I have calculated the potential difference between two atomic centres and transmission spectrum for different bias using the following script:
# -------------------------------------------------------------
# Transmission spectrum
# -------------------------------------------------------------
def transmission(configuration):
# Calculate the transmission spectrum and save it in a file
transmission_spectrum = TransmissionSpectrum(
configuration=device_configuration,
energies=numpy.linspace(-3,3,200)*eV,
kpoints=MonkhorstPackGrid(1,1),
energy_zero_parameter=AverageFermiLevel,
infinitesimal=1e-06*eV,
self_energy_calculator=KrylovSelfEnergy(),
)
nlsave('/home/swapanchem/Desktop/Fe-Fe-complex/fefe-ls-dz/fefe-ls-loop-transmission-iv.nc', transmission_spectrum)
# Read in the converged zero-bias calculation
device_configuration = nlread('/home/swapanchem/Desktop/Fe-Fe-complex/fefe-ls-dz/fefe-ls-loop-iv.nc', DeviceConfiguration)[0]
calculator = device_configuration.calculator()
# Calculate and save the transmission spectrum for zero bias
transmission(device_configuration)
# Define the bias voltages for the I-V curve
voltage_list=[0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5,-0.1,-0.15,-0.2,-0.25,-0.3,-0.35,-0.4,-0.45,-0.5,]*Volt
# Loop over the bias voltages
for voltage in voltage_list:
# Set electrode voltages and use the self-consistent state
# of the previous calculation as starting guess
device_configuration.setCalculator(
calculator(electrode_voltages=(voltage, 0.0*Volt)),
initial_state=device_configuration)
# Calculate and save the transmission spectrum for each bias
transmission(device_configuration)
# -------------------------------------------------------------
# Effective potential
# -------------------------------------------------------------
def EfffectivePotential(configuration):
# Calculate the transmission spectrum and save it in a file
effective_potential = EffectivePotential(
configuration=device_configuration,
)
nlsave('fefe-ls-loop-pd.nc', effective_potential)
# Read in the converged zero-bias calculation
device_configuration = nlread('fefe-ls-loop-iv.nc', DeviceConfiguration)[0]
calculator = device_configuration.calculator()
# Calculate and save the Electrostatic difference potential for zero bias
EfffectivePotential(device_configuration)
# Define the bias voltages for the I-V curve
voltage_list=[0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5,-0.1,-0.15,-0.2,-0.25,-0.3,-0.35,-0.4,-0.45,-0.5,]*Volt
# Loop over the bias voltages
for voltage in voltage_list:
# Set electrode voltages and use the self-consistent state
# of the previous calculation as starting guess
device_configuration.setCalculator(
calculator(electrode_voltages=(voltage, 0.0*Volt)),
initial_state=device_configuration)
# Calculate and save the esdp for each bias
EfffectivePotential(device_configuration)
Now I want to extract the value of potential drop between the two centres at different bias. I know how to calculate the said potential difference at a single bias. For this I uses the following script:
echo "pot = nlread('ti2c66-fm-epot1v-1v.nc', EffectivePotential)[0]
p1 = pot.evaluate(2.07218823*Ang,3.57884614*Ang,13.28806914*Ang)
p2 = pot.evaluate(2.38069829*Ang,3.55537652*Ang,22.30382852*Ang)
print p1
print p2
print (p2-p1)*27.2" > pot-ti2c66-fm-epot1v-1v.py
atkpython pot-ti2c66-fm-epot1v-1v.py > pot-ti2c66-fm-epot1v-1v.out
Now my question is how to extract the value of potential difference from a single netcdf file where it has been calculated for different biases in a loop. kindly help me to sort out this problem.
