Example of atom_style hybrid input and data file

Hi,
I’m trying to use atom_style hybrid for two types of atomic and full. I know how to make read_data for each single of atom_styles alone, but not exactly for hybrid_style. I couldn’t find any example of atom_style hybrid and a corresponding read_data file. Does anyone have an example of this that can help me figure out how to make one?
Thanks,
Masoumeh

Hi,
I'm trying to use atom_style hybrid for two types of atomic and full. I know

there is no point to use this kind of hybrid style.
atomic is a subset of full, so just use full.

how to make read_data for each single of atom_styles alone, but not exactly
for hybrid_style. I couldn't find any example of atom_style hybrid and a
corresponding read_data file. Does anyone have an example of this that can
help me figure out how to make one?

there are several examples for atom style full in the examples folder.

axel.

Thanks Axel,
I want to simulate a combination of molecules of water and some ionic crystal, say NaCl. When making the data file, as the number of molecules, should I disregard the number of ions and count only water molecules, so set the molecule-id of ions to 0, or count each atom of NaCl as a new molecule?

For the charge of ions that I need to specify in the Atoms section, should I set charge to 0?

Is it possible that I specify the coordinates of a crystal using lattice and create_atoms command and for the rest of atoms (say water molecules), choose a data file? I.e. a combination of create_atoms and read_data?
Thanks,
Masoumeh

Thanks Axel,
I want to simulate a combination of molecules of water and some ionic
crystal, say NaCl. When making the data file, as the number of molecules,
should I disregard the number of ions and count only water molecules, so set
the molecule-id of ions to 0, or count each atom of NaCl as a new molecule?

That is your choice. I usually give them different molecule IDs.
The molecule-ID does not effect the simulation because most (nearly
all) LAMMPS force fields do not consider the molecule ID when choosing
the force between atoms. The molecule-ID is a number which exists for
your bookkeeping convenience and for analysis and display software.
(For example, in VMD/topotoos, I think molecule-ID number is converted
to a "resid" number by topotools and this can be used by VMD to decide
how to wrap coordinates across periodic boundaries without splitting
molecules in half when displaying them.)

For the charge of ions that I need to specify in the Atoms section, should I
set charge to 0?

Check out the file named "data.peptide", located in the
"examples/peptide/" subdirectory of your LAMMPS installation (assuming
you have the source code). In that example, the two amino acids are
covalently bonded together, so the author decided to give them the
same molecule-ID. (Other authors might decide to give them different
molecule-IDs, based on their location in the chain.)

Is it possible that I specify the coordinates of a crystal using lattice and
create_atoms command and for the rest of atoms (say water molecules), choose
a data file? I.e. a combination of create_atoms and read_data?

I don't think the built-in lammps input script commands can duplicate
water molecules, but these tools can do that for you:
http://lammps.sandia.gov/prepost.html#builders

I don't know if it helps, but attached a data file containing water
and ions. The ions are at the end of the "Atoms" section (with
atomIDs from 3001-3016.) This data file was made with moltemplate
(discussed in the manual, section 4.1 & 4.2), but you can easily make
similar data files with topotools or the other tools on that web page.

I hope this gets you started.
Andrew

README_visualize.txt (2.85 KB)

water+ions.data (168 KB)