim_1_labels = dim_1_labels*1e-6 + ref_freq_1*1e-3
*** Plotting the output ****************************
* Create THREE plots (on the same figure) from the output data:
* 1) full scale plot, 2) zoom on the baseline, and 3) zoom on one of the peaks
* -pu option is used to force plotting output solely from fig_options
X = f"--widths 0.8 --save [name_]_re.pdf "
A = "Mn55_re.dat --title '$^{55}$Mn(II) EPR' --xlabel 'Frequency, GHz' --axes 0.1,0.1,0.8,0.8 "
B = "Mn55_re.dat --ylim=-0.05,0.25 --axes 0.60,0.63,0.28,0.25 "
C = "Mn55_re.dat --xlim=328.39,328.53 --axes 0.16,0.63,0.28,0.25"
fig_options = X & A & B & C
******* Options *************************************
rho0 I1x
observables I1p
EulerAngles asgind200o
n_gamma *
line_broaden(Hz) 2e+6 2e+6
zerofill *
FFT_dimensions 1
options -re -py -pu -px
options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
******************************************************
-- Note the space at the end of the strings we use to build fig_options
-- --axes option arguments: x0,y0,width,height, where x0,y0 are the coordinates of the lower left corner of the axes box, and width,height are its sizes; all four parameters are given as fractions of the corresponding full figure sizes (WxH)
-- $^{55}$Mn(II) is the title written using mathtext (~TeX) formatting
-- -px option saves Mn55_pl.json file, which can be used to create exactly the same figure by running "plot Mn55" from the command line (i.e. without re-running the whole spinev calculation). One can also edit this file manually to adjust the placement of the axes and other figure options
-- --widths option sets the width of the plot lines (in points, 1 point = 1/72 inch)
-- 'f' in front of a string instructs to format it, i.e. to expand all bracketed exressions inside the string; name_ is the name (or path), from which all output file names are constructed by appending _re.dat etc.
-- Run "plot -h" from the command line to see more details on plot options
spinev('dnp/static-se-profiles', opts)
***************************************************************************************
*** This simulation reproduces Fig. 8 from: Y. Hovav, A. Feintuch, S. Vega (2010).
*** Theoretical aspects of dynamic nuclear polarization in the solid state - The solid
*** effect. Journal of Magnetic Resonance, 207(2), 176–189.
****** The System *********************************************************************
spectrometer(MHz) 144
spinning_freq(kHz) *
channels e H1
nuclei e H1
atomic_coords *
cs_isotropic *
csa_parameters *
j_coupling *
spin-spin_coupling 1 2 868 -2125 0 0 30 0
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei *
******* Pulse Sequence ******************************
CHN 1
timing(usec) (10000)x512
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
CHN 2
timing(usec) 10000
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
******* Variables ***********************************
spin_temp=100
** DQ Solid Effect
scan_par1d freq_1_1_1/-146e3:5:-142e3/
** ZQ Solid Effect
*scan_par1d freq_1_1_1/142e3:5:146e3/
scan_par2d power_1_1_1/1000 100 20/
T2SQ_1=0.01 // T2e, ms
T2SQ_2=1 // T2n, ms
T1SQ_1=5 // T1e, ms
T1SQ_2=1000 // T1n, ms
** Additional T2 relaxation parameters to use with -rmz model
*T2ZQ_1_2_1=0.01
*T2DQ_1_2_1=0.01
** Hyperfine coupling used in the paper: -460*I1zI2z+690*(I1zI2p+I1zI2m) [kHz]
** The fact that we are using the same parameters here can be verified by
** commenting out the scan paramaters above and dim_1_units below, uncommenting
*disp(H_("I1zI2z",0))
*disp(H_("I1zI2p+I1zI2m",0))
** and running the simulation in the analytic mode (with the -am option)
dim_1_units="MHz"
y_label = "$\epsilon_B$"
fig_options="--yrot --ysize 12"
fig_title = "Solid Effect Field Profiles in Static Samples (e-H spin system)"
******* Options ***********************************************
rho0 Ieq
observables I2z
EulerAngles *
n_gamma *
line_broaden(Hz) *
zerofill *
FFT_dimensions *
options -ns1 -dp -re -id1e6 -lv -py
options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
