Dear all,
I have a question about the units of ‘micro’ in LAMMPS.
Now I have a bulk system composed of bead-spring fibers, and I used ‘lj’ and ‘micro’ units respectively to check how the simulation runs.
For the lj unit, the simulation runs well. But when I use ‘micro’, some errors occur. The following is my script using ‘micro’ uints, can anyone give me some advice?
Best
###########################################################
units micro
atom_style molecular
dimension 3
boundary p p p
timestep 2
###################### Interactions ######################
bond_style harmonic
angle_style cosine
pair_style soft 8.0
special_bonds lj 0 0 1
read_data fiber.data
mass * 0.956
################## Coefficients ############################
bond_coeff * 72 5.5
angle_coeff * 1
pair_coeff * * 10.0
thermo_style custom step temp press etotal pe ke epair ebond eangle lx ly lz vol density
thermo 100
velocity all create 310 4679874
variable prefactor equal ramp(0,300)
fix rampSoft all adapt 1 pair soft a * * v_prefactor
################## Output ###################################
timestep 2
thermo_style custom step temp press etotal pe ke epair ebond eangle lx ly lz vol density
thermo 100
dump 1 all custom 500 min.lammpstrj id type mol x y z
minimize 1.0e-12 1.0e-12 20000 20000 # 500000 500000
write_data min.data
unfix rampSoft
undump 1
################## Weeks-Chandler-Anderson ##################
pair_style lj/cut 20
pair_coeff * * 1 8 9
pair_modify shift yes
################## Dynamics ##################
reset_timestep 0
thermo 1
thermo_style custom step temp press etotal pe ke epair ebond eangle lx ly lz vol density
dump 3 all custom 1 relax.lammpstrj id type mol x y z
fix 0 all nve
fix 1 all langevin 310 310 100 699483
run 500000
undump 3
write_data Equil.data
write_restart Equil.rest
print "ALL DONE"
The error is like this, the temp blows up:
Total # of neighbors = 822
Ave neighs/atom = 0.36696429
Ave special neighs/atom = 6.3267857
Neighbor list builds = 53821
Dangerous builds = 53177
System init for write_data ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Setting up Verlet run ...
Unit style : micro
Current step : 0
Time step : 2
Per MPI rank memory allocation (min/avg/max) = 7.407 | 7.491 | 7.684 Mbytes
Step Temp Press TotEng PotEng KinEng E_pair E_bond E_angle Lx Ly Lz Volume Density
0 310 2.2685207e-09 0.29099682 0.27662238 0.014374435 -0.13765038 3.6334669e-05 0.41423643 200 200 200 8000000 0.00026768
1 52266797 0.00020305861 2429.4986 5.932048 2423.5666 -0.12470287 5.6364512 0.42029968 200 200 200 8000000 0.00026768
ERROR on proc 9: Bond atoms 2195 2196 missing on proc 9 at step 2 (src/lammps/src/ntopo_bond_all.cpp:59)
Last command: run 500000
ERROR on proc 0: Bond atoms 892 893 missing on proc 0 at step 2 (src/lammps/src/ntopo_bond_all.cpp:59)
Last command: run 500000
ERROR on proc 1: Bond atoms 221 222 missing on proc 1 at step 2 (src/lammps/src/ntopo_bond_all.cpp:59)
Last command: run 500000
ERROR on proc 2: Bond atoms 929 930 missing on proc 2 at step 2 (src/lammps/src/ntopo_bond_all.cpp:59)
Last command: run 500000
ERROR on proc 3: Bond atoms 2151 2152 missing on proc 3 at step 2 (src/lammps/src/ntopo_bond_all.cpp:59)
Last command: run 500000
ERROR on proc 5: Bond atoms 1854 1855 missing on proc 5 at step 2 (src/lammps/src/ntopo_bond_all.cpp:59)
Last command: run 500000
ERROR on proc 8: Bond atoms 1003 1004 missing on proc 8 at step 2 (src/lammps/src/ntopo_bond_all.cpp:59)
Last command: run 500000
ERROR on proc 6: Bond atoms 1669 1670 missing on proc 6 at step 2 (src/lammps/src/ntopo_bond_all.cpp:59)
Last command: run 500000
ERROR on proc 7: Bond atoms 1564 1565 missing on proc 7 at step 2 (src/lammps/src/ntopo_bond_all.cpp:59)
Last command: run 500000