Creating a Custom Sequence

autoEPR can be used to script and develop EPR pulse sequences in Python.

Pulse sequences are built up of two main object: Sequences and Pulses. In its simplest form, a pulse sequence is just a train of pulses. Here, we consider a pulse in its general form. I.e. Pulses are not just MW pulses but also delays and detection events.

A sequence also contains additional information about the experiment, such as: the LO frequency; the B0 field; Averages and shots; and the shot repetition time.

There are two ways of thinking about and writing down a pulse sequence:

  1. Delay-focused (Like PulseSpel)

  2. Pulse-focused (Like Tables)

When many EPR spectrometrists think about pulse sequences they think of pulses separated by delays, and these delays increase and decrease in length to change the position of the pulses. However, most AWGs and spectrometers think in terms of pulses with a time position and it is this time position that moves. Both of these approaches are physically equivalent, and both approaches can be used in autoEPR. However, most interfaces can only take sequences of one type. Sequences can be converted between each other with the Sequence.convert() command.

Creating your first sequence

Here I will demonstrate how to build a simple Hahn Echo sequence using rectangular pulses.

import autodeer as ad
import numpy as np
from autodeer import Sequence, RectPulse, Detection
HahnEcho = Sequence(
    name="Hahn Echo", B=12220, LO=34.0,reptime=3e3,
    averages=1, shots=100
    )
HahnEcho.addPulse(RectPulse(t=0, tp=16, freq=0, flipangle=np.pi/2))
HahnEcho.addPulse(RectPulse(t=200, tp=32, freq=0, flipangle=np.pi))
HahnEcho.addPulse(Detection(t=400, tp=32))

This sequece can also be created using delays.

import autodeer as ad
import numpy as np
from autodeer import Sequence, RectPulse, Delay, Detection
HahnEcho = Sequence(
    name="Hahn Echo", B=12220, LO=34.0,reptime=3e3,
    averages=1, shots=100
    )
HahnEcho.addPulse(RectPulse(tp=16, freq=0, flipangle=np.pi/2))
HahnEcho.addPulse(Delay(tp=200))
HahnEcho.addPulse(RectPulse(tp=32, freq=0, flipangle=np.pi))
HahnEcho.addPulse(Delay(tp=200))
HahnEcho.addPulse(Detection(tp=32))

Adding Progression

A single static echo is only of limited use. To make a pulse move we need to add a progressive axis. In this example, we will increase the delays of the above sequence from 200ns to 6us in 100ns steps.

HahnEcho.addPulsesProg(
    pulses=[1,3],
    variables=["tp","tp"]
    axis_id = 0,
    axis = np.arange(2e2,6e3,100)
    multipliers = [1,1]
    )

Adding Phase Cycles

In nearly all EPR pulse sequences a phase cycle is required to remove additional unwanted echoes and coherence pathways. This is possible in autoEPR without having to multiply out the full cycle, by adding the phase cycle individually to each pulse.

This is done by adding an extra dictionary to the pulse declaration. This dictionary consists of two lists: phases (“phases”), detection signs(“dets”).

For example, if we wanted to add the standard DC offset cycle on the first pi/2 pulse we can simply do.

HahnEcho.addPulse(RectPulse(
    tp=16, freq=0, flipangle=np.pi/2,
    pcyc={"phases":[0, np.pi], "dets":[1, -1]}))

Viewing the sequence

The simplist way to look at a pulse sequence is to print it. Printing a Sequence will generate a table containing all the import paramaters and infomation.

print(HahnEcho)

Standard Sequences

Since a Hahn Echo is such a standard sequence it comes pre-built as HahnEchoSequence. A full list of standard sequences can be found here

Using Shaped and Chirped pulses

So far we have only looked at monochromatic rectangular pulses. It is often advantageous to use wideband-shaped and chirped pulses. Chirped pulses allow for a wider excitation bandwidth at a lower power level, and shaped pulse is used to reduce excitation side-lobes.

Many standard pulses are included, however, custom pulses can also be created. A full list of standard pulses can be found here

Chirped pulses

The simplest type of chirped pulse is a linear chip and it is implemented in the:ref:ChirpPulse <ChirpPulse> method. ChirpPulse requires the parameters as RectPulse when being declared as well as two frequency parameters. Options: Bandwidth: BW; Initial Frequency init_freq; Final Frequency final_freq.

from autodeer import *
test_pulse = ChirpPulse(
    tp = 128, init_freq = -0.1, BW=0.2,
    flipangle = np.pi
    )

Just like with Sequences, Pulses can also be printed to get a table of the import infomation.

print(test_pulse)

Custom pulses

Unlike when making custom sequences it is not recommended that you use an an instance of the class, instead it is recommended that create a new class which inherits from the class Pulse.

All pulses have the attributes AM and FM which describe their shape and frequency dependencies. The recommended way of creating these is to create a function called func and build AM and FM for this specific pulse length. For a rectangular pulse this is simply:

def func(self, ax):
    nx = ax.shape[0]
    AM = np.ones(nx)
    FM = np.zeros(nx)
    return AM, FM

from autodeer import Pulse
class new_pulse(Pulse):

    # First we need to create the class init statment
    def __init__(
    self, tp, freq, t=None, flipangle=None, pcyc=[0],
    name=None) -> None:
    # Next we need to fill the parent-class with its infomation.
    Pulse.__init__(
    self, tp=tp, t=t, flipangle=flipangle, pcyc=pcyc, name=name)
    # All non standard parameters are now declared
    self.freq = Parameter("freq", freq, "GHz", "Frequency of the Pulse")
    self.Progression = False
    # Here we build the FM and AM using our custom function.
    self._buildFMAM(self.func)
    pass

    # Here we define the custom function.
    def func(self, ax):
    nx = ax.shape[0]
    AM = np.ones(nx)
    FM = np.zeros(nx)
    return AM, FM

What is not currently supported?

  1. RF pulses (No ENDOR or DNP)