Rerun error

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!

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.

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

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

Thanks!

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.

  1. I have generated dump files where I just output x, y, z, and per atom potential energy ‘c_eng’.

  2. After finishing the simulations, I realized that I needed the forces as well.

  3. 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

  4. 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.

Any thoughts on this?

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!

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