Dear LAMMPS users ,
How can I have cluster size evolution at a period of time ?
I use cluster/atom , chunk/atom and also property/chunk commands for cluster size calculation .
When I use fix ave/time command i can have number of clusters and their sizes but I want to have just size of them at simulation time.
Thanks in advance .
Best,
Saeed.
Dear LAMMPS users ,
How can I have cluster size evolution at a period of time ?
I use cluster/atom , chunk/atom and also property/chunk commands for
cluster size calculation .
When I use fix ave/time command i can have number of clusters and their
sizes but I want to have just size of them at simulation time.
if you average only over 1 step, you get the instantaneous cluster sizes.
axel.
Dear Axel ,
Can you please give an example about this kind of averaging ?
I want to calculate size of clusters that probably will be created along simulation time .
Best ,
Saeed.
See Section howto 6.23, the last example (5).
Steve
Dear Steve ,
Thanks for your reply.
With using of that example ( you addressed it to me ) I can get cluster size for my system .
Actually I want to use The mean first-passage time in my system so I need to have cluster size evolution per time but I can’t extract it from fix ave/histo !
I have attached an example of what I want to have with it’s process and also my fix ave/histo command results with this Email.
This is also a part of my input file :
compute cluster all cluster/atom 4.0 # STILLINGER Radius
compute cc1 all chunk/atom c_cluster compress yes
compute size all property/chunk cc1 count
variable temperature equal temp
fix 3 all ave/histo 10 1 1000 -57.0 53.0 100 c_size mode vector ave running beyond ignore file tmp.histo
Thanks for your attention.
Best ,
Saeed.
tmp.histo (1.4 MB)
If you use fix ave/histo with 10 1 1000, then every 1000 steps
you will get a histo of the current cluster sizes, with no
effective time averaging. Isn’t that what you are calling "cluster size evolution
per time" ?
Steve