Create atoms

Dear Lammps users
I want to create atoms for PDMS (3 types of atoms) in molecule and when I run it, it showing only two types by ovito? any suggestion please

The PDMS I know has 4 types of atoms. So perhaps you need to explain what PDMS is an abbreviation for.

run what?

what is showing what?

Please provide sufficient information to show what you are doing, what you expect to see, what the output is, and where exactly it differs from what you expect.

As a scientist you should know that you have to carefully document and describe your experiments and measurements. Using computer software is no different; so you need to apply the same process. Otherwise you are depending on people reading your mind (or hacking your computer?) to see what it is that you are doing and how it is going in the wrong direction.

Many thanks Sir Akohlmey
I want to simulate PDMS considering CH3 as a single atom so I have (CH3, Si, O) and I built PDMS structure by vmd topotool to get data file as in attached file. Also in my input script I used (create_atoms 0 random 1 45678 NULL mol poly 175649) but when visualized it by ovito it showing only two types. Am sorry for bothering you
in.input.test.8.lmp (1.8 KB)

PDMS.mol (2.2 KB)

This is not a “data” file in LAMMPS nomenclature, but a “molecule” file.

Your molecule file has 12 atoms of type 1 and 1 atom of type 2. How should there be more than two atoms types then? LAMMPS cannot read minds, but does exactly what you ask it to do and uses only data you provide. So unless there is a bug (which is rather unlikely for these kind of things), you will get out of it what you feed it.

With your create_box command you reserve space for 3 atom types, but if you don’t create atoms of all 3 types, you cannot visualize them or assign force field parameters to them.

Many thanks Sir it is works now I don’t know how it changed into two types, but I fix it now and it work
Many thanks again


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