Re: colvars: How to implement a collective variable of vector type?

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Sun Mar 11 2018 - 16:54:15 CDT

Hi,

You might be able to implement at least proof-of-concept versions of your
custom variable using either scriptedFunction or even customFunction
(depending on the complexity of the expressions involved). Of course that
will not use your C++ code directly, for that Giacomo's message gives you
the path to follow. I just wanted to state that both scriptedFunction and
customFunction let you define vector variables.

Best,
Jerome

On 11 March 2018 at 13:05, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:

> Hi Haochuan, you need to derive a new class from the colvar::cvc, whose
> structure is described here.
> http://colvars.github.io/doxygen/html/classcolvar_1_1cvc.html#details
> The rest of the webpage shows you also the current inheritance structure
> (what classes are derived from what).
>
> Among the variables that have vector values, a good example to take a look
> at could be distance_pairs. Presumably you only need to wrap your C++ code
> in the correct functions, and add the calls that read coordinates or send
> forces.
>
> See also:
> http://colvars.github.io/doxygen/html/index.html
> for documentation on the other classes.
>
> Giacomo
>
> On Sat, Mar 10, 2018 at 4:27 AM, yjcoshc <yjcoshc_at_gmail.com> wrote:
>
>> Hello,
>>
>> I want to implement a vector collective variable in NAMD through the
>> colvars module. It can calculate the least square fitted plane among
>> multiple atomgroups and return the normal vector of the plane. The example
>> pathCV script in colvartools folder seems scalar type only. Any suggestion
>> of implementing a vector type one? I have finished a sample C++ code to
>> calculate this. How do I incorporate it in colvars?
>>
>> Thanks,
>>
>> Haochuan Chen
>>
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>

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