Dear LAMMPS Users,
I have around 6000 atoms and i wanted to assign each atom as different temperature in langevin command.
The command currently which am i using
fix 3 all langevin 1.0 1.0 1.0 129877
Using this command all the atom will be assigned to temp 1.
I want something like this
atom 1: temp 1
atom 2: temp 1.003
atom 3: temp 1.006
…
atom 6000: temp 20
Do in need to write 6000 fix command or Is there any other way to implement this in lammps?
Thanks
Ankit Agrawal
Institute of Mathematical Sciences
Computational Biology
India
Dear LAMMPS Users,
I have around 6000 atoms and i wanted to assign each atom as different
temperature in langevin command.
The command currently which am i using
fix 3 all langevin 1.0 1.0 1.0 129877
Using this command all the atom will be assigned to temp 1.
I want something like this
atom 1: temp 1
atom 2: temp 1.003
atom 3: temp 1.006
...
atom 6000: temp 20
Do in need to write 6000 fix command or Is there any other way to implement
this in lammps?
please keep in mind that temperature is not a well defined entity for
a finite number of atoms. the smaller the number of atoms, the less
meaning it has. the fact that people do still compute a temperature on
a per atom basis roots in the assumption of equipartitioning. applying
a thermostat to individual atoms makes no sense.
that being said, you can still assign a variety of (initial)
velocities e.g. a ramp or based on an atom style variable or manually
through scripts commands, but they have no meaning as temperature and
will have to have the ability to fluctuate and exchange between atoms
to produce a meaningful trajectory.
before continuing please explain what you want to achieve and why you
want to go such an unphysical route to do this.
axel.
Thank you for explaining the Physics in details.
Actually in my case atom is equivalent to Gene.
And these genes are connected in a polymer chain.
So I have N chain of variable length equivalent to 6000 atoms.
Now this temp is equivalent to activity of Gene.
Higher temperature referred to more active gene and
Lower temperature corresponds to less active gene.
I wanted to see how the activity define the correlation among the genes.
That’s why i asked that question.
Thank you for explaining the Physics in details.
Actually in my case atom is equivalent to Gene.
And these genes are connected in a polymer chain.
So I have N chain of variable length equivalent to 6000 atoms.
Now this temp is equivalent to activity of Gene.
Higher temperature referred to more active gene and
Lower temperature corresponds to less active gene.
there are two concerns with this.
1) can you really resolve differences in temperature as small as what
you intend to use? remember to approximate "temperature" for a small
sample size (e.g. one atom), you need to average over a significant
amount of time. thus, would you see the difference, if there were only
6 or 60 thermostats? this seems quite doable, and still i would not
use a langevin thermostat (as it changes the dynamics significantly),
but rather use nose-hoover chains. in fact, the probably cleanest way
to do what you are a looking for would be to implement a so-called
"massive nose-hoover" thermostat, where each individual degree of
freedom (not just each atom) is coupled to an individual nose-hoover
chain (and thus additional, fictitious DOFs).
2) if you are looking for correlations, how can you know you are not
monitoring correlations between the thermostats, which are also
influenced by the characteristic (relaxation) time of the thermostat
algorithm. how can you prove that what you will find is not simply a
direct result of your input and can thus be changed massively through
changing the thermostat settings.
axel.