[CPMD-list] some question on NOSE CAFES.

[Tengfei Luo]

Dear Apsi:

>Dear Tengfei,

 >  Adding a bit to Axel's answer:

 > - If the MD does what you want, you could easily extract the temperatures
>of the sub-system with a small shell script employing e.g. perl, awk,
>python, ... to process the atomic velocities in the file 'TRAJECTORY' (32
>atoms per sub-system would be VERY small, but probably this is just a test
>for the feasibility of the approach anyway)

Yes, I'm testing if I can model the thermal transportation at materials 
interface. I want to go to larger systems using QM/MM.

>  - What is the highest phonon frequency in silicon? A time step of only 4
>atu sounds quite low for me, it's like the ones people use for water
>nowadays (and there the cut-off energy is usually 70-100 Ry plus the
>highest, stretching modes are at 2200-2400 cm^-1). This would also affect
>the frequency of the Nosé thermostat

I just wanted to start with safe parameters to test NOSE CAFES. Larger time 
steps are OK when I used silicon for other purposes.

>  - I would suggest you to check the sub-option 'SAMPLE' for 'TRAJECTORY'
>(unless you have lots of empty disc, anyway the output at each step is not
>necessary)

Yes, I really should always remember this:)

>  - How did you obtain the values for 'NOSE ELECTRONS'? Did you optimise
>the target (0.00045 sounds a bit small, but maybe it is meaningful for a
>small system with such a low cut-off energy)

This is the value I got after I ran without thermostats.

>  - 'PRINT FORCES ON', well please remember that during Car-Parrinello MD
>you are not exactly at the BO surface and you have to judge whether you
>can use the corresponding forces for some analysis; probably the deviation
>is small

I forgot to delete this!

>  - I would doubt any calculation which uses 'LMAX=P' for silicon; maybe it
>IS okay, I'm just used to 'LMAX=D' for most of the elements (LOC=LMAX=D -
>the default - would be okay for silicon)

>  - Like Axel said, that you get any temperature at all is a bit worrying -
>well, probably the thermostats do the job here, combined with a finite
>numerical precision

Yes, but why I don't need to specify an initial temperature when I used NOSE 
IONS MASSIVE?

>   Good luck! :)

>     Greetings from the suburbs of Paris,

>        apsi

>PS What is the purpose of the option 'RESTART ... RESTART'??

This is to retart from the geometry optimization.

Thank you for your patient email.

Tengfei
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
   Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
   IMPMC, CNRS & Université Pierre et Marie Curie
   Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820

On Sun, 25 Feb 2007, Tengfei Luo wrote:

>
> Here is my input file:
> &INFO
> 64 SI atoms half of which is nose to 100K, and the
> other half set to 200K
> &END
>
> &CPMD
>  MOLECULAR DYNAMICS CP
>  RESTART WAVEFUNCTION COORDINATES RESTART
>  TRAJECTORY XYZ
>  NOSE IONS CAFES
>    2
>    1  32  200.0 1500
>    33 64  100.0 1500
>  NOSE ELECTRONS
>    0.00045 5000
>  PRINT FORCES ON
>  MAXSTEP
>   80000
>  TIMESTEP
>   4.0
>  STORE
>   5000
> &END
>
> &DFT
>  FUNCTIONAL LDA
> &END
>
> &SYSTEM
>  SYMMETRY
>  6
>  SCALE S=2
>  CELL
>  20.526204 1.0  1.0  0  0  0
>  CUTOFF
>  20.0
> &END
>
> &ATOMS
> *SI_MT_LDA  KLEINMAN-BYLANDER
>   LMAX=P
>   64
>   0.50 1.00 0.50
>   1.00 0.50 0.50
>   0.50 0.50 0.00
>   1.00 1.00 0.00
> .......
>   1.25 1.25 1.25
>   1.25 1.75 1.75
>   1.75 1.75 1.25
> &END
>
> &BASIS
>  PSEUDO AO 2
>  0 1
> &END
>
> Sorry for the long email! Any suggestion or advice would be greatly 
> appreciated!
>
> Regards,
>
> T.Luo