Messages

1

General Questions and Answers / How to calculate the "charge transfer" with variuos gate voltage

« on: December 22, 2014, 14:24 »

Hi,
   In the tutorial of "Graphene Junction Device", it shows how to calculate the conductance for different gate potentials at 300K.
http://quantumwise.com/documents/tutorials/latest/GrapheneDevice/index.html/chap.gatepotential.html

#make list of relevant temperatures
temperature_list=numpy.linspace(300,300,1)*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="gatescan-6-6.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()


So if i want to calculate the Charge Transfer with gate voltage from(-2,2)V at 300K, how can i modify the script, or how to wirte a new script.

2

General Questions and Answers / Re: conductance with/without gate structure

« on: November 28, 2014, 03:17 »

      I am planing to calculated the conductance under various gate voltage. The system is Al-molecule-Al two probe device. So first I have to know how to add the gate voltage on the system. This tutotial-A graphene junction device-shows adding a gate voltage by building a physically gate region.
      But the conductance would be also varied with gate region`s other parameters like thickness or area, which is not I expected. Gate voltage should be the only influence factor in my plan. This idea is motivated by the following theorical research on gate voltage effect.
      http://journals.aps.org/prb/abstract/10.1103/PhysRevB.73.045411
      I don`t know if the gate voltage can be added without using a physical gate region like the tutorial showed in ATK.  If no, how to decide the gate region`s physical parameters like thickness and position.

3

General Questions and Answers / conductance with/without gate structure

« on: November 27, 2014, 04:37 »

Hi,
   A graphene junction device with gate structure was built as the tutorial showed in: http://quantumwise.com/documents/tutorials/latest/GrapheneDevice/index.html/chap.buildingdevice.html#vnl.buildingdevice.gate
   
   The gate parameters were set as the tutorial, except that the metallic voltage was 0V this time. So the conductance of graphene junction device was calculated at 0V gate voltage and 0V bias voltage. The value is about 1.32E-6 S.

   In order to know whether the gate region has any effect on the transmission properties, a graphene junction device withou gate region was built by deleting the dielectric and metallic region in my previous work. So the conductance of graphene junction device was calculate at  0V bias voltage with gate region. This time the conductance value is about 1.22E-6 S.

  So here I am wondering if the gate region with might affect the device`s transmission peoperties (here I call it gate region effect), and how serious this influence. Is there any way to calculate the transmission properties, like conductance under certain gate voltage but without gate region effect.
 

4

General Questions and Answers / Re: Calculating the conductance for different gate potentials

« on: November 26, 2014, 08:09 »

yes, Thank you!

5

General Questions and Answers / Re: Calculating the conductance for different gate potentials

« on: November 26, 2014, 03:17 »

Another question is that the unit of calculated conductance is "S". So how to translate it into "G0" as unit of conductance. According to my experience, "S"*12906.4="G0". But I am not sure whether it is right.  So is there any relationship or formula between unit of "S" and "G0".

6

General Questions and Answers / Re: Calculating the conductance for different gate potentials

« on: November 26, 2014, 02:40 »

Yes, It works!  Thank you very much!

7

General Questions and Answers / Calculating the conductance for different gate potentials

« on: November 25, 2014, 14:22 »

Hi,
   In the tutorial of "Graphene Junction Device", it shows how to calculate the conductance for different gate potentials and temperature at the same time.
http://quantumwise.com/documents/tutorials/latest/GrapheneDevice/index.html/chap.gatepotential.html
   
But here I want to calculate the  conductance for different gate potentials at 300K lonely. So how to modify this script:

#make list of relevant temperatures
temperature_list=numpy.linspace(0,2000,21)*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="gatescan-6-6.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()

Thanks!

8

General Questions and Answers / effect of gate parameters

« on: November 25, 2014, 06:26 »

Hello,
    The procedure of building a gate is shown in the Graphene Device Tutorial    http://quantumwise.com/documents/tutorials/latest/GrapheneDevice/index.html/index.html
    and the physical parameters (area and dielectric constant) is defined without noting the reason. So I am wondering if the thickness and area of dielectric region and metallic region would affect the the results, such as Effect of the Gate Potential.  If there is any tutorial or reference about building gate parameters.  I would be highly appreciated for it.
 

9

General Questions and Answers / How to calculate the "transferred charge" and transmission eigenchannel

« on: November 17, 2014, 12:37 »

Hello,
   I am trying to calculate a two probe device system using ATK, and I want to know how to get: 1) transferred charge in the system and 2)eigenchannel decomposition of the total transmission spectra of the cluster around the Fermi level.

   Thank you!

10

General Questions and Answers / Convergence at higher electrode voltage

« on: October 31, 2014, 03:49 »

Hello everyone,
      I was trying to calculate a two-probe device transmission spectrum, and it can be converged at low voltage, for example lower than 2V. But when the voltage increased more than 2V, it was difficult to be converged. The K point is (5,5,100) and history step is 20. Tolerance is 0.0001 Hartree. So could I make the result converfed at high voltage>2V.  Thanks !

11

Installation and License Questions / relationship between device structure stability and total energy

« on: March 31, 2014, 12:47 »

I have calculate a series of data about distance between electrode and molecule vs. total energy. The total energy value is minus (e.g. -36027.50038
and -36025.88371). Can I deduce that the smaller this value, the more stable of the device structure? For example, -36027.50038 is smaller than  -36025.88371, So we can say device at former structure is more stable.

12

General Questions and Answers / Re: How to initial decide the molecule position in a two probe device

« on: March 12, 2014, 12:11 »

I  want to model the "Transmission Spectrum" and "Device Density of states" of the device under bias voltage. If I just put the molecule into the center of the electrode like above figure without considering the effect between molecule and the surface of Au electrode, or without optimization the molecule position in Z direction, the results will be still accurate?

13

General Questions and Answers / Re: How to initial decide the molecule position in a two probe device

« on: March 12, 2014, 04:49 »

The parameters of Calculator and OptimizeGeometry were show in figure.

14

General Questions and Answers / Re: How to initial decide the molecule position in a two probe device

« on: March 12, 2014, 04:38 »

But this would change the initial structure of the molecule which is already a perfect construction. Here I just want to find the best position of the molecule between the Au electrodes (i.e. the position in Z direction) without seriously change molecule structure.

 

15

General Questions and Answers / Re: How to initial decide the molecule position in a two probe device

« on: March 11, 2014, 17:23 »

As you said, I converted the Au electrode-molecule-Au electrode device into a bulk configuration and perform a structure optimization in "Script Generator". So I wanted to optimize the molecule position in Z direction. In the "OptimizeGeometry" tool parameters, I was not sure whether to constrain the Au atom position.

# Set up lattice
vector_a = [5.7671629, 0.0, 0.0]*Angstrom
vector_b = [0.0, 5.7671629, 0.0]*Angstrom
vector_c = [0.0, 0.0, 24.27299996]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
            Gold, Gold, Gold, Gold, Gold, Gold, Chlorine, Sodium, Chlorine,
            Sodium, Chlorine, Sodium, Sodium, Chlorine, Gold, Gold, Gold,
            Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
            Gold, Gold, Gold]

constraints = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]
bulk_configuration = OptimizeGeometry(
        bulk_configuration,
        max_forces=0.05*eV/Ang,
        max_steps=200,
        max_step_length=0.5*Ang,
        constraints=constraints,
        trajectory_filename=None,
        disable_stress=True,
        optimizer_method=QuasiNewton(),
        )