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Re: [ESPResSo-users] zero angle (full angle)
From: |
Ulf Schiller |
Subject: |
Re: [ESPResSo-users] zero angle (full angle) |
Date: |
Thu, 16 Apr 2015 16:16:35 +0100 |
User-agent: |
Mozilla/5.0 (X11; Linux x86_64; rv:31.0) Gecko/20100101 Thunderbird/31.6.0 |
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