ERROR: Did not assign all restart atoms correctly (../read_restart.cpp:521)

LAMMPS LAMMPS Mailing List Mirror
1

I am using Lammps 12 dec 2018 version. And I have been having problems reading the restart file, even using the remap option. The simulation has 32000 atoms while the restart simulation reads only 31955.

The simulation consist of two fixed regions (not included in the thermostat and barostat) and a middle region (surface) able to move.

Input is attached. Any suggestions?

# ------------------------ INITIALIZATION ----------------------------

units metal
dimension 3
boundary p p p
atom_style full

# ----------------------- ATOM DEFINITION ----------------------------
suffix opt
fix csinfo all property/atom i_CSID

read read_restart restart.* remap
#read_data data.lammps fix csinfo NULL CS-Info

group cores type 1 2 3
group shells type 4 5 6

region bulk1 prism 0 EDGE 0 EDGE 0 20.1 0.0 0.0 0.0
region surface prism 0 EDGE 0 EDGE 20.1 141.15 0.0 0.0 0.0
region bulk2 prism 0 EDGE 0 EDGE 141.15 EDGE 0.0 0.0 0.0

group bulk1 region bulk1
group bulk2 region bulk2

group surface region surface
group bulk union bulk1 bulk2

neighbor 1.0 bin
comm_modify vel yes
neigh_modify every 4 delay 0

# ------------------------ FORCE FIELDS ------------------------------
kspace_style ewald 1.0e-6
pair_style hybrid rydb/coul/long/cs 6.5 11.0 buck/coul/long/cs 6.5 11.0 # A, rho, sigma=0, C, D
pair_modify tail no
pair_coeff * * rydb/coul/long/cs 0.0 1.000 0.00
pair_coeff 4 6 rydb/coul/long/cs 0.096 2.420131 -12.5665 #Pb-Ti(shell)
pair_coeff 4 5 rydb/coul/long/cs 6766.270 0.273805 127.7793 #Pb-O(shell)
pair_coeff 5 6 rydb/coul/long/cs 1125.01 0.359723 -170.8363 #Ti-O(shell)
pair_coeff 5 5 buck/coul/long/cs 3634.861 0.314424 331.6058 #O-O(shell)

bond_style class2
#nro de resorte #ro #k2 #k3 #k4
bond_coeff 1 0.0 59.75 0.0 750.02083
bond_coeff 2 0.0 11.645 0.0 188.3333
bond_coeff 3 0.0 750 0.0 0.0

pair_modify table 0
reset_timestep 0

thermo 100
thermo_style custom step etotal pe ke temp press &
              epair evdwl ecoul elong ebond fnorm fmax vol cella cellb cellc pxx pyy pzz pxy pxz pyz

compute CSequ all temp/cs cores shells
compute press all pressure CSequ

thermo_modify temp CSequ

#velocity surface create $Tstart 12315416 dist gaussian mom yes rot no bias yes temp CSequ
#velocity surface scale $Tstart temp CSequ

timestep 0.0004
restart 10 restart.*
fix nose surface npt temp Tstart Tfinal 0.12 tri 0.0 0.0 0.4
fix_modify nose temp CSequ press press
dump Info all custom 10 phasetransition2.dat id type x y z
dump_modify Info sort id format line "%10i %10i %20.10f %20.10f %20.10f"

2

I am using Lammps 12 dec 2018 version. And I have been having problems
reading the restart file, even using the remap option. The simulation
has 32000 atoms while the restart simulation reads only 31955.

The simulation consist of two fixed regions (not included in the
thermostat and barostat) and a middle region (surface) able to move.

Input is attached. Any suggestions?

the input uses a custom pair style not distributed with LAMMPS.
does the same thing happen, when this pair style is not used?

axel.

3

Yes, I tryed just with buckingham potential and the same happens.

4

Yes, I tryed just with buckingham potential and the same happens.

can you provide me with a minimal input deck, that creates the restart
(e.g. from an initial data file)
and then tries to read it. that way i can try to reproduce it on my
local machine and if i am able to do that, it would be much easier to
figure out what it happening. doing this from remote without knowing
more details is difficult.

can you also let me know your platform and compiler choices and settings.

thanks,
      axel.