Jupyter Interface¶
Advanced users will likely want to have more control over their experiments, beyond what the GUI can provide. For this reason, autoDEER has a Jupyter interface that allows users to run experiments from within a Jupyter notebook. In this mode, the user can intercede and take control when necessary or provide modifications to the alogoithm.
In this example, we show how to run a five-pulse DEER experiment using rectangular pulses.
Setup¶
First, we must import all the necessary packages and the interface. In this example we are using a custom ETH-AWG interface.
In [1]:
import matplotlib.pyplot as plt
import numpy as np
import autodeer as ad
from autodeer.hardware.ETH_awg import ETH_awg_interface
from autodeer.sequences import *
import autodeer.hardware.criteria as criteria
import time
Here we define a few starting parameters as well as initialise the interface. It is at this step that a connection between autoDEER and your spectrometer API is made.
In [2]:
gyro_N = 0.0028087 # This is just an initial guess of the gyromagnetic ratio, a more precise value will be calculated from the field sweep.
LO = 34.2172 # The is the central frequency of your resonator
reptime = 2e3 # This should be 3-5e3 when using 50K
interface = ETH_awg_interface()
Field Sweep¶
An Echo Detected Field Sweep (EDFS) is detected. This allows a more precise gyromagnetic ratio to be calculated. Before we can do this, we must first tune a pair of rectangular pulses.
In [3]:
p90, p180 = interface.tune_rectpulse(tp=12, LO=LO, B=LO/gyro_N, reptime = reptime)
In [4]:
fsweep = FieldSweepSequence(
B=LO/gyro_N, LO=LO,reptime=2e3,averages=1,shots=120,
Bwidth = 500,
pi2_pulse=p90, pi_pulse=p180,
)
print(fsweep)
Output
[4]:
###############################################################################
autoDEER Sequence Definition
###############################################################################
Sequence Parameters:
Name Value Unit Description
B 12183 Gauss The static B0 field for the experiment
LO 34.217 GHz The local oscillator frequency.
reptime 2000 us The shot repetition time
averages 1 None The number of averages to perform.
shots 120 None The number of shots per scan.
det_window 128 None The length of the default detection gate
time 0:4:0 HH:MM:SS Estimated sequence run time
Bwidth 500 Gauss Field sweep width
Events (Pulses, Delays, etc...):
iD t (ns) tp (ns) scale type Phase Cycle
0 0 12 0.14 RectPulse [+(+x) -(-x)]
1 500 24 0.14 RectPulse [+(+x)]
2 1000 128 N/A Detection
Progression:
Pulse Prog. Axis Parameter Step Dim Unit
Seq 0 B 1 501 Gauss
###############################################################################
Built by autoDEER Version: 0.4_dev
###############################################################################
In [5]:
interface.launch(fsweep,savename="autoDEER_fieldsweep",IFgain=2)
while interface.isrunning():
time.sleep(10)
dataset = interface.acquire_dataset()
fsweep_analysis = ad.FieldSweepAnalysis(dataset)
gyro_exp = fsweep_analysis.calc_gyro(LO)
fsweep_analysis.plot();
Resonator Profile¶
A resonator profile allows us to find the central frequency and optimise the frequency so that most of the spins are inside our ‘dip’.
In [6]:
RPseq = ResonatorProfileSequence(
B=LO/gyro_exp, LO=LO,reptime=2e3,averages=1,shots=200,
pi2_pulse=p90, pi_pulse=p180,
)
print(RPseq)
Output
[6]:
###############################################################################
autoDEER Sequence Definition
###############################################################################
Sequence Parameters:
Name Value Unit Description
B 12182 Gauss The static B0 field for the experiment
LO 34.217 GHz The local oscillator frequency.
reptime 2000 us The shot repetition time
averages 1 None The number of averages to perform.
shots 200 None The number of shots per scan.
