Output temperature of a group of atoms

[Lukas Reicht]

Hi,

I want to do approach-to-equilibrium molecular dynamics (AEMD) with i-Pi. I have everything set up, but as a final step I would need to output the temperature of a group of atoms. Specifically, I would like to know the temperature of the atoms, that are in each half of my simulation box. I am using LAMMPS as a force calculator. I would know how to output the desired temperature in LAMMPS, but when I use it as a client with i-Pi, LAMMPS always gives zero temperature (not surprisingly, as this information is not provided to it by i-Pi).

Any help is greatly appreciated.

Best Regards,

Lukas Reicht

[Venkat Kapil]

Hi Lukas,

You can print out the temperature of an atom using the temperature property.
`
temperature{kelvin}(atom=0)
`

It can take arguments like the index of an atom or an atomic species "O", "H", etc. I don't think we can pass a set of indices but if you are simulating a solid and the atoms do not flow across the central atom, you can assign atoms (manually) a different label based on their positions. In that case you can overwrite the new sets of labels in the initialize xml tag  from a different file (say labels.xyz, an xyz  formatted file with different labels for left and right hand side atoms)
`
      <initialize nbeads="1">
        <file mode="xyz">./init.xyz</file>
        <labels mode="xyz">./labels.xyz</labels>
        ...
      </initialize>

`

Hope this helps.

[Lukas Reicht]

Thanks very much, Venkat. It worked out nicely.