Doubt and Error with rerun command

Dear Lammps Users

I wanted to calculate the coloumbic forces for system I simulated using Lammps.I did the simulation with the pair style lj/cut/coul/long and now want to rerun the simulation.I have some conceptual and implementation doubts,

The rerun command reads the snapshot from the dump file and calculates the forces and energy at the snapshot.

Now I am not sure how does this happens with just coordinates/velocities for a single frame gives the forces/energy as the two

are calculated using the classical equation of motion.

Regarding the implementation, the manual says fix style like fix npt/nve are not allowed ,does that also includes the fix shake.

Further with the syntax defining the rerun defines the time step at which the snapshot from the dump file is read.Then I hope the
commands like timestep and run are redundant.

Finally the rerun script of mine which seems to showing error is
dimension 3
units real
boundary p p p

kspace_style ewald 1.0e-4

kspace_modify order 3
atom_style full
pair_style coul/long 15.0
bond_style harmonic
angle_style harmonic
pair_modify mix arithmetic

read_restart z.restart.1000000

group oxy type 1
group hyd type 2
group wtr type 1 2

neighbor 3.0 bin
neigh_modify delay 0 every 1 one 6000

fix 1 wtr shake 0.0001 20 0 a 1 b 1 t 1 2

thermo 10000
thermo_style custom step pe ke etotal temp press vol

restart 20000 z.restart

rerun z1.output.dump dump x y z

The error reads “WARNING: Inconsistent image flags (…/domain.cpp:645)”

If i simultaneously want to read two dump files then the rerun command

rerun z1.output.dump,z2.output.dump dump x y z fx fy fz also ends with

an error “Illegal read_dump command (…/read_dump.cpp:693)”

Thanks

DeepaK Ojha
School Of Chemistry

“Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live”

Dear Lammps Users

I wanted to calculate the coloumbic forces for system I simulated using
Lammps.I did the simulation with the pair style lj/cut/coul/long and now
want to rerun the simulation.I have some conceptual and implementation
doubts,

The rerun command reads the snapshot from the dump file and calculates the
forces and energy at the snapshot.

Now I am not sure how does this happens with just coordinates/velocities
for a single frame gives the forces/energy as the two
are calculated using the classical equation of motion.

no they are not. in rerun, there is no time integration, instead data
is overwritten from the trajectory file. of course, *only* the data
that you read from the trajectory file will be overwritten, i.e. if
you read only positions, only those will be updated.

Regarding the implementation, the manual says fix style like fix npt/nve are
not allowed ,does that also includes the fix shake.

there is no reason to use fix shake, since you only take data from the
trajectory file as it is.

Further with the syntax defining the rerun defines the time step at which
the snapshot from the dump file is read.Then I hope the
commands like timestep and run are redundant.

Finally the rerun script of mine which seems to showing error is
dimension 3
units real
boundary p p p

kspace_style ewald 1.0e-4

kspace_modify order 3
atom_style full
pair_style coul/long 15.0
bond_style harmonic
angle_style harmonic
pair_modify mix arithmetic

read_restart z.restart.1000000

group oxy type 1
group hyd type 2
group wtr type 1 2

neighbor 3.0 bin
neigh_modify delay 0 every 1 one 6000

fix 1 wtr shake 0.0001 20 0 a 1 b 1 t 1 2

thermo 10000
thermo_style custom step pe ke etotal temp press vol

restart 20000 z.restart

rerun z1.output.dump dump x y z

The error reads "WARNING: Inconsistent image flags (../domain.cpp:645)"

as mentioned above, rerun overwrites data. since you have a periodic
box, first read a restart file, and then (wrapped!) coordinates, you
likely have inconsistent image flags. you will have to re-read those
as well. similarly about velocities. they will not be updated and thus
should be reset to zero unless you also read them from the dump.

If i simultaneously want to read two dump files then the rerun commanddf
rerun z1.output.dump,z2.output.dump dump x y z fx fy fz also
ends with
an error "Illegal read_dump command (../read_dump.cpp:693)"

it makes no sense to read forces from the dump. the whole point of
rerun is to recompute those.

axel.