Hello everybody,
I’m running NVE simulations in LAMMPS and monitoring the energy transfer of an excited molecule to the bath gas. When I use LJ parameters I see the energy transfer but when I use the Buckingham I do not see any relaxation even after a long time of simulation, 10ns. if I take the LJ parameters and convert them to the Exp-6 parameters and use them again I see no relaxation. I also used the hybrid style but the relaxation decreases when I mix the Buck and LJ. It seems that there is something about the Buckingham potential.
The following is my input file. I read the manual, checked everything but maybe there is something that I’m missing.
echo both
units real
boundary p p p
atom_style molecular
#pair_style hybrid lj/cut 10.0 buck 10.0
pair_style buck 10.0
#pair_style lj/cut 10.0
bond_style morse
read_data data.new
bond_coeff 1 106.6 2.294 0.9706
#pair_coeff 1 1 buck 695954.00 0.248 1294.79
#pair_coeff 1 1 0.285 3.75
#pair_coeff 2 2 lj/cut 0.032 2.98
#pair_coeff 3 3 lj/cut 0.110 2.47
#pair_coeff 1 2 lj/cut 0.095 3.36
#pair_coeff 1 3 lj/cut 0.177 3.11
pair_coeff 1 1 695954.00 0.248 1294.79
pair_coeff 2 2 2202.0289 0.267 32.5948
pair_coeff 3 3 69414.639 0.253 347.3414
pair_coeff 1 2 70054.94 0.299 815.1259
pair_coeff 1 3 130826.4 0.277 957.2115
pair_coeff 2 3 12363.3750 0.260 106.4027
This is a question about Buckingham potential not about LAMMPS. There is no rule that Buckingham should everything LJ does. You might want to discuss this with your advisor and colleagues and search relavant articles in the Literature.
Ray
Ray,
I checked the parameters and read different papers related to the Buckingham potential and parameters that I use and compared them. I wanted also to be sure about my input file. Seems there is an error somewhere that is hard to find.
Best,
Leila
If you want people to check your input script for this kind of details, then your chance of getting a reply is quite slim - this is ultimately your job.
Ray
Well, I didn’t send my input one and ask people to check it. I have a problem and I checked everything, the parameters, the potentials and the input file and up to now I was not successful to find the error so I thought maybe someone has had this problem and can help me and I usually see that people in the user group send their input files.
Best,
Leila
Well, I didn't send my input one and ask people to check it. I have a
problem and I checked everything, the parameters, the potentials and the
input file and up to now I was not successful to find the error so I thought
maybe someone has had this problem and can help me and I usually see that
people in the user group send their input files.
leila,
providing your input as part of your inquiry is indeed a good idea. it
allows to rule out the obvious issues (which may not be obvious to the
person asking).
if that doesn't help, however, you will have to apply "the scientific
method(tm)":
the base hypothesis is that there is something wrong. now that can be
either a problem with your input or a problem with LAMMPS. despite
your repeated checking, chances are that the problem is something on
your side (incorrect unit conversion, misinterpretation of parameter
data, typos, bad geometry, bad simulation protocol), but if they are
on the LAMMPS side, you need to have conclusive proof.
in both cases, you need to simplify your system and try something very
simple, ideally with only one component and see if the parameters that
you believe are equivalent do indeed give equivalent answers. if yes,
then you can add one complication at a time and thus gradually build
your system to the point where it fails and then you can see, which
step is the problematic one. at that point, you will be able to craft
an input that contains only the problematic part of your input and
then you can investigate further whether it is a case where LAMMPS
doesn't behave as it should or perhaps you'll find that your checking
of parameters and/or input wasn't as thorough as you currently believe
it is.
another option would be to use the pair_write option to write out the
energy/force graphs of each interacting pair of atom types and compare
those across the different potentials and check whether your
parameters are indeed equivalent visually.
and the list goes on. depending on what else you see and do, you'll
have to verify each step and each detail always assuming that you
messed it up.
in any case, there is a lot that you can do by yourself.
axel.
In addition to Axel’s comments one more thing that in my personal opinion should go first is to always try the ANALYTICAL expressions (not yelling but almost to make a strong point). If you know the interaction params you can just plot the energy vs distance for your two types in all cases using gnuplot or any other plotting tool. If energy is not dissipated particles are not interacting, or at least this would be a physical reason for such observation. Plotting the interactions while leaving Lammps aside would allow you to simplify the process and focus more on the fundamentals. If the interactions are to be equivalent in magnitude the plots should be comparable when the smae unit system is employed.
Carlos
Dear Axel and Carlos
Thank you for your comments.
Best,
Leila