Dear lammps developers/users,
The lammps version I’m using is LAMMPS (2 Aug 2023), my platform is MacOS13.2
I’m working on polymer grafted nanoparticle. At first I grafted the nanoparticle with 10 chains(attached data file) and use this as my initial configuration to run a minimization and then I tried to run nvt and decrease box size at same time, in the end I will equilibrate system with a npt.
################################### SimulationBox Parameters
units lj
atom_style molecular
special_bonds fene
pair_style lj/cut 2.5
bond_style fene
neighbor 0.4 bin
neigh_modify every 1 delay 1
comm_modify cutoff 4.0
angle_style harmonic
dihedral_style harmonic
atom_style molecular
################################### Adding Data to the SimulationBox
read_data graftedNano.data #onechain graftedNano1.data
mass * 1
angle_style harmonic
angle_coeff 1 60.0 120.0
dihedral_style harmonic
dihedral_coeff 1 40.0 1 2
######################################## Energy Minimization
group Nano_P type 2
group Grafts type 1
timestep .001
fix 1 Nano_P setforce 0.0 0.0 0.0
fix 2 all momentum 1 linear 1 1 1 angular
dump 2 all custom 10 dump.minimized_graftsnano_onechain id mol type x y z vx vy vz
thermo 10
run 100
unfix 2
unfix 1
#min_style cg
min_style fire
minimize 1e-8 1e-9 1000 10000
#minimize 1.0e-4 1.0e-6 100 1000
write_data data.Test
##################################### Equilibration
#fix 4 all nve
fix 4 Grafts nvt temp 0.5 0.5 0.1
fix 5 Grafts deform 2 x final -32 32 y final -32 32 z final -32 32 units box
thermo 1000
run 50000
Before minimization step, from run 100, I get a lot of FENE bond too long error and for fire style minimization, I get ERROR on proc 0: Bond atoms 1 11 missing on proc 0 at step 103 (src/ntopo_bond_all.cpp:59)
Last command: minimize 1e-8 1e-9 1000 10000
Then I changed minimization style to cg, it works until same error occurs again before last command run 50000. Since I’m getting FENE bond too long and the bond atoms 1 11 missed is on grafted polymer chain, then I think I need to start to debug the problem from the graft chains.
I tried to change the initial configuration to 1. only one chain in the system and 2. only one chain and nanoparticle, no bond between them. 3. one chain grafted to nanoparticle. And I only run minimization and then a NVE.
units lj
atom_style molecular
special_bonds fene
pair_style lj/cut 2.5
bond_style fene
neighbor 0.4 bin
neigh_modify every 1 delay 1
comm_modify cutoff 4.0
angle_style harmonic
dihedral_style harmonic
atom_style molecular
read_data #onechain #graftedNano1.data #onechain_and_nano
mass * 1
angle_style harmonic
angle_coeff 1 60.0 120.0
dihedral_style harmonic
dihedral_coeff 1 40.0 1 2
group Nano_P type 2
group Grafts type 1
timestep .001
fix 1 Nano_P setforce 0.0 0.0 0.0 #comment out for only onechain
fix 2 all momentum 1 linear 1 1 1 angular
dump 2 all custom 10 dump.minimized_graftsnano_onechain id mol type x y z vx vy vz
thermo 10
run 100
unfix 2
unfix 1#onechain
min_style cg
minimize 1e-8 1e-9 1000 10000
write_data data.Test
fix 4 all nve
thermo 1000
run 50000
For first system with only one single chain, no error occurs, log file looks normal.
For second system with one chain and a nanoparticle, I’m having ERROR on proc 0: Angle atoms 12 13 14 missing on proc 0 at step 106 (src/ntopo_angle_all.cpp:62)
For third system with grafted nanoparticle, I’m having ERROR on proc 0: Bond atoms 1 2 missing on proc 0 at step 116 (src/ntopo_bond_all.cpp:59)
It seems after nanoparticle is added to system, this problem arises. The initial configuration looks fine in the Ovito with no overlap and the potential coefficients I used works for similar system before. I will highly appreciate if anyone could kindly give me some suggestions. Thank you for your time and help in advance!
Sincerely,
Sakuma
graftedNano1.data (923.9 KB)
onechain (4.3 KB)
onechain_and_nano (835.0 KB)