Dear LAMMPS developers,

I appreciate it if you could tell me what I’m doing wrong here with rerun command. This is a part of the log file:

# VARIABLES

variable restart_name index 1.restart

variable settings_name index system.in.settings

package omp 1 neigh yes

using multi-threaded neighbor list subroutines

suffix omp

processors * * * grid numa map cart

#===========================================================

# SETUP SIMULATIONS

#===========================================================

# READ IN COEFFICIENTS/COORDINATES/TOPOLOGY

read_restart ${restart_name}

read_restart 1.restart

Reading restart file …

restart file = 28 Mar 2023, LAMMPS = 15 Jun 2023

WARNING: Restart file used different # of processors: 56 vs. 28 (src/read_restart.cpp:661)

restoring atom style full from restart

triclinic box = (0.0020454446 -0.038241733 -0.4878597) to (35.785955 35.473842 39.83486) with tilt (-0.13147505 0.090169957 0.047554098)

2 by 2 by 7 MPI processor grid

2 by 2 by 7 core grid within node

restoring pair style hybrid from restart

restoring bond style harmonic/omp from restart

restoring angle style harmonic/omp from restart

restoring dihedral style fourier/omp from restart

3264 atoms

2496 bonds

4608 angles

5184 dihedrals

Finding 1-2 1-3 1-4 neighbors …

special bond factors lj: 0 0 0.5

special bond factors coul: 0 0 0.8333333333333334

4 = max # of 1-2 neighbors

6 = max # of 1-3 neighbors

12 = max # of 1-4 neighbors

16 = max # of special neighbors

special bonds CPU = 0.002 seconds

read_restart CPU = 0.038 seconds

compute eng all pe/atom

compute eatoms all reduce sum c_eng

#===========================================================

# DEFINE PAIR, BOND, AND ANGLE STYLES

#===========================================================

special_bonds amber

pair_style hybrid buck/coul/long 17.0 17.0 lj/cut/coul/long 17.0 17.0

pair_modify shift yes

bond_style harmonic

angle_style harmonic

dihedral_style fourier

kspace_style pppm 1.0e-7

include ${settings_name}

include system.in.settings

pair_coeff 1 1 buck/coul/long 70359906.62970 0.131258 0.00

pair_coeff 2 2 buck/coul/long 22793.33858 0.482217 696.94954

bond_coeff 1 443.528 1.028

bond_coeff 2 443.528 1.028

.

.

.

pair_coeff 9 19 lj/cut/coul/long 0.01570 1.96000

pair_coeff 9 17 lj/cut/coul/long 0.01570 1.96000

pair_coeff 9 22 lj/cut/coul/long 0.01570 1.96000

# DECLARE RELEVANT OUTPUT VARIABLES

variable cfac equal 0.101325

variable my_step equal step

variable PXX equal -pxx*{cfac}
variable PXX equal -pxx*0.101325
variable PYY equal -pyy*{cfac}

variable PYY equal -pyy*0.101325
variable PZZ equal -pzz*{cfac}
variable PZZ equal -pzz*0.101325
variable PXY equal -pxy*{cfac}

variable PXY equal -pxy

*0.101325*

variable PXZ equal -pxz{cfac} variable PXZ equal -pxz*0.101325 variable PYZ equal -pyz*{cfac}

variable PXZ equal -pxz

variable PYZ equal -pyz

*0.101325*

variable LX equal lx

variable LY equal ly

variable LZ equal lz

variable XY equal xy

variable XZ equal xz

variable YZ equal yz

variable my_temp equal temp

variable my_rho equal density

variable my_ke equal ke

variable my_pe equal pe

variable my_ebon equal ebond

variable my_eang equal eangle

variable my_edih equal edihed

variable my_emol equal emol

variable my_evdw equal evdwl

variable my_eel equal (ecoul+elong)

variable my_ent equal enthalpy

variable my_P equal press${cfac}

variable LX equal lx

variable LY equal ly

variable LZ equal lz

variable XY equal xy

variable XZ equal xz

variable YZ equal yz

variable my_temp equal temp

variable my_rho equal density

variable my_ke equal ke

variable my_pe equal pe

variable my_ebon equal ebond

variable my_eang equal eangle

variable my_edih equal edihed

variable my_emol equal emol

variable my_evdw equal evdwl

variable my_eel equal (ecoul+elong)

variable my_ent equal enthalpy

variable my_P equal press

variable my_P equal press*0.101325

variable my_vol equal vol

variable Time equal “time/1000”

neigh_modify every 1 delay 0 check yes cluster yes one 10000

# SET OUTPUTS

thermo_style custom step temp vol density etotal pe c_eatoms eangle edihed ecoul elong evdwl enthalpy press

thermo_modify format float %14.6f

thermo 1000

run 0 post no

WARNING: No fixes with time integration, atoms won’t move (src/verlet.cpp:60)

PPPM initialization …

using 12-bit tables for long-range coulomb (src/kspace.cpp:342)

