[lammps-users] Converting from (*.car ) to LAMMPS input format

Hi Navdeep,

I tried this again (attached) and got the error below:
(1 1 1 20.000000000 0.000000000)

Thanks.

Jide
<<<
Reading data file ...
  orthogonal box = (-60 -60 -60) to (60 60 60)
  1 by 1 by 1 processor grid
ERROR: Incorrect atom format in data file

data.Cu_Testing2.txt (5.58 KB)

jide,

please note, that it is very difficult to debug your
data file, if you don't provide the corresponding
input file. if you want good help, you have to make
it easy to help you. the format of the data file
depends your choice of atom_style. i'm guessing
that you are using the style molecular.

Hi Navdeep,

I tried this again (attached) and got the error below:
(1 1 1 20.000000000 0.000000000)

Thanks.

Jide
<<<
Reading data file ...
  orthogonal box = (-60 -60 -60) to (60 60 60)
  1 by 1 by 1 processor grid
ERROR: Incorrect atom format in data file
>>>

please read the description of the data file carefully.
the very first line of a data file is a comment.
thus lammps is missing the essential "atoms" line
and trying to read your Atoms section as part of
the header. just insert one line at the beginning
and lammps will be able to read your data file.

cheers,
   axel.

Dear Axel,

Thanks.

I have a systems of over 10000 atoms, and l am using a set of 100 atoms to test the initialization - whether lammps would be able to read it.
(since l am converting from a *car file)

It has read the atoms successfully with the following format:

1 1 20.000000000 0.000000000 -30.0000000002
2 2 20.000000000 1.807454944 -28.192546844 ......

My input script :
( I am new to LAMMPS and l am still trying to figure out a lot of things )

units metal
boundary f f s
atom_style atomic
pair_style morse 3.4

read data.Cu_Testing
..

The next question is, how do l specify a group of atoms with the group command - so as to use <group example type 1> ?

I used the '1' in the column that l have now deleted to specify atom group type. I would like to have up to 4 groups of atoms. (I have deleted the column for it to read the file.)

Cheers.

Jide

Dear Axel,

Thanks.

I have a systems of over 10000 atoms, and l am using a set of 100 atoms to test the initialization - whether lammps would be able to read it.
(since l am converting from a *car file)

It has read the atoms successfully with the following format:

1 1 20.000000000 0.000000000 -30.0000000002
2 2 20.000000000 1.807454944 -28.192546844 ......

as i wrote, the format of the data file depends on the
atom_style command. your data file was suitable for molecular
but not for atomic. thus you had to delete that one column.

My input script :
( I am new to LAMMPS and l am still trying to figure out a lot of things )

units metal
boundary f f s
atom_style atomic
pair_style morse 3.4

read data.Cu_Testing
..

The next question is, how do l specify a group of atoms with the group
command - so as to use <group example type 1> ?

well, please turn on your common sense. this is very clearly documented
in the docs for the "group" command. there are _many_ ways to define
groups of atoms. if you want to group atoms by type, then you have to
set the second column in your data file correspondingly as it defines
the atom type.

I used the '1' in the column that l have now deleted to specify atom group type. I would like to have up to 4 groups of atoms. (I have deleted the column for it to read the file.)

that deleted column would correspond to the molecule or residue id
which can only be used with the atom_style molecular. again, i strongly
recommend to re-read in detail the descriptions of the various commands,
i.e. read_data, atom_style, and group.

from the example coordinates that you have posted, your initial
structure looks very regular. thus are you sure that it is better
to convert the coordinates from some other format over using the
lattice and create atoms commands intrinsic to LAMMPS?

finally - but i am biased in that respect - it looks to me, as if you
might be better off using VMD and its topotools plugin to do the kind
of conversion task that you seem to be doing. yet, that depends on
how well you know VMD, and i know it very well and have written
said plugin...

cheers,
    axel.