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 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
Geewatercorrettonuovonuovo.txt (203 KB)
simboxcorrettoconbonds.txt (220 KB)
Geewaterbondsecharge.txt (299 KB)
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 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?
if you want LAMMPS to merge those two data files, you have to make certain, they use the same atom style. for water, you likely need full, so you’ll have to use that for your germanium system as well (you can always use an atom style that is a superset of what a specific system requires).
please note, that when using read_data multiple times, there are special rules and restrictions to pay attention to, and particularly, you have to reserve room for all types required in the first call. it is likely easier to read the water system first. details are in the documentation for read_data.
an alternate approach is to read and merge the data files with an external tool. my personal preference for that is VMD, where you can read both data files. then make sure that you renumber atom types as needed with VMD/Tcl scripting and then merge them and write out a combined data file. there is an example for the latter here: https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial—various-tips-tricks#TOC-Combine-multiple-data-files-with-overlap-detection-and-removal.
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)
keep looking. there are some “generic” force fields (GAFF?, UFF?). perhaps one of those has suitable parameters.
axel.