******************************************************************************************
-- Option -id1e6 is required here to prevent SpinEvolution from interpreting pulses with power >=500kHz as ideal; the option sets this limit to 1000MHz
-- The simulatiom is performed via the Liouville space propagator (option -lv)
spinev('dnp/mas-se-powder', opts)
*********************************************************************************** **** MAS Solid Effect: field profile (powder averaging over 50 crystallites) ***** ****** The System ***************************************************************** spectrometer(MHz) 500 spinning_freq(kHz) 10 channels e H1 nuclei e H1 atomic_coords * cs_isotropic * csa_parameters 1 500 0.7 20 30 40 j_coupling * spin-spin_coupling 1 2 868 -2125 0 0 30 0 quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) (100)x65536 power(kHz) 500 phase(deg) 0 freq_offs(kHz) 0 CHN 2 timing(usec) 100 power(kHz) 0 phase(deg) 0 freq_offs(kHz) 0 ******* Variables *********************************** spin_temp=100 ** ZQ SE scan_par freq_1_1_1/499e3:100:501e3/ ** DQ SE *scan_par freq_1_1_1/-501e3:100:-499e3/ T2SQ_1=0.01 // T2e, ms T2SQ_2=1 // T2n, ms T1SQ_1=5 // T1e, ms T1SQ_2=1000 // T1n, ms dim_1_units="MHz" y_label = "$\epsilon_B$" fig_options="--yrot --ysize 12 --markers ." fig_title = "Solid Effect Field Profile (e-H spin system)" ******* Options ************************************* rho0 Ieq observables F2z EulerAngles leb50 n_gamma * line_broaden(Hz) * zerofill * FFT_dimensions * options -ns1 -dp -re -id1e6 -lv -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb **************************************************************************************** -- Option -id1e6 is required here to prevent SpinEvolution from interpreting pulses with power >=500kHz as ideal; the option sets this limit to 1000MHz -- MAS DNP simulations are always performed using automatically chosen integration steps -- Powder averaging: no need to average over gamma; average only over alpha and beta -- Note that we are not averaging here over different mutual orientations of the hyperfine coupling tensor and the g-tensor, i.e. over the various locations of the 1H around e
spinev('dnp/btbk', opts)
****************************************************************************** * Cross-effect field profile for the bTbK molecule * This is a simplified (e-e-H) version of the full 5-spin btbkn example ****** The System ************************************************************* spectrometer(MHz) 200 spinning_freq(kHz) 5 channels e H1 nuclei e e H1 atomic_coords * cs_isotropic * csa_parameters * g-tensor 1 2.0097 2.0065 2.0024 0 0 0 g-tensor 2 2.0097 2.0065 2.0024 -58 79 -118 j_coupling * spin-spin_coupling 1 2 0 -60e3 0 0 65 0 spin-spin_coupling 1 3 0 3e3 0 0 0 0 quadrupole * dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ****************************** CHN 1 timing(usec) (200)x65536 power(kHz) 1000 phase(deg) 0 freq_offs(kHz) 0 CHN 2 timing(usec) 200 power(kHz) 0 phase(deg) 0 freq_offs(kHz) 0 ******* Variables *********************************** spin_temp=100 ref_freq_1=131.725e+3 scan_par B0_field/4.679:0.001:4.707/ T2SQ_[1 2]=0.001 // T2e, ms T1SQ_[1 2]=0.15 // T1e, ms T1SQ_3=100 // T1n, ms fig_title = "bTbK Field Profile: 3-spin vs 5-spin systems" y_label = "$\epsilon_B$" fig_options="--yrot --ysize 12 --markers . --colors kr" legend_labels="e$_2$H, e$_2$N$_2$H" ******* Options ************************************* rho0 Ieq observables I3z EulerAngles leb50 n_gamma * line_broaden(Hz) * zerofill * FFT_dimensions * options -ns1 -dp -re -id1e6 -v1 -lvc -xtol8e-4 -py -refbtbkn options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb **************************************************************************************** -- Option -id1e6 is required here to prevent SpinEvolution from interpreting pulses with power >=500kHz as ideal; the option sets this limit to 1000MHz -- MAS DNP simulations are always performed using automatically chosen integration steps
spinev('dnp/dp', opts)
