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Messages - AsifShah

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1
General Questions and Answers / Re: Optimization issue
« on: November 27, 2022, 07:44 »
Try keeping max stress 0.001 eV/[A][/-3]
change the gpa unit to eV/A-3

2
General Questions and Answers / Re: Error - Exit Code : 9
« on: November 23, 2022, 06:25 »
Thankyou.

3
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.

4
General Questions and Answers / Re: Hook Method for Partial Charge
« on: November 12, 2022, 09:49 »
Thanks yes it did work.

5
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?

6
General Questions and Answers / Re: Hook Method for Partial Charge
« on: November 10, 2022, 12:41 »
I already tried this one but it returns nothing.

7
I have attached the script below.

8
General Questions and Answers / Re: Simulating protein
« on: October 31, 2022, 08:29 »
Probably memory issue. I faced same in other simulations especialy DOS calculations.

My guess would be you are taking too much stringent conditions such as high density of k points, mesh, large energy intervals, high density for energy sampling points, or other convergence parameters.

9
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?

10
I will rerun with other Grimme corrections and see if the spike repeats.

11
YOu can do some literature survey to see the concentration of gases used in experiments. :)

12
But I am not using any forcefield potential. It is an ab-initio Molecular Dynamic Run.

What could possibly be wrong?

13
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

14
General Questions and Answers / Re: BSSE & Possible ATK Bug
« on: October 3, 2022, 20:42 »
Thanks Anders Blom.
This was helpful.

15
General Questions and Answers / Re: BSSE & Possible ATK Bug
« on: October 3, 2022, 11:58 »
You are welcome.
Also, with regard to Q1. I had a question. For a structure ABC with two interfaces AB & BC, if we include BSSE during optimization the computational time increases crazily for a big system since each BSSE calculation requires 5 internal optimizations making it a total of 10 optimization calculations per structure which is computationally very expensive.

Therefore, I was thinking instead of using BSSE during optimization how about the following:
1. Optimize ABC without BSSE.
2. Use optimized structure from step 1, put A as rigid, B as rigid & C as rigid then perform BSSE optimization again.

Since here we are interested in estimating the interfacial distance accurately, would this method be the correct one (given I understand it is a crude method)?

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