Dear all,
I’m trying to run simulations on “graphene layer deposited on amorphous silicon dioxide” structure. which potential should i use to run the simulations for Si C O bonding ?
Can I take two potential files one for Si C and other Si O bonding at a time ?
Thanks & Regards,
Venkata Pavan Kumar. Miriyala
pavan.kumar9111@…24…,
contact number: +91-9032307746
Dear all,
I’m trying to run simulations on “graphene layer deposited on amorphous silicon dioxide” structure. which potential should i use to run the simulations for Si C O bonding ?
Can I take two potential files one for Si C and other Si O bonding at a time ?
No.
Your 1st Q is better answered by looking
in the literature.
Steve
Dear Steve,
Can you give me the link for that literature?
I can’t find that…
Dear Steve,
Can you give me the link for that literature?I can't find that....
well, that is *your* problem then. i don't believe it is for lack of
publications, but rather an indication that you need to spend more effort
or search smarter or get better training in how to do a literature search.
steve didn't say he knows where it is that you are looking for, but only
that if there is a place where this discussed, it will be in the published
literature.
axel.
Dear axel,
Thank you, In some papers, it is mentioned that airebo potential is used for graphene and charmm potential is used sio2 and for the interactions they used lj potential.
I think this is not possible through lammps.
Dear axel,
Thank you, In some papers, it is mentioned that airebo potential is used for graphene and charmm potential is used sio2 and for the interactions they used lj potential.
I think this is not possible through lammps.
Why should that be not possible?
Taking two potentials and calling them through input file is not possible right ?
Taking two potentials and calling them through input file is not possible right ?
Wrong.
Seemingly AIREBO can be used as part of a hybrid pair style. You can look up the manual for that.
Dear all,
I have 3 types of atoms in my system of graphene layer on amorphous SiO2. (C, O, Si ).
So the interactions possible are
Si-Si
Si-O
O-O
these interactions can be obtained by SiO.tersoff potential.
Later by using pair_style hybrid, C-C interactions can be done by airebo potential and Si- C interactions can be done by lj potential. But for C-O interactions, REBO- CHO potential and ffreax.cho are there.
I can’t any REBO-CHO potential in lammps.
How to use this REBO-CHO potential in my script ? Please Help.
Your 1st Q was about using REBO with CHARMM. The
way to do that is with pair hybrid. Now you are asking about
Tersoff. The answer is the same. You are also asking about
REBO-CHO. I don’t know what that is. REBO in LAMMPS simply
takes an input parameter file. If you give it one for CHO
then it will use it. That is independent of pair hybrid.
Steve
Dear steve,
It is very clear that with pair_style hybrid, we can create Si-Si, C-C, Si-C, Si-O interactions. But to create C-O interactions I have chosen REBO-CHO.
Here is my data file :
17361 bonds
0 angles
0 dihedrals
0 impropers
13 atom types
1 bond types
0 angle types
0 dihedral types
0 improper types
-0.496500 56.810499 xlo xhi
0.264000 57.570999 ylo yhi
-59.116999 -0.943999 zlo zhi
Dear steve,
It is very clear that with pair_style hybrid, we can create
Si-Si, C-C, Si-C, Si-O interactions. But to create C-O interactions I have
chosen REBO-CHO.
You need a CHO potential file for REBO to run this, which is not available
in LAMMPS format currently.
Here is my data file :
17361 bonds
0 angles
0 dihedrals
0 impropers
13 atom types
1 bond types
0 angle types
0 dihedral types
0 improper types
-0.496500 56.810499 xlo xhi
0.264000 57.570999 ylo yhi
-59.116999 -0.943999 zlo zhi# Pair Coeffs
#
# 1 C
# 2 O1
# 3 O2
# 4 O3
# 5 O4
# 6 O5
# 7 O6
# 8 O7
# 9 O8
# 10 SI1
# 11 SI2
# 12 SI3
# 13 SI4# Bond Coeffs
#
# 1Masses
1 12.010700 # C
2 15.999400 # O1
3 15.999400 # O2
4 15.999400 # O3
5 15.999400 # O4
6 15.999400 # O5
7 15.999400 # O6
8 15.999400 # O7
9 15.999400 # O8
10 28.085501 # SI1
11 28.085501 # SI2
12 28.085501 # SI3
13 28.085501 # SI4Here is the hybrid pair style I used
pair_style hybrid lj/cut tersoff airebo 3.0
pair_coeff 10*11*12*13 2*3*4*5*6*7*8*9 tersoff SiO.tersoff.custom Si O
pair_coeff 1 1 airebo CH.airebo NULL C
pair_coeff 10*11*12*13 1 lj/cut 1.0 1.5but can't establish interactions between C-O. Please suggest me.
