Hello all Lammps users,
I am trying to understand how “fix bond/create command” works in Lammps.
At the beginning of my simulation, there are three kinds of types-- beads-spring modeled linear polymers (edges of chains=type 1; others=type 3) and nanoparticles (type 2).
When type 1 beads are close enough to type 2, they are connected by creating a new harmonic bond. When they bond, type 1 changes to type 4.
To simplify the situation, type 2 is always set to ‘stop’ and only the polymers (type 1 and 3) move. When type 1 changes to type 4, I want type 4 to ‘stop’ as well.
In the dump file, I can confirm that type 1 has correctly changed to type 4, but it seems that the new type 4 can still move around the surface of the nanoparticles. How can I make type 4 ‘stop’?
For your information, I use lammps 2013 May version. Of course I used the latest version (lammps 2016 14May), but I got same results.
I have read previous threads about “fix bond/create”, but I couldn’t find related ones.
I’d appriciate it if you give me advises.
Sincerely,
Makoto Asai
My input file that I used is as follows:
///////////////////////////////////////////////////////////////////////////////////////////////////////////
units lj
atom_style full
read_data NP_chains.np
neighbor 0.5 bin
group Edges type 1
group NP type 2
group Chains type 3
group GP type 4
special_bonds fene extra 100
bond_style hybrid fene harmonic
bond_coeff 1 fene 30.0 1.5 1.0 1.0
bond_coeff 2 harmonic 1.0 10.5
neigh_modify every 1 delay 0 check yes page 100000
pair_style lj/expand 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 0.00 1.12
pair_coeff 1 2 1.0 1.0 6.50 1.12
pair_coeff 1 3 1.0 1.0 0.00 1.12
pair_coeff 1 4 1.0 1.0 0.00 1.12
pair_coeff 2 2 1.0 1.0 13.0 1.12
pair_coeff 2 3 1.0 1.0 6.50 1.12
pair_coeff 2 4 1.0 1.0 6.50 1.12
pair_coeff 3 3 1.0 1.0 0.00 1.12
pair_coeff 3 4 1.0 1.0 0.00 1.12
pair_coeff 4 4 1.0 1.0 0.00 1.12
fix 1 Chains nve
fix 2 Chains langevin 1.0 1.0 1.0 9024297
fix 3 Edges nve
fix 4 Edges langevin 1.0 1.0 1.0 9024297
fix 5 NP setforce 0.0 0.0 0.0
fix 6 GP setforce 0.0 0.0 0.0
fix 7 all bond/create 1 1 2 7.6 2 iparam 1 4 jparam 0 2
dump 1 all custom 10000 dump.s id type x y z
thermo 10000
thermo_style custom step temp ke etotal press vol
timestep 0.005
restart 100000 restart_temp_s1 restart_temp_s2
run 1000000
write_restart restart_s
///////////////////////////////////////////////////////////////////////////////////////////////////////////