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Topics - AsifShah

Pages: [1] 2
1
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.

2
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?

3
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?

4
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

5
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?

6
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?

7
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?

8
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?

9
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?

10
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?

11
General Questions and Answers / Multiple Node issue
« on: July 23, 2022, 15:16 »
Dear Admin,

When using the following command for 2 node with 25 cores per node:
mpiexec -n 50 -ppn 25 atkpython test.py > test.log
I see from CPU activity all calculations run on single node.

& when I use following command (host_names is a file that contains compute node addresses):
mpiexec -f host_names -n 50 -ppn -25 atkpython test.py > test.log
I see this error:
bash: /opt/QuantumATK/QuantumATK-T-2022.03-SP1/libexec/pmi_proxy: No such file or directory
bash: /opt/QuantumATK/QuantumATK-T-2022.03-SP1/libexec/pmi_proxy: No such file or directory


Kindly help resolve this error.

12
Dear Admin, I want to run QATK on multiple nodes.
I have added paths of license, mpiexec.hydra (from libexec) & atkpython (bin) in ~/.bashrc added.
next I run the following commands on terminal.

1. mpiexec.hydra -f host_file -n 200 -ppn 40 atkpython filename.py > output.log
(host_file contains list of node information)
I get the following errors:
            i) /etc/tmi.conf: No such file or directory
 
              ii) DAPL startup: RLIMIT_MEMLOCK too small


2. mpiexec.hydra  -n 200 -ppn 40 atkpython filename.py > output.log
In this case although I mention 200/40= 5 nodes but it runs all calculation on single node & not on expected 5 nodes.


KIndly provide a solution!

13
Dear Admin/Others,
When doing device from bulk, it chooses minimal electrode length as one atom. However, I want to keep 2 or 3 atoms as my electrode I tried changing +/-  as shown in attachment, also tried changing left & right values below (see attachment) & electrode extension length but it does not help change the electrode length & keeps it fixed as one atom. How to rectify it? I found that changing left & right values below had no effect on the electrode size. Kindly help.
Check the attachments below.

(The reason why I want to change it to 2 or 3 atoms is because in electrode validator it says large matrix elements error & asks to increase electrode size)

14
General Questions and Answers / Bandstructures
« on: June 30, 2022, 11:28 »
Dear Admin/Anyone,
Could you kindly explain why any multiple of 3 chosen for a supercell (in this case for moS2) produces a different bandstructure than other sizes. It can be seen below that for a supercell of 3x3 & 9x9 we have VBM & CBM along G point whereas for other sizes such as 4x4,5x5 it is along KM points?
 Is it something with software or I am missing something here?
See the attachment below


15
I am calculating the dissociation energy of Hydrogen molecule.
The formula used is E(disso)=E(H2)-2E(H)
where E(H2) is the total energy calculated using two methods as:
1. Spin unpolarised/polarized using B3LYP functionals giving energies - 32, -32 respectively.
2. Spin unpolarised/polarised using PBE functionals giving energies - 31.651, -27.181 respectively.
Since H2 is spin unpolarised molecule & when choosing unpolarised/polarised using B3LYP both give same energy -32 which makes sense but why does PBE give different results for spin polarised & spin unpolarised?

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