G vector (1/distance) = 0.21351548

grid = 45 45 48

stencil order = 5

estimated absolute RMS force accuracy = 3.6918559e-05

estimated relative force accuracy = 1.1117914e-07

using double precision KISS FFT

3d grid and FFT values/proc = 13500 4050

Generated 0 of 351 mixed pair_coeff terms from geometric mixing rule

Hybrid pair style last /omp style lj/cut/coul/long

Last active /omp style is kspace_style pppm/omp

Neighbor list info …

update: every = 1 steps, delay = 0 steps, check = yes

max neighbors/atom: 10000, page size: 100000

master list distance cutoff = 19

ghost atom cutoff = 19

binsize = 9.5, bins = 4 4 5

3 neighbor lists, perpetual/occasional/extra = 3 0 0

(1) pair buck/coul/long, perpetual, skip from (3)

attributes: half, newton on, omp

pair build: skip/omp

stencil: none

bin: none

(2) pair lj/cut/coul/long, perpetual, skip from (3)

attributes: half, newton on, omp

pair build: skip/omp

stencil: none

bin: none

(3) neighbor class addition, perpetual

attributes: half, newton on, omp

pair build: half/bin/newton/tri/omp

stencil: half/bin/3d/tri

bin: standard

Per MPI rank memory allocation (min/avg/max) = 22.39 | 23.04 | 23.8 Mbytes

Step Temp Volume Density TotEng PotEng c_eatoms E_angle E_dihed E_coul E_long E_vdwl Enthalpy Press

3000000 1.016615 51240.545975 3.075966 -77858.802173 -77868.690160 -77868.690160 117.355672 -798.271652 -42794.418220 -42763.822508 8351.063979 -77866.424380 -10.199786

Loop time of 5.74211e-05 on 28 procs for 0 steps with 3264 atoms

balance 1.0 shift xyz 10 1.0 weight time 0.8 weight neigh 0.8

Balancing …

PPPM initialization …

using 12-bit tables for long-range coulomb (src/kspace.cpp:342)

G vector (1/distance) = 0.21351548

grid = 45 45 48

stencil order = 5

estimated absolute RMS force accuracy = 3.6918559e-05

estimated relative force accuracy = 1.1117914e-07

using double precision KISS FFT

3d grid and FFT values/proc = 13500 4050

Generated 0 of 351 mixed pair_coeff terms from geometric mixing rule

Hybrid pair style last /omp style lj/cut/coul/long

Last active /omp style is kspace_style pppm/omp

WARNING: Balance weight neigh skipped b/c no suitable list found (src/imbalance_neigh.cpp:65)

rebalancing time: 0.003 seconds

iteration count = 30

time weight factor: 0.8

neighbor weight factor: 0.8

initial/final maximal load/proc = 180 130

initial/final imbalance factor = 1.5441176 1.1151961

x cuts: 0 0.49951172 1

y cuts: 0 0.50048828 1

z cuts: 0 0.095563616 0.20354353 0.41169085 0.55957031 0.65332031 0.83021763 1

# CREATE COORDINATE DUMPS FOR EQUILIBRIUM

dump Deform all custom 1000 1.rerun.lammpstrj id type x y z fx fy fz c_eng

dump_modify Deform sort id

rerun 1.lammpstrj dump x y z

WARNING: No fixes with time integration, atoms won’t move (src/verlet.cpp:60)

PPPM initialization …

using 12-bit tables for long-range coulomb (src/kspace.cpp:342)

G vector (1/distance) = 0.21351548

grid = 45 45 48

stencil order = 5

estimated absolute RMS force accuracy = 3.6918559e-05

estimated relative force accuracy = 1.1117914e-07

using double precision KISS FFT

3d grid and FFT values/proc = 15300 5290

Generated 0 of 351 mixed pair_coeff terms from geometric mixing rule

Hybrid pair style last /omp style lj/cut/coul/long

Last active /omp style is kspace_style pppm/omp

Hybrid pair style last /omp style lj/cut/coul/long

Last active /omp style is kspace_style pppm/omp

ERROR on proc 0: Out of range atoms - cannot compute PPPM (src/KSPACE/pppm.cpp:1839)

Last command: rerun 1.lammpstrj dump x y z

And here is the format of the dump file ‘1.lammpstrj’ that I generated in the previous run:

ITEM: TIMESTEP

0

ITEM: NUMBER OF ATOMS

3264

ITEM: BOX BOUNDS xy xz yz pp pp pp

-1.2924208554267189e-01 3.5872141067650290e+01 -1.2990216942643038e-01

-4.2131316647385120e-02 3.5525677432202926e+01 8.4801151608821596e-02

-4.8480739176730836e-01 3.9831807391657790e+01 4.7946115586054987e-02

ITEM: ATOMS id type x y z c_eng

1 1 6.40301 32.0487 9.5538 -299.269

2 1 1.9643 27.716 9.61621 -299.952

…

3262 25 30.7191 21.7794 22.3138 -0.509143

3263 26 29.5206 20.4816 22.0947 -0.676045

3264 27 31.2469 20.1477 21.8721 -0.72018

ITEM: TIMESTEP

1000

ITEM: NUMBER OF ATOMS

3264

ITEM: BOX BOUNDS xy xz yz pp pp pp

-1.3092946535011762e-01 3.5881323947150868e+01 -1.3216621701229059e-01

-4.1327792795581075e-02 3.5545610888821457e+01 9.4560698887709821e-02

-4.8020894547762438e-01 3.9827208945368184e+01 6.8683096056307777e-02

ITEM: ATOMS id type x y z c_eng

1 1 6.40193 32.0351 9.56041 -298.972

2 1 1.95405 27.7102 9.61271 -298.491

Please let me know if more information is needed to resolve this issue.

Thanks!