Dear LAMMPS Users
First, Thank you, Dr. Plimpton, for your advice.
I have created my input script where my simulation box is changing its volume. The box contains 4 polymer chains each consisting 10 atoms which is being read from the external data file, polymer_4c10m.
The polymer chains consist of 3 types of bonds: Type 1 bonds connect the beads in each chain, Type 2 bonds are crosslink bonds which one atom from one chain connects to another atom from another chain, Type 3 bonds are harmonic bonds contained in each chain.
As the simulation box size is inflating, I am inserting water molecules into the box. The water molecules are contained in the file molecule.dimer where the two atoms are Type 2 and the bond that connects these two atoms are Type 4.
Adhering to your advice, I have allowed extra space for the Type 2 atoms and the Type 4 bond by modifying my read_data command.
However, when I run my simulation, I am running into an issue where my Type 2 bonds are exceeding its critical bond length (FENE bond too long).
I confirmed that the fix deform command which is inflating the simulation box size is not responsible for the excessive bond length.
Therefore, I was curious if I could request for any suggestions or advice on why my Type 2 FENE bonds in my original input script is exceeding their critical length when I insert the water molecules.
Reading the documentation, I am expecting that my dump files will consist of Type 1 and 2 atoms and Type 1, 2, 3, and 4 bonds since I specified the offset as â0â in my fix deposit command.
A portion of my original script is as follows:
units lj
atom_style full
neighbor 0.36 bin
neigh_modify delay 2
pair_style lj/cut 2.5
bond_style hybrid harmonic fene
special_bonds lj 0.0 1.0 1.0
read_data polymer_4c10m extra/atom/types 1 extra/bond/types 1
mass * 1.0
pair_coeff * * 1.0 1.0 2.5
bond_coeff * fene 30.0 1.5 1.0 1.0
bond_coeff 3 harmonic 1000.0 1.20
pair_modify shift yes
timestep 0.010
reset_timestep 0
fix 1 all langevin 1.0 1.0 2.0 542305
fix 2 all press/berendsen iso 0.0 0.0 10.0
fix 3 all nve
thermo 100
thermo_style custom step temp pe etotal epair pxx pyy pzz lx ly lz
run 1000
unfix 2
variable tmp equal âlxâ
variable L0 equal {tmp}
print "Initial Length, L0: {L0}"
Perform Volume Inflation
reset_timestep 0
fix 7 all deform 1 x erate 0.01 y erate 0.01 z erate 0.01 remap v
region vol block EDGE EDGE EDGE EDGE EDGE EDGE side in
molecule dimer molecule.dimer
group Add_Atom id 2
fix 8 Add_Atom deposit 50 0 100 12345 region vol near 0.0 &
mol dimer vx -1.0 -1.0 vy -1.0 -1.0 vz -1.0 -1.0
fix 9 Add_Atom nve
fix 10 Add_Atom langevin 0.1 0.1 0.1 587283
fix 11 Add_Atom nve
compute p all pressure thermo_temp
fix 12 all ave/time 4 25 100 c_p[1] c_p[2] c_p[3] c_p[4] c_p[5] c_p[6] file press.1
run 1000
My water molecule data is as follows:
2 atoms
1 bonds
Coords
1 0 0 0
2 1 0 0
Types
1 2
2 2
Bonds
1 4 1 2
Special Bond Counts
1 1 0 0
2 1 0 0
Special Bonds
1 2
2 1
Thank you.
Sincerely,
Masato Koizumi