It is impossible that LJ parameters for C-O pairs cannot be found in the
Literature.
Ray
Dear Ray,
Can you suggest me any other way?
Might I ask any other way for what? CHO potential file? It is not
available unless someone makes an effort to make it available. C-O LJ
parameters? It is in the Literature.
Ray
Dear steve,
It is very clear that with pair_style hybrid, we can create
Si-Si, C-C, Si-C, Si-O interactions. But to create C-O interactions I have
chosen REBO-CHO.
no, no and NO!
it is not very clear and while you may be technically able to do what you
say, it would be a big mistake to do so. your simulation is practically
*guaranteed* to be wrong.
you are looking at this from the wrong perspective. you cannot just mix and
match any kind of potentials for any pairs of elements as you like.
interactions have to be *balanced*. particularly when using manybody
potentials.
you are not doing ab initio quantum chemistry here (and even there you need
some degree of consistency), so you have to respect for which kind of
systems parameters were derived and how you can use them to build you
entire system.
now you have a bit of a problem with your setup, since you want to model a
hybrid compound where you have well established potentials for each part of
your hybrid, but no single and consistent parameter set that describes them
all.
this is where the hybrid pair style in LAMMPS comes to your rescue, it
allows you to run each compound with the preferred potential type and
parameter set.
thus the remaining problem is how to describe the interactions *between*
those two compounds. if you want a clean model, this *has* to be done with
a pairwise additive potential type (i.e. no many-body, no long-range
electrostatics), hence the use of CHARMM parameters in the paper you
quoted. this gives you a clean separation and no inconsistencies when
computing the potential for each compound, the cross terms between them and
adding everything up.
there is only one drawback: models like CHARMM are less sophisticated than
manybody potentials, and thus you may not get the level of detail and
accuracy that you want. but since you seem to be new to the business, i
*strongly* urge you to set that up first and study how bad (or how good) it
is for your needs. having a baseline with a consistent interaction model is
always a good thing and helps to tell, if more complex approaches actually
provide and improvement or not.
if you want to have a many-body description for *all* components, you will
have to look for a potential type, that has parameters for *all* atom types
in your system. it is a bad idea to use a many-body potential for
interactions between two types of atoms since it will neglect many-body
terms that would be included, if you had a potential suitable for all atom
types. this inconsistency will likely render your simulation worse than
using the CHARMM parameters. however, using two types of tersoff, and REBO
in this weird way is a certain way to doom.
please spend some more time on the concepts of what you are doing and less
on what is technically possible. in classical MD, many things are
technically possible that are complete and utter garbage. many of the older
papers give good introductions into the motivation why certain combinations
of potentials were used. study those and learn from them (but do not
blindly copy them, since things have changed since).
axel.
Dear Axel,
Thanks for your patience and valuable suggestions axel.
Dear Pavan,
The situation is even more complicated for weakly bound
systems such as graphene on various substrates.
In a recent paper it has been pointed out that the simple
pairwise interface potentials, such as the Lennard-Jones (LJ) one,
are inadequate for properly describing orientation effects
at the interface.
For instance, in graphene/Ru(0001) and gr/Cu(111) we used a carefully fitted Abell-Tersoff potential which gives reasonable results.
For the gr layer the AIREBO potential has been employed.
However, the simple LJ improperly binds gr on various metals giving
completely bad binding registry: the holow regions are bound more strongly
than the hcp(fcc) regions, while the contrary is true as obtained by
vdw-DFT calculations. The inadequate nanomesh morphology occurs for LJ.
Therefore I suggest to use LJ only for preliminary calculations
and for special problems where limited accuracy is still acceptable.
Also other potentials not specifically optimized for gr/SiO2 should also be avoided, such as e.g. the reax potential fitted to other special
problems including Si and O.
Refs.:
- The classical molecular dynamics simulation of graphene on Ru(0001) using a fitted Tersoff interface potential
DOI: 10.1002/sia.5344,
P. Süle, M. Szendrő, Surf. Interf. Anal., 46, 42. (2014).
- Time-lapsed graphene moiré superlattice on Cu(111)
P. Süle, M. Szendrő, arXiv:1402.4692 (2014)
- Rotation misorientated graphene moire superlattices on Cu(111): classical molecular dynamics simulations and scanning tunneling microscopy studies
P. Süle, M. Szendrő, C. Hwang, L. Tapasztó, arXiv:1401.1716 (2014)
Best regards, Péter Süle