[lammps-users] questions to make data file for posistional data and force field parameter data

I’d like to make data file to insert positional data file (pdb file) of graphene and AIREBO force field parameter data to my input file.
What should I do for it in detail?

Is there available utility to make it automatically?
Otherwise, should I make all of it by hand (e.g., assignment the parameters to various cases)?
If so, I suppose that it will be a very troublesome task.

Is it correct that I should read “read data” part (page 625~) of the manual to learn the format of LAMMPS input data file for positional data and force field parameters (which
are assigned to various cases according to atom type)?

Incidentally asking, I installed LAMMPS but it seems that there is no force field file for AIREBO in potentials directory. Should I install it additinally?

Best wishes,

Luke

You just need the coordinates of graphene. The AIREBO potential should be stored in your potential directory as CH.airebo file. Just link to that file in your pair_style command as discussed on the doc page. For the input datafile, write a code (there may be one already) which converts pdb format to lammps data format for coordinates. Put in atom type and box dimensions by hand.

Best Regards,
Vikas

2010/5/18 JhonY. I. <yijhon@…8…>

2010/5/21 Vikas Varshney <[email protected]...>:

You just need the coordinates of graphene. The AIREBO potential should be
stored in your potential directory as CH.airebo file. Just link to that file
in your pair_style command as discussed on the doc page. For the input
datafile, write a code (there may be one already) which converts pdb format
to lammps data format for coordinates. Put in atom type and box dimensions
by hand.

yes. there is a code. the topotools package can help with that.
for AIREBO it is particularly simple, since one does not need
to specify any bonds.

to generate an initial data file loading the .pdb file in VMD
and then typing into the command line:

topo writelammpsdata data.graphene atomic

should do most of the job. there are more tweaks on this for
more complex systems. i've been explaining strategies for
different cases on this list and the VMD mailing list several
times. just search for my name and topotools in google and
you should find additional help.

cheers,
      axel.

Incidentally asking, I installed LAMMPS but it seems that there is no force
field file for AIREBO in potentials directory. Should I install it
additinally?

There is a file potentials/CH.airebo, which is part of LAMMPS.

Steve

2010/5/18 JhonY. I. <[email protected]...>:

First many thanks for your answer really, axel.
I’ve made data file using VMD following your advice.
However, if I’ve run the job using this data file, it showed folowing error message.

Scanning data file …
3 = max bonds/atom
Reading data file …
orthogonal box = (0.341 0.606 0.132) to (17.384 35.046 10.132)
1 by 1 by 1 processor grid
ERROR: Incorrect atom format in data file

The visualzation of pdb file looks fine in VMD and the data file was produced only by typing “topo writelammpsdata data.graphene atomic”.
The content of data file is as follows.

ERROR: Incorrect atom format in data file

This error means the atom lines in your
data file don't match the atom_style of your
input script. It looks like your atom lines
just list: ID, type, x, y, z
but you also have bonds defined. So you
probably need a molecule ID in each line.

The read_data doc page explains all of this.

Steve

2010/5/26 JhonY. I. <[email protected]...>: