1
Installation and License Questions / Re: Cannot assign more than 5 cores for AKMC
« on: October 23, 2024, 06:08 »
Yes, threading solved the issue. Thank you!
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2
General Questions and Answers / Re: configuration for Training set created by random displacement parameters
« on: October 23, 2024, 06:07 »
Thank you for your response.
After running the Defect Training Workflow, I was unable to locate any file containing the Training Set. However, I do have the 'mtp' object, which I can open in the Movie Tool. In my case, two defect configurations were generated by the defect block, and I used a sample size of 10, 20, and 10 for Rattle Atom, Rattle Cell, and Rattle Volume parameters, respectively.
I am curious about the resulting trajectory, as it consists of 140 steps, whereas I was expecting 80 steps (40 configurations per defect). Could you help clarify why this might be the case?
Thank you for your assistance.
After running the Defect Training Workflow, I was unable to locate any file containing the Training Set. However, I do have the 'mtp' object, which I can open in the Movie Tool. In my case, two defect configurations were generated by the defect block, and I used a sample size of 10, 20, and 10 for Rattle Atom, Rattle Cell, and Rattle Volume parameters, respectively.
I am curious about the resulting trajectory, as it consists of 140 steps, whereas I was expecting 80 steps (40 configurations per defect). Could you help clarify why this might be the case?
Thank you for your assistance.
3
General Questions and Answers / configuration for Training set created by random displacement parameters
« on: October 14, 2024, 10:53 »
Hello,
I have successfully used the Defect Training Workflow template to obtain the Moment Tensor Potential (MTP). I would now like to review the structures used in the training set, specifically those generated by applying the Rattle Atom, Rattle Cell, and Rattle Volume random displacement parameters.
While I can see that these random displacement parameter objects have been added to the table, I am unsure how to visually inspect or view them. Could you please guide me on how to access or visualize the specific configurations generated by these displacement parameters?
Thank you in advance for your assistance.
I have successfully used the Defect Training Workflow template to obtain the Moment Tensor Potential (MTP). I would now like to review the structures used in the training set, specifically those generated by applying the Rattle Atom, Rattle Cell, and Rattle Volume random displacement parameters.
While I can see that these random displacement parameter objects have been added to the table, I am unsure how to visually inspect or view them. Could you please guide me on how to access or visualize the specific configurations generated by these displacement parameters?
Thank you in advance for your assistance.
4
Installation and License Questions / Re: Cannot assign more than 5 cores for AKMC
« on: October 14, 2024, 06:37 »
Hello,
I’m revisiting this topic because I encountered the same license error while running AKMC with a trained MTP. Specifically, when I use the forcefield calculator and assign more than 7 cores, I get a license error that says, “licensed number of users already reached.”
You previously mentioned that I could set processes_per_saddle_search in the ParallelParameters object to distribute the cores per saddle search. However, it seems that this option isn’t available when I’m using the forcefield calculator (TremoloXCalculator())
Is there another way to manage core allocation for the forcefield calculator under the same license restrictions? I want to make full use of the available cores to speed up this calculation.
Thanks!
I’m revisiting this topic because I encountered the same license error while running AKMC with a trained MTP. Specifically, when I use the forcefield calculator and assign more than 7 cores, I get a license error that says, “licensed number of users already reached.”
You previously mentioned that I could set processes_per_saddle_search in the ParallelParameters object to distribute the cores per saddle search. However, it seems that this option isn’t available when I’m using the forcefield calculator (TremoloXCalculator())
Is there another way to manage core allocation for the forcefield calculator under the same license restrictions? I want to make full use of the available cores to speed up this calculation.
Thanks!
5
General Questions and Answers / Plotting fermi surface by tag (like fatbandstructure)
« on: September 19, 2024, 07:00 »
Is it possible to plot a 2D Fermi surface while assigning weights to specific tags, similar to how fat band structures are visualized? For instance, if the surface and bulk states are tagged in the configuration, can these tags be used to indicate their respective contributions to the bands in the Fermi surface plot? I have already generated a 2D Fermi surface plot (ka vs kb), but I would like to differentiate between the contributions from bulk and surface states.
6
General Questions and Answers / Re: Discrepancy in bulk and device transmission
« on: September 19, 2024, 06:45 »
I realize there may have been some confusion. The screenshots I attached represent the total transmission, while the transmission values I mentioned earlier refer to the per-spin transmission. I apologize for any misunderstanding this may have caused. So per-spin or total transmission, both matches the device and bulk transmission when bulk transmisison are repeated 2x in transverse plane.
7
General Questions and Answers / Re: Discrepancy in bulk and device transmission
« on: September 13, 2024, 07:18 »
Hello, I have tried several methods to match the results between bulk and device transmission.