det_window 128 None The length of the default detection gate
time 0:13:38 HH:MM:SS Estimated sequence run time
Events (Pulses, Delays, etc...):
iD t (ns) tp (ns) scale type Phase Cycle
0 0 4 1 RectPulse [+(+x)]
1 2000 12 0.14 RectPulse [+(+x) -(-x)]
2 2500 24 0.14 RectPulse [+(+x)]
3 3000 512 N/A Detection
Progression:
Pulse Prog. Axis Parameter Step Dim Unit
0 0 tp 2 33 ns
Seq 1 B 7.1201 31 Gauss
Seq 1 LO 0.02 31 GHz
###############################################################################
Built by autoDEER Version: 0.4_dev
###############################################################################
In [7]:
interface.launch(RPseq, savename="autoDEER-resonator_profile", IFgain=2)
while interface.isrunning():
time.sleep(10)
dataset = interface.acquire_dataset()
respro = ad.ResonatorProfileAnalysis(
nuts = dataset.data.T,
freqs = RPseq.LO.prog[0][1],
dt=2
)
respro.process_nutations(threshold=1)
respro.plot(fieldsweep=fsweep_analysis);
DEER¶
Now we have the necessary setup experiments it is time to start thinking about DEER. A DEER experiment is normally formed from three types of pulses. An excitation π/2 pulse, a refousing π pulse and finally a pump π pulse. There will be a frequency seperation between the excitation pulse and the pump pulse.
In [8]:
exc_pulse = RectPulse(
tp=12, freq=0, flipangle=np.pi/2, scale=0
)
ref_pulse = RectPulse(
tp=12, freq=0, flipangle=np.pi, scale=0
)
pump_pulse = RectPulse(
tp=12, freq=0, flipangle=np.pi, scale=0
)
det_event = Detection(tp=512, freq=0)
In [9]:
fpump,fobs = ad.calc_optimal_deer_frqs(
fsweep_analysis,pump_pulse,exc_pulse,exc_limits=(-0.08,0.025))
exc_pulse.freq.value += fobs
ref_pulse.freq.value += fobs
det_event.freq.value += fobs
pump_pulse.freq.value += fpump
ad.plot_optimal_deer_frqs(fsweep_analysis,pump_pulse,exc_pulse);
In [10]:
p90, p180 = interface.tune_rectpulse(
tp =12, LO=LO+exc_pulse.freq.value, B=LO/gyro_exp, reptime = reptime)
p90.freq.value = exc_pulse.freq.value
p180.freq.value = p90.freq.value
CPseq = CarrPurcellSequence(
B=LO/gyro_exp, LO=LO,reptime=2e3,averages=1,shots=200,
n=2,tau=32e3, pi2_pulse=p90, pi_pulse=p180, det_event=det_event)
print(CPseq)
interface.launch(CPseq, savename="autoDEER-CarrPurcell", IFgain=2)
Output
[10]:
###############################################################################
autoDEER Sequence Definition
###############################################################################
Sequence Parameters:
Name Value Unit Description
B 12182 Gauss The static B0 field for the experiment
LO 34.217 GHz The local oscillator frequency.
reptime 2000 us The shot repetition time
averages 1 None The number of averages to perform.
shots 200 None The number of shots per scan.
det_window 128 None The length of the default detection gate
tau 32000 ns Total sequence length
n 2 None The number of pi pulses
time 0:10:16 HH:MM:SS Estimated sequence run time
Events (Pulses, Delays, etc...):
iD t (ns) tp (ns) scale type Phase Cycle
0 0 12 0.16 RectPulse [+(+x) -(-x)]
1 8000 24 0.16 RectPulse [+(+x)]
2 24000 24 0.16 RectPulse [+(+x)]
3 32000 512 N/A Detection
Progression:
Pulse Prog. Axis Parameter Step Dim Unit
1 0 t 10 770 ns
2 0 t 30 770 ns
3 0 t 40 770 ns
###############################################################################
Built by autoDEER Version: 0.4_dev
###############################################################################
In [11]:
while interface.isrunning():
time.sleep(10)
dataset = interface.acquire_dataset()
dataset.axes[0] = dataset.axes[0]/1e3
CP_data = ad.CarrPurcellAnalysis(dataset)
CP_data.fit()
CP_data.plot();
tau = CP_data.find_optimal(
averages=800,SNR_target=20/0.3, target_time=4,
target_shrt=reptime*1e-6, target_step=0.015)
print(tau)
In [12]:
exc_pulse = p90
ref_pulse = interface.tune_pulse(
ref_pulse, mode="amp_nut", B=LO/gyro_exp, LO=LO, reptime=reptime )
pump_pulse = interface.tune_pulse(
pump_pulse, mode="amp_nut", B=LO/gyro_exp, LO=LO, reptime=reptime )
In [13]:
deer = DEERSequence(
B=LO/gyro_exp, LO=LO,reptime=2e3,averages=30,shots=80,
tau1=tau, tau2=tau, tau3=0.2, dt=15,
exc_pulse=exc_pulse, ref_pulse=ref_pulse,
pump_pulse=pump_pulse, det_event=det_event)
deer.five_pulse()
deer.select_pcyc("16step_5p")
print(deer)
Output
[13]:
###############################################################################
autoDEER Sequence Definition
###############################################################################
Sequence Parameters:
Name Value Unit Description
B 12182 Gauss The static B0 field for the experiment
LO 34.217 GHz The local oscillator frequency.
