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_ peratom or pergroup 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 WIgnerSeitz cells around the atoms in the precascade 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 precascade 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