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
change the gpa unit to eV/A-3
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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.
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
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?
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
General Questions and Answers / Re: Hook Method for Partial Charge
« on: November 9, 2022, 07:16 »
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.
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?
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
General Questions and Answers / Re: Unexplainable Glitch in NPT Molecular Dynamics (Possible ATK Numerical Error?)
« on: October 20, 2022, 12:49 »
I will rerun with other Grimme corrections and see if the spike repeats.
11
General Questions and Answers / Re: Can we know the concentration used of the studied gas ?
« on: October 20, 2022, 06:26 »
YOu can do some literature survey to see the concentration of gases used in experiments. 
12
General Questions and Answers / Re: Unexplainable Glitch in NPT Molecular Dynamics (Possible ATK Numerical Error?)
« on: October 20, 2022, 06:25 »
But I am not using any forcefield potential. It is an ab-initio Molecular Dynamic Run.
What could possibly be wrong?
What could possibly be wrong?
13
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
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.
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)?
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)?