Closed kedhar1992 closed 3 years ago
pierrehirel
commented
3 years ago Dear Sir,
Thank you for using Atomsk. I did not experience what you describe with the version beta-0.11.
Can you please provide an example file ? (input file, or final polycrystal configuration)
Regards
kedhar1992
commented
3 years ago Dear Sir,
Kindly find the attached xsf and voronoi files. Sorry, I couldn't attach the final configuration due to heavy file size. I ran the program using the line ""C:\Program Files (x86)\Atomsk\atomsk.exe" --polycrystal Zr.xsf voronoi.txt 500_4.cfg -wrap"
Regards
On Mon, Mar 1, 2021 at 2:03 PM Pierre Hirel notifications@github.com wrote:
Dear Sir,
Thank you for using Atomsk. I did not experience what you describe with the version beta-0.11.
Can you please provide an example file ? (input file, or final polycrystal configuration)
Regards
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box 500 500 500 lattice fcc
pierrehirel
commented
3 years ago Dear Sir,
I have run multiple times the command with your parameters, and I never found a system where there is void between grains.
Can you please provide the following:
Regards
kedhar1992
commented
3 years ago Dear Sir,
I ran several times with the following version(s) and got the same configuration: version of Window: Windows 10 Pro for workstation version of Atomsk: Version 0.11 (I check this while running atomsk command line)
Kindly find the attached screenshot of the configuration and the output from the terminal window while running Atomsk code (output.txt).
Thank you & Regards A. Kedharnath
On Wed, Mar 3, 2021 at 7:52 PM Pierre Hirel notifications@github.com wrote:
Dear Sir,
I have run multiple times the command with your parameters, and I never found a system where there is void between grains.
Can you please provide the following:
- version of Windows you are running (Windows 7, 10?)
- version of Atomsk (confirm it is beta-0.11 downloaded from the Website)
- a screenshot of your terminal (Power Shell) after you run the command inside
- a picture of your final system
Regards
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| | | o---o A T O M S K | | o---o| Version 0.11 | | | |o (C) 2010 Pierre Hirel | | o---o https://atomsk.univ-lille.fr | |____|
Constructing a polycrystal using Voronoi method. Opening the input file: Zr.xsf ..> Input file was read successfully (2 atoms). Reading parameters for Voronoi construction from: voronoi.txt ..> File was successfully read. ..> Number of grains to be constructed: 4 ..> Using a 3-D Voronoi tesselation. Generating grain #1... Rotating the system to change the crystal orientation... ..> System was successfully rotated, new orientation: Placing the center of mass at the center of the box... ..> System was re-centered, shift vector: (382.509,-83.732,803.236). ..> Number of atoms in this grain: 1333507. Generating grain #2... Rotating the system to change the crystal orientation... ..> System was successfully rotated, new orientation: Placing the center of mass at the center of the box... ..> System was re-centered, shift vector: (883.647,431.971,269.575). ..> Number of atoms in this grain: 1323885. Generating grain #3... Rotating the system to change the crystal orientation... ..> System was successfully rotated, new orientation: Placing the center of mass at the center of the box... ..> System was re-centered, shift vector: (888.048,331.623,395.732). ..> Number of atoms in this grain: 1330919. Generating grain #4... Rotating the system to change the crystal orientation... ..> System was successfully rotated, new orientation: Placing the center of mass at the center of the box... ..> System was re-centered, shift vector: (349.667,654.035,-261.691). ..> Number of atoms in this grain: 1332202. Wrapping atoms... ..> 3998671 atoms were wrapped. Writing output file(s) (5320513 atoms): ..> Successfully wrote CFG file: 500_4.cfg Writing output file(s) (4 atoms): ..> Successfully wrote XSF file: 500_4_nodes.xsf Writing output file(s) (4 atoms): ..> Successfully wrote XSF file: 500_4_grains-com.xsf ..> Successfully wrote DAT file: 500_4_size-dist.txt \o/ Program terminated successfully! Total time: 156.844 s.; CPU time: 187.688 s.
pierrehirel
commented
3 years ago Dear Sir,
Despite all my efforts I cannot reproduce the bug that you describe.
I ran the following commands using Atomsk version beta-0.11 under Windows 10:
atomsk.exe --create hcp 3.239 5.172 Zr Zr.xsf
atomsk.exe --polycrystal Zr.xsf voronoi.txt Zr_poly.cfg
The file "voronoi.txt" contains the following:
box 500 500 500
lattice fcc
This is what I obtained:
As you can see, there is no void between the grains. Using "-wrap" with Atomsk results in the same configuration as using the option "Wrap at periodic boundaries" in OVITO.
I do not understand what is going on here. If you still have this issue, here is what I can recommend:
Best regards
kedhar1992
commented
3 years ago Dear Sir,
I used the values of the lattice constants of Zr from your previous mail and it worked. I think the generation of void like defect/problem was arising due to the variation in the coordinates of the atoms in the primitive cell. Thank you so much for your kind help.
Thank you A. Kedharnath
On Tue, Mar 9, 2021 at 6:23 PM Pierre Hirel @.***> wrote:
Dear Sir,
Despite all my efforts I cannot reproduce the bug that you describe.
I ran the following commands using Atomsk version beta-0.11:
atomsk.exe --create hcp 3.239 5.172 Zr Zr.xsf
atomsk.exe --polycrystal Zr.xsf voronoi.txt Zr_poly.cfg
The file "voronoi.txt" contains the following:
box 500 500 500 lattice fcc
This is what I obtained:
[image: Screenshot_20210309_134204] https://user-images.githubusercontent.com/20334353/110472741-05015300-80de-11eb-9b5f-05180ee52a88.png [image: Screenshot_20210309_134308] https://user-images.githubusercontent.com/20334353/110472756-0c286100-80de-11eb-8fec-2db0bc43ac74.png
As you can see, there is no void between the grains. Using "-wrap" with Atomsk results in the same configuration as using the option "Wrap at periodic boundaries" in OVITO.
I do not understand what is going on here. If you still have this issue, here is what I can recommend:
- Use the option "-nthreads 1" to force Atomsk to use only one thread. During my tests I used multiple threads and didn't run into a problem, but maybe it causes problems in your case. Anyway it would be nice to rule that out.
- Try running the same commands on another computer.
- If you are in a hurry, you may still use older versions of Atomsk to construct this polycrystal, however I would like to help you figure out how to fix the new version.
Best regards
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Dear Sir/Madam,
Latest update on Atomsk is so useful but I encountered a situation with polycrystal command and related commands (similar to https://atomsk.univ-lille.fr/tutorial_polycrystal.php) while creating a polycrystal configuration. The final wrapped configuration is having cavities/unfilled spaces. It seems the voronoi cells are not getting completed or touching each other. Earlier versions of Atomsk was working fine in this issue.
Thank you