1
General Questions and Answers / Re: Setting different temperature for different regions
« on: September 6, 2024, 22:32 »
Thanks a lot.
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2
General Questions and Answers / Re: Setting different temperature for different regions
« on: August 31, 2024, 21:35 »
Dear Ander Bloms,
It's for simulating Joule's heating in a small region.
I would love to share but I am still improving upon the code. I am not able to maintain temperature properly. I used manual code in hook method but I was thinking if I could utilize velocity distribution from class MaxwellBoltzmannDistribution in QuantumATK. I have been trying to obtain velocities from this distribution but i run into errors.
Can you help me with that? I am trying to set velocities using this method for a configuration but it runs into error. Kindly help in this case.
Also, is there a direct way to extract say 10 random velocities from class MaxwellBoltzmannDistribution?
It's for simulating Joule's heating in a small region.
I would love to share but I am still improving upon the code. I am not able to maintain temperature properly. I used manual code in hook method but I was thinking if I could utilize velocity distribution from class MaxwellBoltzmannDistribution in QuantumATK. I have been trying to obtain velocities from this distribution but i run into errors.
Can you help me with that? I am trying to set velocities using this method for a configuration but it runs into error. Kindly help in this case.
Also, is there a direct way to extract say 10 random velocities from class MaxwellBoltzmannDistribution?
Code
# %% Molybdenite (1)
# Set up lattice
lattice = Hexagonal(3.1604*Angstrom, 12.295*Angstrom)
# Define elements
elements = [Molybdenum, Sulfur, Molybdenum]
# Define coordinates
fractional_coordinates = [[ 0.333333333333, 0.666666666667, 0.25 ],
[ 0.666666666667, 0.333333333333, 0.121 ],
[ 0.666666666667, 0.333333333333, 0.379 ]]
# Set up configuration
molybdenite_1 = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates,
)
molybdenite_1_name = "molybdenite_1"
molybdenite_1.setVelocities(
velocities=MaxwellBoltzmannDistribution(
temperature=300*Kelvin
)
)3
General Questions and Answers / Re: Setting different temperature for different regions
« on: August 27, 2024, 07:27 »
Dear Anders Blom,
Thanks for your response.
I was able to do it manually using post_step_hook. Looks like post_step_hook is a nice way to do many things.
Thanks for your response.
I was able to do it manually using post_step_hook. Looks like post_step_hook is a nice way to do many things.
4
General Questions and Answers / Setting different temperature for different regions
« on: August 16, 2024, 21:55 »
Dear Admin,
How can one set a heating rate only for a specific tag of atoms? In QuantumATK by default heating rate is set for all atoms.
How can one set a heating rate only for a specific tag of atoms? In QuantumATK by default heating rate is set for all atoms.
5
General Questions and Answers / Re: Relaxation of devices (optimize the geometry of a two-probe system)
« on: July 5, 2024, 12:20 »
As a rule, you need to optimize electrodes separately first and then create the structure you want.
After that the central region should include some portion of electrodes and your molecule and then optimize all of central region.
PS: During optimization - electrode and electrode extensions will be fixed.
Thanks
After that the central region should include some portion of electrodes and your molecule and then optimize all of central region.
PS: During optimization - electrode and electrode extensions will be fixed.
Thanks
6
General Questions and Answers / Re: Geometric optimization
« on: July 5, 2024, 12:18 »
You can do it in the device optimizer in QATK. You can set voltage values in LCAO calculator. However, there maybe convergence issues due to high bias.
7
General Questions and Answers / Re: Questions about MD reservoir temperature and its analysis
« on: June 17, 2024, 16:01 »
The instan. temperature will always fluctuate around reservoir temperature and it is normal.
May I know:
1. What type of forcefield you are using?
2. If you can provide a longer time scale graph?
3. What time do you set for thermostat timescale and barostate timescale?
May I know:
1. What type of forcefield you are using?
2. If you can provide a longer time scale graph?
3. What time do you set for thermostat timescale and barostate timescale?
8
General Questions and Answers / Re: Questions about MD reservoir temperature and its analysis
« on: June 14, 2024, 11:53 »
yes you can see after 10ps both are coming close to each other..
If you are using DFT then 2-3 ps is enough for equilibration however for classical forcefield, do use longer timescales maybe up to 100 ps.
If you are using DFT then 2-3 ps is enough for equilibration however for classical forcefield, do use longer timescales maybe up to 100 ps.
9
General Questions and Answers / Re: Questions about MD reservoir temperature and its analysis
« on: June 13, 2024, 08:32 »
I think this is the equilibration period since the simulation has only progressed a few femtoseconds. Can you show behavior after 10 ps?
10
General Questions and Answers / Re: Questions about MD reservoir temperature and its analysis
« on: June 12, 2024, 09:27 »
I will try to answer:
1. Reservoir temperature is like the temperature you set on the AC in your room, i.e., the reference temperature you want. Then there is instantaneous temperature- which is the actual temperature calculated from kinetic energy of atoms. Insta. temp. oscillates around the reservoir temperature.
2. I would suggest to heat the system slowly from 300 to 3000K. (The term slowly is generic here- it depends on how much computational resources you have, type of study you want to conduct etc. Also, more slow means more time taking process).
3. Can you please the graph? I don't understand.
1. Reservoir temperature is like the temperature you set on the AC in your room, i.e., the reference temperature you want. Then there is instantaneous temperature- which is the actual temperature calculated from kinetic energy of atoms. Insta. temp. oscillates around the reservoir temperature.
2. I would suggest to heat the system slowly from 300 to 3000K. (The term slowly is generic here- it depends on how much computational resources you have, type of study you want to conduct etc. Also, more slow means more time taking process).
3. Can you please the graph? I don't understand.
11
General Questions and Answers / Re: Radial distribution
« on: June 12, 2024, 09:21 »
You can use inbuilt function in QATK to plot radial and angular distribution.
When you single click on MD trajectory, there will be an option to the right where you can choose "MD Analyzer"
When you single click on MD trajectory, there will be an option to the right where you can choose "MD Analyzer"
12
General Questions and Answers / Re: Implementing a new Reactive Forcefield
« on: June 8, 2024, 08:46 »
Dear Anders Blom,
Thanks a lot.
Yes, now I can run it very well.
Thanks a lot.
Yes, now I can run it very well.
13
General Questions and Answers / Re: Implementing a new Reactive Forcefield
« on: June 5, 2024, 10:46 »
Dear Anders Blom,
Thanks a lot for your response.
Thanks a lot for your response.
14
General Questions and Answers / Re: Implementing a new Reactive Forcefield
« on: June 4, 2024, 07:25 »
Dear Anders Blom,
How should one include effects due to electric field?
Is it possible to include optimized trajectories under electric fields?
Moreover, if the MTP is designed in this way, can it predict material distortions when subjected to high electric fields?
How should one include effects due to electric field?
Is it possible to include optimized trajectories under electric fields?
Moreover, if the MTP is designed in this way, can it predict material distortions when subjected to high electric fields?
15
General Questions and Answers / Re: Implementing a new Reactive Forcefield
« on: June 2, 2024, 09:32 »
Dear Anders Blom,
Thanks for your response. I thought about it earlier but the problem is that I am not sure how accurate the MTP will be for studying the properties that I want to study. Also, generating AIMD training data for those properties is very time consuming. That's why I wanted to use something that is already tested.
Thanks for your response. I thought about it earlier but the problem is that I am not sure how accurate the MTP will be for studying the properties that I want to study. Also, generating AIMD training data for those properties is very time consuming. That's why I wanted to use something that is already tested.