Counting new bonds dynamically

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1

Hello

I am running a simulation where (harmonic) bonds are formed as time elapses
following a simple distance threshold condition.

Bonds are formed between particles of type 2 (fixed) and of type 1 (diffusing).
The latter become type 4 upon formation of a new bond.

I would like to count those bound particles (type 4) as a function of time and
access their coordinates. I could not find a meaningful way to define a dynamic
group to do so. Or any other work-around, for that matter.
Any help would be strongly appreciated.

Here it is the part pf the script where I define the bond creation process:

Bonds (dynamic)

bond_style harmonic
bond_coeff 1 100. {d_bond} fix bonds all bond/create 2 1 2 {Rmin} 1 prob ${prob_bind} 85784 iparam 1 4 jparam 1 2

Best wishes

Francesco

2

Hello

I am running a simulation where (harmonic) bonds are formed as time elapses
following a simple distance threshold condition.

Bonds are formed between particles of type 2 (fixed) and of type 1 (diffusing).
The latter become type 4 upon formation of a new bond.

I would like to count those bound particles (type 4) as a function of time and
access their coordinates. I could not find a meaningful way to define a dynamic
group to do so. Or any other work-around, for that matter.
Any help would be strongly appreciated.

you should be able to build a dynamic group based on an atom style variable. if you use the expression “type==4”, it should select only type 4 atoms in the dynamic group, as this variable evaluates to 1 for all of those atoms and to 0 for all others.

axel.