[lammps-users] No output

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1

I am doing MD Simulations on water using SPC/E Water model . I have minimized and equilbrated the system in periodic conditions and then I am trying to transfer the system into another box which is non-periodic in z dimension and introduce a surface . However there is no processing going on . My input is as follows :
read_restart restart.spce800eq
change_box all boundary p p f remap

kspace_style pppm 1.0e-4
kspace_modify slab 3.0

pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000

bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none

bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47

special_bonds lj/coul 0.0 0.0 0.5

neighbor 1.0 bin
neigh_modify every 1 delay 0 check no

reset_timestep 2

thermo_style one
thermo_modify lost ignore
thermo 50

fix 1 all shake 0.0001 20 0 b 1 a 1
fix 2 all nvt temp 300.0 300.0 100.0
run 10000

dump 1 all custom 200 s.comp_*. id xs ys zs type type

region zlow plane 0.02645 0.02645 0.02641 0 0 1 units box

fix 3 all wall/region zlow lj93 0.155 3.166 10

run 20000

In the output , after few steps there isn’t any further processing .
…
All restart file global fix info was re-assigned
Neighbor list info …
update every 1 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/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 : 2
Time step : 0.5

I am getting no output after this step nor is the Software showing any error .

2

this is impossible to debug from remote.
however, you should not have

thermo_modify lost ignore

as that could hide problems and associated warnings/error from LAMMPS.
to narrow down you should set thermo and dump output to be done at every step so you can see if energies are well behaving and atoms moving normally until LAMMPS gets stuck.

when it gets stuck, you can try looking up the process ID (or the process IDs if running in parallel) and then attach a debugger with gdb -p and then at the gdb prompt you would hit ctrl-c to interrupt and then you can type the “where” command to get a stack trace showing where exactly the calculation gets stuck.

without more specific information like stack traces or a minimal input deck that would quickly reproduce this behavior with minimal effort and time there is nothing else that I can think of to debug from remote.

axel.

3

Thanks, I’ll check it out.