How to start a new simulation from a data file

Dear lammps users

I simulate a structure consisting of 2 elements. The structure base consists of element 1 (E1) and the coating upon the base consists of element 2 (E2). The simulation runs for 510000 timesteps, so even though I use many threads it takes some time. I want to use the state that the simulation is at when TIMESTEP = 100000 to start another simulation in which the applied load is reversed. I have checked the forum threads and I wonder:

1.) To start a simulation from a data file, is it correct to just append “the simulation instructions (computes, fixes, loads, dumps etc)” after the data file as in the thread LAMMPS not reading data file from 28th Oct 2015? If not, how should I do?

2.) How do I inherit the atom groups from the original simulation to the new simulation, so I can applied the reverse loading on the same atoms that are subjected to loading in the original simulation, apply boundary conditions make computes for certain groups etc?

My lammps version is 15 May 2015.

Sincerely

Dan Johansson

Dear lammps users

I simulate a structure consisting of 2 elements. The structure base
consists of element 1 (E1) and the coating upon the base consists of
element 2 (E2). The simulation runs for 510000 timesteps, so even though I
use many threads it takes some time. I want to use the state that the
simulation is at when TIMESTEP = 100000 to start another simulation in
which the applied load is reversed. I have checked the forum threads and I
wonder:

1.) To start a simulation from a data file, is it correct to just
append “the simulation instructions (computes, fixes, loads, dumps etc)”
after the data file as in the thread *LAMMPS not reading data file* from
28th Oct 2015? If not, how should I do?

​without a specific URL, nobody will look up an old thread.​ ​there are
plenty of examples bundled with LAMMPS that show​ how to run a simulation.
certain things need to be set *before* the read_data command others can
only be set later. this is easy to find out and there are explanations in
the manual for the individual commands and also explanations in the various
tutorials posted online.

2.) How do I inherit the atom groups from the original simulation to
the new simulation, so I can applied the reverse loading on the same atoms
that are subjected to loading in the original simulation, apply boundary
conditions make computes for certain groups etc?

group assignments are not stored in the data file. you have to redo the
group definition, although that may not always be easy, if the group
definition was dependent on atom locations, that are no longer given. in
that case, you can store group assignments with the group2ndx command to an
external file, and it should be straightforward to write a little script to
convert those back to lammps input.

axel.

I’ll just add that you also restart a simulation from a restart file, and

the restart file does store group assignments.

Steve