cp2k COMBINE_COLVAR/FUNCTION define exponential form function

Marcella Iannuzzi marci... at gmail.com
Fri Jan 20 18:02:31 CET 2017


Hi, 

yes, this would be an option. 
Other possibilities are the DISTANCE_POINT_PLANE variable, or the 
displacement variable, called XYZ_DIAG
regards
Marcella



On Friday, January 20, 2017 at 4:56:09 PM UTC+1, Sun Tao wrote:
>
> Hi Marcella:
>
> Thanks for your response! Another question is how could I define a 
> collective variable as the z-coordinate of a specific atom? In the COLVAR 
> session I only found DISTANCE which defines the distance between 2 specific 
> atoms and COORDINATION which defines the coordination number of a specific 
> atom. I did not find anything like COORDINATES. Shall I fix the position of 
> some atoms and use DISTANCE to define the z-coordinate? 
>
> Thanks ~
>
> Tao
>
>
> Dear Tao,
>>
>> yes this is the right way, but please keep the same name of the variable 
>> in the expression of the FUNCTION as the one you assign with the keyword 
>> VARIABLES 
>>
>> regards
>> Marcella
>>
>>
>> On Friday, January 20, 2017 at 5:19:28 AM UTC+1, Sun Tao wrote:
>>>
>>> Dear All:
>>>
>>> I am trying to set up some collective variables in cp2k. I need to 
>>> calculate the exponential-form value of a defined collective variable, 
>>> which is the distance between certain 2 atoms, the form is as the following:
>>>
>>> f = 1/{1 + exp([distance(i, j) - 0.5]/1.5)}
>>>
>>> Shall I define the CV as the following?
>>>
>>>   &SUBSYS
>>>     &COLVAR
>>>        &COMBINE_COLVAR
>>>           &COLVAR
>>>              &DISTANCE
>>>                 ATOMS 1 5
>>>
>>>              &END
>>>           &END COLVAR
>>>           FUNCTION 1/(1+exp((CV-0.5)/1.5))
>>>           VARIABLES CV1 
>>>           ERROR_LIMIT 1.0E-8
>>>        &END
>>>     &END
>>>
>>>    &END
>>>
>>>
>>>
>>> Or the correct form should be something else? Thanks ~
>>>
>>>
>>> Tao
>>>
>>>
>>>
>>>
>>>
>>>
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