Hi all,
I am running the simulation in lammps where during the initial first minimization the lammps dump the atom id properly in the trajectory but during the production run the atom ids are not sorted correctly. I tried running it in my system and the dumping happens correctly but when I run it in the cluster the ids are not getting sorted correctly only during the production run. Could anyone help me with this issue?
the lammps input script that i used
variable temperature equal 150
variable randomSeed equal 15973
## Lammps Input File Creating data file for multi chain condensate
#----------------- Box and units (use real units and periodic boundaries)----------------
variable input string input
units real
atom_style full
dimension 3
boundary p p f
#---------- Pair interactions require lists of neighbours to be calculated -------------
neighbor 3.5 multi
neigh_modify every 10 delay 0 check no
#-------------- READ "start" data file ------------------------------------------------
read_data data_Multi.${input}
include forcefield.${input}
#---------- Output thermodynamic info(temperature, energy, pressure, etc.) ------------
thermo_style custom step temp pe ke etotal lx ly lz pxx pyy pzz
thermo 100
#--------------- Dump configurations at regular intervals -----------------------------
dump 2 all custom 100 input1.lammpstrj id mol type q x y z ## wrap coordinate
dump_modify 2 sort id
timestep 10
fix botwall all wall/lj93 zlo -130.0 1.0 6.0 10.0 # lz epsilon sigma cutoff
fix topwall all wall/lj93 zhi 130.0 1.0 6.0 10.0
fix cg_npt all npt temp 100.0 100.0 100.0 x 1.0 1.0 1000.0 y 1.0 1.0 1000.0 couple xy
run 30000
unfix botwall
unfix topwall
unfix cg_npt
change_box all z final -300 300 boundary p p p
fix fxnve all nve
fix fxlange all langevin 100 100 1000.0 548669595
run 10000
# Initital pair style and bond parameters
bond_style harmonic
dielectric 80.0
# Set pair parameters
include forcefield.input
reset_atom_ids
velocity all create ${temperature} ${randomSeed}
special_bonds fene
# neighbour list settings
neighbor 3.5 multi
# Timestep and computational parameters
comm_style tiled
timestep 10
# Relax sim by performing minimisation (this is helpful if we change the potential or sequence)
min_style fire
timestep 0.0000001
minimize 0.0 1.0e-8 1000 100000
timestep 0.00001
minimize 0.0 1.0e-8 1000 100000
timestep 0.1
minimize 0.0 1.0e-8 1000 100000
timestep 10
minimize 0.0 1.0e-8 1000 100000
neigh_modify every 10 delay 0
fix fxnve all nve
fix fxlange all langevin ${temperature} ${temperature} 100000.0 ${randomSeed}
fix fxbal all balance 1000 1.1 rcb
variable binsize equal lz/200
compute dens all chunk/atom bin/1d z lower ${binsize}
fix 6 all ave/chunk 1000 1 1000 dens density/mass density/number file density.profile
fix fixCOM all recenter INIT INIT INIT # this helps to prevent drift of the interfaces and makes it easier to average over many measurements
# Thermo output settings
thermo 100000
thermo_style custom step pe ecoul ke temp press density
thermo_modify flush yes
dump 3 all custom 200000 result.lammpstrj id mol type q x y z
dump_modify 3 sort id
dump 4 all custom 200000 result_nopbc.lammpstrj id mol type q xu yu zu
dump_modify 4 sort id
#dump 2 all molfile 1800 melt2.pdb pdb .:/usr/local/lib/vmd/plugins/LINUXAMD64/molfile
#dump_modify 2 unwrap yes
# Equilibration
run 50000
# Run simulation
restart 10000000 restart
run 20000000
# write final configuration
write_data final-structure.dat nocoeff
output example :
input1.lammpstrj
ITEM: ATOMS id mol type q x y z
1 1 11 0 562.467 73.907 97.042
2 1 3 -0.75 564.166 76.43 94.528
3 1 18 0 566.861 74.486 92.722
4 1 5 0 564.636 72.313 90.495
5 1 11 0 563.008 75.167 88.592
result.lammpstrj
ITEM: ATOMS id mol type q xu yu zu
1 89 18 0 -76.0925 -95.8928 -29.1919
2 89 18 0 -74.9051 -97.133 -38.0792
3 89 16 0 -63.4815 -84.9568 -35.4658
4 89 6 0 -73.9764 -99.3464 -22.3573
5 89 1 0 -73.8377 -96.2179 -26.2333
6 89 18 0 -75.1316 -101.996 -19.5842
7 100 4 -0.75 -6.34979 -120.171 -52.5064
Thank you