Why can I not compute the voronoi/atom at the beginning of the simulation,
and compare it to a compute later in the simulation to find the defects?
Sure, you can do that. The options in the latest voronoi/atom compute
version (nt yet merged by Steve, but posted on the ML) should help a
lot.
But that way you can only identify "Defects" in general. Pinpointing
what type of defect you have is a bit more difficult.
I might add the functionality for occupation checks on a set of fixed
voronoi cells sometime. But this is not a silver bullet either!
Daniel
Daniel,
I must still be confused on the functionality of the command. All I want to do right now is to determine where vacancies and interstitials are occurring. If I did a compute voronoi/cell, would it not return the number of cells in the lattice site? If there is 0 cells, then that is a vacancy, if there is >1, that is an interstitial. What am I missing?
Ben
I must still be confused on the functionality of the command. All I want to
Yes, you do sound confused 
do right now is to determine where vacancies and interstitials are
occurring. If I did a compute voronoi/cell, would it not return the number
of cells in the lattice site? If there is 0 cells, then that is a vacancy,
if there is >1, that is an interstitial. What am I missing?
No, you are confusing cells, lattice sites, and atoms.
The voronoi compute has no concept of "lattice sites". It just knows
current atom positions and will compute a tessellation, resulting in
exactly one cell per atom.
Each cell ALWAYS has an occupation of 1, per the definition of the VT.
The compute helps you in defining _a_ per-atom or per-group volume
(caveat emptor), defines _a_ surface area (again per atom, per group,
etc.), it gives you a neighbor relationship, and it can give you a
characterization of the local crystal structure (via face count and
edge count histograms).
Daniel
Hi.
Probably I am adding to the confusion :-).
AFAIK, currently two methods seem to be followed to determine radiation damage in a MD cascade (R. E. Stoller - Comprehensive Nuclear Materials - Vol.1):
-
Build WIgner-Seitz cells around the atoms in the pre-cascade atomic positions. After or during cascade, from the output of atomic positions see if the cells are empty (vacancy) or occupied. If more than one atom occupies a cell, one of them is an interstitial (or both form a interstitial configuration - dumbell, etc).
-
Build spheres around the atoms (of radius 30 % of unit cell size) in the pre-cascade atomic positions. Again from the output of atomic positions after or during the cascade, a empty cell signifies vacancy. If the position of any atom does not fall in a sphere, it is an interstitial.
(2) seems to work pretty well (inspite of being less exact than (1)). Therefore if you construct a voronoi cell of initial atomic positions and carry out similar analysis as (1) for atomic positions after or during the cascade, you may get the correct results.
Best Regards
Manoj