Hello all,
1 - Where do I find the result of rerun command ?
2 - I my system I have two kind of particles ( see myRDF all rdf 100 1 1 1 2).
How do to known what kind of particles were used rerun command ?
There is no “result” of the rerun command. It just executes whatever
other commands are in your input script, as if you were running a simulation
that produced the snapshots that are in the dump file it reads.
So if you have a compute rdf and fix ave/time command defined that
writes a file, they will get invoked. In the script you included, they will
likely overwrite whatever data you already had from the initial run.
The usual way to use “rerun” is to make a 2nd script that defines the
new commands you want to execute on the snapshots. Presumably
those are different than the commands you used for the initial run.
Re: what particles are used? All the ones that are in the snapshot.
Steve
Hi Steve, sorry for the late. I’m using units LJ and style atomic. As shown under :
units lj
atom_style atomic
boundary p p p
dimension 3
timestep 0.001
In my snapshot (dump file) the label of particles are :
1 8.19723 0.299016 8.39318
1 3.94509 8.49487 5.51578
1 4.36332 2.34575 7.68791
1 6.21362 4.64014 5.60117
2 8.33722 9.14922 6.92168
2 7.64217 5.26774 4.29112
2 3.98182 1.36069 1.28927
2 8.38455 7.22515 6.16822
2 3.84858 2.32143 9.86296
…
where the first number, 1 or 2 are kind of particles and the other are x,y,z of each particle.
How I use rerun in this dump file ?
Best regards
Alexandre
You setup a similar simulation model to what
you had when you wrote out the dump file,
including new commands to calculate,
average, and write out the RDF
(e.g. compute rdf and fix ave/time).
Then you invoke the rerun command.
I suggest you first just use a read_dump command
to read a single snapshot from your dump file.
Use it to verify that you can read the file correctly
and compute an energy/pressure that agrees with
your original simulation. Then move on to rerun.
Steve
I suggest you first just use a read_dump command
to read a single snapshot from your dump file.
Hi Steve…I don’t know the correct form of use read_dump.
Me xyz file was generated using :
dump 1 all xyz 10000 movie.xyz
the file is :
812
Atoms. Timestep: 20000
1 1.40632 5.32093 0.716731
1 3.37399 5.39947 3.27782
1 10.9362 2.5549 9.19836
1 11.6618 11.9632 2.46185
1 8.28242 7.12111 1.9737
.
.
.
.
2 4.85609 10.2858 3.00324
2 0.766773 8.58636 1.34618
2 0.58483 10.1745 8.90157
812
Atoms. Timestep: 30000
1 1.67468 4.27434 0.0779386
1 2.14671 3.67373 3.97551
1 5.0006 2.95303 9.14601
1 12.3894 10.9145 4.2409.
.
.
.
.
and so on. My read_dump is :
read_dump movie.xyz 0 id x y z box no format xyz
but lammps returns :
LAMMPS (17 Jun 2012)
Lattice spacing in x,y,z = 1 1 1
Created orthogonal box = (0 0 0) to (12.6992 12.6992 12.6992)
1 by 1 by 1 MPI processor grid
ERROR: Illegal read_dump command (read_dump.cpp:554)
Where is the error ?
Best
Alexandre
your lammps version is *ancient*. please upgrade. most likely your
executable does not support the .xyz file format (which is not a good
choice anyway).
axel.
Hi Axel and Steve. I'm using a new version of LAMMPS. But the
output of LAMMPS is the same.
LAMMPS (11 Nov 2013)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1 1 1
Created orthogonal box = (0 0 0) to (12.6992 12.6992 12.6992)
1 by 1 by 1 MPI processor grid
ERROR: Illegal read_dump command (../read_dump.cpp:607)
Axel, you told me that xyz file is not a good choice. What is your
suggestion?
Best regards
Alexandre
Hi Axel and Steve. I'm using a new version of LAMMPS. But the
output of LAMMPS is the same.LAMMPS (11 Nov 2013)
this is not a "new" version. current is 18 Sep 2014.
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1 1 1
Created orthogonal box = (0 0 0) to (12.6992 12.6992 12.6992)
1 by 1 by 1 MPI processor grid
ERROR: Illegal read_dump command (../read_dump.cpp:607)Axel, you told me that xyz file is not a good choice. What is your
suggestion?
the native LAMMPS dump format, of course. it is more structured, more
flexible and contains more information.
axel.