[CP2K:8638] Re: Questions about AdBF-QM/MM in cp2k

[Ivan Gladich]

Dear Noam,

Dear Rolf,


thank you for your reply, they helped me to better understand the meaning
of R_QM, R_CORE and EXTENDED and the differences with to the paper.


Concerning the labels I still have some unclear point. For example, I got
for the last step


> QMMM FORCE MIXING final count (not including links):  N_QM core_list
2 N_QM core     0 N_QM extended    12 N_QM buffered    66


but, if I look at my non-zero labels I see


    6482

 i =       50, time =       25.000, E =      -108.8420993135

 BR        10.0000000000       10.0000000000       10.0000000000

  O        10.0000000000       10.0000000000       10.0000000000

  O         5.0000000000        5.0000000000        5.0000000000

  H         5.0000000000        5.0000000000        5.0000000000

  H         5.0000000000        5.0000000000        5.0000000000

  O         7.0000000000        7.0000000000        7.0000000000

  H         7.0000000000        7.0000000000        7.0000000000

  H         7.0000000000        7.0000000000        7.0000000000

  O         5.0000000000        5.0000000000        5.0000000000

  H         5.0000000000        5.0000000000        5.0000000000

  H         5.0000000000        5.0000000000        5.0000000000

  O         5.0000000000        5.0000000000        5.0000000000

  H         5.0000000000        5.0000000000        5.0000000000

  H         5.0000000000        5.0000000000        5.0000000000

  O         5.0000000000        5.0000000000        5.0000000000

  H         5.0000000000        5.0000000000        5.0000000000

  H         5.0000000000        5.0000000000        5.0000000000


So, two questions

a) 10 should be the core list atoms but which is the meaning of labels 7
and 5?
b) I cannot match the numbers because the labels tells me that I have 17 QM
atoms in the extended or extended plus buffer.
The Output points toward much higher number  (66)

You can find my inputs at the following link

goo.gl/C15cBY

Thank you again for your help, it was extremely useful.

Ivan




On Fri, Feb 3, 2017 at 1:41 PM, Rolf David <rolf.d... at gmail.com> wrote:

>
>
> For the force-mixing labels, for me it works
> I have 10.0 for list/core, 7.0 for extended and 5.0 for buffered. (for
> CP2K version 3.0)
>
> I have a parell question if I may:
>
> How can we restart a ad-qmmm calculations ?:
>
> I run a first dynamics, at the last step at the end i got:
>
> QMMM FORCE MIXING final count (not including links):  N_QM core_list
> 11 N_QM core     0 N_QM extended    42 N_QM buffered   111
>
>
>
> And restarting it, the very first step :
>
> QMMM FORCE MIXING final count (not including links):  N_QM core_list
> 11 N_QM core     0 N_QM extended    33 N_QM buffered    87
>
>
> + the WFN:   READ RESTART : WARNING : DIFFERENT natom, returning
> 131         164
>
>
> So for the minimal QM region, I got only core_list, so it doesen't change
> and it can read the WFN restart files
>
> But for the extended, since it is buffer in buffer out related, it varies.
>
>
> Is there a way to let CP2K now which atoms where in the extended/buffered
> ? (Except putting the min/max the same for R_*** distances)
>
>
> For info, these test were run on the 2.x (rev 16205) and i used:
>
>
> R_CORE [angstrom] 0.0 0.0
>
> R_QM [angstrom]   2.5 3.0
>
> R_BUF [angstrom]  2.5 3.0
>
>
>
>
>
> A part for the restart issues, which can be penalising when using
> national/eu clusters where there is a wall time, it runs smoothly
>
>
> Thanks
>
>
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