Print Page - How to save selfconsistent_configurations for every voltage

Title: How to save selfconsistent_configurations for every voltage
Post by: ATK-user-zuox on January 10, 2016, 11:21

Dear sir:
Recently i tested to restart I-V calculations from a checkpoint . i learned from http://quantumwise.com/forum/index.php?topic=3306.msg15142#msg15142 (http://quantumwise.com/forum/index.php?topic=3306.msg15142#msg15142) andhttp://quantumwise.com/forum/index.php?topic=1358.msg9062#msg9062 (http://quantumwise.com/forum/index.php?topic=1358.msg9062#msg9062) about how to restart a suspended job.i modify the code as

Code

# -------------------------------------------------------------
# IV Curve
# -------------------------------------------------------------
calculator=device_configuration.calculator()

biases = [0.000000, 0.100000, 0.200000, 0.300000, 0.400000, 0.500000,
          0.600000, 0.700000, 0.800000, 0.900000, 1.000000]*Volt
for bias in biases:
    calculator=calculator(
            electrode_voltages=(bias/2, -bias/2))

    device_configuration.setCalculator(
          calculator(),
          initial_state=device_configuration)
    device_configuration.update()
    nlsave("ivcurve_selfconsistent_configurations.nc", device_configuration)
    
#----------------------------------------
# Transmission spectrum
#----------------------------------------
configurations = nlread('ivcurve_selfconsistent_configurations.nc', DeviceConfiguration)
     for device_configuration in configurations:
         transmission_spectrum = TransmissionSpectrum(
             configuration=device_configuration,
             energies=numpy.linspace(-2,2,201)*eV,
             kpoints=MonkhorstPackGrid(4, 4),
             energy_zero_parameter=AverageFermiLevel,
             infinitesimal=1e-06*eV,
             self_energy_calculator=RecursionSelfEnergy(),
             )
         nlsave("TS_analysis.nc", transmission_spectrum)
         nlprint(transmission_spectrum)

.

So here is my idea:
For the initial calculation script(not restaring script) i want to use "nlsave" statement to make a new file for each converged bias and calculate the transmission spectrum for each bias using each converged bias(i want to exactly know output bias file and restart from it ),
my problem is :
How to modify the above code in the I-V and transmission module to realise the these two underlined functions.

Title: Re: How to save selfconsistent_configurations for every voltage
Post by: Jess Wellendorff on January 14, 2016, 09:22

Perhaps this code is what you need:

Code

# -------------------------------------------------------------
# IV Curve
# -------------------------------------------------------------
calculator = device_configuration.calculator()

biases = [0.000000, 0.100000, 0.200000, 0.300000, 0.400000, 0.500000,
          0.600000, 0.700000, 0.800000, 0.900000, 1.000000]*Volt

files = []
for bias in biases:
    myfile = "iv_%.3fV" % bias
    files.append(myfile)
    
    calculator=calculator(
            electrode_voltages=(bias/2, -bias/2))
    device_configuration.setCalculator(
          calculator(),
          initial_state=device_configuration)
    device_configuration.update()
    nlsave(myfile, device_configuration)

#----------------------------------------
# Transmission spectrum
#----------------------------------------
for myfile in files:
    device_configuration = nlread(myfile, DeviceConfiguration)[0]

    transmission_spectrum = TransmissionSpectrum(
        configuration=device_configuration,
        energies=numpy.linspace(-2,2,201)*eV,
        kpoints=MonkhorstPackGrid(4, 4),
        energy_zero_parameter=AverageFermiLevel,
        infinitesimal=1e-06*eV, 
        self_energy_calculator=RecursionSelfEnergy(),
        )
    nlsave(myfile, transmission_spectrum)  
    nlprint(transmission_spectrum)

Title: Re: How to save selfconsistent_configurations for every voltage
Post by: ATK-user-zuox on January 17, 2016, 13:14

Thanks for your kind reply , i whill check it tonight .I have already solved it in another way ,the code is :

Code

# -------------------------------------------------------------
# IV Curve
# -------------------------------------------------------------
calculator=device_configuration.calculator()

biases = [0.000000, 0.100000, 0.200000, 0.300000, 0.400000, 0.500000,
          0.600000, 0.700000, 0.800000, 0.900000, 1.000000]*Volt
for bias in biases:
    calculator=calculator(
            electrode_voltages=(bias/2, -bias/2))

    device_configuration.setCalculator(
          calculator(),
          initial_state=device_configuration)
    device_configuration.update()
    nlsave("ivcurve_selfconsistent_configurations_bias_%g.nc" % bias.inUnitsOf(Volt), device_configuration)
    
#----------------------------------------
# Transmission spectrum
#----------------------------------------
for bias in biases:
    configurations = nlread('ivcurve_selfconsistent_configurations_bias_%g.nc' % bias.inUnitsOf(Volt), DeviceConfiguration)
    for device_configuration in configurations:
           transmission_spectrum = TransmissionSpectrum(
               configuration=device_configuration,
               energies=numpy.linspace(-2,2,201)*eV,
               kpoints=MonkhorstPackGrid(4, 4),
               energy_zero_parameter=AverageFermiLevel,
               infinitesimal=1e-06*eV,
               self_energy_calculator=RecursionSelfEnergy(),
               )
           nlsave("TS_analysis.nc", transmission_spectrum)
           nlprint(transmission_spectrum)

This way to save the checkpoint is very helpful and it's easy to restart from the I-V converged state .Hope it could help the new learnrers.

Title: Re: How to save selfconsistent_configurations for every voltage
Post by: Anders Blom on January 18, 2016, 10:20

That's a really excellent suggestion!!!

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QuantumATK => General Questions and Answers => Topic started by: ATK-user-zuox on January 10, 2016, 11:21