reptime 2000 us The shot repetition time
averages 30 None The number of averages to perform.
shots 80 None The number of shots per scan.
det_window 128 None The length of the default detection gate
time 6:49:36 HH:MM:SS Estimated sequence run time
Events (Pulses, Delays, etc...):
iD t (ns) tp (ns) scale type Phase Cycle
0 0 12 0.16 RectPulse [+(+x)]
1 2400 12 0.3 RectPulse [+(+x)]
2 2600 12 0.36 RectPulse [+(+x) -(+y) +(-x) -(-y)]
3 2800 12 0.3 RectPulse [+(+x) +(+y) +(-x) +(-y)]
4 7800 12 0.36 RectPulse [+(+x)]
5 10400 512 N/A Detection
Progression:
Pulse Prog. Axis Parameter Step Dim Unit
3 0 t 15 320 ns
###############################################################################
Built by autoDEER Version: 0.4_dev
###############################################################################
In [14]:
interface.launch(deer,savename="autoDEER_4hr",IFgain=2)
interface.terminate_at(
criteria.DEERCriteria(tau1=tau,tau2=tau,tau3=0.2,mode="speed"),verbosity=2)
In [15]:
while interface.isrunning():
time.sleep(10)
dataset = interface.acquire_dataset()
fit,ROI,new_tau = ad.DEERanalysis(
dataset.axes[0]/1000 - tau, dataset.
data, tau, tau, tau3=0.2,
num_points=100, compactness=True, plot=False, precision="speed")
ad.DEERanalysis_plot(fit,background=False,ROI=ROI);
In [16]:
tau = np.around(new_tau/2,1)
deer = DEERSequence(
B=LO/gyro_exp, LO=LO,reptime=2e3,averages=1000,shots=50,
tau1=tau*1e3, tau2=tau*1e3, tau3=0.2*1e3, dt=15,
exc_pulse=exc_pulse, ref_pulse=ref_pulse,
pump_pulse=pump_pulse, det_event=det_event)
deer.five_pulse()
deer.select_pcyc("16step_5p")
print(deer)
Output
[16]:
###############################################################################
autoDEER Sequence Definition
###############################################################################
Sequence Parameters:
Name Value Unit Description
B 12181 Gauss The static B0 field for the experiment
LO 34.217 GHz The local oscillator frequency.
reptime 2000 us The shot repetition time
averages 1000 None The number of averages to perform.
shots 50 None The number of shots per scan.
det_window 128 None The length of the default detection gate
time 332:0:0 HH:MM:SS Estimated sequence run time
Events (Pulses, Delays, etc...):
iD t (ns) tp (ns) scale type Phase Cycle
0 0 12 0.14 RectPulse [+(+x)]
1 5600 12 0.3 RectPulse [+(+x)]
2 5800 12 0.32 RectPulse [+(+x) -(+y) +(-x) -(-y)]
3 6000 12 0.3 RectPulse [+(+x) +(+y) +(-x) +(-y)]
4 17400 12 0.32 RectPulse [+(+x)]
5 23200 512 N/A Detection
Progression:
Pulse Prog. Axis Parameter Step Dim Unit
3 0 t 15 747 ns
###############################################################################
Built by autoDEER Version: 0.4_dev
###############################################################################