Input script
clear
units real
boundary p p p
dimension 3
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
pair_style hybrid lj/cut/tip4p/long 1 2 1 1 0.1594 12 12 lj/charmm/coul/long 8.0 12.0 lj/cut/coul/long 8.5 12.0
kspace_style pppm/tip4p 1.0e-5
read_data data.lmp
#read_restart restart.mini.*
pair_coeff 1 1 lj/cut/tip4p/long 0.212801 3.166550 # Ow Ow
pair_coeff 2 2 lj/cut/tip4p/long 0.000000 0.000000 # Hw Hw
pair_coeff 3 3 lj/charmm/coul/long 0.170000 3.250000 # NCO NCO
pair_coeff 4 4 lj/charmm/coul/long 0.105000 3.750000 # CO CO
pair_coeff 5 5 lj/charmm/coul/long 0.210000 2.960000 # CO OC
pair_coeff 6 6 lj/charmm/coul/long 0.065999 3.500000 # CTN CTN
pair_coeff 7 7 lj/charmm/coul/long 0.065999 3.500000 # CT2 CT2
pair_coeff 8 8 lj/charmm/coul/long 0.065999 3.500000 # C2H C2H
pair_coeff 9 9 lj/charmm/coul/long 0.030000 2.500000 # H H
pair_coeff 1 3 lj/cut/coul/long 0.1902043638 3.208003663 # Ow NCO
pair_coeff 1 4 lj/cut/coul/long 0.1494826077 3.445948708 # Ow CO
pair_coeff 1 5 lj/cut/coul/long 0.2114003311 3.061533603 # Ow OC
pair_coeff 1 6 lj/cut/coul/long 0.2114003311 3.061533603 # Ow CTN
pair_coeff 1 7 lj/cut/coul/long 0.1185126457 3.329102732 # Ow CT2
pair_coeff 1 8 lj/cut/coul/long 0.1185126457 3.329102732 # Ow C2H
pair_coeff 1 9 lj/cut/coul/long 0.07990181475 2.813605338 # Ow H
pair_coeff 2 3 lj/cut/coul/long 0 0 # Hw NCO
pair_coeff 2 4 lj/cut/coul/long 0 0 # Hw CO
pair_coeff 2 5 lj/cut/coul/long 0 0 # Hw OC
pair_coeff 2 6 lj/cut/coul/long 0 0 # Hw CTN
pair_coeff 2 7 lj/cut/coul/long 0 0 # Hw CT2
pair_coeff 2 8 lj/cut/coul/long 0 0 # Hw C2H
pair_coeff 2 9 lj/cut/coul/long 0 0 # Hw H
neighbor 3.0 bin
neigh_modify every 1 delay 0 check yes
timestep 1.0
thermo 100
thermo_style custom step time cpu etotal ke pe evdwl ecoul elong temp press vol density
#minimize 1.0e-4 1.0e-6 100 1000
#write_restart restart.mini.*
dump dcd all dcd 100 nmp_pd3.dcd
dump_modify dcd unwrap yes
compute myent all entropy/atom 0.25 5 avg no 5 local yes
#dump myent all custom 100 dump.entropy c_myent
group water type 1 2
fix SHAKE water shake 0.0001 20 0 b 1 a 1
fix mynve all nve
run 1000
unfix mynve
write_restart restart.equil.*
output when dump myent is disabled “#dump myent all custom 100 dump.entropy c_myent”
LAMMPS (23 Jun 2022 - Update 2)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
WARNING: Using a tip4p sub-style with other sub-styles that include coulomb interactions can result in inconsistent calculation of the coulomb interactions (src/pair_hybrid.cpp:365)
Reading restart file …
restart file = 29 Sep 2021, LAMMPS = 23 Jun 2022
WARNING: Old restart file format revision. Switching to compatibility mode. (src/read_restart.cpp:613)
WARNING: Restart file used different # of processors: 4 vs. 1 (src/read_restart.cpp:658)
restoring atom style full from restart
orthogonal box = (0 0 0) to (60 60 60)
1 by 1 by 1 MPI processor grid
restoring pair style hybrid from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style opls from restart
26400 atoms
22400 bonds
31000 angles
34200 dihedrals
Finding 1-2 1-3 1-4 neighbors …
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
15 = max # of special neighbors
special bonds CPU = 0.010 seconds
read_restart CPU = 0.023 seconds
12000 atoms in group water
14400 atoms in group nmp
Finding SHAKE clusters …
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
4000 = # of frozen angles
find clusters CPU = 0.007 seconds
PPPM initialization …
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.25627018
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.0032540938
estimated relative force accuracy = 9.7996067e-06
using double precision KISS FFT
3d grid and FFT values/proc = 140608 91125
Generated 22 of 36 mixed pair_coeff terms from geometric mixing rule
Neighbor list info …
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.3188
ghost atom cutoff = 15.3188
binsize = 7.6594, bins = 8 8 8
5 neighbor lists, perpetual/occasional/extra = 4 1 0
