Out of range

Thanks Axel,
For tiny system this file is work. And yes, I run my simulation with a lot of processors, but I think that is not the problem, because I run it in a large computing center, and it did work with same file for almost same structure ( it did work for PETG with water for example).
Here is my output file:(a little bit long, sorry about that)
LAMMPS (4 Jan 2019)

OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)

using 1 OpenMP thread(s) per MPI task

units real

atom_style full

pair_style lj/class2/coul/long 9.5 9.5

bond_style class2

angle_style class2

dihedral_style class2

improper_style class2

pair_modify mix sixthpower tail yes

special_bonds lj/coul 0 0 1

Interaction potential definition

read_data data.300000

Reading data file …

orthogonal box = (5.92908 5.92908 5.92908) to (182.02 182.02 182.02)

6 by 8 by 10 MPI processor grid

reading atoms …

500054 atoms

reading velocities …

500054 velocities

scanning bonds …

4 = max bonds/atom

scanning angles …

6 = max angles/atom

scanning dihedrals …

12 = max dihedrals/atom

scanning impropers …

4 = max impropers/atom

reading bonds …

520386 bonds

reading angles …

898264 angles

reading dihedrals …

1265730 dihedrals

reading impropers …

428696 impropers

Finding 1-2 1-3 1-4 neighbors …

special bond factors lj: 0 0 1

special bond factors coul: 0 0 1

4 = max # of 1-2 neighbors

9 = max # of 1-3 neighbors

13 = max # of special neighbors

Integration conditions (check)

timestep 0.5

kspace_style pppm 1e-5

fix mom all momentum 100 linear 1 1 1 angular

#--------------- Variables Definition---------

thermo 1000

thermo_style custom step dt temp vol density etotal ke lx ly lz press pxx pyy pzz pe evdwl ecoul ebond eangle edihed eimp

variable temp index 300

variable tmp equal “lx”

variable L0 equal ${temp}

variable L0 equal 300

variable srate equal “1.0e-5” # change it from 5-7

variable srate1 equal “v_srate”

variable strain equal “(lx-v_L0)/v_L0”

variable p1 equal “v_strain”

variable p2 equal “-pxx/10000*1.01325”

variable p3 equal “-pyy/10000*1.0132”

variable p4 equal “-pzz/10000*1.0132”

variable p5 equal “lx”

variable p6 equal “ly”

variable p7 equal “lz”

variable p8 equal “press”

variable p9 equal “pxy”

variable p10 equal “pxz”

variable p11 equal “pyz”

variable step equal step

variable dt equal dt

variable vol equal vol

variable dens equal density

variable etotal equal etotal

variable ke equal ke

variable pe equal pe

variable evdwl equal evdwl

variable ecoul equal ecoul

variable ebond equal ebond

variable eangle equal eangle

variable edihed equal edihed

variable eimp equal eimp

#--------------- Deformation ------------------

reset_timestep 0

timestep 0.5

fix 1 all npt temp 300 300 50 y 0 0 500 z 0 0 500 drag 0.2 nreset 1000

fix 2 all deform 1 x trate ${srate1} units box remap x

fix 2 all deform 1 x trate 1e-05 units box remap x

fix def1 all print 1000 “{step} {dt} {temp} {vol} {dens} {etotal} {ke} {pe} {evdwl} {ecoul} {ebond} {eangle} {edihed} ${eimp}” file energies_npt.dat screen no title “step dt temp vol density etotal ke pe evdwl ecoul ebond eangle edihed eimp”

fix def2 all print 1000 “{step} {dt} {temp} {vol} {etotal} {p1} {p2} {p3} {p4} {p5} {p6} {p7} {p8} {p9} {p10} {p11}” file tension_npt.dat screen no title “step dt temp vol etotal p1 p2 p3 p4 p5 p6 p7 p8 p9 p10 p11”

dump 1 all cfg 1000 dump.tensile_* mass type xs ys zs fx fy fz id q mol

dump_modify 1 element o_2 ho2 oh c hc c1 c_1 o_1 cp ho

run 200000

PPPM initialization …

using 12-bit tables for long-range coulomb (src/kspace.cpp:321)

G vector (1/distance) = 0.288226

grid = 108 108 108

stencil order = 5

estimated absolute RMS force accuracy = 0.0040415

estimated relative force accuracy = 1.21709e-05

using double precision FFTs

3d grid and FFT values/proc = 8500 3240

Neighbor list info …

update every 1 steps, delay 10 steps, check yes

max neighbors/atom: 2000, page size: 100000

master list distance cutoff = 11.5

ghost atom cutoff = 11.5

binsize = 5.75, bins = 31 31 31

1 neighbor lists, perpetual/occasional/extra = 1 0 0

(1) pair lj/class2/coul/long, perpetual

attributes: half, newton on

pair build: half/bin/newton

stencil: half/bin/3d/newton

bin: standard

Setting up Verlet run …

Unit style : real

Current step : 0

Time step : 0.5

Per MPI rank memory allocation (min/avg/max) = 19.07 | 19.44 | 19.55 Mbytes

Step Dt Temp Volume Density TotEng KinEng Lx Ly Lz Press Pxx Pyy Pzz PotEng E_vdwl E_coul E_bond E_angle E_dihed E_impro

