Messages

16

General Questions and Answers / Re: How to set spin multiplicity in ATK？

« on: March 3, 2017, 10:13 »

See:
https://quantumwise.com/documents/manuals/ATK-2008.10/chap.oxspin.html
Although this is the document for the old version of ATK, it is basically suitable for calculation procedure of triplet state of O2 by using the new version of ATK.

17

General Questions and Answers / Re: How to calculate the enthalpy of reaction in ATK?

« on: March 3, 2017, 10:10 »

Assume that the contribution from phonons of substrates can be cancelled before and after the gas adsorption.
1. Calculate the vibration frequencies of an isolated gas molecule (i.e., the adsorbate);
2. Calculate the vibration frequencies only for the atoms belonging to the adsorbed molecules;
Following the formula in the following webpage to calculate the enthalpy for the adsorbate molecules before and after adsorption:
https://wiki.fysik.dtu.dk/ase/ase/thermochemistry/thermochemistry.html

18

General Questions and Answers / Re: Processes per saddle search

« on: March 2, 2017, 01:04 »

"What is purpose of including_"Shift to Gamma" in k-point sampling??"
Impose the Gamma point being included in the k-point sampling, because the BZ center (Gamma point) is the most important k point.

19

General Questions and Answers / Re: AKMC or KMC simulations

« on: March 1, 2017, 03:18 »

I am  aware of that but we want to see the influence of temperature on barriers.

The influence of temperature on barriers could be taken into account by post-processing the calculated vibration frequencies of diffusion particles in  saddle points and end points on the basis of quasi-harmonic approximation.  Please refer to the following paper:
Vacancy migration in hexagonal boron nitride
A. Zobelli, C. P. Ewels, A. Gloter, and G. Seifert
Phys. Rev. B 75, 094104 – Published 8 March 2007

20

General Questions and Answers / Re: Core-Shell nanowire

« on: March 1, 2017, 00:35 »

You may first create a silicon nanowire and then replace some of silicon atoms by Ge atoms.

21

General Questions and Answers / Re: AKMC or KMC simulations

« on: February 27, 2017, 11:25 »

The purposes of NEB and KMC are different. Please refer to wiki for KMC:
https://en.wikipedia.org/wiki/Kinetic_Monte_Carlo

22

General Questions and Answers / Re: How to figure out complex band structure at G-K?

« on: February 24, 2017, 04:45 »

choose the Miller indices (1,0,-1) to cleave the surface.

23

General Questions and Answers / Re: asking computer configuration for running ATK

« on: February 23, 2017, 02:26 »

In your case, the following parameters should be irrelevant to the transmission spectrum calculations:
 processes_per_neb_image=1,
 processes_per_individual=1,
 processes_per_saddle_search=1,

Because the NEB calculations and geometry optimization  aren't specified in your script.
Please refer to the manual: http://docs.quantumwise.com/manuals/Types/ParallelParameters/ParallelParameters.html

Only the 'processes_per_bias_point ' may affect the parallel jobs of your transmission spectrum calculations.
If processes_per_bias_point =1, it means only 1 process is used for each bias point. Actually there is only one bias voltage (zero V) in your script file. In this case, you will do the serial calculation and the whole memory will be used for this single serial calculations.  If the 'processes_per_bias_point ' value is determined automatically,  the whole memory will be shared by the  multiple processes. For each process, the memory will be insufficient, so your job failed. 

'The "Processor Main Features" of my computer is "Quad-Core", what does it mean? How can I use it for parallel calculation?'

To use all of these 4 cores,  one need to run the code via openmp (OMP_NUM_THREADS=4) or mpi. Please refer to the manual for the parallel job of ATK:
https://quantumwise.com/documents/manuals/ATK-2008.10/chap.parallel.html

24

General Questions and Answers / Re: unexpected low running speed

« on: February 19, 2017, 08:19 »

Please check the explanation of SG15 basis set from the manual:
http://docs.quantumwise.com/technicalnotes/atk_pseudo_basis/atk_pseudo_basis.html

You need to make a trade-off between the accuracy and the efficiency.

