91
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. 
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92
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?
93
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
94
General Questions and Answers / Re: BSSE & Possible ATK Bug
« on: October 3, 2022, 20:42 »
Thanks Anders Blom.
This was helpful.
This was helpful.
95
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)?
96
General Questions and Answers / Re: BSSE & Possible ATK Bug
« on: October 1, 2022, 08:03 »
This issue happens only when we tick counterpoise for BSSE. Otherwise, I never faced this issue.
It also concerns me whether this only happens with K point sampling or other parameters also. Nevertheless, I always check file content post saving.
It also concerns me whether this only happens with K point sampling or other parameters also. Nevertheless, I always check file content post saving.
97
General Questions and Answers / Re: BSSE & Possible ATK Bug
« on: September 30, 2022, 21:10 »
Q2. I have attached a screenshot below. (It shows default 3x3x1 in saved file.py though i choose to keep 5x5x1) You can test on graphene maybe as: Set k sampling , then choose DFTD2 for vDw then tick BSSE counterpoise, when you get back you see k sampling has already changed then change again to desired and save. The saved file has again default. I use same version that of yours.
Q1. Thanks for the hack. Will try it.
Q1. Thanks for the hack. Will try it.
98
General Questions and Answers / Re: BSSE & Possible ATK Bug
« on: September 30, 2022, 12:20 »
Q1. No, what I am saying is I need to take BSSE at AB interface & BC interface. I am not taking AC interaction. How to do between AB & BC interface simultaneously?
Q2. yes i am sure its K points sampling (not density) that comes automatically na=2, nb=2 when saving the file after including BSSE.
Q2. yes i am sure its K points sampling (not density) that comes automatically na=2, nb=2 when saving the file after including BSSE.
99
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?
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?
100
General Questions and Answers / Re: I can't see UI of LabFloor
« on: September 27, 2022, 05:40 »
I think you should create a new project when QATK starts.
I faced similar issue sometime ago & creating a new project with proper path helped.
I faced similar issue sometime ago & creating a new project with proper path helped.
101
General Questions and Answers / Re: Reason for sudden jump in stress optimization
« on: September 21, 2022, 11:29 »
Thank you for all the help.
102
General Questions and Answers / Re: Reason for sudden jump in stress optimization
« on: September 21, 2022, 06:26 »
Dear Anders Blom,
Yes, I did grep -rni Warning/not converge but found no results which show I should not then worry about a single calculation jump as you said.
Also, I would like to ask, about restarting an MD simulation due to power shutdown. I use the following method:
1. I extract the last minus 1 image from the trajectory, send it to the script generator then use same calculators & MD block with same parameters as in the original script that was interrupted.
2. Further I send it to the editor where I replace the default initial velocity using Boltzmann (300K) by initial_velocity = Configuration_velocity(remove_center_of_mass=True)
I have attached the file below also.
My concern is whether I should keep equilibration time for pressure & temperature again in this restart or not as the trajectory had already reached equilibration (temperature, pressure) in the previous run. Is there any better method to restart the MD simulation?
Kindly help in this regard.
Thanking you in anticipation.
Yes, I did grep -rni Warning/not converge but found no results which show I should not then worry about a single calculation jump as you said.
Also, I would like to ask, about restarting an MD simulation due to power shutdown. I use the following method:
1. I extract the last minus 1 image from the trajectory, send it to the script generator then use same calculators & MD block with same parameters as in the original script that was interrupted.
2. Further I send it to the editor where I replace the default initial velocity using Boltzmann (300K) by initial_velocity = Configuration_velocity(remove_center_of_mass=True)
I have attached the file below also.
My concern is whether I should keep equilibration time for pressure & temperature again in this restart or not as the trajectory had already reached equilibration (temperature, pressure) in the previous run. Is there any better method to restart the MD simulation?
Kindly help in this regard.
Thanking you in anticipation.
103
General Questions and Answers / Re: Reason for sudden jump in stress optimization
« on: September 20, 2022, 02:52 »
The temperature I am talking of is the broadening temperature (1000K) & the system(Semiconductor) is in the vacuum.
Also, the calculator is NPT- Maryna Tobias Klein.
Also, if i run simulation for say 1500fs I see "grep -rni converge file.log | wc" gives me 1502. Should I be worried about these sudden jumps in temperature or just consider it some glitch due to numerical error as output file generates no warning or error sign?
Thanks
Also, the calculator is NPT- Maryna Tobias Klein.
Also, if i run simulation for say 1500fs I see "grep -rni converge file.log | wc" gives me 1502. Should I be worried about these sudden jumps in temperature or just consider it some glitch due to numerical error as output file generates no warning or error sign?
Thanks
104
General Questions and Answers / Re: Reason for sudden jump in stress optimization
« on: September 16, 2022, 06:26 »
Yes I tried increasing K point also. On the positive it is converging towards tolerance value however, the speed of convergence is very very slow.
Apart from damping factor are there any other crucial parameters that can help increase speed of convergence?
Also, talking of increase in temperature I read from QATK manual that increasing it too much can give incorrect results. (I use 1000K)
Apart from damping factor are there any other crucial parameters that can help increase speed of convergence?
Also, talking of increase in temperature I read from QATK manual that increasing it too much can give incorrect results. (I use 1000K)
105
General Questions and Answers / Re: Reason for sudden jump in stress optimization
« on: September 13, 2022, 11:39 »
Thankyou Anders Blom