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Topics - AsifShah

Pages: 1 [2] 3
16
General Questions and Answers / QATK unable to read files
« on: March 25, 2023, 12:10 »
Dear ADmin,

I have observed that sometimes QATK is unable to read files upon restarting as shown below in the attached pic.

This has happened many times. Please let me know what is the issue?

It also shows some source scanning error. More than 100000 files in /directory

17
General Questions and Answers / Machine Learning Prerequisites
« on: March 23, 2023, 09:35 »
Dear Admin,

To work with ML force fields provided in QuantumATK, what are the prerequisites required to begin with?
Is there any background course/subjects one should be familiar with?
Also, can you recommend any course to start with?

18
General Questions and Answers / Two Reactive ForceField
« on: December 26, 2022, 07:40 »
Is it possible to combine multiple Reactive Forcefield in an MD simulation for different pairs of atoms?

19
General Questions and Answers / How to save movie from MD trajectory?
« on: December 18, 2022, 01:04 »
Dear Admin,
how does one save MD trajectory as movie for ppt?

20
General Questions and Answers / Effective potential
« on: December 8, 2022, 06:49 »
Dear Admin,

What is the physical meaning of effective potential in QATK? I understand it is the potential in the Hamiltonian of system, however it is difficult to understand what do all the crust and trough mean? or what is the eff. pot actually represent in a system?
I have attached a pic from a paper. This paper mentions relative difference between maximas at interface as tunneling barrier.
https://pubs.acs.org/doi/pdf/10.1021/acsanm.2c00995


21
General Questions and Answers / Error - Exit Code : 9
« on: November 22, 2022, 10:18 »
Dear Admin,
I was performing some HSE06 calculations & got the following error:

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 17811 RUNNING AT node8
=   EXIT CODE: 9
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 17811 RUNNING AT node8
=   EXIT CODE: 9
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
   Intel(R) MPI Library troubleshooting guide:
      https://software.intel.com/node/561764
===================================================================================


Kindly help in this regard.

22
General Questions and Answers / PDOS projection on orbitals used in pseudopotential basis set
« on: November 12, 2022, 09:38 »
Is there a way to project density of states on the valence orbitals used in basis set in a pseudopotential?

for eg, When using pseudodojo pseudopotential, I can get projections on d orbitals of Mo but that includes both 3d and 4d orbitals?
However, I want only to project on 4d orbitals?

From manual I saw QATK allows projection on angular quantum numbers only, but how does one select the principal quantum number?

23
General Questions and Answers / Hook Method for Partial Charge
« on: October 30, 2022, 07:40 »
Dear Admin,

I am trying to call partial charges on configuration inside a hook method as:

def post_step_hook(step, time, configuration, forces, stress):
    PC=PartialCharges(configuration)

md_trajectory = MolecularDynamics(
    bulk_configuration,
    constraints=constraints,
    trajectory_filename='File1.hdf5',
    steps=3000,
    log_interval=10,
    post_step_hook=post_step_hook,
    method=method
)


But I get the following error:
Traceback (most recent call last):
  File "Electric_Field_F_Migration.py", line 923, in <module>
    md_trajectory = MolecularDynamics(
  File "zipdir/NL/Dynamics/MolecularDynamics/MolecularDynamics.py", line 776, in MolecularDynamics
  File "zipdir/NL/Dynamics/MolecularDynamics/HookFunctionContainer.py", line 252, in callAllHookFunctions
  File "Electric_Field_F_Migration.py", line 914, in post_step_hook
    PC=PartialCharges(configuration)
  File "zipdir/NL/Analysis/PartialCharges.py", line 85, in __init__
  File "zipdir/NL/Analysis/Analysis.py", line 282, in __init__
  File "zipdir/NL/Analysis/Analysis.py", line 253, in _supportConfigurationWithCalculator
  File "zipdir/NL/Analysis/Analysis.py", line 209, in _supportConfiguration
  File "zipdir/NL/Analysis/AnalysisUtilities.py", line 176, in checkConfiguration
NL.ComputerScienceUtilities.Exceptions.NLTypeError: The parameter 'configuration' must be an instance of one of the following: BulkConfiguration, MoleculeConfiguration, DeviceConfiguration


Kindly help in this case, as how to calculate partialcharges inside hook?

