Hi,
It might be very stupid question but please bear with me :-). I want to use relaxed structure for my further calculations but also want to look at and work with relaxed structure (that's why I don't want to use minimize and run in the same file). Here is what I do:
1. Minimize the structure
2. Edit output structure file and make it compatible as a input structure file (see question relating to this step below)
3. Run the further simulation
My Questions:
1. My rlx.str file generates structure twice and also output coordinates are fractional (between 0-1). Can I use it as it is? I did make changes and wrote input structure file but program is giving error message "unexpected end of data file". even though I have all the atoms are there.
2. Is there any better way to write output structure after minimization is complete.
3. As I want to further introduce vacancy in the system, can I just choose one atom by its coordinates to delete ?
Thanks in advance
~Priyank
Here is my input script for minimization
Comments below.
Steve
Hi,
It might be very stupid question but please bear with me :-). I
want to use relaxed structure for my further calculations but also want
to look at and work with relaxed structure (that's why I don't want to
use minimize and run in the same file). Here is what I do:
1. Minimize the structure
2. Edit output structure file and make it compatible as a input
structure file (see question relating to this step below)
3. Run the further simulation
My Questions:
1. My rlx.str file generates structure twice and also output coordinates
are fractional (between 0-1). Can I use it as it is? I did make changes
and wrote input structure file but program is giving error message
"unexpected end of data file". even though I have all the atoms are there.
undoubtably the format of your data file is incorrect. LAMMPS wouldn't
complain if it wasn't. See the read_data doc page.
2. Is there any better way to write output structure after minimization
is complete.
As with any LAMMPS simulation, you can write out dump or restart files
at the end of a minimization. You have to cut/paste coords from a dump
file into a data file. The tools/restart2data code will convert a restart
file to a data file.
3. As I want to further introduce vacancy in the system, can I just
choose one atom by its coordinates to delete ?
You can just whack a line from the data file if you like. Or use
the delete_atoms command in an input script.