*******************************************************
**** Depolarization ****
****** The System *************************************
spectrometer(MHz) 500
spinning_freq(kHz) 10
channels e H1
nuclei e e H1
atomic_coords e2h.cor
cs_isotropic *
csa_parameters 1 800000 0.8 0 0 0
csa_parameters 2 800000 0.8 0 30 70
j_coupling *
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei *
******* Pulse Sequence ******************************
CHN 1
timing(usec) (100)x65536
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
CHN 2
timing(usec) 100
power(kHz) 0
phase(deg) 0
freq_offs(kHz) 0
******* Variables ***********************************
scan_par1d spinning_freq/0.2:0.2:1 1.5 2/
scan_par2d T1e/0.1 1 10/
spin_temp=100
pulse_[1 2]_1_1=1000/spinning_freq
T2SQ_[1 2]=0.01 // T2e, ms
T1SQ_[1 2]=T1e // T1e, ms
T1SQ_3=1000 // T1n, ms
dim_2_name="$T_{1e}$"
dim_2_units="ms"
y_label="Depolarization"
fig_title="Depolarization (e-e-H spin system)"
fig_options="--markers . --colors krg"
******* Options *************************************
rho0 Ieq
observables I3z
EulerAngles leb50
n_gamma *
line_broaden(Hz) *
zerofill *
FFT_dimensions *
options -ns1 -dp -re -id1e6 -v1 -lv -py
options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb
****************************************************************************************
-- Option -id1e6 is required here to prevent SpinEvolution from interpreting pulses with power >=500kHz as ideal; the option sets this limit to 1000MHz
-- MAS DNP simulations are always performed using automatically chosen integration steps
In the following spectrum, each sideband in represented by a signle point that gives the integral intensity of the sideband. Hence a bar plot is used to visualize the spectrum. The central peak is erased.
spinev('quadrupoles/quad1_full', opts)
****** The System ***************************** spectrometer(MHz) 500 spinning_freq(kHz) 10 channels X(200 3/2) nuclei X atomic_coords * cs_isotropic * csa_parameters * j_coupling * quadrupole 1 1000 0.25 0 0 0 dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ************************ CHN 1 timing(usec) (0)128 power(kHz) 0 phase(deg) 0 freq_offs(kHz) 0 ****** Variables ******************************* pulse_1_1_1=1000/spinning_freq/128 x_lim=["-600 600"] y_lim=["0 1.6"] fig_title="Full Sideband Manifold (integral peak intensities)" fig_options="--markers b --text 0.85,0.9,$I=3/2$" ******* Options ******************************** rho0 I1x observables I1p EulerAngles lebind65o n_gamma 128 line_broaden(Hz) * zerofill * FFT_dimensions 1 options -re -fft0 -ws -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb ************************************************ -- This computes the intensities of the spinning sidebands -- The -fft0 option sets the number of frequency bins for collecting the spectral intensities during the g-COMPUTE algorithm to the number of points in D1 (i.e. 128). The spacing between the centers of the bins is made to coincide with the spinning frequency by choosing the dwell time equal to the 1/128-th of the rotor period, which makes the spectral width equal to 128 spinning frequencies. With this choice, each sideband, although broadened by the the 2nd-order quadruplar interaction, is collected in just one bin. The total intensity collected in that bin (i.e. the intensity of the point in the spectrum on the output) then reflects the total sideband intensity over all orientations in the powder. -- Since the 2nd-order quadruplar interactions (although present in the Hamiltonian) do not affect the total intensities of the sidebands, exactly the same spectrum can be obtained with the -quad1 option. -- The -ws option is specified to disable the interpolation of the spectal frequencies (as functions of the orientation), which is useless in this case since the frequencies are made orientation-independent by the way they are binned. Enabling interpolation would produce the same result, but it would take longer to compute. -- This kind of input file is easily remade into a sideband fitting task (see csa-sb-fitting example).
