Examples

A complete tutorial, starting from pristine Si nanowire to the movie of oxidation is presented here. The corresponding directory with the necessary input files is in path_to_poxy/examples/nw_110_D15_L8. (Downloadable tarball here: nw_110_D15_L8.tar).

Below, a few details concerning the approach.

An example bash-script (oxidise.sh) is currently used to handle the flow of incorporating a desired number of oxygen atoms within a given atomic structure (Si, or Si/SiO2). It may be replaced by a poxy command in the future.

The script is invoked with three command-line arguments:

1. Input atomic structure;
2. Number of O atoms to be added;
3. (optional) type of bonds (surface/subox/either) to consider when incorporating oxygen.

Note that currently the type of structure is hard-coded as ‘wire’, but could be easily modified along with other tunings for a particular oxidation run.

An example invocation will be:

./oxidise.sh output/heat.prd 100 either 2>&1 | tee oxidise.log

It assumes output/heat.prd exists (e.g. from heating up pristine Si NW to desired temperature). The output and log files from the MD run will be placed in output directory, the structure files and png-images will be placed in the structures directory. The MD engine is lammps.

The script realizes the flow depicted in the diagram at the bottom, and takes care of the cases, where O cannot be added due to the potential overlap of atoms, or an atom is lost during MD due to interaction being too strong. In either case, the cure is some more MD at the selected annealing temperature.

If all goes well, at the end of the run, a video will be produced, illustrating the individual incorporation and anneal of each O atom, as below:

An atom-by-atom incorporation of O, followed by equilibration anneal, leading to layer-by-layer oxidation of the Si-NW.

The flow diagram mentioned above:

Implementation of oxidation flow, one atom at a time with safe handling of situations where MD looses atom or O cannot be safely incorporated in a specific bond.