Save atomic numbers instead of atom type

LAMMPS LAMMPS Beginners
1

Consider this dump simulation all xyz 1 simulation.xyz

Then the ouput is something like:

128000
 Atoms. Timestep: 200
1 0.0160486 114.643 114.619
2 1.43427 1.39655 1.44747
1 2.86522 114.582 114.653
2 4.29715 1.39228 1.42944
1 5.70815 114.58 114.647

I know I can do "dump_modify simulation element Fe Cr He" and then get:

128000
 Atoms. Timestep: 200
Fe 0.0160486 114.643 114.619
Cr 1.43427 1.39655 1.44747
Fe 2.86522 114.582 114.653
Cr 4.29715 1.39228 1.42944
Fe 5.70815 114.58 114.647

But for the purposes of other programs, it would be better to have the atomic numbers, instead of the atomic symbols. Is that possible without external tools or shell commands? (I don’t want to modify atom types, since that breaks the LAMMPS simulation.)

2

You can use any string you want in that dump_modify atom type to element map, including numbers.

3

I see, not so dificult dump_modify simulation element 26 24 2 :slight_smile:

4

Hi again,
I don’t know what I’m missing here (maybe because it’s a custom dump and not xyz?):

units metal
atom_style atomic
boundary p p p
atom_modify map yes
lattice bcc 2.8664999
region R1 block 0 1 0 1 0 1
create_box 1 R1
create_atoms 1 box
group Region1 region R1

fix integrate all nve
fix reset all dt/reset 10 1e-05 0.001 0.028664999 units box
pair_style eam/alloy
pair_coeff * * fe_mendelev_eam_alloy.potential Fe

dump simulation all custom 1 simulation.xyz id type x y z
dump_modify simulation element 26
run 0

Dumps:

ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
2
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+00 2.8664999000000000e+00
0.0000000000000000e+00 2.8664999000000000e+00
0.0000000000000000e+00 2.8664999000000000e+00
ITEM: ATOMS id type x y z
1 1 0 0 0
2 1 1.43325 1.43325 1.43325

The type is not being replaced by the atomic number.

5

Why should it? What LAMMPS does is completely logical and following the documentation.
Your dump_modify command modifies the “element” property, not “type” itself (which you cannot). In dump style xyz the type value is used as fallback, if no elements have been set.

1 Like
6

I see, thanks again, I was confused.