Use "Avogadro"

Hi

I try use avogadro(molecular-modeling soft).
So it have function “Build-Cartesian editor”
It can make .xyz file.

I want to use it .xyz files ,command read_data.

but appear error.

please tell me how to use .xyz(by avogadro) in read_data(LAMMPS)

No where in the read_data doc page says LAMMPS reads conventional xyz format files. You will have to convert it to a LAMMPS data file format.

Ray

But you can probably use the read_dump command. Please read its doc page for more details.

Ray

Hi

I try use avogadro(molecular-modeling soft).
So it have function "Build-Cartesian editor"
It can make .xyz file.

I want to use it .xyz files ,command read_data.

but appear error.

please tell me how to use .xyz(by avogadro) in read_data(LAMMPS)

you cannot. not without further processing of the information, which
depends on the requirements of force field that you are using.

read_data gives and error because the .xyz file is in a different
format and is lacking essential information that is required in the
data file.
the data file format is described in detail here:
http://lammps.sandia.gov/doc/read_data.html

I’ve found it is easiest to use external(free) geometry visualization/processing software like OVITO for this puropse - just import the .xyz into ovito and then export it in lammps data file format, which can be read by the read_data command.

Best,

Kristian Kuppart

Dear Murai

   You have a lot of hard work ahead of you. XYZ files only contain
atom coordinates and atom names (which are frequently too vague to be
useful). You need to generate topology information (bonds, angles,
dihedrals, impropers), as well as a (long) list of force-field
parameters. See below....

I've found it is easiest to use external(free) geometry
visualization/processing software like OVITO for this puropse - just import
the .xyz into ovito and then export it in lammps data file format, which can
be read by the read_data command.

It looks like the current version of OVITO only supports atom_style
atomic. That means that the DATA file will not contain any topology
information (bonds,angles,...)

Here are a list of alternative programs which can generate bonds,
angles, dihedrals, and impropers:
http://lammps.sandia.gov/threads/msg45535.html
http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1
http://montecarlo.sourceforge.net/emc/Welcome.html (EMC)
http://sourceforge.net/projects/moleculardynami/
http://lammps.sandia.gov/prepost.html

Without knowing more about what kind of system you are simulating, it
is impossible to recommend a force-field.

Cheers
Andrew