Query about delete_atoms

Hi all,

I try to use ‘delete_atoms porosity’ command to randomly delete specified atoms but found failed. The error is: ERROR: Could not find delete_atoms region ID (…/delete_atoms.cpp:425)
What shall I do if I did not set region but only set group of different kinds of atoms?
Input file are pasted below.

Thank you very much,
Zizhen Zhou

Declaration of variables

- lattice parameters -

variable Naas equal 5.568
variable Bias equal 5.568
variable Tias equal 5.568
variable O1as equal 5.568
variable O2as equal 5.568
variable O3as equal 5.568

- simulation box -

variable slbx equal 0.0
variable subx equal 16.0
variable slby equal 0.0
variable suby equal 16.0
variable slbz equal 0.0
variable subz equal 16.0

Principal simulation options

units metal
atom_style charge
neighbor 3.0 bin
neigh_modify every 1 delay 5 check yes

Lattice and geometry

lattice sc {Naas} origin 0.5 0.5 0.5 lattice sc {Bias} origin 0.5 0.5 0.5

region simbox block {slbx} {subx} {slby} {suby} {slbz} {subz} units lattice

create_box 6 simbox
create_atoms 3 box
lattice sc {Tias} origin 0.0 0.0 0.0 create_atoms 4 box lattice sc {O1as} origin 0.0 0.5 0.5
create_atoms 5 box
lattice sc {O2as} origin 0.5 0.0 0.5 create_atoms 6 box lattice sc {O3as} origin 0.5 0.5 0.0
create_atoms 1 box
lattice sc ${Naas} origin 0.5 0.5 0.5

set half of Na to Bi

set type 1 type/fraction 2 0.5 1234

Species and interatomic potential

group A1 type 1
group A2 type 2
group A3 type 3
group A4 type 4
group A5 type 5
group A6 type 6
set group A1 charge 1.0
set group A2 charge 3.0
set group A3 charge 3.988
set group A4 charge -2.0
set group A5 charge -2.0
set group A6 charge -2.0
mass 1 22.98
mass 2 208.98
mass 3 47.867
mass 4 15.9994
mass 5 15.9994
mass 6 15.9994

Definition of output

delete_atoms porosity A2 0.01 86754321
thermo_style multi
thermo 1000

Run simulation

velocity all create 500.0 376847 loop geom
fix 1 all npt temp 500.0 500.0 0.02 iso 0.0 0.0 0.1

Hi all,

I try to use ‘delete_atoms porosity’ command to randomly delete specified atoms but found failed. The error is: ERROR: Could not find delete_atoms region ID (…/delete_atoms.cpp:425)
What shall I do if I did not set region but only set group of different kinds of atoms?

you must provide a region id. the syntax requires it. why don’t you simply use the “simbox” region that defines the entire simulation box?

axel.