Author Topic: Why I-V calculation dead? (Read 3054 times)

Pagani · « **on:** November 24, 2012, 12:04 »

I calculate the I-V curves of a two-probe system according to the mini script "Molecular device" on the quantumwise Web. But the calculation of transmission spectra at the first cycle is dead. Why? Is there anybody met the same situation?
How to solve this problem?

zh · « **Reply #1 on:** November 27, 2012, 01:59 »

please post your script file and the error message.

Pagani · « **Reply #2 on:** November 27, 2012, 13:31 »

The script I used is:

# -------------------------------------------------------------
# TwoProbe configuration
# -------------------------------------------------------------

# -------------------------------------------------------------
# Left electrode
# -------------------------------------------------------------

# Set up lattice
vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom
vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom
vector_c = [0.0, 0.0, 7.06373620597]*Angstrom
left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
left_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold]

# Define coordinates
left_electrode_coordinates = [[ 0.72107876, 1.24846289, 1.17728937],
[ 3.60483699, 1.24846289, 1.17728937],
[ 6.48859522, 1.24846289, 1.17728937],
[-0.72080035, 3.74587078, 1.17728937],
[ 5.04671611, 3.74587078, 1.17728937],
[ 2.16295788, 3.74587078, 1.17728937],
[ 3.60483699, 6.24327867, 1.17728937],
[-2.16267947, 6.24327867, 1.17728937],
[ 0.72107876, 6.24327867, 1.17728937],
[ 2.16295788, 2.08093219, 3.5318681 ],
[-0.72080035, 2.08093219, 3.5318681 ],
[ 5.04671611, 2.08093219, 3.5318681 ],
[-3.60455858, 7.07574796, 3.5318681 ],
[-2.16267947, 4.57834008, 3.5318681 ],
[ 2.16295788, 7.07574796, 3.5318681 ],
[ 3.60483699, 4.57834008, 3.5318681 ],
[ 0.72107876, 4.57834008, 3.5318681 ],
[-0.72080035, 7.07574796, 3.5318681 ],
[ 7.93047434, 0.4159936 , 5.88644684],
[ 0.72107876, 2.91340148, 5.88644684],
[ 2.16295788, 5.41080937, 5.88644684],
[-0.72080035, 5.41080937, 5.88644684],
[ 5.04671611, 5.41080937, 5.88644684],
[ 2.16295788, 0.4159936 , 5.88644684],
[ 3.60483699, 2.91340148, 5.88644684],
[ 5.04671611, 0.4159936 , 5.88644684],
[ 6.48859522, 2.91340148, 5.88644684]]*Angstrom

# Set up configuration
left_electrode = BulkConfiguration(
bravais_lattice=left_electrode_lattice,
elements=left_electrode_elements,
cartesian_coordinates=left_electrode_coordinates
)

# -------------------------------------------------------------
# Right electrode
# -------------------------------------------------------------

# Set up lattice
vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom
vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom
vector_c = [0.0, 0.0, 7.06373620597]*Angstrom
right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
right_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold]

# Define coordinates
right_electrode_coordinates = [[ 0.72080035, 4.57882217, 1.17728937],
[-0.72107876, 7.07623006, 1.17728937],
[ 2.16267947, 7.07623006, 1.17728937],
[-2.16295788, 4.57882217, 1.17728937],
[-0.72107876, 2.08141429, 1.17728937],
[ 3.60455858, 4.57882217, 1.17728937],
[-3.60483699, 7.07623006, 1.17728937],
[ 5.0464377 , 2.08141429, 1.17728937],
[ 2.16267947, 2.08141429, 1.17728937],
[ 7.93019593, 0.4164757 , 3.5318681 ],
[ 3.60455858, 2.91388358, 3.5318681 ],
[ 6.48831681, 2.91388358, 3.5318681 ],
[ 2.16267947, 5.41129147, 3.5318681 ],
[ 5.0464377 , 0.4164757 , 3.5318681 ],
[ 5.0464377 , 5.41129147, 3.5318681 ],
[-0.72107876, 5.41129147, 3.5318681 ],
[ 0.72080035, 2.91388358, 3.5318681 ],
[ 2.16267947, 0.4164757 , 3.5318681 ],
[ 2.16267947, 3.74635288, 5.88644684],
[-2.16295788, 6.24376076, 5.88644684],
[ 0.72080035, 6.24376076, 5.88644684],
[-0.72107876, 3.74635288, 5.88644684],
[ 6.48831681, 1.24894499, 5.88644684],
[ 0.72080035, 1.24894499, 5.88644684],
[ 5.0464377 , 3.74635288, 5.88644684],
[ 3.60455858, 1.24894499, 5.88644684],
[ 3.60455858, 6.24376076, 5.88644684]]*Angstrom

