Hi,eveyone:
I have installed the latest version of lammps (LAMMPS 64-bit 20140411) and simulate a chemical reaction.The initial configuration is generated randomly with 500 beadtype1s bead and 500 beadtype2 beads.
1+2->3=4 (after reaction,beadtype1 will become beadtype 3,beadtype2 will become beadtype4, “=“stand for a chemical bond)
=3+2->=5=4 (the newly formed product beadtype3 can still reacte with beadtype2 and form beadtype5,”*=3” stand for random beads that connect beadtype3 with a chemical bond )
I use the following commands in lammps to simulate the reaction process:
fix cratebond1 all bond/create 200 1 2 1 1 iparam 1 3 jparam 1 4 prob 0.5 1126546
fix cratebond2 all bond/create 200 3 2 1 1 iparam 2 5 jparam 1 4 prob 0.5 16464221
with “special_bonds” and “extra bond per atom” set in datafile. (special_bonds lj 0 1 1 extra 2 ; 2 extra bond per atom)
I still got the error:New bond exceeded bonds per atom in fix bond/create
I do not think this should happen.
Can anyone tell me why?
in (1.41 KB)
test.data (52.4 KB)
Hi,eveyone:
I have installed the latest version of lammps (LAMMPS 64-bit 20140411) and
simulate a chemical reaction.The initial configuration is generated randomly
with 500 beadtype1s bead and 500 beadtype2 beads.
1+2->3=4 (after reaction,beadtype1 will become beadtype 3,beadtype2 will
become beadtype4, "="stand for a chemical bond)
*=3+2->*=5=4 (the newly formed product beadtype3 can still reacte with
beadtype2 and form beadtype5,"*=3" stand for random beads that connect
beadtype3 with a chemical bond )
I use the following commands in lammps to simulate the reaction process:
fix cratebond1 all bond/create 200 1 2 1 1 iparam 1 3 jparam 1 4 prob 0.5
1126546
fix cratebond2 all bond/create 200 3 2 1 1 iparam 2 5 jparam 1 4 prob 0.5
16464221
with "special_bonds" and "extra bond per atom" set in datafile.
(special_bonds lj 0 1 1 extra 2 ; 2 extra bond per atom)
I still got the error:New bond exceeded bonds per atom in fix bond/create
I do not think this should happen.
Can anyone tell me why?
if you pay close attention, you should see that unlike in your
previous input example, you now get a bit of trajectory until the
problem hits. if you crank space for potential bonds to a larger
number than 2, you'll see that some atoms actually have more than 2
bonds.
this has to be a consequence of your input, thus you have to debug
your input more carefully to figure out why this happens.
axel.
p.s.: your input creates tons of "dangerous builds", so there is
something else that needs to be corrected.