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

From: yjcoshc (yjcoshc_at_gmail.com)
Date: Mon Mar 12 2018 - 05:01:52 CDT

Hi Giacomo,

Is there any way to parse unlimited atom groups (group1,...,groupN)? I
decide to write a loop checking groupN by cvc::parse_group and break the
loop when cvc::parse_group return NULL, but cvc::parse_group seems
raising an error when groupN is not defined.

Haochuan Chen

在 2018年03月11日 20:05, Giacomo Fiorin 写道:
> 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
> <mailto: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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