[CP2K-user] [CP2K:17317] Re: Metadynamics in CP2K

[Marcella Iannuzzi]

Dear Meili

I am not sure that I understand what you mean and what the problem is.
Just two comments:
- PBC are taken into account working with distances
- CP2K works with atomic units

Regards
Marcella

On Wednesday, July 13, 2022 at 2:45:28 PM UTC+2 meilil... at gmail.com wrote:

> 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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