[lammps-users] Creating a Molecule with 10 atoms

Dear All,

I have lammps 29oct20 installed.

I’m trying to simulate a nano fluid of a ethylene glycol and copper.

When I simulate this I get a simulation box with only 3 different types of atoms 2,3,4 for my molecule. However, my molecule contains 10 different atoms.

What am I doing wrong here?

my input file look like this:

------------------------ INITIALIZATION ----------------------------

units real
dimension 3
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic

variable latparam equal 5.0553

----------------------- ATOM DEFINITION ----------------------------

region whole block -50 50 -50 50 -50 50 units lattice
create_box 11 whole bond/types 9 angle/types 14 extra/bond/per/atom 9 extra/angle/per/atom 14 extra/special/per/atom 10
lattice fcc ${latparam} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1

molecule ethylene_glycol lammps.data
info system
create_atoms 1 region whole mol ethylene_glycol 52874

region nanoparticle sphere 0 0 0 7 units lattice
lattice fcc ${latparam} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
create_atoms 11 region nanoparticle

Outlook-glxkiqb5.png

Outlook-glxkiqb5.png

Dear All,

I have lammps 29oct20 installed.

I’m trying to simulate a nano fluid of a ethylene glycol and copper.

When I simulate this I get a simulation box with only 3 different types of atoms 2,3,4 for my molecule. However, my molecule contains 10 different atoms.

What am I doing wrong here?

Your input is mostly correct, your thinking less so. And you apparently have not read the documentation with sufficient care. LAMMPS is correctly doing exactly what you are asking for.

You have a Types section in your molecule file where you assign only 3(!) atom types to your 10 atoms (types 1,2, and 3) which will become 2, 3, 4 because your create_atoms command uses atom type 1 (instead of 0), which means that 1 is added to the atom type from the atoms in the molecule file.

There is one more issue: didn’t you notice the warning from the molecule command that you have inconsistent data? That is because you have a Masses section. However, that should only be provided, for an atom style that has per-atom masses. Atom style full, however, has per-type masses and thus they need to be set in the input file using the “mass” command.

Axel.

Dear Axel,

Thank you so much for your comment and clarification.

Best regards,
Yunes Salman