31
General Questions and Answers / error in GUI
« on: May 31, 2014, 10:01 »The GUI is suddenly stopped with following error
line 8: 25422 Segmentation fault (core dumped) $EXEC_DIR/vnl_exec $*
Kindly help me.
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The GUI is suddenly stopped with following error
line 8: 25422 Segmentation fault (core dumped) $EXEC_DIR/vnl_exec $*
Kindly help me.
32
General Questions and Answers / erro while creating a two-probe geometry with GUI
« on: April 14, 2014, 10:31 »
When tried to attach a molecule (from builder section) to molecular junction part the gui shows following error
Traceback (most recent call last):
File "./zipdir/NL/GUI/Core/Runner.py", line 230, in run
File "./zipdir/NL/GUI/Tools/CustomBuilder/Builders/MolecularJunction.py", line 152, in configuration
IndexError: index out of bounds
Kindly help me sorting out this issue.
Sabyasachi Sen
Traceback (most recent call last):
File "./zipdir/NL/GUI/Core/Runner.py", line 230, in run
File "./zipdir/NL/GUI/Tools/CustomBuilder/Builders/MolecularJunction.py", line 152, in configuration
IndexError: index out of bounds
Kindly help me sorting out this issue.
Sabyasachi Sen
33
General Questions and Answers / electron transfer rate from electrode to the molecule
« on: October 18, 2013, 08:21 »
Kindly suggest me, how electron transfer rate from a specific electrode to the molecule (usually denoted as gamma) is obtained using ATK?
34
General Questions and Answers / increasing layers in the electrode part of the central region
« on: October 4, 2013, 12:50 »
During transport calculation through a two-probe system, such as, Au(111)-molecule-Au(111); number of Au atomic layer is three in the central region. Is it possible to increase the number of layers in electrode part of the central region. If possible, kindly intimate me the related keyword/script to be use.
35
General Questions and Answers / Iteration control parameters not effective to remove a convergence problem
« on: January 12, 2013, 07:50 »
Dear ATK Forum
I attach herewith an input file where iteartion control parametrs have been included. The output is too large to be attached.
Sabyasachi Sen
I attach herewith an input file where iteartion control parametrs have been included. The output is too large to be attached.
Sabyasachi Sen
36
General Questions and Answers / Assigning spin-polarization of magnetic electrode when molecule is nonmagnetic
« on: January 10, 2013, 18:01 »
Dear ATK Forum
In a spin-polarized transport calculations involving magnetic electrode (e.g Nickel electrode) and a non-magnetic molecule placed between the two electrodes how can I assign the spin-polarization of the electrode keeping one of the electrode in spin-up state and the other one in spin-down state.
Sabyasachi Sen
In a spin-polarized transport calculations involving magnetic electrode (e.g Nickel electrode) and a non-magnetic molecule placed between the two electrodes how can I assign the spin-polarization of the electrode keeping one of the electrode in spin-up state and the other one in spin-down state.
Sabyasachi Sen
37
General Questions and Answers / change in Iteration Control Settings not become effective in convergence problem
« on: January 10, 2013, 07:18 »
Dear ATK Forum
In a calculation with
Warning: The calculation did not converge to the requested tolerance
I have tried to use Iteration Control Settings as mentioned below but the same is not affecting the output.
Number of iterations has been increased to 200 but still the scf stops after the 100th cycle. Tolerance value has been lowered to 0.001 but the same is not affecting the run it is showing similar warning message.
Kindly help me in sorting out this issue.
Sabysachi Sen
In a calculation with
Warning: The calculation did not converge to the requested tolerance
I have tried to use Iteration Control Settings as mentioned below but the same is not affecting the output.
Number of iterations has been increased to 200 but still the scf stops after the 100th cycle. Tolerance value has been lowered to 0.001 but the same is not affecting the run it is showing similar warning message.
Kindly help me in sorting out this issue.
Sabysachi Sen
38
General Questions and Answers / the script is not working
« on: December 22, 2012, 08:56 »
if I write a script with following lines for getting spin polarized current for a series of bias(using single .nc file,
t_list = nlread('myfile.nc', TransmissionSpectrum)
for t in t_list:
print t.bias(), t.current(Spin.Up), t.current(Spin.Down)
then we are getting the following errors.
Traceback (most recent call last):
File "/tmp/2852876685689547.py", line 5, in <module>
print t.bias(),t.current(Spin.Up),t.current(Spin.Down)
File "./zipdir/NL/Analysis/TransmissionSpectrum.py", line 368, in current
File "./zipdir/NL/Analysis/TransmissionSpectrum.py", line 816, in checkElectrodeVoltages
NL.ComputerScienceUtilities.Exceptions.NLValueError: The electrode voltages must be given as two physical quantities with the unit Volt.
