R: Re: Re: R: Re: Re: temperature in NVE ensembles

Ok, So I hope this is the final question. I wanted to be sure that after a
command:

velocity all create c_termo_themp 312231 dist gaussian

the total kinetic energy after the command should not have changed (exactly)
and does what I need. Am I right? I used a compute that should be automatically
defined.

----Messaggio originale----
Da: [email protected]
Data: 14/08/2013 0.17
A: "[email protected]"<[email protected]>
Cc: "Axel Kohlmeyer"<[email protected]>, "LAMMPS Users Mailing List"<lammps-

[email protected]>

Ogg: Re: Re: [lammps-users] R: Re: Re: temperature in NVE ensembles

Thanks to the chaotic nature of atom dynamics and also perhaps blind
faith in the ergodic hypothesis, you should be able to generate an
independent simulation as follows:

1. Read in a system with the desired geometry and total energy
2. Use the "velocity create" command to assign new random velocities,
but exactly the same kinetic energy (read the manual for technical
details, like how the nominal temperature is related to the kinetic
energy)
3. Run NVE dynamics

To get a different trajectory at the same E, just change the random
number seed in the velocity create command.

Aidan

----Messaggio originale----
Da: [email protected]
Data: 13/08/2013 19.00
A: "[email protected]"<[email protected]>
Cc: "Axel Kohlmeyer"<[email protected]>, "LAMMPS Users Mailing List"

<lammps-

[email protected]>

Ogg: Re: [lammps-users] R: Re: Re: temperature in NVE ensembles

The temperature of the NVE simulation should depend only on the value
of E at the end of the NVT run. It does not matter how you thermostat,
you will never come closer to the desired temperature than deltaT ~
sqrt(1/N). During an NVT run, the total energy fluctuates about an
average value that is determined by the set temperature. The
fluctuations are proportional to sqrt(heat capacity). When you switch
from NVT to NVE, you are taking a sample from that energy
distribution, not the average of the distribution.

Ok great, thanks for this analysis one learns by doing mistakes I'll study
better nvt dynamics.

To do what you want, you should follow Axel's original suggestion and
generate a master plot of <T>_NVE versus E.

also, regarding

"because I'd like to study different replicas of the same system."

If you want to generate *equivalent* independent replicas, it is
sufficient that they have the same value of some state variable, in
this case either E or T. There is no strong reason to favor one or the
other and choosing E eliminates your problem. If it ain't broke, don't
fix it, especially if you don't know how to.

Ok, actually I don't want to stick to an exact value of the "mean"
temperature, so I can choose E as my state variable without problem. But

now

it's not clear to me how I can easily generate independent configurations

in

lammps with the same total energy. When I mean independent, I mean not
"directly connected" one to the other by a lammps NVE dynamics. Was this

the

solution you were proposing?

I tried to modify in the fix nvt the damp parameter, but I see no

particular

difference.

When plotting istantenous temperature (given as output by lammps) versus

time

during nvt integration, I see that the frequency of oscillation of

temperature

depends upon the damp parameter but the amplitude of oscillations is
independent. Is this correct?

I am not a frequent user of nosè hoover integration. Maybe when I switch

off

nvt integration and shitch on nve, the new temperature will try to

oscillate

around the istantenous value of the temperature at which I switched off

nosè

hoover?

Maybe as you say these oscillations in nvt are a finite size effect,

since

I'm

using quite small systems (hundreds of atoms), but I think there is a

brute

force way to overcome the problem, that is starting NVE integrations from
different configurations that have the same fixed total energy and

equilibrate

using an NVE ensemble. I don't know if this is a good and feasible idea

in

lammps and which is the best way to implement it.

Again, thanks a lot for the help!

----Messaggio originale----
Da: [email protected]
Data: 13/08/2013 15.27
A: "[email protected]"<[email protected]>
Cc: "LAMMPS Users Mailing List"<[email protected]>
Ogg: Re: Re: [lammps-users] temperature in NVE ensembles

----Messaggio originale----
Da: [email protected]
Data: 13/08/2013 15.02
A: "[email protected]"<[email protected]>
Cc: "LAMMPS Users Mailing List"<[email protected]>
Ogg: Re: [lammps-users] temperature in NVE ensembles

Hi everybody,

      I've got a basic question I think. I'd like to create several

different

NVE ensembles in a simple system (say a crystal sylicon, or LJ

Argon).

Temperature in equilibrium is not a well defined quantity in such

ensembles

but

oscillates around a mean value T , that depends in a non trivial way

on

the

total energy, and that we call the 'temperature' of the system.

The point is that I'd like to run different NVE simulations fixing a

priori

this mean value of the temperature. Which is the best efficient way

in

lammps

to achieve that ? (equilibrating with an NVT thermostat and than

switch

to

NVE

gets me close to the right temperature but not close enough)

what is close enough? if you run your simulation long enough with a
proper thermalization until it is well equilibrated, then it should
maintain that (average) temperature. if not, then you need to
investigate your settings, how long you ran the MD, how well you
sampled phase space, how well it is equilibrated, how well you
conserve energy. when running with a thermostat reduce the intensity
of the thermal coupling, you should transition from NVT to NVE
ensemble.

First of all, thanks for your reply.

I'll try to check this. What I observed till now is that if I try to
equilibrate using NVT at a certain temperature T and after

equilibration

I

switch to NVE, temperature will start oscillating aroung a value close

to