Re: [ESPResSo-users] zero angle (full angle)

[Ulf Schiller]

Hi Dusan,

On 16/04/15 16:02, Dudo wrote:
> Hi Ulf,
> 
> well, I'm pretty sure the Espresso with current definition of bond angle
> won't allow creating a zero angle (or full angle, doesn't matter).
> You may set phi0 to whatever value, it will always end up with an angle
> in between pi/2 and pi..

I'm not sure what definition you are referring to - I reckon you mean
that a certain potential would give this configuration a high energy
penalty and thus it would be sampled with a lower probability. But in
principle

cos_phi = scalar(vec21, vec31) / (vec21_magn * vec31_magn)

can give you an angle in the range [0,pi].

> It's a good remark however, that I wrongly defined the shift which
> should have been introduced as cosine of the value at least.
> However, it won't resolve the problem with defining two bond angle
> potential simultaneously which Espresso seems to dislike at the moment.

You could always use tabulated potentials to implement an arbitrary
functional form or a superposition of different potentials.

Cheers,
Ulf

> On Thu, Apr 16, 2015 at 4:08 PM, Ulf Schiller <address@hidden
> <mailto:address@hidden>> wrote:
> 
>     Hi,
> 
>     On 16/04/15 14:44, Dudo wrote:
>     > Hi,
>     >
>     > I'm trying to implement a zero angle potential with minima at 0 or 2*pi
>     > respectively.
> 
>     How would you decide whether the angle is in [0,pi] or [pi,2*pi] ?
> 
>     > For this I just added a phase shift into the former angle_harmonic.hpp
>     > potential:
>     >
>     > cos_phi = scalar(vec21, vec31) / (vec21_magn * vec31_magn) -
>     > (3.141592653589793238462 / 2.000000000000000);
> 
>     This does not seem to make sense. cos_phi should be in the range [-1,1].
> 
>     > However, in my model I would need also flat angle and right angle
>     > definitions.
> 
>     For zero angle cos_phi=1, for right angle cos_phi=0, for flat angle
>     cos_phi=-1.
> 
>     Cheers,
>     Ulf
> 
>     --
>     Dr Ulf D Schiller
>     Centre for Computational Science
>     University College London
>     20 Gordon Street
>     London WC1H 0AJ
>     United Kingdom
> 
> 
> 
> 
> 
> -- 
> ____________________
> Ing. Dusan Racko, PhD
> https://www.researchgate.net/profile/Dusan_Racko
> Polymer Institute of the Slovak Academy of Sciences
> Dubravska cesta 3
> 845 41 Bratislava, Slovak Republic
> tel: +421 2 3229 4321


-- 
Dr Ulf D Schiller
Centre for Computational Science
University College London
20 Gordon Street
London WC1H 0AJ
United Kingdom

Phone: +44 (0)20 7679 5300