Please help us resolve the issue.
t_list = nlread('myfile.nc', TransmissionSpectrum)
for t in t_list:
print t.bias(), t.current(Spin.Up), t.current(Spin.Down)
then we are getting the following errors.
Traceback (most recent call last):
File "/tmp/2852876685689547.py", line 5, in <module>
print t.bias(),t.current(Spin.Up),t.current(Spin.Down)
File "./zipdir/NL/Analysis/TransmissionSpectrum.py", line 368, in current
File "./zipdir/NL/Analysis/TransmissionSpectrum.py", line 816, in checkElectrodeVoltages
NL.ComputerScienceUtilities.Exceptions.NLValueError: The electrode voltages must be given as two physical quantities with the unit Volt.
Please help us resolve the issue.
39
General Questions and Answers / current calculation in a loop
« on: December 1, 2012, 20:13 »
I am facing problems in estimating iv curve for certain values of applied by ruining the calculation over a loop. In the script I added following lines at the end of zero bias calculation but the program does not run at a loop.
The program does not run at all kindly hep me in sorting out this problem.
The script is
# -------------------------------------------------------------
# Transmission spectrum
# -------------------------------------------------------------
def transmission(configuration):
# Calculate the transmission spectrum and save it in a file
transmission_spectrum = TransmissionSpectrum(
configuration=device_configuration,
energies=numpy.linspace(-3,3,50)*eV,
)
nlsave('/home/swapanchem/Desktop/lih2-loop/li-h2_iv.nc', transmission_spectrum)
# Read in the converged zero-bias calculation
device_configuration = nlread('/home/swapanchem/Desktop/lih2-loop/lih2-loop1.nc', device_configuration)[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=[0.5,1.0]*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)),
initial_state=device_configuration)
# Calculate and save the transmission spectrum for each bias
transmission(device_configuration)
.
The program does not run at all kindly hep me in sorting out this problem.
The script is
# -------------------------------------------------------------
# Transmission spectrum
# -------------------------------------------------------------
def transmission(configuration):
# Calculate the transmission spectrum and save it in a file
transmission_spectrum = TransmissionSpectrum(
configuration=device_configuration,
energies=numpy.linspace(-3,3,50)*eV,
)
nlsave('/home/swapanchem/Desktop/lih2-loop/li-h2_iv.nc', transmission_spectrum)
# Read in the converged zero-bias calculation
device_configuration = nlread('/home/swapanchem/Desktop/lih2-loop/lih2-loop1.nc', device_configuration)[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=[0.5,1.0]*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)),
initial_state=device_configuration)
# Calculate and save the transmission spectrum for each bias
transmission(device_configuration)
.
40
General Questions and Answers / how to know current of both spin channels in vnl analyzer
« on: August 28, 2012, 19:34 »
When the analyzer window of vnl is used to estimate the current (I-V) of a spin polarized calculation we are getting only one value of current. Kindly highlight me how could I get the numeric value of spin polarized current of both spin channels in a spin polarized twoprobe run.
Sabyasachi Sen
Sabyasachi Sen
41
General Questions and Answers / numeric value of electrostatic difference potential
« on: August 28, 2012, 19:31 »
i) In electrostatic difference potential plot colored contour plot does not produce exact numeric value on a specific atom. Can you suggest any modification in python script which will give us the numeric value of the electrostatic potential difference between any two atom of choice.
ii) In a calculation with Au electrode-Central region-Au electrode run I noticed that Fermi energy of Au electrodes (both left and right) with LSDA functional and SZ basis is -0.74 eV while the same for the central region considering equivalent bulk as -4.0 eV. However, in transmission run Femi energy is shifted to zero as per the energy of the electrodes. Since, there is a huge difference in Fermi energy between the central region and the electrodes. Could you please clarify what is the importance of the Fermi energy of central region? or How does it influences the transport run.
ii) In a calculation with Au electrode-Central region-Au electrode run I noticed that Fermi energy of Au electrodes (both left and right) with LSDA functional and SZ basis is -0.74 eV while the same for the central region considering equivalent bulk as -4.0 eV. However, in transmission run Femi energy is shifted to zero as per the energy of the electrodes. Since, there is a huge difference in Fermi energy between the central region and the electrodes. Could you please clarify what is the importance of the Fermi energy of central region? or How does it influences the transport run.