Question about fix bond/create

LAMMPS LAMMPS Mailing List Mirror
1

Dear Lammps-users,

I am writing to ask about “fix bond/create” command.

I try to create an epoxy crosslinked structure using “fix bond/create” command. I wrote lammps input and data files, and then ran it. When the simulation was done, I visualized the trajectory file via OVITO. It seems that a bond was created between two reactive atoms, because two reactive atoms became close and moved together. However, when I convert restart file to data file, bond information was not updated. I mean that the number of bonds in the restart data file is the same as one in the initial data file.

I read “fix bond/create section” in lammps doc. It said that “When a bond is created, you might wish to induce new angle and dihedral interactions that include that bond. However, LAMMPS does not create these angles and dihedrals, even if your simulation defines an angle_style or dihedral_style.”

As far as I understood, the bond information must be updated in the restart data file because the document does not mention that new bond is not induced.

If there is no updated information for a new bond in the restart file, how can I verify that the new bond was created?

Data file and input file are attached here for your information. I compiled all packages except for USER-CUDA, GPU, and USER-ATC.

Thanks in advance.

Best regards,
Changwoon Jang

data.test1 (106 KB)

in.crosslink (2.48 KB)

2

From the fix bond/create doc page:

You can dump out snapshots of the current bond topology via the dump
local command.

New bonds are also written to restart files.

Steve

3

You can dump out snapshots of the current bond topology via the dump
local command.

Incidentally, there's an example of how to do this here:
http://lammps.sandia.gov/doc/compute_bond_local.html
(I don't know if this addresses your issue.)

On Thu, Nov 15, 2012 at 10:34 PM, Chang Woon Jang

I mean that the number of
bonds in the restart data file is the same as one in the initial data file.

Really?

I read "fix bond/create section" in lammps doc. It said that "When a bond is
created, you might wish to induce new angle and dihedral interactions that
include that bond. However, LAMMPS does not create these angles and
dihedrals, even if your simulation defines an angle_style or
dihedral_style."

Incidentally, are you trying to add angle/dihedral/improper
interactions after a bond is formed? There is a script to help do
that here:
http://www.moltemplate.org/other.html
(gen_all_angles_topo.sh. It uses the same topology-generator used by
moltemplate.)
It's not trivial to use. Feel free to post any questions about it.