Topics

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 / 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.
 

3

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!

4

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.
 

5

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!

6

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 !

7

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.

8

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

« on: March 11, 2014, 03:46 »

    The left and right electrode had been completed and the distance between the two electrode was set. Then the molecule was put in the center of the device by using "center" option in the "Coordinate Tools".
    But I was not sure whether the center was the perfect position for the molecule. And It would cost much time by using the "Optimize Geometry" in "Script Generator" to optimize the position of the molecule.
   Another problem was the it would change the molecule structure during optimization.
   I didn`t know how to deal with that.

9

General Questions and Answers / DOS difference

« on: February 21, 2014, 13:23 »

     I have used VNL 13.8.0 to calculate electrode-molecule-electrode Device Density of State and the result is shown in figure1. So I used VNL2008.10 calculate this device`s DOS again and the result is shown in figure2. Both the result shows that they have the similar trend, but their value are very different, about one order of magnitude difference. I`m not sure which one is right?
     The primary parameters in VNL2008.10 are set as attachment3.
      
  

10

General Questions and Answers / "internal error"

« on: February 21, 2014, 03:05 »

  There is always an error happens when I try to use the VNL 2008.10 to open a "py" file. Restarting or reinstallation still cannot solve this problem. Is it because the incomplete software i got or it is incompatible with my computer?

11

General Questions and Answers / "PeriodicAtomConfiguration" error

« on: February 19, 2014, 08:09 »

Dear all,
I had constructed a two probe configuration-[Au electrode-Molecule-Au electrode] by using VNL 2008.10. Now I want to use VNL 13.8.0 to run the script. But there`re always error existing. I don`t know how to adjust my code to VNL13.8.0. The attachment is the code.

12

General Questions and Answers / error message

« on: January 18, 2014, 04:10 »

Dear all,
   When I run a complete .VNL file using Virtual nanoLab 13.8.0, there was always an error message:

   The following error message was generated when attempting to read a file:
The format of the file C:/Users/think/Desktop/1.vnl cannot be determined
If the message does reveal the cause of the error, please report the issue to QuantumWise, and make sure to include the traceback (click "Show Details...").
  Traceback (most recent call last):
  File ".\zipdir\NL\GUI\DnD\MimeData.py", line 253, in _urlTypes
  File ".\zipdir\NL\IO\ConfigurationsImporter.py", line 151, in __init__
  File ".\zipdir\NL\IO\ConfigurationsImporter.py", line 254, in inspect
NLIOError: The format of the file C:/Users/think/Desktop/1.vnl cannot be determined

   The file cannot be open. Is this the reason of different computer system or anything else. How to deal with it.
   Thanks in advance!

13

General Questions and Answers / How to optimize the molecule in device.

« on: January 16, 2014, 13:54 »

Dear friends,
  I have made a two probe configuration:[Au electrode]-[molecule]-[Au electrode]. The structure of molecule(a cubic) had been optimised individually before used to construct the two probe device.
The distance between two electrode was based on experience parameter.

  The initial structure of the device is shown in figure1.
  The electrode is two layers, and the Unit Vector is:
           vector_a = [5.89465425896, 0.0, 0.0]*Angstrom
           vector_b = [0.0, 5.89465425896, 0.0]*Angstrom
           vector_c = [0.0, 0.0, 4.16814999926]*Angstrom
  Five layers of Au slab were chosen in z direction as left electrode and electrode extension just for a fast computational speed.  
  The perpendicular distance between the left electrode and the leftmost atom of the molecule as well as counterpart in the right is 2.0 Å as experience.
  More detail parameters are in the attached script.
  
  So I decided to optimized structure of the molecule in this device. We kept all gold atoms fixed and relax the molecule in the center until the forces on each atom are smaller than 0.05 eV/ Å in the
optimization.

  But the result I got was unstatisfied, because the change of molecule`s shape is too big, not cubic any more, as in figure2. So I think there must be someting wrong.
  1.The perpendicular distance between the left electrode and the leftmost atom of the molecule is 2.0 Å according to experience. But I am not sure whether it is the cause of the mistake.
  2. In this work, only five layers of Au slab are used because they are enough for such small molecule. Also I am not sure it is reasonable.
  
  The two above is just the reasons I speculated. And this problem is still making me confused.
  
 Thanks in advance!

14

General Questions and Answers / construct Au electrode with 2 × 2 layers in x and y directions

« on: January 12, 2014, 12:45 »

Dear friends,
   I am trying to construct Au electrodes with  2 × 2 layers in x and y directions and eight slabs in Z direction. As i don`t know the experimental parameter of Au electrode, so i have tried a lot of times to optimize the structure of Au electrode. No matter what i did, the results were not what i want. So if you could give me some directions or help. I would very appreciate it.

15

General Questions and Answers / Fcc NaCl including 8 atoms

« on: January 6, 2014, 03:23 »

when i use the ATK to construct a Fcc NaCl including 8 atoms, there is always existing the same mistake reminder:

{Back Engine Exception : Diagonalization error, overlap matrix not positive definite. This may be caused by atoms that are too close to each other or situated in equivalent positions, or (in the Extended Huckel model) a too low value of interaction_max_range
** Location of Exception : mathutils.cpp:687
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.}

So, i don`t know how to do with it. Please help me.
Thanks!