Question about export a file in Dream.3D as LAMMPS file

[Raffaello Chen]

Hi, I am trying to export a structure I made via Dream.3D as a LAMMPS file for later processing. But the 'insert atoms' filter keeps making error message like the photo I attached here. Would you mind kindly helping to take a look into it?

Thanks

[Michael Jackson]

Dear Raffaello, 

    The Insert Atoms filter is pretty picky about what it can and cannot do. Could you tell me what the voxel dimensions and spacing of your generated microstructure are? Also what version of DREAM3D are you using currently?

--
Mike Jackson                    mike.j...@bluequartz.net
BlueQuartz Software         www.bluequartz.net

President/Owner               Dayton, Ohio

Principal DREAM.3D Developer

On Jan 2, 2024 at 4:49:07 PM, Raffaello Chen <raffae...@gmail.com> wrote:

Hi, I am trying to export a structure I made via Dream.3D as a LAMMPS file for later processing. But the 'insert atoms' filter keeps making error message like the photo I attached here. Would you mind kindly helping to take a look into it?

Thanks

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[Raffaello Chen]

Hi, Thanks for your response. My version is 6.5.171 and I have attached the setting of all parameters here with the error message and another .csv file I output. Would you mind taking a look to that kindly?

---Raffaello

[Michael Jackson]

Dear Raffaello, 

    You can make this a bit easier by saving the pipeline to a file (Use the File menu) and then just send me the file. I was able to recreate most of the pipeline from the images but on macOS at least the pipeline crashes when it gets to the InsertAtoms filter. Please note that the InsertAtoms filter combined with even a modest sized microstructure can generate more atoms that can be stored in memory. DREAM3D 6.5 did not do a great job of explaining this. I think the later nightly builds of DREAM3D did a better job. You can grab one from here.

https://dream3d.bluequartz.net/binaries/experimental/2023-12-25/

I would try that nightly and see if there are any better results.

--
Mike Jackson

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[Raffaello Chen]

Thank your for your response. Yes, the crash while running to the filter of InsertAtoms is what I am confused with. Sorry for the trouble caused by these pictures. I have attached the save pipeline here
--Raffaello

[Michael Jackson]

Essentially that filter is probably unusable. Let’s do some math to help us both realize that who ever wrote the filter was probably running on a VERY large memory machine.

Let us assume that you have a microstructure that is 1 micron on a side and you are using a lattice constant of 1 angstrom. That means that there are at least 10000 x 10000 x 10000 atoms in that small microstructure. This is 1x10E12 atoms or 1 Tera worth of atoms. Since we store the location of each atom as 3x4byte floats, that is 12 bytes for each position which gives us 12 Terabytes of memory that is needed just to allocate for this filter.

Unfortunately the InsertAtoms filter was hard coded to assume the position values that were passed into the filter are in micrometers so there isn’t much you can do. If your microstructure is really in nanometers you could try to save the .dream3d file, use something like Python to open the .dream3d file, find the vertices of the mesh and scale them  to be expressed as nanometers instead. (So multiply each vertex by 1000). This might get you close as you would remove 9 orders of magnitude from the calculation.

Sorry for the bad news.

--
Mike Jackson                   

BlueQuartz Software         www.bluequartz.net

President/Owner               Dayton, Ohio

Principal DREAM.3D Developer

To view this discussion on the web visit https://groups.google.com/d/msgid/dream3d-users/2083d189-03e9-48e5-aae2-e6f191130201n%40googlegroups.com.

[Raffaello Chen]

Thanks for your response. For the model I am doing with I just wanna build up a polycrystal structure of cubic diamond with about 2000 atoms for LAMMPS running. That is why I am using this InsertAtoms filter which is required for another filter called 'ExportLammpsDataFile'. Or would you mind sharing another more simple way to achieve this rather than doing the insertatoms filter.  What I wanna get is like the photo I attached here. I can get the left side figure via imput the .xdmf file into the Paraview and may I ask how can I get the figure like right side one which will show the distribution of atoms? Thanks

[Michael Jackson]

I don't know how that image was generated. I do know that DREAM3D was involved just looking at the left and center. But the right side probably was not generated with DREAM.3D but instead used some other method. Maybe you could email the original authors and inquire with them how the image was made.

—

Mike Jackson

Principal DREAM.3D Developer

BlueQuartz Software

To view this discussion on the web visit https://groups.google.com/d/msgid/dream3d-users/9022810c-8768-4203-bda7-d87f99472008n%40googlegroups.com.

[Hanyu Xu]

Dear Michael,

If I want an atomic system containing 1000 × 1000 × 1000 atoms, can I create a simple geometry in DREAM.3D—such as a single-grain structure—and then use the Export LAMMPS Data File filter to generate the corresponding atomic configuration? Is this possible?  

Best Regards,

Hanyu

[Michael Jackson]

Hello Hanyu, 

   This is possible. I have included a pipeline that places a single atom type on a 1000 x 1000 x 1000 grid and writes out the LAMMPS file. The file will be VERY Large since it is a text file so you will need to give it some time to finish.

You will need to use DREAM.3D Version 6.5.171 to run the pipeline as we have not yet ported that filter into DREAM3D-NX.

--
Mike Jackson                    mike.j...@bluequartz.net
BlueQuartz Software         www.bluequartz.net

President/Owner               Dayton, Ohio

Principal DREAM.3D Developer

To view this discussion visit https://groups.google.com/d/msgid/dream3d-users/677af1d8-7392-4e88-9732-44aa9892b7e1n%40googlegroups.com.