[CP2K-user] [CP2K:17316] Re: Metadynamics in CP2K

[Meili Liu]

Dear Marcella,

I will try XYZ_DIAG or XYZ_OUTERDIAG. And Please allow me to ask question.

I tried the &DISTANCE (ATOMS 1 97) to set up the CVs. Below is part of my 
input file for your reference: 
#1 is a fixed Fe atom in the metal during MTD. Its coordinates are (0, 0, 
-9.7). 
#97 is the Oxygen atom and is flexible. 
Picture 2 is the output file including CV1 and CV2 and size of cell box(ABC 
information). 
Picture 1 is sketch showing the box  size and position of O atom and Fe 
atom in 2D plot.

 I found a different description for CV1. I try to use picture 1 and 
picture 2 to describe it. 
I add the WALL of position at Lx/2 and Ly/2. The input file(MD_meta.inp) is 
attached. 
However, the trajectory looks strange. I guess the problems are between PBC 
and distance 
instead of Position to result in the WALL setup maybe wrong. I am not sure 
other description for distance
will have this issue or not. However, I didn't find the description for 
position of one atom. 

Thanks so much for any advice and ideas.

%%%%%%COLVAR%%%%%%%%
    &COLVAR

       &DISTANCE

         ATOMS 1 97

         AXIS X

       &END

    &END COLVAR

    &COLVAR

       &DISTANCE

         ATOMS 1 97

         AXIS Y

       &END

    &END COLVAR

%%%%%%WALL setup%%%%%%%%

     &METAVAR

       SCALE 0.1

       COLVAR 1

         &WALL

            POSITION 4.8

            TYPE QUARTIC

            &QUARTIC

               DIRECTION WALL_PLUS

               K  100.0

            &END

         &END

     &METAVAR

       SCALE 0.1

       COLVAR 2

         &WALL

            POSITION 4.2

            TYPE QUARTIC

            &QUARTIC

               DIRECTION WALL_PLUS

               K  100.0

            &END

         &END

%%%%%%%%%%%%%%


Best,
Meili
University of Miami

在2022年7月13日星期三 UTC-4 07:51:54<Marcella Iannuzzi> 写道：

> Dear Meili
>
> You can try
>
>    - XYZ_DIAG 
>    <https://manual.cp2k.org/cp2k-9_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/XYZ_DIAG.html>
>
> or
>
>    - XYZ_OUTERDIAG 
>    <https://manual.cp2k.org/cp2k-9_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/XYZ_OUTERDIAG.html>
>
> or the distance from a point.
> The wall is applied via
>
>    - WALL 
>    <https://manual.cp2k.org/cp2k-9_1-branch/CP2K_INPUT/MOTION/FREE_ENERGY/METADYN/METAVAR/WALL.html>
>
> It can be used multiple times to define a confinement region
>
> Regards
> Marcella
>
>
> On Tuesday, July 12, 2022 at 6:11:25 PM UTC+2 meilil... at gmail.com wrote:
>
>> Dear CP2K users
>>
>> I am using Metadynamics to research the adsorption of one O atom on the 
>> surface of metal. I plan to use x-axis of O atom as CV1 and y-axis of same 
>> O atom as CV2. 
>>
>> I am wondering how to  set up the position (instead of distance) 
>> of &COLVAR. and how to  set up the WALL to constrain the O atom within a 
>> certain small region on the metal surface.  
>>
>> Please let us know if any advices, and many thanks in advance!
>>
>> Best,
>> Meili
>> University of Miami
>>
>>
>>
>>

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