Hi
I am very new for lammps. I want simulate iron core Iron oxide structure. I know there are many things need to run the simulation. but for the beginning i need the geometry structure of iron core iron oxide.
Can any one help me about that?
Hi, you can use nanocut https://bitbucket.org/aradi/nanocut/
or Ovito https://ovito.org/ to import the unit cell, replicate and cut it in the desired shape. The same for the oxide layer. I dont know how is the interface, but if the iron core surface bonds do not match the bonds of the shell you should anneal your system.
Andrea
Hi Andrea Pedrielli
Thank you very much for your response. You have mention to that import the unit cell but how should I get unit cell for import. Because I never used ovito so before learning the ovito, i should make sure that it will work for me.
You can download the .cif file from http://rruff.geo.arizona.edu/AMS/minerals/Magnetite, the same for iron.
Then you can use this program to convert it in lammps file
https://github.com/andeplane/cif2cell-lammps
Or you can import the .cif file in Avogadro or any other software that reads it and export as .xyz. The xyz files can be imported in Ovito and using the commands "show periodic images" "expression select" and "delete selected atoms" you should be able to create a spherical core and a hollow shell. If you have to repeat the procedure for many samples you can save the program state to change only the radius of the core and the thickness of the shell.
Hi Andrea Pedrielli
Thank you very much for you help with explanation. I will let you know about my update.
Hi Andrea Pedrilli
I have tried your steps and Avogadro and then ovito and load file but did not get show periodic images" "expression select" and "delete selected atoms".
You have to click "add modification" in the panel on the right.
Further details can be found at
http://www.ovito.org/manual_v2.2.1/particles.modifiers.html
HI Khan
I think you can use Material Studio for building your initial files in PDB or xyz format. Then you could use packmol which is very convenient to make different geometrical shapes and they explained those in there manual very thoroughly. Then you could use maltemplate for building data file for your system which you could use your lammps simulation. Alternatively, you can use VMD which is also able to change the shape of your surface and write lammps data file.
Hope its help
- Badges
- Science topic
- Similar topics
- Biological Science
- Kinesiology
- Running