Dear Lammps Users,
I have accounted the following problem and thus seek for guidance.
A Carbon nanotube coordinate file was generated from VMD and nanotube builder.
File 1 : From VMD the file looks as :
1640 atoms
1 atom types
Hello Prakhar,
Did you define the computational box limits for the VMD version? If so, what did you define them as?
Cheers,
Derek Thomas
Dear Lammps Users,
I have accounted the following problem and thus seek for guidance.
A Carbon nanotube coordinate file was generated from VMD and nanotube
builder.
[...]
With same input file (Program file) the output differs. Moreover with the
why on earth should it not be different?
you have different coordinates.
help of File 1 the CNT vibrates and it is not seen with File 2.
there are no dynamics in a minimization.
so how can there be a "vibration". the
minimizer algorithm moves the atoms towards
the minimum. or are you saying that
the calculation doesn't converge?
axel.
The CNT oscillates about mean position throughout the simulation. Moreover with the help of File 2 I am getting my results correct but this is not same with File 1 (and with same Simulation box used as of File 2 ).
nobody can give you any proper advice,
if you provide incomplete information.
- there was no mention of any "simulation"
only minimization.
- there were only input data fragments.
if it "doesn't work", chances are, you are doing it wrong.
if you think it is a LAMMPS problem, you have to provide
proof or at the very least sufficient evidence that somebody
else can check it.
please remember that MD always follows the
"garbage in, garbage out" principle.
axel.
Sir,
I mean to say that the input file (program ) is same, only the coordinate file of same type (10,10) is changed and the results are so changed…Thats what my curosity.
I know MD depends on coordinates.
Sir,
I mean to say that the input file (program ) is same, only the coordinate
file of same type (10,10) is changed and the results are so changed....Thats
what my curosity.
again, chances are that your calculations are simply not done properly,
and it shows more in one of the two cases. but nobody can tell without
seeing what you have done and how.
I know MD depends on coordinates.
...and on many other things.
axel.
Dear Axel Sir,
Here is the input data and the files attached.
in.cnt (2.76 KB)
file1.xyz (66.4 KB)
File2.xyz (47.8 KB)
Dear Axel Sir,
Here is the input data and the files attached.
there is one major flaw in your lammps input script.
after doing the minimization, you don't re-initialize
the velocities. minimization doesn't touch them, so
if you have specific vibrational modes excited due to
your initial geometry, those won't go away quickly.
dissipation of kinetic energy across bonds and particularly
a resonant system like you have can take a very, very
long time.
if i re-initialize the velocities after the minimization,
there is no qualitative difference between the two
different starting geometries.
axel.
p.s.: it would have helped me *massively* if you
had first removed all the stuff that doesn't affect
the dynamics.