Greetings LAMMPS users,
We are interested in using ‘fix phonon’ to get the phonon dispersion information for functionalized graphene. That is, we have a regular periodic structure which we’d normally write a map file for (the graphene lattice) however the presence of functional groups on the edges of the material breaks this periodicity.
We would like to find a way to implement ‘fix phonon’ without treating the entire system as one unit cell. Does anyone know of a way we could still define a map file for this type of system which gives accurate phonon information even though the material is not entirely periodic? I suppose we could place the atoms of the graphene lattice into a group and create a map file only for the “periodic part” of the material, however I imagine we would lose information that way (since the functional groups change the vibrational modes of the system).
Thanks in advance!
For details on fix phonon you probably have to contact the author of the package. I can only give you some general perspective.
But you also need to think about the physics of what you are looking into. Basically, you are asking to treat something as “regular” that is not. Now let us for a moment assume you have a perfectly regular and periodic system. Then if you look at the reciprocal space when choosing a larger unit cell with multiple periodic copies of the same unit cells, you will get a correspondingly smaller representation in reciprocal space with all features folded back into the smaller volume. On the other hand, if you try to represent a larger system with a smaller unit cell, you will get the equivalent of an average over the multiple different unit cells. Now that latter option can make sense when you have a setup where you have an atom replaced by a different element with a certain probability. Then you can model such a system by creating a “virtual” atom type that is an average of the interactions of the two atom types involved at the ratio of the different occupations. However, I cannot see how you can interpret the results of a study like you want to conduct, where you do not have such a simple replacement.
So before even looking into how to measure the phonon dispersion for your system, you probably need to think about what any such results would mean. From my perspective this is not exactly trivial.
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