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Messages - hol28

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1
Thanks!
The conductance in your calculation takes into account only the ballistic conduction.  What you expect is true for the  resistance of the Ohmic contact.

2
Hi everyone:
I calculated the conductance of Li-wires with different lengths and found that the values of conductance are almost the same. But as I know, the electrical conductivity is a material property and indepedent on the length and cross section of the material. However, the conductance, which equals conductivity*(cross section)/length, should be inversely proportional to the length. Could someone tell me why my calculated conductance is independent on the length?
Thanks very much! 

3
General Questions and Answers / Re: Is the gate added correctly?
« on: September 6, 2012, 16:05 »
OK. Thank you all the same!
It's a bit hard to tell, the system is after all rather artificial, but I guess it means you can't really expect to have a H+ ion in this place, in this system.

4
General Questions and Answers / Re: Is the gate added correctly?
« on: September 4, 2012, 16:52 »
Hi, I have tried other site shifts, but the results are still very strange. When no site shift is added, the mulliken charge for H is 0.903. When the site shift is +10, the value is 1.463; when -10, it is 1.751. +8: 1.299; -8: 1.257. +5:1.095;-5:0.951. +3:0.994;-3:0.903. The charge of H atom is always increased. Could you please give me other suggestions? Thank you so much!
It looks correct. But I think a shift of 15 eV is also not suitable, it's probably way too much, which may explain the strange results.

5
Hi, thank you very much! Yes, I think the result should be like what you say, but what I get is weird. I have read the document you mentioned to add the site shift, but since the case is a little different, I'm not sure whether it is right in my case. Could you please help me check if the method I use to add the site shift is correct? 
Thank you so much!
You cannot instruct the H atom to be in a particular charge state, since the Mulliken population of each atom will be determined by the self-consistent state of the whole system. Thus the relevant quantity to compare to is not the isolated H atom, but the self-consistent state of the H atom in the given atomic environment. I am sure (or at least I very much hope) that if you compare the 3 calculations with +15 eV, 0 eV, and -15 eV, you will see a net additional positive/negative charge on the H atom in the two cases with a finite shift, compared to no shift.


6
Hi, I have tried your suggestion, but another thing puzzled me. When I added an onsite shift of +15*eV on H atom, the  Mulliken Population Report for H is 1.745; when onsite shift is -15*eV, the value is 2.327. It seems that the charge of H should be larger than ~1.00 for one case and smaller than ~1.00 for another. Could you please give me some suggestions for this problem? Thank you so much!
That's probably a bit too violent :) I would suggest adding an onsite shift on the H atom instead (see http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.atomicshift.html).

7
Thank you very much! I will have a try.
Hmm, an alternative to the Mulliken population could be using the ElectronDensity.
A rough example I have made:
Code
ed = nlread('analysis.nc', ElectronDensity)[0]
cut = 20
s = ed[:, :, :].sum()
print ed[:,:, :cut].sum()/s
print ed[:,:, cut:].sum()/s
Where 20 is some grid number in the z-direction.

Also take a look at the manual entry for ElectronDensity :)

8
General Questions and Answers / Is the gate added correctly?
« on: August 28, 2012, 16:27 »
Hi everyone,
I'm now considering studying the conductance of a device with H+ involved. The geometry is included in the file Pt.py. In order to simulate the H+, I add a gate just on the bottom of the atom H. By adjusting the gate, the atom H can be turned into H+. But I'm not sure whether it is reasonable using this method. In addition, what boundary condition should I use in this case?
Any suggestion would be appreciated. Thank you very much!

9
Hi everyone:
In this topic, http://quantumwise.com/forum/index.php?topic=369.0, the author calculated the charge transfer in the system. I'm also studying the effect of the gate voltage on the charge of the central region in a two-probe system. I know that the mulliken population can give the charge of an given atom. Is there another way to calculate the charge transfer?
Any advice would be appreciated!

11
Hi everyone,
I am puzzled about one issue in the two-probe system. When I add voltages of -0.5V and +0.5V to the left and right electrodes, respectively, the Fermi level of the left electrode is shifted up and  the right is shifted down. When calculating the transmission, I think it is more easier for the electrons to transfer from left to right, which should lead to a larger transmission at the Fermi level. But in my calculation, the value is decreased. On the other hand, when I add a voltage of +0.5V and -0.5V to the left and right electrodes, respectively, the value is increased. I'm puzzled by the results. Could anyone help me? Thanks!

12
Hi nori:
I have tried the method you suggested. It just the same as GGA.PW91.
Thanks!

13
Hi Nordland,
Thank you for your suggestion. Since that's always the way to treat a molecule in other software, I'm used to use that method. 
Yes, I find in ATK the way to treat a molecule. That's great! 

14
Hi Nordland,
Thanks for your patient reply.
   (1) I put the molecule HCl in a large enough box so that there are no interactions among the neighboring molecules and treat it as a periodic bulk. I think this can simulate the situation of a molecule HCl.
   (2) Yes, you are right. In H-Cl the electron is not transfered to the Cl atom completly. In my original post, I got the result that H get partial electron from Cl. I think this is not reasonable. I have read the reference you recommended, the result therein is -0.17 for Cl and +0.17 for H. I finally got a similar result by changing the basis set in the input file.
Thanks again for your suggestions.

15
Hi everyone,
I want to use the ATK to calculate the mulliken population, so I did a simple test on a HCl molecule. The result is:
 Mulliken Population Report                                                   |
|                                                                              |
| ---------------------------------------------------------------------------- |
|                        |                                                     |
| Element   Total  Shell | Orbitals                                            |
|                        |                                                     |
|                        |      s                                              |
|   0   H   1.044  0.129 |  0.129                                              |
|                        |      s                                              |
|                  0.773 |  0.773                                              |
|                        |      y      z      x                                |
|                  0.142 |  0.058  0.042  0.042                                |
|                        | --------------------------------------------------- |
|                        |      s                                              |
|   1  Cl   6.956  0.090 |  0.090                                              |
|                        |      y      z      x                                |
|                  0.630 |  0.153  0.239  0.239                                |
|                        |      s                                              |
|                  1.674 |  1.674                                              |
|                        |      y      z      x                                |
|                  4.525 |  1.091  1.717  1.717                                |
|                        |     xy     zy  zz-rr     zx  xx-yy                  |
|                  0.037 |  0.002  0.002  0.008  0.000  0.025                  |
+------------------------------------------------------------------------------+
But as is know, for the HCl, the result should be H+ and Cl- and the electrons for H and Cl should be 0.0 and 8.0, respectively.
My input file is:
# -------------------------------------------------------------
# Bulk configuration
# -------------------------------------------------------------

# Set up lattice
vector_a = [10.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 10.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 9.999945]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Hydrogen, Chlorine]

# Define coordinates
cartesian_coordinates = [[ 5.       ,  4.36     ,  4.9999725],
                         [ 5.       ,  5.64     ,  4.9999725]]*Angstrom

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    cartesian_coordinates=cartesian_coordinates
    )

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = GGABasis.DoubleZetaPolarized

#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = GGA.PW91

numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=(10, 10, 10),
    )

calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    )

bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('HCl.nc', bulk_configuration)

# -------------------------------------------------------------
# Mulliken population
# -------------------------------------------------------------
mulliken_population = MullikenPopulation(bulk_configuration)
nlsave('HCl.nc', mulliken_population)
nlprint(mulliken_population)

Could anyone give me any suggestions? Look forward to your reply! Thanks!

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