25

General Questions and Answers / Re: error in transmission spectra run at a specific vibrational modes

« on: February 19, 2017, 08:02 »

Thanks for your information.

Now I roughly know what cause the error.   It is no necessary to install atkpython separately, since you can run atkpython command. 
The error you met was because you may run the atkpython on the remote computer server and try to launch the X-windows (due to calling the matplotlib).

1) add the following lines into your script file at the beginning lines:
import matplotlib
# Force matplotlib to not use any Xwindows backend.
matplotlib.use('Agg')

or  2) when you login into your remove computer sever, add the "-X" into the ssh command, that is,  ssh  -X  hostname_your_computer_sever

or 3) install Xming (https://sourceforge.net/projects/xming/) on your local computer with Windows system.

Please refer to the following websites:
http://stackoverflow.com/questions/19309085/no-display-name-and-no-display-environment-variable-using-tkinter-through-ssh
http://stackoverflow.com/questions/2801882/generating-a-png-with-matplotlib-when-display-is-undefined

26

General Questions and Answers / Re: bending AGNR

« on: February 19, 2017, 07:46 »

The length of ribbon may too short, so it couldn't be bent into a tube by 360 degree.

27

General Questions and Answers / Re: asking computer configuration for running ATK

« on: February 18, 2017, 11:11 »

"Estimated Peak memory requirement         3519473 Mbyte  "-------->3519.473 GB memory

This exceeds the memory of computer too much. It can't be run on your computer definitely.

You need make a proper adjustment for the size of your simulated system, which seems to be a perfect MoS2 nanoribbons. In this case, it may be reasonable to use a shorter length of MoS2 in center region.

28

General Questions and Answers / Re: Optimization geometry at different electron temperature

« on: February 18, 2017, 11:01 »

To understand the difference among them, my suggestion is to first understand the "Born–Oppenheimer approximation" used in the DFT calculations:
https://en.wikipedia.org/wiki/Born%E2%80%93Oppenheimer_approximation

29

General Questions and Answers / Re: error in transmission spectra run at a specific vibrational modes

« on: February 18, 2017, 10:48 »

I have tried but again it failed. I reattach the input and screen shot taken showing the error.

Sabyasachi Sen

The errors in this time aren't related to atkpython.  First, you should ensure that you use atkpython (not the other python installed by yourself or provided by your computer system) to run the script file.  Second, make a proper setup for the python path.

The error indicates that you have used the matplotlib package from your own installment (./build/.....).

30

General Questions and Answers / Re: error in transmission spectra run at a specific vibrational modes

« on: February 17, 2017, 01:46 »

This may be caused by the different length of data in the "pl.plot()".

Please add the following line before "for i in modes:" to check the dimension of "SymP_LOE", "SymN_LOE", and so on:
print SymP_LOE.shape()

According to the manual:
http://docs.quantumwise.com/manuals/Types/InelasticTransmissionSpectrum/InelasticTransmissionSpectrum.html#NL.Analysis.InelasticTransmissionSpectrum.InelasticTransmissionSpectrum.inelasticTransmissionAsymmetricNegativeBias

The shape of "SymP_LOE" should be (number_of_energies, number_of_kpoints, number_of_qpoints, number_of_spins) for mode = integer.
pl.plot(E,SymP_LOE[i,:,0,0],'-',label='mode %d, + (LOE)' %i)
So if you change it to following line, it may work:
pl.plot(E,SymP_LOE[i,:,0,0,0],'-',label='mode %d, + (LOE)' %i)

The same changes are applied to other three lines:
pl.plot(E,AsymP_LOE[i,:,0,0,0],'-',label='mode %d, + (LOE)' %i)
pl.plot(E,SymP_XLOE[i,:,0,0,0],'-',label='mode %d, + (XLOE)' %i)
pl.plot(E,AsymP_XLOE[i,:,0,0,0],'-',label='mode %d, + (XLOE)' %i)

Please try it.