Hi, LAMMPS users,
I used fix bond/react to create polymer cross-linking between two liner polymer chains.
I used harmonic bond and angle potentials between beads in each polymer, and Lennard-Jones potentials used as non-bonded interactions. The molecule template included two linear polymer chain, each chain includes two atom types, in which, one type of atoms can form cross-linking bond between tow atoms when they get closed to each enough. I set pre-reacted template, post-reacted, map file, input file and data file. When I run these files, there’s no error appeared. But the dumped file of fix bond/react indicated that there’s no reaction have been happened. What’s wrong? Any help will be appreciated.
The LAMMPS version is 5May, 2020.
The follows are input file and pre-reacted and post-reacted files:
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I’ve run your files and I think your problem was that you specified 0 edgeIDs in the map file when you actually have 4 edge atoms (1, 3, 4, and 6). When I made that change, the thermo output IS showing bonds being created, but I’m not seeing them in OVITO (a visualizer). I’ve attached the modified files.
Linear_Chain_map.txt (102 Bytes)
Linear_Chain_Crosslinking.dat (2.44 KB)
Linear_Chain_post.template (399 Bytes)
Linear_Chain_Crosslinking.in (2.8 KB)
Linear_Chain_pre.template (384 Bytes)
Hi Bo (and thanks Will!),
It looks like you do not have enough atoms in your pre- and post reaction templates. Just one more next to each current ‘edge atom’ should do it, because you only have angles (and no dihedrals) defined. This is necessary, because all reacting atoms must have fully-defined topology in the reaction templates. Bond/react gives a warning about this in your output.