[lammps-users] Regarding calculation of the asphericity of aggregates

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1

Dear All,

I have a system containing several aggregates after equilibration. I am aiming to calculate the asphericity of each aggregate. With the following commands I could calculate the average gyration tensor eigenvalues over all the aggregates in the system per time.

compute cc1 all chunk/atom c_agg
compute myChunk all gyration/chunk cc1 tensor
compute myShape all gyration/shape/chunk myChunk

variable P1 equal ave(c_myShape[1])
variable P2 equal ave(c_myShape[2])
variable P3 equal ave(c_myShape[3])
variable P4 equal ave(c_myShape[4])
variable P5 equal ave(c_myShape[5])
variable P6 equal ave(c_myShape[6])
fix shape all print 1 “{P1} {P2} {P3} {P4} {P5} {P6}” file shape.out

Would it be possible to store these three variables per chunk by time?
Any advice would be appreciated!

Regards,
Katerina

2

you should be able to do something like this:

fix 2 all ave/time 50 1 50 c_myShape[1] c_myShape[2] c_myShape[3] mode vector file shapes.txt

this will print out the first three shape parameters for all clusters in a table every 50 steps.

axel.

3

Many thanks for your advice!

Best Regards,
Katerina

you should be able to do something like this:

fix 2 all ave/time 50 1 50 c_myShape[1] c_myShape[2] c_myShape[3] mode vector file shapes.txt

this will print out the first three shape parameters for all clusters in a table every 50 steps.

axel.