I don't think the method in post is going to help in the case of example as it is run in manual/direct mode rather than in firmware. In manual/direct mode the every time the output voltage is changed and the current is sampled, as the test is run, requires USB/serial communication with the host PC. In this manner the schedule for the waveform output is running PC side and the voltage is set using set_volt and the current is sample using the get_curr methods. So each sample requires two USB/Serial command/response pairs - one to set_volt and one to get_curr.. Each of these commands take some time to complete. Because of this tests run in manual /direct mode cannot achieve as high a sample rate as those implemented in firmware and run using the 'run_test' method. Unfortunately, at this time, there isn't an AC voltammetry test implement in the firmware. That said even if it was implemented in firmware the maximum sample rate would be about 1000Hz with the stock firmware - and you might be able to achieve up to around 10kHz for very short bursts with the firmware modifications in post.
Regarding the manual/direct mode AC voltammetry test you are running I'm not quite sure what is happening. I'm not able to replicate this myself - I'm guessing it might be something specific to your system. That said this manual/direct mode test can't achieve very high sample rates as the 'set_volt' and 'get_curr' method calls take some time to complete. So as you lower dt more and more eventually the actually time taken per sample will plateau as it is dominated by the time required for the 'set_volt' and 'get_curr' method calls.
One thing that is useful to look to help diagnose the timing of manual/direct mode test is the time difference between samples. You can get this by converting the list of samples returned to an array an then looking at the consecutive differences e.g.
t = scipy.array(t)
dt = scipy.diff(t)
plt.plot(t[1:], dt)
This is what I get for dt = 0.05 and dt = 0.005
and
Note, that in when dt parameter is set to 0.005 the measured "actual' dt between time steps much more erratic and has a median value of only 0.0143. this is due to the fact that the sampling time is being dominated by the time required for the 'set_volt' and 'get_curr' calls.
I've also attached the modified AC voltammetry script I used for generating these plots.
from __future__ import print_function
from potentiostat import Potentiostat
import time
import sched
import math
import scipy
import matplotlib.pyplot as plt
def run_manual_test(pstat, volt_func, dt, t_stop):
"""
Run a voltammetric test in maunal/direct mode.
pstat = potentiostat
volt_func = output voltage function
dt = sample time step
t_stop = duration of the trial
"""
t = 0
cnt = 0
t_start = time.time()
time_list, volt_list, curr_list = [], [], []
scheduler = sched.scheduler(time.time, time.sleep)
while t < t_stop:
# Set potentiostat output voltage and samle current
volt = volt_func(t)
pstat.set_volt(volt)
curr = pstat.get_curr()
print('{0:1.2f}, {1:1.2f}, {2:1.2f}'.format(t, volt, curr))
time_list.append(t)
volt_list.append(volt)
curr_list.append(curr)
# Run scheduler to until time for the next sample (dt seconds)
t_next = t_start + (cnt+1)*dt
scheduler.enterabs(t_next, 1, lambda:None, ())
scheduler.run()
t = time.time() - t_start
cnt+=1
return time_list, volt_list, curr_list
def create_sin_linear_func(t0, t1, v0, v1, amp, per):
"""
Returns a function which in the interval [t0,t1] is a sum of linear
function and a sine wave.
t0 = time at which linear transition, from v0 to v1, begins
t1 = time at which linear transition, from v0 to v1, ends
v0 = initial value
v1 = final value
amp = amplitude of superimposed sinewave
per = period on superimposed sinewave
"""
def func(t):
if t < t0:
return v0
elif t < t1:
dt_trans = t1-t0
v_lin = (v1-v0)*(t-t0)/dt_trans + v0
v_sin = amp*math.sin(2*math.pi*(t-t1)/per)
return v_lin + v_sin
else:
return v1
return func
if __name__ == '__main__':
# Run parameters
t0 = 0.0 # Transition start time (s)
t1 = 8.0 # Transition stop time (s)
v0 = -0.1 # Initial voltage (V)
v1 = -0.9 # Final voltage (V)
amp = 0.1 # Sinusoid ampliude (V)
per = 0.5 # Sinusoid period (s)
dt = 0.05 # Time step for setting voltage and measurements
t_total = t0 + t1 # Total experiment duration
volt_func = create_sin_linear_func(t0,t1,v0,v1,amp,per)
# Create device object, set voltage/current ranges and run test
pstat = Potentiostat('/dev/ttyACM0')
pstat.set_volt_range('2V')
pstat.set_curr_range('100uA')
t, volt, curr = run_manual_test(pstat, volt_func, dt, t_total)
t_array = scipy.array(t)
dt_array = scipy.diff(t)
dt_median = scipy.median(dt_array)
print('median dt: {}'.format(dt_median))
# Plot results
plt.figure()
plt.subplot(311)
plt.plot(t,volt)
plt.ylabel('potential (V)')
plt.title('param dt = {:0.3}, median actual dt = {:0.4}'.format(dt,dt_median))
plt.grid(True)
plt.subplot(312)
plt.plot(t,curr)
plt.xlabel('time (s)')
plt.ylabel('current (uA)')
plt.grid(True)
plt.subplot(313)
plt.plot(t,curr)
plt.plot(t_array[1:], dt_array)
plt.grid(True)
plt.xlabel('time (s)')
plt.ylabel(r'$\Delta t$ (s)')
plt.ylim(0.0, dt_array.max()*(1 + 0.1))
plt.show()
