(no subject)

I wish to place few hydrogen atoms in only one grain of bcc/fcc bicrystal at octahedral and tetrahedral sites.
Is it right to place H atoms randomly first using create_atom random and then do thermal stabilization to shift H atoms to octahedral and tetrahedral sites.
Will thermal stabilization will place H atoms at O and T sites?

how about you just do a simulation and find out?

axel.

I wish to place few hydrogen atoms in only one grain of bcc/fcc bicrystal at octahedral and tetrahedral sites.
Is it right to place H atoms randomly first using create_atom random and then do thermal stabilization to shift H atoms to octahedral and tetrahedral sites.
Will thermal stabilization will place H atoms at O and T sites?
Navjot Kaur

If you want to manually specify precisely where all of the atoms in your system should go, you need to create a “DATA” file and use the read_data command. The basic format of a DATA file is explained here. For small systems, you can create one with a simple text editor. The format is not that complicated, but if there are a lot of atoms, it may be helpful to use 3rd-party program to build the DATA file:
There’s a list of 3rd-party “molecule builders” here:
https://lammps.sandia.gov/prepost.html

and there’s a few more choices (left off that list) here:
https://github.com/sgsaenger/vipster #<- graphical user interface (still glitchy unfortunately)

https://sourceforge.net/projects/moleculardynami/

All these tools differ in how much freedom they give you to control the details of the system you want to build, how many assumptions they make about the atoms in your system, how automated they are and what force fields they support, and whether or not they allow graphical user input. Most tools are text only. VIPSTER has a primitive GUI that allows you to click on where you want the atoms to go. It gives you a great deal of freedom to make what you want, but the GUI is still pretty glitchy. It is under active development and I think that will change. Moltemplate and Topotools give you a large amount of freedom to build what you want and have built in commands that make it easy to build crystals. But these tools have a text-only interface. (Perhaps VMD has a GUI for building crystals. Topotools runs within VMD.) I am not familiar enough with the other tools on that list to comment. (Disclaimer: I wrote moltemplate.)

If you want to test whether a physical process would give rise to a particular spatial pattern, then (as Axel said), run a simulation.

Hope this helps.

Andrew