Messages

1

General Questions and Answers / parallelization and ATK

« on: January 12, 2016, 11:22 »

Hi,

I want to understand parallelism in ATK , so can you please tell me the levels of parallelization implemented ?

For ex.
If N is the group of all processors
how to specify (or rather how do these parameters vary when we pass N as an argument to mpirun ?)
Processors that can then be divided into different "images", each corresponding to a different self-consistent or linear-response calculation, loosely coupled to others.
Each image can be subpartitioned into "pools", each taking care of a group of k-points.
Bands: each pool is subpartitioned into "band groups", each taking care of a group of Kohn-Sham orbitals (also called bands, or wavefunctions)
Orbitals: orbitals in the LCAO set

Also is there a way to account for the amount of memory per thread ? I see messages from the simulation in ATK 2015.1 about real space sampling etc.

Hoping for a detailed clarification !

Thanks
Sathyajit

2

General Questions and Answers / Chlorographene

« on: January 3, 2016, 14:25 »

Hi,

How to get the structure of Chlorographene in VNL ?

3

General Questions and Answers / tunneling across van der waal's structures

« on: December 5, 2015, 12:24 »

Hi,

What is the methodology to have tunneling across van der waal's structures ? for ex. tunneling between MoS2 and another layer MoS2. It doesnt converge when I use the same script I use for other structures.

4

General Questions and Answers / temperature distribution along the device length

« on: October 4, 2015, 15:36 »

Hi,

Can we have temperature distribution along the length of a device for a specified current ?

Regards
Sathyajit

5

General Questions and Answers / creating ions

« on: September 25, 2015, 12:07 »

Hi,

How do I create ions (ex. Na+, Cl-) to simulate the ion dissociation in water  and its effect on a bulk configuration ?

I know how to get the element Na or Cl, but I am not sure about getting the individual ions in place.

Thanks
Sathyajit

6

General Questions and Answers / Re: Contour plot of the C component of the linear response current density

« on: August 31, 2015, 16:20 »

Pls reply...

7

General Questions and Answers / Re: Contour plot of the C component of the linear response current density

« on: August 28, 2015, 15:40 »

Hi,

I wanted to know what is the significance of spectral weight in the definition given at
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.currentdensity.html

Also what do you mean by
"positive weight corresponds to calculating right to left going modes (positive current), while a negative weight corresponds to calculating left to right going modes (negative current)."

I am not able to understand what you mean by positive current and negative current w.r.t. the plot given in the post.

8

General Questions and Answers / Re: plotting eigenstate and determining corresponding energy of the state

« on: August 25, 2015, 17:05 »

Dr.Blom,

I am facing the same error after I have modified the script looking into the documentation. Can you pls take a look at the modified script and the log file ?

Also when we define our own basis sets to include principal quantum numbers for 3d orbitals what is the expected computation increase ? I want to do the orbital calculation for a small 2 terminal device.

Regards
Sathyajit

9

General Questions and Answers / Re: plotting eigenstate and determining corresponding energy of the state

« on: August 25, 2015, 12:46 »

Dr. Blom,

I am unable to get the 3s and 3p orbital strucutre from the script below. Can you please let me know what I am missing ?

The error I am getting is

Traceback (most recent call last):
  File "/tmp/3336602494981770.py", line 45, in <module>
    eigenstate=Eigenstate(molecule_configuration,3,proj_list)
  File "./zipdir/NL/Analysis/Eigenstate.py", line 62, in __init__
  File "./zipdir/NL/Analysis/Eigenstate.py", line 391, in calculateEigenstate
  File "./zipdir/NL/Analysis/AnalysisUtilities.py", line 133, in setAndCheckQuantumNumber
NL.ComputerScienceUtilities.Exceptions.NLValueError:  The parameter, quantum_number, must lie in the range [0,number of orbitals - 1], which is [0,1] in this case.

Regards
Sathyajit

10

General Questions and Answers / Re: plotting eigenstate and determining corresponding energy of the state

« on: August 24, 2015, 19:47 »

Thanks Dr.Blom.
The description of ProjectionList in
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.eigenstate.html

must read as atoms instead of orbitals. Am I missing something here ?

11

General Questions and Answers / plotting eigenstate and determining corresponding energy of the state

« on: August 24, 2015, 10:40 »

Hi,

According to the documentation I can calculate the eigenstate of a quantum number with Eigenstate method.
1. Is it possible to do it for a device configuration, if so, what method must I use ?

projection_list
Specifies the orbitals within the configuration to include in the calculation.

Type: ProjectionList.

Default: All atoms included : ProjectionList(All)

2.In the above does ProjectionList imply atoms in the device configuration or the orbitals within a single atom ? :
This is contrary to what is said here:
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.projectionlist.html
3. How do I know the energy value of the eigenstate ?
4. How do I extract the 3D matrix for the eigenstate so that I can plot it ? (Is this option already there in VNL ?)

Thanks
Sathyajit

 

12

General Questions and Answers / Re: calculating band diagram along Y axis

« on: August 11, 2015, 13:00 »

Hi,

Can you please let me know if there is a possibility to do this ?
I saw the documentation but it appears the DOS can be calculated only along left or right electrode or average of device length

13

General Questions and Answers / Re: calculating band diagram along Y axis

« on: August 9, 2015, 09:06 »

Pls reply.

14

General Questions and Answers / calculating band diagram along Y axis

« on: August 6, 2015, 06:10 »

Hi,

I am trying to modify the script given in (By Dr.Anders)
http://quantumwise.com/forum/index.php?topic=1551.0

so that I can plot the band diagram along Y axis. I have marked the places where I replaced Z coordinates with Y coordinate in the script (please see attachment, the modifications are in
line 20 and line 124)
Can you please verify that this is correct ?

Also can you please tell me how do I calculate the band diagram along a specific line (set of atoms along a particular point in Z axis, with band diagram along Y axis) ?
I am thinking of using DOS calculation along a specific set of atoms and then using the obtained DOS in band diagram calculation.

Code

conf = nlread('device.nc',DeviceConfiguration)[0]

#setup energies
energies = numpy.linspace(-2,3,100) * eV

#calculate the dos from the Left electrode
dos = DeviceDensityOfStates(conf, energies=energies, contributions=Left)

#calculate the projections on the atoms in the central region
dos_projection = [
     dos.evaluate(projection_list = ProjectionList([i])) for i in range(3,11)
     ]

#plot the data
import pylab
pylab.figure()
for i in range(3,11):
    label = conf.elements()[i].symbol()+'('+str(i)+')'
    pylab.plot(
        energies.inUnitsOf(eV),
	dos_projection[i-3].inUnitsOf(eV**-1),
	label=label
	)
pylab.legend()
pylab.xlabel("Energy (eV)")
pylab.ylabel("dos (1/eV)")
pylab.show()

The above code calculates the DOS only on the left electrode, Is there a way to specify some atoms along the transport direction (Z axis in this case) ?

15

General Questions and Answers / Re: Contour plot of the C component of the linear response current density

« on: July 15, 2015, 16:28 »

Hi,

I am using the scripts attached here and have obtained the png file.
Can you please help me interpret the reason why the red regions and blue regions are alternating ? (positive and negative current densities)

Regards
Sathyajit