24
General Questions and Answers / Unexplainable Glitch in NPT Molecular Dynamics (Possible ATK Numerical Error?)
« on: October 12, 2022, 06:48 »
Dear Admin,

I have been running NPT simulations (at 300K, details in attached file below) using Martyna Tobias Klien's calculator. The files are attached below.
However, I see my system suffers from a sudden glitch (shown in the pic below). I re-ran my script again but it still shows the glitch.
This has happened for other temperatures also.

Kindly state the possible reasons for this sudden change in temperature. Although grep -rni warning file.log  shows no error or warning.

(The .log file was very large, so I have grep MD in the attached file. It shows how suddenly instant temperature changes to very high values of 1000K+)

Thanks

25
General Questions and Answers / BSSE & Possible ATK Bug
« on: September 27, 2022, 12:13 »
Q1. How to use BSSE correction for three parts of a system such as A-B-C with two interfaces between AB & BC?

Normally we have for single interface as:
CounterpoiseCorrectedLCAOCalculator = counterpoiseCorrected(
    LCAOCalculator,
    tag_list=['Left', 'Right'],
    )


For two interfaces should it be as? :
CounterpoiseCorrectedLCAOCalculator = counterpoiseCorrected(
    LCAOCalculator,
    tag_list=['Left', 'Middle', 'Right'],
    )

where left, middle, right are adjacent & comprise of full system.

Q2. In the QuantumATK version released in 2022, I see when I use BSSE correction (inbuilt) & the set K point sampling to some value say (7x7x1). I have found that in the saved .py file it always shows 2x2x1 as k point sampling. Is this some internal error with QuantumATK?

26
General Questions and Answers / Reason for sudden jump in stress optimization
« on: August 20, 2022, 19:27 »
Dear All,
I am running optimization for a metal-semiconductor structure. I ran it earlier for 24 hours then it got interrupted & I took last minus 2 image from trajectory & rerun the calculation. However, I observed the following sudden increase in stress as shown in image below.
Also the simulation is converging very slowly.

Kindly provide any reason for why it is converging slowly? & why this sudden increase in stress?

27
General Questions and Answers / 3D plots
« on: August 16, 2022, 16:15 »
Dear Admin,
How can one visualize 3D plots of band decomposed charge density? Like 3D charge accumulation & depletion regions?

28
General Questions and Answers / Using GPUCompute Nodes
« on: August 13, 2022, 08:44 »
Dear Admin,
Is it possible to run QATK on GPU compute nodes?
If so, how can I do that?
Also, will there be a speedup in comparison to running a optimization calculation on CPU?

29
General Questions and Answers / Interface Relaxation
« on: August 6, 2022, 07:30 »
Dear Admin,
Are these methods same or different? (Kindly mention the difference if any) {Assume A & B are pre-relaxed before building interface}
Method 1: I make interface between two materials A & B using interface builder with a strain of 3%. Then I do interface relaxation using DFT keeping layers away from interface as rigid.

Method 2: I make interface between two materials A & B using interface builder with a strain of 0.8% (using large supercell). Then I do interface relaxation using DFT keeping layers away from interface as rigid.

Method 3: I just drag & drop two materials with (say) 4x4  supercell in builder & adjust interface distance to some value from experiments. Then perform a full DFT optimization.

Will all methods yield same end configuration? Also, how is method 3 different from 1 & 2 and if it is same what is then the purpose of interface builder?

30
General Questions and Answers / AKMC License
« on: August 2, 2022, 13:16 »
I was running adaptive kinetic monte carlo (AKMC) on 80 cores using the following command:
mpiexec.hydra -n 80 atkpython akmc_test.py > akmc_test.log
however i get this error, though we already have more than 80 licenses of ATK.

License Error: Unable to obtain a required license for the
requested license feature. It could mean there are no valid
licenses left, a problem with the connection to the license
server, or the license file does not contain the requested feature.
See below for more details.

Licensed number of users already reached.
Feature:       qatk_forcefield
License path:  27020@XXXXXXXXX:
FlexNet Licensing error:-4,234



Kindly help resolve it. Also, are there separate licenses required to use AKMC module.


Also, is there a way to add external potential energy contributions in CINEB/NEB calculations? I am interested in observing how the migration barrier is affected by some external potential energy/ applied field? If it is possible how to do it?

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