Messages

1

General Questions and Answers / Re: How to build this molecule structure?

« on: September 25, 2012, 18:49 »

It is just the molecule I showed above and then sandwiched between two gold electrodes (similar to the tutorial, which is exactly the same with the tutorial, except for the molecule, which is originally benzene in tutorial then replaced by my molecule here).

2

General Questions and Answers / Re: How to build this molecule structure?

« on: September 25, 2012, 15:04 »

My computer has 3 Gb RAM. This is still not enough for this simulation?! Wa....

3

General Questions and Answers / Re: How to build this molecule structure?

« on: September 25, 2012, 11:45 »

So, does it mean the RAM in my computer is not big enough for this simulation?

4

General Questions and Answers / Re: How to build this molecule structure?

« on: September 21, 2012, 16:37 »

Hi Dr Blom,

I have successfully built the model in your method, thank you.

I build the molecule junction by repeating the method of tutorial with this molecule (-S terminated, the same as tutorial), and I just repeat the exact same process to simulate the I-V properties of this junction using the same parameters sa tutorial. The only parameter I changed it that I set the lattice parameter in C direction to be 70 rather than 45, to make it long enough for my molecule.

I successfully get the device transmission spectrum. However, unfortunately, when I run the program to simulate the I-V curve (Chapter 4 in tutorial), it always stop at the beginng (pro1.jpg, attachment) and reply the error (pro2.jpg).

I have simulated some other molecule junction before, but this is the first time I face this problem. I tried to, for example, turn the benzene ring by 90 degree, and simulate again, but the same error happens.

Could you please give me a hand?

5

General Questions and Answers / Re: About the molecular wires junction.

« on: September 19, 2012, 13:42 »

Thanks for your kind reply.

I have one more question: it seems that there is still considerable difference between the literature (1.jpg)  (Reed et al. Science, 1997) and the simulation. The simulated results (2.jpg) are around 30 times bigger than the literature. The shape also has a little bit difference between them. Could you please give me some suggestion on it?

6

General Questions and Answers / About the molecular wires junction.

« on: September 19, 2012, 13:29 »

Hi,

I built the molecule junctions with a benzene completely following the tutorial and then calculated the I-V curve. May I ask, whether this calculation includes the tunneling (or noise) current between two electodes, because the space between two electrodes are very small?

Thanks ahead.

7

General Questions and Answers / How to build this molecule structure?

« on: September 18, 2012, 12:41 »

The molecule is put in the attachment. I tried to build it by insert benzene and repeat replacing H by C and adding H again, but VNL reports error.

What is the correct way to build it?

8

General Questions and Answers / Re: Mistake in modelling graphene nanoribbon with CONDUCATNCE VS. Vg

« on: September 6, 2012, 17:55 »

Hi Dr. Blom,

I found one possible problem in my method. To calculate the Conductance vs. gate voltage, I directly used the code on Page 19 of the tutorial "Graphene junction device".

The model the tutorial used is the one which has been built in software. However, my device is built by myself (as shown in previous attachment).

I am not quite familiar with the ATK language, but is this code also suitable for my model (such as defining the correct gate field at the correct region)?

If not, how to modify it?

Thanks ahead!
 

9

General Questions and Answers / Re: Mistake in modelling graphene nanoribbon with CONDUCATNCE VS. Vg

« on: August 29, 2012, 13:23 »

Sorry. I forget to mentioned last time, I adjusted the first two (A ,B) boundary conditions to Neu, and the third one  (C) to Dir, which was the same as the one mentioned on Tutorial.  I just repeat the one on tutorial step by step, so I don't know why my result is different from the one on tutorial.

10

General Questions and Answers / Re: Mistake in modelling graphene nanoribbon with CONDUCATNCE VS. Vg

« on: August 28, 2012, 12:21 »

I choose calculator and transmission spectrum:
in calculator, I choose: n = 1, 1, 100, with SCF, and then change basic set to Cerda carbon.

In spectrum, I change energy range to -4 ~ 4, and calculation model to Krylov. Others are all in default.

there is a lot of repeated warning as follows:
################################################################################
# WARNING                                                                      #
#                                                                              #
# The computed multigrid residual is greater than the required accuracy.       #
#                                                                              #
# Computed residual :   7.91855e-012                                            #
# Required accuracy :   1.00000e-012                                            #
#                                                                              #
################################################################################

And then the final result was shown as before. Could you please tell me the reason?

