[CPMD-list] some question on NOSE CAFES.

[Tengfei Luo]

Dear Axel:


> On Sun, 25 Feb 2007, Tengfei Luo wrote:
>
> TL> Dear all:
> TL> I'm simulating the thermal energy equilibrating on a 64 Si atoms 
> system.
> TL>
>
> TL> Here comes the questions: How can I check whether each of the two
> TL> part is at there set temperature? or how to monitor the temperatures
> TL> of the two parts separately? Do I need to modify the code? or there
> TL> is some other software can analyze the trajectory to see the
> TL> temperature of different parts of a system?
>
> no, you only need to read the manual:
>
> A new file, \texttt{CAFES} is created containing the temperature
>      of each group (cols. 2 \dots \textsl{ncafesgrp+1}) and the energy
>      of the Nose-Hoover chains of that group (last columns).\\
>      Using CAFES with different temperatures only makes sense if the
>      different groups are decoupled from each other by increasing the
>      masses of the involved atoms. The
>

Oh, I didn't see the file. I should have looked more closely at the manual. 
I checked the file and the temperature of the two parts are oscillating 
around the set temperature. But I haven't changed any mass at all, why this 
works? or the trajectory isn't physically meaningful?

Here is a portion of the CAFES file:
.............
   64780   223.055398   85.242507   -1.164740    1.220325
   64781   223.217170   85.198965   -1.164813    1.220345
   64782   223.364599   85.157363   -1.164883    1.220364
.............
   66126   229.914950   99.289693   -1.202579    1.248588
   66127   230.176053   99.413485   -1.202640    1.248572
   66128   230.419875   99.533537   -1.202699    1.248556
............
   67380   166.164382  121.215046   -1.215219    1.265484
   67381   165.854535  121.563279   -1.215208    1.265499
   67382   165.550833  121.906464   -1.215197    1.265514


> TL> Another question is that after I began the CP-MD steps, it took 5000
> TL> steps before the atoms start to move(please see the following part
> TL> of the output). Why does this happen?
>
> if your structure is in the potential energy minimum (or close to it)
> and you assign no initial temperature, where should the kinetic energy
> come from?? why _should_ the atoms move at all?
> check out the TEMPERATURE keyword. (RTFM again).
>

I got that, the atoms shouldn't move at all. Maybe the computational error 
played the role of perturbation.

> [...]
> TL>
> TL> Sorry for the long email! Any suggestion or advice would be greatly 
> appreciated!
>
> well, you could have just copied smaller parts of the output,
> e.g. beginning and end of the trajectory. the message would
> have been the same.
>
> cheers,
>   axel.
>

Thank you very much for your answers!

Regards,

Tengfei