Inquiry on Special Bonds section in molecule.dimer

Dear Dr. Axel Kohlmeyer,

Hello Dr. Kohlmeyer. Thank you for your many help on LAMMPS.

I would like to ask a simple question on “Special Bonds” section in the molecule.dimer in the LAMMPS example “deposit” directory which contains the input file, in.deposit.atom.

The molecule.dimer reads the following:

dimer molecule

2 atoms
1 bonds

1 0 0 0
2 1 0 0

1 2
2 3

1 1 1 2

Special Bond Counts
1 1 0 0
2 1 0 0

Special Bonds
1 2
2 1

However, when I look at the Special Bonds section, I see two lines which should corresponds to the number of atoms.

If this is the case, should not the first line of “Special Bonds” read “1 1” instead of “1 2” since Atom 1 only has one 1-2 interaction?

(I tried with “1 1” and obtained an error “Invalid special atom index in molecule file” so I may be misunderstanding something.)

Thank you so much for your time.


Masato Koizumi

Dear Dr. Axel Kohlmeyer,

Hello Dr. Kohlmeyer. Once again, thank you for all of your help on LAMMPS. I resolved my confusion to my previous inquiry.

I am currently trying to insert 1000 molecules into an empty enclosed simulation box using fix deposit under NVE ensemble. However, the simulation terminates without any error message. Looking at my simulation through OVITO, I see that molecules are being inserted and I only see a handful of molecules inside the simulation box before the simulation terminates.

Although I am expecting 1000 molecules to be inserted into the simulation domain, I could not find out why the simulation terminates. I would greatly appreciate if I could request for any advice.

I have attached a small input script with the molecule file that replicates this issue.

Thank you so much for your time and consideration


Masato Koizumi

in.deposit.molecule (1.5 KB)

molecule.TetraPEG (563 Bytes)

Special Bond Counts is the count of 1-2, 1-3, 1-4 interactions
for each atom int the molecule. So 1 0 0 for atom 1 means
there is one 1-2 bond, and no 1-3 or 1-4 bonds. For a total
of 1 special bond.

Special Bonds is the list of atom IDs for the special bonds for
each atom. So atom 1 lists a single bond since that was its
total. That one 1-2 bond is with atom 2. So the line is 1 2.