Initial Atoms and Final Atoms Present are of Different Type

LAMMPS LAMMPS Mailing List Mirror
1

Dear lammps-users,

I am a physical chemistry student who is beginning to use LAMMPS to run simulations in battery research. I am continually getting an error where the initial atoms present transform to some different atom after the simulation has run. For example, in the files I attached, for a water molecule, the initial Oxygen atom is converted to a Helium atom in the output. I attached all relevant files - the h2o.xyz file I used to generate my .lmpdat file, my LAMMPS input script, the LAMMPS log file , and the output file (out.xyz). As a beginner, I cannot figure out why this error is happening and have tried a lot of things. I would appreciate any help with why this is happening, and how to fix it.

Thank you in advance,
Peter

out.xyz (5.89 KB)

h2o.lmp (560 Bytes)

log.lammps (2.92 KB)

h2o.lmpdat (646 Bytes)

h2o.xyz (155 Bytes)

2

Dear lammps-users,

I am a physical chemistry student who is beginning to use LAMMPS to run simulations in battery research. I am continually getting an error where the initial atoms present transform to some different atom after the simulation has run. For example, in the files I attached, for a water molecule, the initial Oxygen atom is converted to a Helium atom in the output. I attached all relevant files - the h2o.xyz file I used to generate my .lmpdat file, my LAMMPS input script, the LAMMPS log file , and the output file (out.xyz). As a beginner, I cannot figure out why this error is happening and have tried a lot of things. I would appreciate any help with why this is happening, and how to fix it.

​there is nothing really to fix. you are interpreting the data wrong.
LAMMPS internally has no concept of eleme​nts, but only sees atom types as numbers. that is what you see in the output. atoms of type 1 and type 2. if you want to associate element names with those, you have to do this explicitly, e.g. via the dump_modify command or by post-processing the .xyz file. BTW: .xyz files are the smallest common denominator type file format, and thus not recommended to use. they drop a lot of useful information (e.g. box dimensions).

axel.