[CP2K-user] [CP2K:17318] Re: Metadynamics in CP2K

[Meili Liu]

Dear Marcella,

Thanks for your comments and all helps. I keep try XYZ_DIAG or 
XYZ_OUTERDIAG. 

Best,
Meili
University of Miami

在2022年7月13日星期三 UTC-4 09:01:20<Marcella Iannuzzi> 写道：

> 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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