# Set up configuration
right_electrode = BulkConfiguration(
bravais_lattice=right_electrode_lattice,
elements=right_electrode_elements,
cartesian_coordinates=right_electrode_coordinates
)

# -------------------------------------------------------------
# Central region
# -------------------------------------------------------------

# Set up lattice
vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom
vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom
vector_c = [0.0, 0.0, 21.4537368239]*Angstrom
central_region_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
central_region_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold, Nitrogen, Carbon,
Hydrogen, Hydrogen, Carbon, Carbon, Carbon, Carbon, Hydrogen,
Hydrogen, Carbon, Nitrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold]

# Define coordinates
central_region_coordinates = [[ 0.72107876, 1.24846289, 1.17728937],
[ 3.60483699, 1.24846289, 1.17728937],
[ 6.48859522, 1.24846289, 1.17728937],
[ -0.72080035, 3.74587078, 1.17728937],
[ 5.04671611, 3.74587078, 1.17728937],
[ 2.16295788, 3.74587078, 1.17728937],
[ 3.60483699, 6.24327867, 1.17728937],
[ -2.16267947, 6.24327867, 1.17728937],
[ 0.72107876, 6.24327867, 1.17728937],
[ 2.16295788, 2.08093219, 3.5318681 ],
[ -0.72080035, 2.08093219, 3.5318681 ],
[ 5.04671611, 2.08093219, 3.5318681 ],
[ -3.60455858, 7.07574796, 3.5318681 ],
[ -2.16267947, 4.57834008, 3.5318681 ],
[ 2.16295788, 7.07574796, 3.5318681 ],
[ 3.60483699, 4.57834008, 3.5318681 ],
[ 0.72107876, 4.57834008, 3.5318681 ],
[ -0.72080035, 7.07574796, 3.5318681 ],
[ 7.93047434, 0.4159936 , 5.88644684],
[ 0.72107876, 2.91340148, 5.88644684],
[ 2.16295788, 5.41080937, 5.88644684],
[ -0.72080035, 5.41080937, 5.88644684],
[ 5.04671611, 5.41080937, 5.88644684],
[ 2.16295788, 0.4159936 , 5.88644684],
[ 3.60483699, 2.91340148, 5.88644684],
[ 5.04671611, 0.4159936 , 5.88644684],
[ 6.48859522, 2.91340148, 5.88644684],
[ 2.16296 , 3.74587 , 7.88344 ],
[ 2.16296 , 3.74587 , 9.32715 ],
[ 1.07985 , 5.62137 , 9.47628 ],
[ 3.24595 , 1.87058 , 9.47677 ],
[ 1.55661 , 4.79582 , 10.02683 ],
[ 2.76905 , 2.69637 , 10.02705 ],
[ 1.55659 , 4.79585 , 11.42669 ],
[ 2.76903 , 2.69641 , 11.42691 ],
[ 1.07969 , 5.62165 , 11.97696 ],
[ 3.24579 , 1.87085 , 11.97746 ],
[ 2.16268 , 3.74635 , 12.12659 ],
[ 2.16268 , 3.74635 , 13.5703 ],
[ 2.97945788, 4.21687078, 7.54944143],
[ 1.34645788, 4.21687078, 7.54944143],
[ 2.97945788, 3.27487078, 13.9043 ],
[ 1.34645788, 4.21687078, 13.9043 ],
[ 0.72080035, 4.57882217, 15.56729 ],
[ -0.72107876, 7.07623006, 15.56729 ],
[ 2.16267947, 7.07623006, 15.56729 ],
[ -2.16295788, 4.57882217, 15.56729 ],
[ -0.72107876, 2.08141429, 15.56729 ],
[ 3.60455858, 4.57882217, 15.56729 ],
[ -3.60483699, 7.07623006, 15.56729 ],
[ 5.0464377 , 2.08141429, 15.56729 ],
[ 2.16267947, 2.08141429, 15.56729 ],
[ 7.93019593, 0.4164757 , 17.92186873],
[ 3.60455858, 2.91388358, 17.92186873],
[ 6.48831681, 2.91388358, 17.92186873],
[ 2.16267947, 5.41129147, 17.92186873],
[ 5.0464377 , 0.4164757 , 17.92186873],
[ 5.0464377 , 5.41129147, 17.92186873],
[ -0.72107876, 5.41129147, 17.92186873],
[ 0.72080035, 2.91388358, 17.92186873],
[ 2.16267947, 0.4164757 , 17.92186873],
[ 2.16267947, 3.74635288, 20.27644746],
[ -2.16295788, 6.24376076, 20.27644746],
[ 0.72080035, 6.24376076, 20.27644746],
[ -0.72107876, 3.74635288, 20.27644746],
[ 6.48831681, 1.24894499, 20.27644746],
[ 0.72080035, 1.24894499, 20.27644746],
[ 5.0464377 , 3.74635288, 20.27644746],
[ 3.60455858, 1.24894499, 20.27644746],
[ 3.60455858, 6.24376076, 20.27644746]]*Angstrom

