[lammps-users] SiO2- Couple structure, potential and energy

Hi,

I need to couple the structure, potential and energy for SiO2. I have the following queries:

Structure of SiO2
I have a particular form of bulk amporphous silica as a .xsd file through Materials Studio. Can I input that into LAMMPS?

Coupling the potential to the structure
Once I input my structure, how do I couple my potential to the structure?
I intend to use the Tersoff potential without Coloumbic interactions.

Choosing a particular atom in the structure and providing an energy
How do I choose a particular atom in the structure and provide it with an initial energy?

Thanks for the support.

Answers below.

Steve

Hi,

I need to couple the structure, potential and energy for SiO2. I have the
following queries:

Structure of SiO2
I have a particular form of bulk amporphous silica as a .xsd file through
Materials Studio. Can I input that into LAMMPS?

LAMMPS inputs atom coords via the read_data command and a
data file which has a simple format. You'll need to convert your XSD
file into that format. Several tools for this exist in the tools dir,
like for PDB files, but I don't think there is one for XSD files. But
maybe it is a simple cut/paste.

Coupling the potential to the structure
Once I input my structure, how do I couple my potential to the structure?
I intend to use the Tersoff potential without Coloumbic interactions.

Just use the pair tersoff command. See the doc page for how it
assigns coeffs to atom types.

Choosing a particular atom in the structure and providing an energy
How do I choose a particular atom in the structure and provide it with an
initial energy?

If by energy, you mean velocity, then use the velocity command.
You can also use the set command for a single atom.