Messages

46

General Questions and Answers / Re: Structure in polyhedron graph

« on: February 19, 2018, 08:05 »

Send your structure to the Viewer, then click Properties, and select the polyhedra to visualize. See also attached PNG.

47

General Questions and Answers / Re: vacuum

« on: February 19, 2018, 00:05 »

In the Builder, use the Lattice Parameters tool to increase the length of the appropriate lattice vector (most likely C).

48

General Questions and Answers / Re: Error in Total Readenergy calculation for Single Electron Transistor

« on: February 16, 2018, 15:08 »

Dear Shivani,
thanks for uploading the files. I would really like to help you here, but the NC files seem somehow corrupted:

> nlread('gatescan0.nc')
> NLIOError: Error: gatescan0.nc is not a valid NetCDF 3 file

49

General Questions and Answers / Re: Error in Total Readenergy calculation for Single Electron Transistor

« on: February 8, 2018, 12:53 »

OK, so it's a bit more complicated than I thought. Could you possibly upload the relevant file somewhere online so we can test and give you a proper solution? the relevant files are python scripts, nc-datafiles, and log files.

50

General Questions and Answers / Re: Error in Total Readenergy calculation for Single Electron Transistor

« on: February 7, 2018, 13:13 »

The nlinspect function was changed from 2017 version. I think your problem is fixed if you in line 24 replace

Code

if (id[0] == 'TotalEnergy'):

with

Code

if id[0].cls == TotalEnergy:

51

General Questions and Answers / Re: picture of the charge transfer

« on: February 2, 2018, 09:14 »

Sounds like you need to compute the Muilliken population for the system both before and after charge transfer, and then subtract one from the other.

52

General Questions and Answers / Re: How to use ATK to correctly analyze the charge layout

« on: January 29, 2018, 08:10 »

What exactly do you mean "charge layout" ?

53

General Questions and Answers / Re: About Tracking the coordinates of each atom

« on: January 19, 2018, 15:50 »

The script below reads the images in a saved MD trajectory and prints the coordinates of a particular atom (identified by the index i) in each image. Pretty easy to expand this script to also store the coordinates in a list for plotting purposes.

Code

trajectory = nlread('MD_trajectory.hdf5', MDTrajectory)[-1]
images = trajectory.coordinates()
i = 0
for image in images:
    position = image[i]
    print position

54

General Questions and Answers / Re: Computational time approximation for 192 atom Transport devise

« on: January 19, 2018, 15:27 »

Would be much easier to help you if you attach the ATK Python script that you are running, and the current log file.

55

General Questions and Answers / Re: device k-point convergence

« on: January 10, 2018, 08:17 »

The simple answer is that you do not really need to think about such details. You just need to select one single set of k-points (kA, kB, kC) in the VNL Scripter, then the k-point sampling for both electrode calculations and for the device calculation are automatically set up correctly.

The more advanced answer is that 3 calculations are needed (electrode #1, electrode #2, device NEGF), so 3 k-point grids are set up in the ATK Python script. But they are all identical. Example:

Code

left_electrode_k_point_sampling = MonkhorstPackGrid(
    na=5,
    nb=5,
    nc=165,
    )
left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=left_electrode_k_point_sampling,
    density_mesh_cutoff=140.0*Hartree,
    )

right_electrode_k_point_sampling = MonkhorstPackGrid(
    na=5,
    nb=5,
    nc=165,
    )
right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=right_electrode_k_point_sampling,
    density_mesh_cutoff=140.0*Hartree,
    )

device_k_point_sampling = MonkhorstPackGrid(
    na=5,
    nb=5,
    nc=165,
    )
device_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=device_k_point_sampling,
    density_mesh_cutoff=140.0*Hartree,
    )

56

General Questions and Answers / Re: Running atk on linux

« on: January 10, 2018, 08:10 »

Hi Rose. You report 2 different problems: (A) problems with the display, and (B) problems running ATK Python. Let's consider (B) first.

Please tell me
1) Which Linux distribution do you use? And is this on your laptop or on some computing cluster?
2) Which version of VNL-ATK do you use?
3) Do you know if the ATK calculation actually runs (i.e. the problem is just that the log file is empty), or does the calculation crash?
4) Please tell me the results from running attached script in the following 2 different ways:

Code

atkpython Silver.py 2>&1 | tee serial.log
mpirun -np 2 atkpython Silver.py 2>&1 | tee parallel.log

57

General Questions and Answers / Re: Iso value

« on: January 10, 2018, 07:54 »

There is really not general answer to your questions. I think you need to try different approaches and decide on which one gives the best insight into the physics/chemistry you are studying.

58

General Questions and Answers / Re: About the repeatability and correctness of the calculation using ATK

« on: January 8, 2018, 07:46 »

I agree with your assessment.

59

General Questions and Answers / Re: About the repeatability and correctness of the calculation using ATK

« on: January 4, 2018, 16:33 »

Line 431 needs to be changed like this:

Code

Value = transmission_spectrum.current().inUnitsOf(Ampere)*1.e9

The reason is that

Code

transmission_spectrum.current

just points to the Python method "current", while

Code

transmission_spectrum.current()

executes the method and returns the value of the current. The

Code

.inUnitsOf(Ampere)*1.e9

makes sure the stored value of the current is in units of nA.

60

General Questions and Answers / Re: VNL - effective mass

« on: January 4, 2018, 11:37 »

Holes are just "missing electrons", so the hole effective mass is calculated the exact same way as the electron effective mass, but for valence bands instead of conduction bands. Hole masses therefore come out with the opposite sign, but that's just a matter of convention.