# Set up configuration
central_region = BulkConfiguration(
bravais_lattice=central_region_lattice,
elements=central_region_elements,
cartesian_coordinates=central_region_coordinates
)

device_configuration = DeviceConfiguration(
central_region,
[left_electrode, right_electrode]
)

calculator = device_configuration.calculator()

# Define bias voltages
voltage_list= 0.2 *numpy.arange(1,16)*Volt
#make loop
for voltage in voltage_list:
# Set new calculator with modified electrode voltages on the configuration
# use the self consistent state of the old calculation as starting input.
device_configuration.setCalculator(
calculator(electrode_voltages=(-0.5*voltage, 0.5*voltage)),
initial_state=device_configuration)

# Calculate the transmission spectrum
transmission_spectrum = TransmissionSpectrum(
configuration=device_configuration,
energies=numpy.linspace(-3,3,100)*eV,
kpoints=MonkhorstPackGrid(3,3),
)

#save the results
nlsave('au_dtb_au.nc', device_configuration)
nlsave('au_dtb_au.nc', transmission_spectrum)

The question is the first cycle of the calculation died! Why? I wrote it following the mini tutorial of "molecular device". Oh, the Version of my ATK is 11.2.2.

kstokbro · « **Reply #3 on:** December 2, 2012, 22:28 »

You need to define a calculator and attach it to the configuration, i.e.
device_configuration = DeviceConfiguration(
central_region,
[left_electrode, right_electrode]
)

calculator = DeviceLCAOCalculator()
device_configuration.setCalculator(calculator)

I recommend that you setup your 0 bias calculation using VNL and then follow:
http://www.quantumwise.com/publications/tutorials/mini-tutorials/98-i-v-curve-and-voltage-drop

QuantumATK Forum

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Author Topic: Why I-V calculation dead? (Read 3054 times)

Pagani

Why I-V calculation dead?

zh

Re: Why I-V calculation dead?

Pagani

Re: Why I-V calculation dead?

kstokbro

Re: Why I-V calculation dead?