Formation & breaking of bonds doubt

Dear All,

If I have a material and and a substrate, I heat them together. Few bonds break (observed by visualization via Ovito). I want it to condense/cool and I want to see if any new bonds are formed, can LAMMPS help me simulate that? I did some literature study and read about fix bond /create and fix bond/break feature of LAMMPS but am not sure how to implement that.

Thanks in advance. Also, happy new year to everyone and thanks on behalf of all students to the LAMMPS developers and the helping community!

Dear All,

If I have a material and and a substrate, I heat them together. Few bonds
break (observed by visualization via Ovito). I want it to condense/cool and
I want to see if any new bonds are formed, can LAMMPS help me simulate that?
I did some literature study and read about fix bond /create and fix
bond/break feature of LAMMPS but am not sure how to implement that.

this is *far* to vague a description to give any specific advice.

however, your line of questioning displays some conceptual problems in
understanding MD force fields and visualization: unless you are
actually using bonding data from the simulation (e.g. what is
specified in a data file or computed by reaxff), visualization
programs usually show bonds based on simple heuristics like distances
and/or element names.
this means, for example, that such a visualization cannot distinguish
between adsorption and bonding. in short, using a visualization tool
to analyze bonding is almost always a bad idea. whether you have bonds
or not is defined by the force field you are using. some force fields
have implicit bonding, others explicit. do you have any
(experimental?) evidence that there are actual chemical bonds formed
between your "material" and your "substrate"? how do you know, this is
not just adsorption?

i don't think that using bond/create is a good idea to study bonding
unless you know exactly what you are doing. it can indeed detect pairs
with distances below a given threshold, but its purpose is also to
change the bond topology and thus the nature of interactions. this
makes sense when preparing a system before equilibrating it (e.g.
introduce polymerization) or when using a force field specifically
tuned and parameterized for this purpose, possibly in connection with
fix bond/break. however, you may be even better off using a force
field with implicit bonding.

how LAMMPS commands are used is described in the documentation.
whenever you have difficulties understanding the description and want
help from the list, you have at least give a summary of what you
understood and where your problems are. any questions of the kind of
"i don't know what to do" is usually an indication, that you need to
have a chat with your adviser about more fundamental things and
concepts of planning simulations which are considered off-topic for
this list.

axel.

Dear Dr Axel,

Thank you for your inputs.

When you say “using a visualization tool to analyze bonding is almost always a bad idea”, then what would be a recommended way to study the bonds?

I have bond data in my input file, is there any way we could extract the bond information at timesteps or some numerical way to establish if the bonds between same type atoms (i-i or j-j) break or the vdW was weak between i-j during simulations?

Dear Dr Axel,

Thank you for your inputs.

When you say "using a visualization tool to analyze bonding is almost always
a bad idea", then what would be a recommended way to study the bonds?

it depends on the system and the force field.

I have bond data in my input file, is there any way we could extract the
bond information at timesteps or some numerical way to establish if the
bonds between same type atoms (i-i or j-j) break or the vdW was weak between
i-j during simulations?

you are not making sense here and i find it particularly annoying,
that you are asking more questions rather than making an effort to
answer mine (which were designed to make you think about important
issues, that you seem to have been ignoring).

if your force field - like most conventional classical force fields -
has explicit bonds, then there is no point in discussing bonds forming
or breaking. the bond topology is an input parameter of your
simulation. your mentioning of van-der-waals interactions in this
context hints that you are mixing up (chemical) bonding and (physical)
adsorption.

at any rate, there is no value in discussing this based on the
extremely vague information you provided. if you want to learn about
how to do and analyze MD simulations in general, please discuss with
your adviser and study relevant sections in text books and suitable
publications. there is a lot of material out there.

axel.