Rerun error

RezaNamakian · July 20, 2023, 6:39pm

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 -pyy0.101325
variable PZZ equal -pzz{cfac} variable PZZ equal -pzz*0.101325 variable PXY equal -pxy*{cfac}
variable PXY equal -pxy0.101325
variable PXZ equal -pxz{cfac} variable PXZ equal -pxz*0.101325 variable PYZ equal -pyz*{cfac}
variable PYZ equal -pyz0.101325
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 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!

simongravelle · July 20, 2023, 8:20pm

Hi

You need to make the minimum effort of providing context to what you try to do, a simplified input, and explain the steps you already took to try to fix the issue. I doubt anybody wants to read a badly formatted log file out of context.

RezaNamakian · July 20, 2023, 8:24pm

1.rerun.log.sh (41.6 KB)
in.Compression_X.sh (2.5 KB)

RezaNamakian · July 20, 2023, 8:24pm

Pls let me know if you can’t read these files.

Thanks!

simongravelle · July 20, 2023, 8:43pm

I can read the files just fine, but you also ignored all my other previous requests, so please understand that I have little to no motivation to look at those.

RezaNamakian · July 20, 2023, 8:52pm

I have generated dump files where I just output x, y, z, and per atom potential energy ‘c_eng’.
After finishing the simulations, I realized that I needed the forces as well.
I thought I could use the rerun command to get those additional quantities through already generated dump file ‘1.lammps.trj’ which has only 'x y z c_eng, but I want ‘x y z fx fy fz c_eng’ now
I failed to do that as it is obvious from the error shown in the log file, and I do not know where I’m making the mistake.

RezaNamakian · July 21, 2023, 9:14pm

Any thoughts on this?

srtee · July 21, 2023, 10:10pm

Please see Search results for 'rerun out of range' - Materials Science Community Discourse

The first thread has answers to your questions, and it also shows

(1) how searching Matsci* first can save you lots of time waiting on answers
(2) how to write a decent first post with just the right amount of detail to sketch out the problem without overwhelming readers

*My own Google search profile is very well optimised just from spending lots of time searching LAMMPS questions, but searching from a fresh Google profile or DuckDuckGo gives much less helpful results. So search the forums directly!