[lammps-users] Water modeling

AEI,

Thanks. It was embarrassing I missed the obvious. Thank you very much. It runs now but collapses after 28 time steps. I don’t think the systems overlaps at the beginning. I am attaching my script and part of the out put file. Please help.

[[email protected]…1180… water]$ cat job.out FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
Warning: no access to tty (Bad file descriptor).cy-2 16water Feb 9 09:32
Thus no job control in this shell.
NODES: 84-91
LAMMPS (21 May 2008)desktop 17960 Feb 6 15:42 a.spc
Scanning data file …sktop 17960 Feb 9 08:44 a.tip4
2 = max bonds/atomdesktop 1819 Feb 9 08:44 data.water
1 = max angles/atomesktop 39144 Feb 6 15:42 data.water_spc
Reading data file …esktop 764 Feb 9 09:32 in.water
orthogonal box = (-0.5 -0.5 -0.5) to (5.7 5.7 5.7)water_ljcl
2 by 2 by 4 processor grid 792 Feb 9 08:41 in.water_spc
24 atoms 1 sfeng desktop 768 Feb 9 08:41 in.water_tip4
16 bonds 1 sfeng desktop 0 Feb 9 09:32 job.err
8 angles 1 sfeng desktop 2146 Feb 9 09:32 job.out
Finding 1-2 1-3 1-4 neighbors …24 Feb 4 13:03 lmp_coyote
2 = max # of 1-2 neighbors 4096 Feb 9 09:32 log.lammps
1 = max # of 1-3 neighbors 593 Feb 6 15:18 myscript
1 = max # of 1-4 neighbors 2904 Feb 9 09:32 rdf.out
2 = max # of special neighbors630 Feb 9 08:44 water.f
Finding SHAKE clusters …p 2642 Feb 6 15:42 water.f_spc
0 = # of size 2 clustersp 2630 Feb 6 14:28 water.f_tip4
8 = # of size 3 clustersp 8632 Feb 9 09:32 xyz.dat
0 = # of size 4 clustersg.lammps
0 = # of frozen anglesdata.water
PPPM initialization … in.water
G vector = 0.2994
grid = 5 5 5
stencil order = 5
RMS precision = 1.38853e-05
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor
G vector = 0.306979
grid = 8 8 8
stencil order = 4
RMS precision = 8.77166e-06
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor
G vector = 0.292018
grid = 12 12 12
stencil order = 3
RMS precision = 2.1486e-05
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor
G vector = 0.285275
grid = 45 45 45
stencil order = 2
RMS precision = 3.1726e-05
brick FFT buffer size/proc = 42588 6348 45630
Setting up run …
SHAKE stats (type/ave/delta) on step 0
1 0.957311 2.23449e-07
Memory usage per processor = 5.89698 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 5382.2062 KinEng = 20.5676 Temp = 390.5660
PotEng = 5361.6386 E_bond = 0.0000 E_angle = 597.6562
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 8.2627
E_coul = 5449.0692 E_long = -693.3494 Press = 97037.5435
---------------- Step 1 ----- CPU = 0.0182 (sec) ----------------
.
.
.
---------------- Step 29 ----- CPU = 0.4830 (sec) ----------------
TotEng = nan KinEng = nan Temp = nan
PotEng = 4949.3204 E_bond = 0.0000 E_angle = 30.9706
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 6.7148
E_coul = 5604.6843 E_long = -693.0492 Press = nan
ERROR: Atom IDs must be consecutive for dump xyz

#3d Lennard-Jones settling

units real
atom_style full

pair_style lj/cut/coul/long/tip4p 1 2 1 1 0.125 10.0 10.0
bond_style harmonic
angle_style harmonic
kspace_style pppm/tip4p 0.00004

read_data data.water
#read_restart arestart.water.160000

set potentials

pair_coeff 2 2 0 0 10.0
pair_coeff 1 2 0 0 10.0

pair_coeff 1 1 0.1550 3.1536 10.0

running conditions

neighbor 1.8 bin
neigh_modify every 1 delay 0 check no

velocity all create 300 57287

fix id1 all nvt 300.0 300.0 1.0
fix 1f all shake 0.0001 20 100000 b 1 a 1

fix 1 all rdf 100 rdf.out 100 1 1

fix 3 all coord/original

dump id4 all xyz 1 xyz.dat

restart 2000 restart.water

thermo 1
thermo_style multi
thermo_modify lost error
thermo_modify norm no

run 20000