11

General Questions and Answers / Mistake in modelling graphene nanoribbon with CONDUCATNCE VS. Vg

« on: August 27, 2012, 18:49 »

I have built the model of the device of a graphene nanoribbon with applied gate electric field, like shown in the .py file below. However, when I run the program in 1 and 2 to get the curve of conductance vs. gate voltage at temperature of 25K and 350 K, the results I obtained is shown in 4.jpg.

This is not correct, since theoretically it should be a "V" shape, with the minimum point at Vg=0. Could you please tell me the reason？

Thanks ahead!

12

General Questions and Answers / Re: How to get the G-S curve from transmission spectral.

« on: August 23, 2012, 18:23 »

Sorry, I did not make my question clearly. I built a graphene nanoribbon as shwon in device.jpg. After I calculate the transmission spectrum (with self-consistent), I run the program above. Then I just run the program shown on the tutor as shown below, but the result I obtained (in result.jpg) is different from the theory, which should be a "V" shaped curve.

#make list of relevant temperatures
temperature_list=numpy.linspace(25,350,2)*Kelvin
#make list of relevant gate voltages
gate_voltage_list=numpy.linspace(-2.0,2.0,17)*Volt
#make list to hold the conductance calculations
conductance_list=numpy.zeros(len(gate_voltage_list)*len(temperature_list))
conductance_list=conductance_list.reshape(len(gate_voltage_list),
len(temperature_list))
#specify the filename for the netcdf data file
filename="gatescanAW8L8.nc"
#loop through the gate voltages
for n in range(len(gate_voltage_list)):
    transmission_spectrum=nlread(filename,
                                 object_id="trans"+str(gate_voltage_list[n]))[0]
    #loop through the temperature list
    for i in range(len(temperature_list)):
        conductance_list[n,i]=transmission_spectrum.conductance(
            electrode_temperatures=(temperature_list,temperature_list))
 
#plot the conductance as function of gatevoltage
import pylab
pylab.figure()
# make curve for each temperature
for i in range(len(temperature_list)):
    pylab.semilogy(gate_voltage_list,conductance_list[:,i])
pylab.xlabel("Gate Voltage (V)")
pylab.ylabel("Conductance (S)")
pylab.show()

13

General Questions and Answers / How to get the G-S curve from transmission spectral.

« on: August 23, 2012, 16:37 »

I have run the following program:
#read in the old configuration
device_configuration = nlread("FGNRARMW8L12.nc",DeviceConfiguration)[0]
calculator = device_configuration.calculator()
metallic_region0 = device_configuration.metallicRegions()[0]

# Define gate_voltages
gate_voltage_list=numpy.linspace(-2.0,2.0,17)*Volt

for gate_voltage in gate_voltage_list:
    device_configuration.setMetallicRegions(
        [metallic_region0(value = gate_voltage)] )

    # make a copy of the calculator and attach it to the configuration
    # restart from the previous scf state
    device_configuration.setCalculator(calculator(),
         initial_state=device_configuration)

    #Analysis
    filename= 'gatescanAW8L12.nc'
    electron_density = ElectronDifferenceDensity(device_configuration)
    nlsave(filename, electron_density,object_id='dens'+str(gate_voltage))

    electrostatic_potential = ElectrostaticDifferencePotential(device_configuration)
    nlsave(filename, electrostatic_potential, object_id='pot'+str(gate_voltage))

    transmission_spectrum = TransmissionSpectrum(
        configuration=device_configuration,
        energies=numpy.linspace(-2,2,200)*eV,
        )

    nlsave(filename, transmission_spectrum,object_id='trans'+str(gate_voltage))
    nlprint(transmission_spectrum)

How can I get the curve of "conductance vs. gate bias voltage" from file I get from the program above? (it gives me the transmission spectrum under different bias.)

14

General Questions and Answers / Re: Problems in applying electric field onto nanoribbon structure.

« on: August 22, 2012, 20:09 »

Sorry. Another problem arise. When I test the I-V curve of the configuation in Figure 1, after I get the transmission spectrum, I run the program in the attachment, which was copied from tutorial. However, I get the following warning, and the simulation has taken more than one day, and haven't been finished. Could you please help me to have a look on this problem?

################################################################################
# WARNING                                                                      #
#                                                                              #
# The computed multigrid residual is greater than the required accuracy.       #
#                                                                              #
# Computed residual :   7.91855e-012                                            #
# Required accuracy :   1.00000e-012                                            #
#                                                                              #
################################################################################

15

General Questions and Answers / Re: Problems in applying electric field onto nanoribbon structure.

« on: August 20, 2012, 21:52 »

I see. Thanks for such a clear explanation!