[lammps-users] Average Bond Length

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1

Hi,

I am using the ‘May 2008 version of LAMMPS’. This is my problem.

I have some hexadecane molecules inside the simulation cell. The simulation is run by thermostating at various temperatures. We know that when the temperature is increased, the energy stored in the intermolecular bonds between atoms changes and as a result, the bond length increases.

Does anybody know of an easy way to calculate (or some method to quantify) the average length of class II bonds during a simulation in lammps?

Any help will be appreciated.

Thanking You

Yours Sincerely
Ajay

2

This wouldn't be hard to do post-processing, by processing the
dump files. If you want to do it on the fly, you'll need to write
a fix or compute that performs this calculation.

Steve

3

Hi Steve and lammps-users

I have a simple script just to check the "variable loop" command. I tried
this script for both May 2008 and Jan 2009 versions and it doesn't loop.
It performs the first iteration and ends immediately. The script is.

variable b loop 5
print "$b:
next b

What am I missing?

Thanks!

Jan-Michael Carrillo

4

Hi Steve and lammps-users

I have a simple script just to check the "variable loop" command. I tried
this script for both May 2008 and Jan 2009 versions and it doesn't loop.
It performs the first iteration and ends immediately. The script is.

variable b loop 5
print "$b:
next b

What am I missing?

Thanks!

Jan-Michael Carrillo

5

Jan-Michael, this is how we’re doing it our scripts:

variable b loop 5
label loop_b
print “$b”
next b
jump my_lammps_input_file loop_b

cheers,
Jeremy

6

I missed type the second line of the script. It should be:
print "$b"
and not
print "$b:

7

Thanks, It works!

8

Add a jump command.

Steve

9

Dear Ajay,
Quick thought. If you can calculate the bond length at one temperature as well as its volume. Then by estimating volume at different temperature, you might get an estimate of bond length increment.