The following shows the spectrum of exactly the same system, but now the spectrum consists of 2 million points, which is enough to digitize the detailed lineshape of each sideband. If zoomed onto, each sideband will show a unique lineshape.
spinev('quadrupoles/quad_full', opts)
****** The System ************************************ spectrometer(MHz) 500 spinning_freq(kHz) 10 channels X(200 3/2) nuclei X atomic_coords * cs_isotropic * csa_parameters * j_coupling * quadrupole 1 1000 0.25 0 0 0 dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ************************ CHN 1 timing(usec) (0.5)2m power(kHz) 0 phase(deg) 0 freq_offs(kHz) 0 ****** Variables ****************************** x_lim=["-600 600"] y_lim=["-5 230"] fig_title="Full Sideband Manifold with 2nd-Order Lineshapes" fig_options="--text 0.85,0.9,$I=3/2$" ******* Options ******************************* rho0 I1x observables I1p EulerAngles asgind100o n_gamma 200 line_broaden(Hz) 0.25 zerofill * FFT_dimensions 1 options -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb ***************************************************** -- See quad_sb for an individual sideband computation and comments
The spectrum below is again computed for exactly the same system as the two spectra above. However, it is now computed centered at the -100 kHz sideband, and with a lowpass filter that leaves only 1024 points in the output spectrum.
spinev('quadrupoles/quad_sb', opts)
****** The System ************************** spectrometer(MHz) 500 spinning_freq(kHz) 10 channels X(200 3/2) nuclei X atomic_coords * cs_isotropic 100 csa_parameters * j_coupling * quadrupole 1 1000 0.25 0 0 0 dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ********************* CHN 1 timing(usec) (0.5)2m power(kHz) 0 phase(deg) 0 freq_offs(kHz) 0 ****** Variables *************************** dim_1_labels = dim_1_labels - cs_iso_1 fig_title="Single Spinning Sideband Lineshape" fig_options="--text 0.85,0.9,$I=3/2$" ******* Options **************************** rho0 I1x observables I1p EulerAngles asgind100o n_gamma 200 line_broaden(Hz) * zerofill * FFT_dimensions 1 lowpass_npoints 1024 options -re -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb ******************************************** -- A single sideband can be obtained by shifting the spectrum to place the sideband at zero frequency and then turning on the lowpass feature. In this example, the "full" spectrum with 2M points is cut down to the 1024 points. The resulting spectum is computed at the same resolution (SW/npoints) as the full spectrum would have been computed. A different resolution can be set by the variable lowpass_sw, in which case the number 2M would be essentially ignored. -- One can verify that the output in this example coincides with the 10th sideband in the spectrum obtained in the quad_full example (except for a much higher resolution). -- Note that the spectral width specified by the pulse sequence should be sufficient to cover the full spectrum to prevent folding.
And finally, we compute the static (no MAS) spectrum of the same system
spinev('quadrupoles/quad1_stat', opts)
****** The System **************************************** spectrometer(MHz) 500 spinning_freq(kHz) * channels X(200 3/2) nuclei X atomic_coords * cs_isotropic * csa_parameters * j_coupling * quadrupole 1 1000 0.25 0 0 0 dip_switchboard * csa_switchboard * exchange_nuclei * bond_len_nuclei * bond_ang_nuclei * tors_ang_nuclei * groups_nuclei * ******* Pulse Sequence ************************************ CHN 1 timing(usec) (0.5)1024 power(kHz) 0 phase(deg) 0 freq_offs(kHz) 0 ****** Variables ****************************************** fig_title="First-Order Static Spectrum" fig_options="--text 0.1,0.9,$I=3/2$" ******* Options ******************************************* rho0 I1x observables 1.73|-1/2><-3/2| 1.73|3/2><1/2| I1p EulerAngles asgind100o n_gamma * line_broaden(Hz) * zerofill * FFT_dimensions 1 options -re -quad1 -rsp -py options_cmd_line -px -py0 -vm -v0 -vf0 -vsf0 --verb *********************************************************** -- This computes the spectra produced by each of the two observable transitions individually (the first two observables), as well as the total spectum obtained by observing I1p. -- Note that I1p=1.73205(|-1/2><-3/2|+|3/2><1/2|) + 2.0|1/2><-1/2| This can be observed, for example by running this input file with options -s -sm, or by running the quad_norm example -- The -rsp (remove singular peaks) option removes coherences with orientation-indepenent frequencies from the spectra. Since the second-order-broadening is not present in the Hamiltonian (due to the -quad1 option), the central transition is removed from the I1p spectrum. -- See quad2_stat for the second-order effects