Increasing the number of energy point for calculation for both bulk and device have almost no effect in transmission result.
Increasing the extended electrode size for device configuration from 8.8Å to 13.2Å very slightly increases the device transmission from 2.1552 to 2.1641 (I assume this value will converge when increasing the extended elecrode size)
Repeating the bulk configuration x2 in the c direction (transport direction) changes bulk transmission from 4.94 to 2.1667, further repeating it to x3 result in 2.1665.
So repeating the bulk configuration in the transport direction solved the issue. Thank you for your suggestions!
Increasing the number of energy point for calculation for both bulk and device have almost no effect in transmission result.
Increasing the extended electrode size for device configuration from 8.8Å to 13.2Å very slightly increases the device transmission from 2.1552 to 2.1641 (I assume this value will converge when increasing the extended elecrode size)
Repeating the bulk configuration x2 in the c direction (transport direction) changes bulk transmission from 4.94 to 2.1667, further repeating it to x3 result in 2.1665.
So repeating the bulk configuration in the transport direction solved the issue. Thank you for your suggestions!
8
General Questions and Answers / Re: Discrepancy in bulk and device transmission
« on: September 6, 2024, 08:02 »
+ additional attachment for device configuraiton
9
General Questions and Answers / Discrepancy in bulk and device transmission
« on: September 6, 2024, 08:01 »
Hello,
I’ve come across previous discussions regarding differences between bulk and device transmission calculations, but none have helped solve my issue.
I am working with a bulk configuration that consists of 3-10 repeated unit cells in the b direction, along with 12.5 Å of vacuum in the top and bottom of the b direction (as shown in the first screenshot attached).
For the device configuration, it is similar to the bulk configuration, but with 10 repeated unit cells in the c direction (the transport direction).
After performing transmission calculations for both the bulk and the device configurations, I noticed a significant discrepancy between the two results. Theoretically, the bulk and device transmission values should be at least somewhat similar, but that’s not the case in my results.
Could you help me understand the possible reasons for this difference?
Thank you!
I’ve come across previous discussions regarding differences between bulk and device transmission calculations, but none have helped solve my issue.
I am working with a bulk configuration that consists of 3-10 repeated unit cells in the b direction, along with 12.5 Å of vacuum in the top and bottom of the b direction (as shown in the first screenshot attached).
For the device configuration, it is similar to the bulk configuration, but with 10 repeated unit cells in the c direction (the transport direction).
After performing transmission calculations for both the bulk and the device configurations, I noticed a significant discrepancy between the two results. Theoretically, the bulk and device transmission values should be at least somewhat similar, but that’s not the case in my results.
Could you help me understand the possible reasons for this difference?
Thank you!
10
General Questions and Answers / Re: How to use workflow iteration for multiple calculation with one calculator?
« on: September 6, 2024, 06:56 »
I have attached the workflow(I provided a link since hdf5 file cannot be attached in the forum) and screenshots below.
However, the workflow resets with "unique string error" whenever I leave the worfklow screen to builder or clicking on any other window.
Basically I created the workflow by
1. Add iteration block
2. attach lcao calculator and optimize geometry block under iteration block
3. Click iteration block and add 4 configurations (tick/unitick iterator, same error appears)
Any additional click on other workflow, or sending the script, will result in an error as shown in the 2nd screenshot attached.
Workflow: https://drive.google.com/file/d/1jBxA2FUcORFVzzFn-nrCRf2Hqkz4gYuH/view?usp=sharing
However, the workflow resets with "unique string error" whenever I leave the worfklow screen to builder or clicking on any other window.
Basically I created the workflow by
1. Add iteration block
2. attach lcao calculator and optimize geometry block under iteration block
3. Click iteration block and add 4 configurations (tick/unitick iterator, same error appears)
Any additional click on other workflow, or sending the script, will result in an error as shown in the 2nd screenshot attached.
Workflow: https://drive.google.com/file/d/1jBxA2FUcORFVzzFn-nrCRf2Hqkz4gYuH/view?usp=sharing
11
General Questions and Answers / Re: How to use workflow iteration for multiple calculation with one calculator?
« on: September 5, 2024, 07:55 »
I can't share the script since the error pops up (the same 'unique string error' ) when I try to create the script 
Also, I've already adjusted the names manually so that the first letter of names for each configuration is not a number.
Also since you mentioned that it is more used to loop over parameters in calculator instead of configuration, maybe iteration block is not used for my needs because I wanted to use different configurations.
Thanks!
Also, I've already adjusted the names manually so that the first letter of names for each configuration is not a number. Also since you mentioned that it is more used to loop over parameters in calculator instead of configuration, maybe iteration block is not used for my needs because I wanted to use different configurations.
