Hello everyone,
I have a system with 12 cellulose chains arranged in rows of 3 in one plane. I am using reax/c potential and lammps 16March, 18 version in serial.
However I am getting the following error:
“step149-hbondchk failed: H=57 end(H)=103734 str(H+1)=103724”
When I try to increase the safezone and mincap, I get the following error "
WARNING: trying to allocate -34359738368 bytes for array list:hbonds. returning NULL.
p0: not enough space for hbonds! total=41204695 allocated=-2147483648"
The polymer chains trajectory as visualized in VMD are just straight as the initial strucrture in the entire simulation.
Can anyone please help? Thank you so much.
The input script and log file are posted below.
INPUT SCRIPT
dimension 3
units metal
atom_style full
read_data data.NFC_Bundle
displace_atoms all random 0.01 0.01 0.01 443322
###SPECIFYING THE POTENTIAL
pair_style reax/c NULL checkqeq yes safezone 100 mincap 1000
pair_coeff * * ffield.reax C H O
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
neighbor 2.0 bin
neigh_modify delay 50 every 10 check yes
thermo_style custom step temp epair etotal press vol
minimize 1.0e-7 1.0e-9 100 10000
velocity all create 300.0 4928459
fix 2 all npt temp 300.0 300.0 0.1 iso 0.0 0.0 1
thermo 50
timestep 0.001
run 100000
unfix 1
LOG FILE
LAMMPS (16 Mar 2018)
dimension 3
units metal
atom_style full
read_data data.NFC_Bundle
orthogonal box = (-40.5 -30.5 -40.5) to (40.5 90.5 90.5)
1 by 1 by 1 MPI processor grid
reading atoms …
3024 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
displace_atoms all random 0.01 0.01 0.01 443322
###SPECIFYING THE POTENTIAL
pair_style reax/c NULL checkqeq yes safezone 100 mincap 1000
pair_coeff * * ffield.reax C H O
Reading potential file ffield.reax with DATE: 2010-02-19
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
neighbor 2.0 bin
neigh_modify delay 50 every 10 check yes
dump 1 all custom 100 NFCs.lammpstrj id type x y z
thermo 100
thermo_style custom step temp epair etotal press vol
minimize 1.0e-7 1.0e-9 100 10000
WARNING: Using ‘neigh_modify every 1 delay 0 check yes’ setting during minimization (…/min.cpp:168)
Neighbor list info …
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 14 21 22
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 4877 | 4877 | 4877 Mbytes
Step Temp E_pair TotEng Press Volume
0 0 -328479.55 -328479.55 83855.617 1283931
100 0 -338779.66 -338779.66 -3589.5212 1283931
Loop time of 85.2903 on 1 procs for 100 steps with 3024 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-328479.550299 -338771.152339 -338779.657696
Force two-norm initial, final = 4170.99 337.387
Force max component initial, final = 197.417 73.3122
Final line search alpha, max atom move = 0.000209336 0.0153469
Iterations, force evaluations = 100 379
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total