def main():
#main machine
machine = Machine(name='machine', dt=0.00005, pushed=True)
# wave generator
machine.AddCircuit(type='waver', name='wave', amp=1, pushed=True)
machine.AddCircuit(type='RCLP',
name='sklp',
fcut=100,
order=1,
pushed=True)
#amplitude detector for the filter
machine.AddCircuit(type='minmax', name='asklp', CheckTime=0.2, pushed=True)
machine.AddCircuit(type='RCHP',
name='skhp',
fcut=100,
order=1,
pushed=True)
#amplitude detector for the filter
machine.AddCircuit(type='minmax', name='askhp', CheckTime=0.2, pushed=True)
machine.AddCircuit(type='SKBP', name='skbp', fc=100, band=60, pushed=True)
#amplitude detector for the filter
machine.AddCircuit(type='minmax', name='askbp', CheckTime=0.2, pushed=True)
#connect oscillator to the filters
machine.Connect("wave.sin", "sklp.signal", "skhp.signal", "skbp.signal")
machine.Connect("sklp.out", "asklp.signal") #filter -> amplitude detector
machine.Connect("skhp.out", "askhp.signal") #filter -> amplitude detector
machine.Connect("skbp.out", "askbp.signal") #filter -> amplitude detector
#output to file - dump=0 means only manual dump
out1 = machine.AddCircuit(type='output',
name='output',
file='test_filters2.log',
dump=0)
out1.Register('wave.freq', 'asklp.amp', 'askhp.amp', 'askbp.amp')
#set the frequency and relax the filter
freq = 5
machine.SetInput(channel="wave.freq", value=freq)
machine.Wait(1)
while freq < 6000:
#assign the frequency to the oscillator
machine.SetInput(channel="wave.freq", value=freq)
#wait some time to charge the capacitors in the filters
machine.Wait(0.5)
out1.Dump() #output to file
freq *= 1.5 #ramp the frequency
def main():
machine = Machine(machine=None, name='machine', dt=5.0e-8)
# canti = machine.AddCircuit(type='Cantilever',name='canti',
# Q=20000, k=26.4, f0=150000, startingz=1, pushed=True)
A0 = 0.2
canti = machine.AddCircuit(type='Cantilever',
name='canti',
startingz=0.5 * A0,
Q=10000,
k=167.0,
f0=150000,
pushed=True)
#machine.AddCircuit(type='waver',name='wave',freq=150000,amp=1)
#Amplitude stuff: I changed the settings a bit so the noise is less than 1 pm
machine.AddCircuit(type="Machine",
name='amp',
fcut=5000,
assembly=aAMPD,
pushed=True)
machine.AddCircuit(type='PI',
name='agc',
Kp=1.0,
Ki=100,
set=A0,
pushed=True)
machine.AddCircuit(type="limiter",
name='agclim',
min=0,
max=10,
pushed=True)
machine.AddCircuit(type="Machine",
name='pll',
fcut=1000,
assembly=aPLL,
filters=[10000, 5000, 2000],
gain=600.0,
f0=150000,
Kp=0.5,
Ki=700,
pushed=True)
machine.AddCircuit(type='opMul', name='pllinv', in2=-1, pushed=True)
machine.AddCircuit(type='opMul', name='exc', pushed=True)
scanner = machine.AddCircuit(type='Scanner',
name='scan',
Process=machine,
pushed=True)
inter = machine.AddCircuit(type='i3Dlin',
name='inter',
components=3,
pushed=True)
inter.Configure(steps=[0.0705, 0.0705, 0.01],
npoints=[8, 8, 201]) # I converted it back to nN
inter.Configure(pbc=[True, True, False])
inter.Configure(ForceMultiplier=1e9) # I converted it back to nN
inter.ReadData('NaClforces.dat')
#Outputs
out1 = machine.AddCircuit(type='output',
name='output',
file='testafm.out',
dump=2)
out1.Register('global.time', 'canti.zabs', 'amp.norm', 'pll.cos',