Thanks!
12
General Questions and Answers / Re: How to use workflow iteration for multiple calculation with one calculator?
« on: August 29, 2024, 06:43 »
Thank you for your answer! I did as you told me and it worked!
One more question, is it possible to use iteration block instead of table iteration for such calculation?
I am curious if there is any difference and also why it keeps on giving me the same "unique string" error even though the names of configurations were adjusted.
Thanks!
+ The main problem is solved but I ask this because I am trying to get used to the features in workflow
One more question, is it possible to use iteration block instead of table iteration for such calculation?
I am curious if there is any difference and also why it keeps on giving me the same "unique string" error even though the names of configurations were adjusted.
Thanks!
+ The main problem is solved but I ask this because I am trying to get used to the features in workflow
13
General Questions and Answers / How to use workflow iteration for multiple calculation with one calculator?
« on: August 21, 2024, 05:11 »
Hello,
I'm working on a workflow where I aim to perform calculations on multiple configurations using a single calculator instance. My goals are to:
1. Understand why the script generated from my workflow isn't functioning as expected. (See attached files 1, 2, and 3, which show the process of optimizing a Cu slab with different thicknesses.)
2. Clarify if the memory consumption for the script is simply the sum of the memory required for each individual calculation. If that's the case, what strategies can I use to reduce the overall memory footprint?
Additionally, when I attempted to use the iteration block (instead of the iteration table block), I encountered an error that prevented script generation. Here is the error message:
Any insights or advice on these issues would be greatly appreciated!
Thank you!
I'm working on a workflow where I aim to perform calculations on multiple configurations using a single calculator instance. My goals are to:
1. Understand why the script generated from my workflow isn't functioning as expected. (See attached files 1, 2, and 3, which show the process of optimizing a Cu slab with different thicknesses.)
2. Clarify if the memory consumption for the script is simply the sum of the memory required for each individual calculation. If that's the case, what strategies can I use to reduce the overall memory footprint?
Additionally, when I attempted to use the iteration block (instead of the iteration table block), I encountered an error that prevented script generation. Here is the error message:
Code
Traceback (most recent call last):
File "zipdir/NL/GUI/Tools/WorkflowTool/WorkflowSendToMenu.py", line 180, in onActionTriggered
File apd/N/601./azWindow/lanindowpy Line 785, in showtool
File "zipdir/NL/GUI/Tools/WorkflowTool/WorkflowBuilder.py", line 176, in deactivate
File "zipdir/NL/GUI/Tools/WorkflowTool/WorkflowBuilderWidget.py", line 206,
saveCurrent
File "zipdir/NL/GUI/Workflow/InteractiveWorkflow.py", line 379, in saveStateString
File "zipdir/NL/GUI/Workflow/FlowTree.py", line 128, in saveStateString File "zipdir/NL/GUI/Workflow/Blocks/Block.py", line 846, in saveStateString File "zipdir/NL/GUI/Store/Utilities.py", line 198, in uniqueString File "zipdir/NL/GUI/Store/Utilities.py", line 219, in uniqueString File "zipdir/NL/GUI/Store/Utilities.py", line 219, in uniqueString File "zipdir/NL/GUI/Store/Utilities.py", line 198, in uniqueString File "zipdir/NL/GUI/Store/Utilities.py", line 219, in uniqueString File "zipdir/NL/GUI/Store/Utilities.py", line 219, in uniqueString File "zipdir/NL/GUI/Store/Utilities.py", line 191, in uniqueString NL. ComputerScienceUtilities.Exceptions.NLNotImplementedError: value ConfigurationListBlock(23375294451984) requires a uniqueString handlingAny insights or advice on these issues would be greatly appreciated!
Thank you!
14
General Questions and Answers / Re: Is Planewave PAW Spin Orbit Coupling not supported?
« on: July 15, 2024, 08:54 »
Hello,
I went through the script and found out it was my mistake. However though, there seem to be problem in the workflow, whenever PW PAW SOC is selected, the workflow can't be saved and the following error message appears (screenshot attached).
++
I am using 2023.12 version and I wasn't trying to load workflow from an older version.
The workflow was created within 2023.12 version
I went through the script and found out it was my mistake. However though, there seem to be problem in the workflow, whenever PW PAW SOC is selected, the workflow can't be saved and the following error message appears (screenshot attached).
++
I am using 2023.12 version and I wasn't trying to load workflow from an older version.
The workflow was created within 2023.12 version
15
General Questions and Answers / Is Planewave PAW Spin Orbit Coupling not supported?
« on: July 12, 2024, 09:39 »
I tried running Planewave PAW SOC but the calculation is run without SOC.
Is it because it is not supported?
Thanks
Is it because it is not supported?
Thanks