Messages

1

General Questions and Answers / Error in readTotalEnergy.py for Single Electron Transistor in ATK2019 or later

« on: February 18, 2020, 04:20 »

Using ATK 2019, I am testing the behaviour of Single electron transistor as per Benzene Single-Electron Transistor Tutorial Version 2015.2. The script went well in old versions of ATK (such as ATK 12.8.2).

However, there is a problem in running the script fig4-1plot.py which uses readTotalEnergy.py to get calculated total energy at  different gate voltages in the new version of ATK.
In version 2019, though the energy has been sucessfully calculated, the error occured, reporting "ValueError: No total energy in hdf5 file".

Please help solving the issue for reading the data sucessfully.

Thank you very much.

PS: relevent files of *.hdf5 and *.py are attached in the zip file.

2

General Questions and Answers / Re: Urgent! Questions on repeating "Properties of an isolated benzene molecule"

« on: March 14, 2014, 16:25 »

Dear kstokbro,
    Thank you very much for your reply. Yeah, you are right. I eye on solid, and is not familiar with chemistry
community. 
    I calculated the a,b,c of the isolated box following your instruction. I am very interested in the detailed theory about solving the Poisson's equation under multipole boundary condition. And I would like to  know if this is the relevant paper: http://onlinelibrary.wiley.com/doi/10.1002/jcc.540160707/references
    And if you can tell me a reference, that would be highly appreciated.

3

General Questions and Answers / Urgent! Questions on repeating "Properties of an isolated benzene molecule"

« on: March 10, 2014, 10:55 »

   I am repeating the example shown in "Properties of an isolated benzene molecule" and I have some questions.

   When using the multipole boundary condition, is the periodic superscell (in which there are periodic images of the benzene molecule) approach used or just a single isolated box (in which there is only one benzene molecule) is used?         
   In this specific example of a charged benzene, the size of the box is not explilcitly given. I would like to know very much the size of the box containing the charged benzene. Can I find the size of the box in the output file?
   I would also like to know, if I calculate a different charged molecule, how can I know the size of the box that is actually used.

   I found a paper about the multipole expansion solution to solve the Poisson's equation
(http://journals.aps.org/prb/abstract/10.1103/PhysRevB.46.4495). I would like to ask you if the method described in this paper is relevant to the multipole method used in ATK.

Thank you for your prompt reply.

4

General Questions and Answers / Re: reference for multipole boundary condition?

« on: March 10, 2014, 05:33 »

Is this method used for multipole boundary condition?
http://journals.aps.org/prb/abstract/10.1103/PhysRevB.46.4495
Poisson equation withperiodic boundary conditions: Multipole-expansion solution

5

General Questions and Answers / reference for multipole boundary condition?

« on: March 10, 2014, 02:44 »

Could you show the reference for multipole boundary condition. It seems the multipole boundary condition is used to simulate isolated systems, but in molecule configuration, why a default "supercell" is used?

6

General Questions and Answers / Re: urgent! how dose ATK deal with charged molecule in molecule_configuration

« on: May 13, 2013, 09:41 »

Thank you very much, sir.
I am very interested in the related theory, could you tell me the references of this method ?

7

General Questions and Answers / urgent! how dose ATK deal with charged molecule in molecule_configuration

« on: May 10, 2013, 15:31 »

When an extra electron is added to molecule, the molecule get charged.
In Siesta, when extra electron is added, the default cell is filled with jellium-like opposite charge for compensation, so the total box is neutral. In order to remove the interaction of charged default cells, a Madelung correction term is applied to the energy to make it converge much faster with cell size.
( for molecules or atoms, this is done only if the cell is SC, FCC or BCC).
However, in the forum I haven't found how ATK remove the effect of extra compensate electron on repeated default cells in calculation ,
I don't know whether ATK use the same method as Siesta ?
In addition, how is the default cell for molecule in molecule_configuration like, especially when molecule is being charged (like SC)?

urgent, please reply soon as possible.

8

General Questions and Answers / Re: How to get the LDOS of a molecule in molecule_configuration?

« on: April 10, 2013, 14:49 »

I have an idea, but some problems stuck in front.
In my opinion, the "eigenstate" of molecule is similar to "bloch state" of bulk system,
So LDOS can be obtained by sum the eigenstates of specific quantum numbers,
because we LDOS of particular  energy range,
energy spectrum of molecule should first be calculated, in this way, we can find out the detailed quantum numbers distributed among the   particular energy range.
then, sum the eigenstates together.

However, there are some doubts:
1. eigenstate is described in red and blue, indicating phase of wavefunction.  But what is the related physics ?
2. can eigenstated be sumed ?
3. In fact, I would like to be surel, wether  LDOS is the electron density of particular energy range, and wether eigenstate of molecule is the electron density of a specific quantum number.
 

9

General Questions and Answers / Re: How to get the LDOS of a molecule in molecule_configuration?

« on: April 10, 2013, 10:12 »

your resolution is ok for bulk_configuration.
but for molecule_configuration,  "BlochState()" is not available, how to deal with it ?

10

General Questions and Answers / How to get the LDOS of a molecule in molecule_configuration?

« on: March 31, 2013, 06:32 »

Local Device Density of States is avialable in device_configuartion.
But when it comes to molecule_configuration and bulk_configuration, LDOS is not acessible.
how to get the LDOS (the partical charge density at fixed energy)of a single molecule ?

11

General Questions and Answers / how to export molecule configuration in cube file ?

« on: March 15, 2013, 10:20 »

In order to visualize electron density in Vesta, electron density was export in *.cub file.
When related molecule configuration was export in *.cif or *. xyz file, it did not fit the *.cub file.
the combination of electron density and molecule configuration are well in Virtual Nanolab as follow

But in Vesta, I get only this


How to deal with it?

12

General Questions and Answers / Re: how to get 3D bandstructure ?exactly Dirac cone

« on: October 12, 2012, 04:42 »

under your instruction, i plot the dirac cone, attached is my work.
i calculated the eigenvalues by vasp, extract them out and plot in origin.
(i admit the plot is ugly and i am trying to do better )

my addtional question:
how to extract the eigenvalues in *.nc under extended huckel method calculated by atk?
because i really don't see the eigenvalues when i just open the *.nc in Editor of Virtual NanoLab.

13

General Questions and Answers / Re: how to get 3D bandstructure ?exactly Dirac cone

« on: October 10, 2012, 08:44 »

would you give some detailed instructions?
actually, i think 3d-bandstructure is beautiful and should be in the galleary.

14

General Questions and Answers / how to get 3D bandstructure ?exactly Dirac cone

« on: October 9, 2012, 16:38 »

ATK calculate bandstructure and plot it along high-symmetry lines.
when I need to plot 3D dirac cones, I am despaired, because i can't do it.
how to extract data from the *.nc and plot the dirac cone of graphene unit ?
attched is the plot i want

15

General Questions and Answers / does gate voltage work in bulk configuration?

« on: July 24, 2012, 05:26 »

   I found the gatevoltage dose not work in bulk configuration, when I do transmission, dos and bandstructure calculations under different gate voltages.
   My configuration is similar with the one in minitoturial(
Transmission spectrum of perfect sheets of graphene and MoS2 in speturm
http://quantumwise.com/publications/tutorials/mini-tutorials/167),but mine have dielect region and metallic region under graphene.
   dose gate voltage work in bulk configuration? or I did something wrong

Moderator edit: Fixed spelling mistake in subject