(1) pair lj/cut/tip4p/long, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/charmm/coul/long, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) pair lj/cut/coul/long, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) compute entropy/atom, occasional
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(5) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run …
Unit style : real
Current step : 200
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 295.4 | 295.4 | 295.4 Mbytes
Step Time CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density
200 200 0 -59553.147 0 -59553.147 4605.5365 477015.44 -556318.29 0 31006.611 216000 1.2398668
300 300 38.361029 -52406.075 8683.5215 -61089.597 3917.8872 478772.11 -556438.62 130.05677 27149.822 216000 1.2398668
400 400 78.308604 -52411.277 10834.183 -63245.46 4677.1501 476570.31 -556493.64 162.26814 25488.472 216000 1.2398668
500 500 119.52826 -52419.215 11732.453 -64151.668 4494.5162 476246.48 -556547.31 175.7219 23408.866 216000 1.2398668
600 600 161.23846 -52427.887 11789.142 -64217.03 4804.9027 476047.37 -556586.45 176.57096 22461.851 216000 1.2398668
700 700 206.16619 -52435.468 11401.483 -63836.951 5281.8035 475835.55 -556605.07 170.76482 22550.298 216000 1.2398668
800 800 251.04665 -52443.005 11179.747 -63622.751 5499.0105 475845.77 -556637.72 167.44378 23018.038 216000 1.2398668
900 900 294.11539 -52444.875 11318.466 -63763.34 4909.322 476279.94 -556639.16 169.52144 22090.887 216000 1.2398668
1000 1000 338.65073 -52442.304 11688.114 -64130.418 3841.2182 476863.23 -556649.07 175.05782 20636.802 216000 1.2398668
1100 1100 381.72083 -52438.483 11997.671 -64436.154 2750.9696 477519.34 -556647.26 179.69418 19435.047 216000 1.2398668
1200 1200 425.16054 -52435.428 12324.931 -64760.359 1827.5006 478062.74 -556656.06 184.59569 18576.438 216000 1.2398668
Loop time of 425.161 on 1 procs for 1000 steps with 26400 atoms
Performance: 0.203 ns/day, 118.100 hours/ns, 2.352 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
Pair | 371.19 | 371.19 | 371.19 | 0.0 | 87.31
Bond | 8.0329 | 8.0329 | 8.0329 | 0.0 | 1.89
Kspace | 28.173 | 28.173 | 28.173 | 0.0 | 6.63
Neigh | 15.558 | 15.558 | 15.558 | 0.0 | 3.66
Comm | 0.65115 | 0.65115 | 0.65115 | 0.0 | 0.15
Output | 0.010354 | 0.010354 | 0.010354 | 0.0 | 0.00
Modify | 1.3566 | 1.3566 | 1.3566 | 0.0 | 0.32
Other | | 0.1842 | | | 0.04
Nlocal: 26400 ave 26400 max 26400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 64747 ave 64747 max 64747 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 6.4318182
Neighbor list builds = 24
Dangerous builds = 0
System init for write_restart …
PPPM initialization …
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.25627018
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.0032540938
estimated relative force accuracy = 9.7996067e-06
using double precision KISS FFT
3d grid and FFT values/proc = 140608 91125
Generated 22 of 36 mixed pair_coeff terms from geometric mixing rule
Total wall time: 0:07:06
the problem is as soon as i turn on the dump myent command “dump myent all custom 100 dump.entropy c_myent”
I am getting following Error:
ERROR on proc 0: Neighbor list overflow, boost neigh_modify one (src/npair_full_bin.cpp:120)
Last command: run 1000
data file
26400 atoms
22400 bonds
31000 angles
34200 dihedrals
9 atom types
7 bond types
13 angle types
16 dihedral types
0.000000 60.000000 xlo xhi
0.000000 60.000000 ylo yhi
0.000000 60.000000 zlo zhi
Masses
1 15.999 # Ow
2 1.008 # Hw
3 14.007 # NCO
4 12.011 # CO
5 15.999 # OC
6 12.011 # CTN
7 12.011 # CT2
8 12.011 # C2H
9 1.008 # H
Bond Coeffs
1 517.630258 0.872400 # Ow-Hw
2 489.997610 1.335000 # C-N
3 570.004780 1.229000 # C-O
4 336.998088 1.449000 # CT-N
5 267.999522 1.529000 # CT-CT
6 340.000000 1.090000 # CT-HC
7 317.005258 1.522000 # CT-C
Angle Coeffs
1 37.950526 103.600000 # Hw-Ow-Hw
2 50.000000 121.900000 # C-N-CT
3 50.000000 118.000000 # CT-N-CT
4 79.995220 122.900000 # N-C-O
why i am getting this errror? anyone please help