Lammps tersoff Ge and water

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1

Hi, lammps users
I’m beginning to use lammps to simulate Ge wettability properties. I have no particular problem in using the tersoff potential when i use Ge alone (110nuovovero.txt and iniziogermanio2.lmp) since i can just create a slab with avogadro and provide an input without explicitly define the number of bonds and so on, it deduces them from the force field parameters
However i don’t understand how to create the data input file for Ge and water together. What i mean is i create the geometric configuration with packmol but since for water it wants an input file in the form “simboxcorrettoconbonds” with number of bonds,angles and so on.

Therefore how to conciliate these two different way of input files? I tried in different ways (the Geewater files) but when i don’t explicit tell the bonds/angles in the datafile it gives me incorrect atom data format, while of course if i define them only fro water it tells me my bond index is out of range when it gets to tersoff, but i don’t see an easy way to tell in advance all the bonds for tersoff potential. Any suggestion on how to build the input file?

Big issue instead, does anyone know about an explicit formulation for non bondend interactions of Ge? I had poor luck searching in the literature so far (i would need something in the form of LJ parameters to mix with water but couldn’t find anything. With some other metallic elements i found some study developing intra layer potential with explicit non bonded just for this purpose but nothing for Ge)

I’m using lammps 22-aug2018

Thank you and sorry for the prolixity

Area degli allegati

mail sourgeforce.rar (301 KB)

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For Ge + water, you need to use an atom style that includes bonds, angles, etc. But you
don’t have to define any bonds or angles for Ge. Then you can use a hybrid pair style
and make sure you only apply Tersoff to the subset of Ge atoms. And a water potential
to the subset of water atoms. For the cross terrm, you can use just LJ interactions
as a simple model. But you have to find a similar model in the literature, if you
cannot parameterize it yourself.

Steve

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Thank you for the answer.

Yeah, i was using full atom style and writing all bonds/angles for water and only coordinates for Ge, it turned out to be a symple mistake in the order of the lines in the script. For the parameters i’ll take for now a similar model since nothing precise seems to be available.

I was trying to output the energies of my system throught the simulation, no problem using the fix print command, however it can’t be used for minization, is there a smart, simple way to write minimization energies to file?

Lorenzo

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What do you mean by “minimization energes” ? Any values you output with
fix print can also be output with a variable in thermo output. So those
values will appear every N iterations of the minimizer where you choose N.
They are output to the screen and the log file.

Steve