'pll.sin', 'exc.in2')
#out1.Register('global.time', 'wave.cos','pll.cos','pll.sin','exc.in2')
out1.Stop()
out2 = machine.AddCircuit(type='output',
name='output2',
file='testafm2.out',
dump=100000)
out2.Register('global.time', 'amp.amp', 'agc.out', 'pll.df', "canti.fz",
'scan.z') #always monitor the amplitude
#Imaging output
imager = machine.AddCircuit(type='output',
name='image',
file='NaCl.dat',
dump=0)
imager.Register("scan.x", "scan.y", "pll.df", "amp.amp")
#feed x and y to interpolation
machine.Connect("scan.x", "inter.x")
machine.Connect("scan.y", "inter.y")
machine.Connect("scan.z", "canti.holderz")
machine.Connect("canti.zabs", "inter.z")
#Force
machine.Connect("inter.F3", "canti.fz")
machine.Connect('canti.ztip', 'amp.signal')
machine.Connect('amp.amp', 'agc.signal')
machine.Connect('amp.norm', 'pll.signal1')
#machine.Connect('wave.cos','pll.signal1')
machine.Connect('pll.cos', 'pll.signal2')
machine.Connect('agc.out', 'agclim.signal')
machine.Connect('agclim.out', 'exc.in1')
machine.Connect('pll.cos', 'pllinv.in1')
machine.Connect('pllinv.out', 'exc.in2')
machine.Connect('exc.out', 'canti.exciter')
machine.Connect("scan.record", "image.record")
'''
machine.Wait(0.01)
out1.Start()
machine.Wait(0.001)
out1.Stop()
machine.Wait(0.05)
out1.Start()
machine.Wait(0.001)
'''
#plot testafm.out 1:3 (canti) 1:4 (pll reference) 1:6 (the exciter)
#u should see 3 distinct waves, canti peaks are in the middle between the other 2
holderstartz = 3 #start at 3nm high
out2.Stop()
scanner.Place(x=0, y=0, z=holderstartz)
machine.Wait(0.1) # prerelaxation we do not want to see in out2
out2.Start()
machine.Wait(
0.5
) #these does not give any visual feedback.... we dont know if the program crashed!
scanner.FastSpeed = 10 # approach faster
#amp is 1nm, to image at a min approach distance of 5 angs,
#we need to approach by 15nm-amp-0.5nm
scanner.Move(x=0, y=0, z=-(holderstartz - A0 - 0.5))
machine.Wait(1)
machine.SetInput(channel="output.record", value=1)
scanner.Recorder = imager
scanner.BlankLines = True
#resolution of the image [# points per line, # lines]
scanner.Resolution = [512, 512]
scanner.ImageArea(1.128, 1.128)
scanner.FastSpeed = 10
scanner.SlowSpeed = 10
#scan
scanner.ScanArea()
Ampgain=2,
assembly=LockInAmp,
pushed=True)
#canti = machine.AddCircuit(type='Cantilever',name='canti', startingz=Az, Q=Q, k=k, f0=f0, pushed=True)
machine.AddCircuit(type='minmax', name='amp', CheckTime=1e-5)
machine.AddCircuit(type='waver', name='WaveGen', freq=f0, amp=1, pushed=True)
machine.AddCircuit(type='opAdd', name='summer', in2=0)
machine.Connect('WaveGen.cos', 'LockInAmp.Signal')
#machine.Connect('LockInAmp.RefWave','canti.exciter')
#machine.Connect('canti.ztip','amp.signal')
machine.Connect('summer.out', 'LockInAmp.CentFreq')
out1 = machine.AddCircuit(type='output',
name='output',
file='LockInTest.dat',
dump=0)
#out1.Register('global.time','canti.ztip','LockInAmp.RefWave','LockInAmp.Amp','LockInAmp.Phase','amp.amp','summer.out')
out1.Register('summer.out', 'LockInAmp.Amp')
freq = f0 - 1000
while freq < (f0 + 1000):
machine.SetInput(channel="summer.in1", value=freq)
machine.Wait(0.1)
out1.Dump()
freq += 100
