automap.data (567 Bytes)
cross.in (1.3 KB)
output.data (577.4 KB)
postpy2.mol (15.1 KB)
prepy2.mol (13.5 KB)
Hello,
I am facing a probelm while using fix bond/react in lammps. the problem is that i am getting no reaction.
PS : I am trying to crosslink DGEBA and DETDA molecules by creating a bond between an N from DETDA and C from DGEBA.
I am using LAMMPS (17 Apr 2024)
This is not a problem, but a consequence of the physical conditions set up in your simulation.
I know it’s not much help, but LAMMPS is only meant to integrate numerically the equations of motion. It’s up to you to provide the right settings to approximate a physical phenomenon with a computational model.
What troubleshooting steps have you tried so far?
I have changed the system by trying two reaction steps with 2 dgeba and one DETDA but still having an an error
ERROR on proc 3: Fix bond/react: Excessive iteration of superimpose algorithm. Please check that all pre-reaction template atoms are linked to an initiator atom, via at least one path that does not involve edge atoms. (…/fix_bond_react.cpp:1400)
the system is
automap1 (915 Bytes)
automap2 (914 Bytes)
react1 (16.7 KB)
in.script (1.5 KB)
system.in.settings (2.2 KB)
react2 (16.2 KB)
system.data (15.3 KB)
unreact (16.7 KB)
Have you checked ‘that all pre-reaction template atoms are linked to an initiator atom, via at least one path that does not involve edge atoms’?
I have checked that and now i am not having the error but I am getting no reaction
automap1 (326 Bytes)
automap2 (394 Bytes)
in.script (1.6 KB)
system.data (15.3 KB)
system.in.settings (2.2 KB)
A couple points. It looks like you have the wrong ‘edgeID’ listed. It should be ID 5 of the pre-reaction template (an oxygen), rather than ID 8 of the pre-reaction template (a hydrogen). Also, are you sure you have the correct type for the phenyl groups (six-membered rings)? They are not planar in your simulation, and are behaving more like cyclohexane. After those two corrections (and minimizing your initial configuration), a reaction occurs. That said, you may have uncovered a bug for your molecule when all the backbone atoms have the same atom type, as you currently have have it. I will look into that sometime this week (hopefully).
I will be very thankfull if you look at the files because i am really desperate
I am confused. I already looked at the files and solved your problem for you. Did you make the corrections above?
Thank you so much it is working 
could you explain why EdgeID should be 5 and not 8
Edge atoms are those that connect to the rest of a larger molecule in the simulation, in other words, those that have incomplete topology in the reaction template.
thank you so much