Hi, lammps users:
I am performing Browian dynamics simulation to study the assembly of ligated nanoparticles in solution(such as toluene).I treat the nanoparticle as a united atom by using a potential table file. my input file and table file is as follows:
input file
#Running a Brownian dynamics simulation
------------------------ INITIALIZATION ----------------------------
units metal
atom_style atomic
dimension 3
boundary p p p
atom_modify sort 0 0
neighbor 0.5 bin
neigh_modify every 1 delay 3 check yes
read_data our1.dat
------------------------ FORCE FIELDS ------------------------------
pair_style table linear 9001
pair_coeff * * NPaticle.table NPs_NPs 120
EQUILIBRATION
minimize 1.0e-12 1.0e-12 100 1000
compute mytemp all temp
compute 1 all gyration
reset_timestep 0
timestep 1.0
fix 1 all langevin 300.0 300.0 100.0 12345
fix 2 all nve
thermo_style custom step c_mytemp c_1 epair etotal press
thermo 500
run 20000
The data file is as follows:
LAMMPS Description
10 atoms
1 atom types
-3840.000000 3840.000000 xlo xhi
-3840.000000 3840.000000 ylo yhi
-3840.000000 3840.000000 zlo zhi
Masses
1 1.0
Atoms
1 1 0.0 0.0 -800.0
2 1 0.0 0.0 -600.0
3 1 0.0 0.0 -400.0
4 1 0.0 0.0 -200.0
5 1 0.0 0.0 0.0
6 1 0.0 0.0 200.0
7 1 0.0 0.0 400.0
8 1 0.0 0.0 600.0
9 1 0.0 0.0 800.0
10 1 0.0 0.0 1000.0
My table file is in the attachment,the range is from 66A to 120 A(for the diameter of nanoparicle is 60A,and the potential curve for two nanoparticles begins at 66A in the reference), meaning that there is no potential expression in the range of 0-66A. so I am always encounting the error " pair distance < table inner cutoff",I am pretty confused about it. I suspect that it may be related with my table file or units(I used units metal), as I seeked a advice that doing Browian dynamics simulation should use units of lj, So I performed a browian dynamics simulation as follows:
input file
units lj
atom_style full
dimension 3
neighbor 0.5 bin
neigh_modify every 1 delay 3 check yes
atom_modify sort 0 0
boundary p p p
read_data SingPart.dat
group sample type 1
velocity all create 1.0 482748 dist uniform
thermo 1000
thermo_style one
timestep 0.01
#pair_style none
mass * 1.0
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
fix 1 all langevin 1.0 1.0 1.0 12345
fix 2 all nve
compute 1 sample msd
variable msd equal c_1[4]
variable ts equal 0.01*step
variable xx equal xcm(sample,x)
variable yy equal xcm(sample,y)
variable zz equal xcm(sample,z)
fix 3 all print 5 “{ts} {msd}” file SingPart.msd screen yes
fix 4 all print 5 “{ts} {xx} {yy} {zz}” file SingPart.xyz screen yes
dump 1 all atom 5 SingPart.atom
dump_modify 1 image yes scale yes flush yes
dump 2 sample custom 5 sample.atom id xu yu zu
dump_modify 1 image yes scale yes flush yes
restart 5 SingPart.r1 SingPart.r2
run 100000
data file
LAMMPS Description
10 atoms
2 atom types
-10.000000 10.000000 xlo xhi
-10.000000 10.000000 ylo yhi
-10.000000 10.000000 zlo zhi
Masses
1 1.0
2 1.0
Atoms
1 1 1 0 0.0 0.0 -4.0
2 2 2 0 0.0 0.0 -3.0
3 3 2 0 0.0 0.0 -2.0
4 4 2 0 0.0 0.0 -1.0
5 5 2 0 0.0 0.0 0.0
6 6 2 0 0.0 0.0 1.0
7 7 2 0 0.0 0.0 2.0
8 8 2 0 0.0 0.0 3.0
9 9 2 0 0.0 0.0 4.0
10 10 2 0 0.0 1.0 0.0
and it did work.
Can you give me some advice? Thank you very much!
best wishes
Xuepeng liu
NPaticle.table (589 KB)