How can I remove an atom´s coordinates in LAMMPS?

The Lammps command to remove an atom is called delete_atoms:

http://lammps.sandia.gov/doc/delete_atoms.html

You need to call this command either for a group or a region. If you know the ID of the atom (maybe, you can find it out using the inspect tool in vmd) you can define a group containing only this atom. Otherwise you have to define a region encompassing your atom and be careful not to remove any additional atoms.

Gourav Shrivastav

Simplest thing, If you know that which atom has to be deleted , open your input file and delete those coordinates directly (i am assuming you don't have molecule).

You can also do this using vmd by making appropriate selection and then writing a lammps input file using that selection.

Jamoliddin Razzokov

I think the easiest way is to use awk command!

awk printf '{$1, $2}' file > output using this command you can save the coulombs that you need.

for the other options follow the link: http://www.chemie.fu-berlin.de/chemnet/use/info/gawk/gawk_7.html

Julian Helfferich

The Lammps command to remove an atom is called delete_atoms:

http://lammps.sandia.gov/doc/delete_atoms.html

Amin Hamzei

I wrote a code in LAMMPS atom and formed a group to delete a number, I got what I wanted.

thank you all...

Mosab Jaser

Hi Amin, even its long time ago question but I just accidentally stopped by it, let me share some tips to do that as someone may find it useful in the future:

1- if you know your atom coordination and you have already the data file, you just simply delete it from the data file to be used with lammps

2- If you use lammps to generate the data file internally you could use these commands :

a- after generation of the data file by lammps, print it out and check it. Assume your atom of interest has the ID 2 and its coordination as (0.5a 0.5a 0.5a), as lammps command define :

group SIA id 2 # define a group

delete_atoms group SIA compress yes # delete atoms belong to SIA group

b- you could also delete atoms belong to a specific region, for example, this command will delete atoms located at 0,0,0 point for a spherical region of radius r:

variable r equal sqrt(${a}^2+${a}^2)/4

# variable defined as (r = radius , a= lattice constant of the element)

region select sphere 0 0 0 ${r} units box

delete_atoms region select compress yes

#region defined_all atoms within this region will be removed

Amin Hamzei

thanks all

Mohammad Imran

Hi Mosab Jaser

Is it possible to delete the atom which belong to a subgroup?

I am making a group of particles which have displaced more than a certain distance. Is it possible to delete them.

compute 1 binded compute/atom

compute 2 binded reduce sum c_1

thermo_style custom step temp pe c_2

run 0

variable eatom atom "c_1 < -3.0"

group hienergy variable eatom

then delete the particles belonging to hienergy group

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