0 0.5 300.20374 5460260.5 1.2159361 1170274.5 447472.59 176.09125 176.09125 176.09125 -17.671264 75.916192 -20.773943 -108.15604 722801.9 -164514.5 2754981.3 189105.51 262266.88 -216038.85 21986.535

1000 0.5 300.65922 5468717.2 1.2140558 1171515.5 448151.52 176.97392 175.86843 175.7067 92.31402 -76.864249 106.38445 247.42186 723363.98 -162854.52 2754859.2 189886.08 261961.75 -217347.33 21846.185

2000 0.5 300.44696 5477506.2 1.2121078 1171917.7 447835.13 177.861 175.46678 175.51217 -29.666899 -487.64224 235.84088 162.80065 724082.56 -162930.12 2755085.5 189714.66 262334.66 -217231.24 22087.686

3000 0.5 300.1992 5481142.7 1.2113036 1171545.4 447465.82 178.75253 175.13071 175.08809 -203.25161 -548.4217 -76.831676 15.498552 724079.58 -162571.07 2754824.3 189746.55 262158.79 -216896.61 21814.808

4000 0.5 299.63825 5485588.3 1.2103219 1170669.5 446629.69 179.64853 174.87844 174.60765 -202.80254 -568.70222 64.937624 -104.64302 724039.76 -163023.67 2754946.8 189178.67 263619.56 -217612.08 21894.958

5000 0.5 300.33376 5489240.1 1.2095168 1172684.6 447666.4 180.54903 174.49429 174.23519 -206.49514 -690.56614 77.028724 -5.9479975 725018.19 -162055.46 2754924.5 189828.63 262339.32 -217004.33 21950.462

6000 0.5 299.8362 5495177.4 1.2082099 1171605.6 446924.74 181.45403 174.13343 173.91336 -167.67184 -663.27447 -59.481514 219.74047 724680.82 -161468.7 2754845.2 189333.93 262760.98 -217842.41 22037.731

7000 0.5 299.9492 5502936.7 1.2065063 1172698.7 447093.18 182.36357 173.83518 173.58762 -364.62372 -1042.873 4.6488149 -55.646957 725605.56 -161399.29 2755039.7 190030.61 262675.33 -217773.46 21975.92

8000 0.5 300.56055 5504801.9 1.2060975 1174080 448004.43 183.27767 173.49172 173.12244 -462.86953 -1067.7371 -255.05794 -65.813585 726075.54 -161529.19 2755170 189963.73 262549.82 -217014.14 21912.762

9000 0.5 299.94134 5510541.8 1.2048412 1173025.8 447081.46 184.19636 173.09169 172.83713 -458.81686 -1339.1729 -122.59704 85.3194 725944.31 -160791.79 2755190.3 189765.95 262727.9 -217846.12 21870.161

10000 0.5 299.55201 5513943.2 1.204098 1173567.2 446501.15 185.11965 172.85194 172.31993 -422.50299 -1329.9498 -17.72488 80.165702 727066.06 -161274.73 2755275.9 190192.83 263023.84 -217168.08 21954.849

11000 0.5 300.03391 5524029.5 1.2018994 1174271.4 447219.44 186.04756 172.49726 172.12732 -647.40481 -1615.1846 -38.518144 -288.51164 727051.91 -160392.66 2755245.9 189765.96 263140.13 -217745.84 22016.122

12000 0.5 299.44989 5529102.1 1.2007968 1174656.2 446348.92 186.98013 172.16961 171.75234 -593.97161 -1547.9273 -50.092047 -183.89552 728307.27 -159809.86 275314.5 190064.13 263161.1 -217252.64 21793.645

until
180000 0.5 300.13987 5988669.7 1.1086482 1226772.2 447377.39 433.1146 116.66728 118.5164 -2324.0424 -6582.833 -227.68542 -161.60889 779394.83 -127516.55 2758646.7 184572.47 275353.03 -208901.18 21727.993

ERROR on proc 165: Out of range atoms - cannot compute PPPM (src/KSPACE/pppm.cpp:1945)

Last command: run 200000

Application 2543161 exit codes: 134

Application 2543161 exit signals: Killed

Application 2543161 resources: utime ~2675s, stime ~27s, Rss ~18036, inblocks ~0, outblocks ~0

Thanks Axel,
For tiny system this file is work. And yes, I run my simulation with a lot of processors, but I think that is not the problem, because I run it in a large computing center, and it did work with same file for almost same structure ( it did work for PETG with water for example).

this is clarifying a little, but not much help. whether something ran
with a different molecule is no proof, you may just have gotten lucky,
or the structure of the other molecule is such, that the problems
doesn't manifest itself to the same degree.

thus my suggestions for what to try out remain the same.

axel.