LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] Colvars Angles
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [lammps-users] Colvars Angles


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 10 Dec 2014 15:10:54 -0500

mike,

do you mind updating your sources using the colvars code from colvars.github.io?
there has been a bugfix commit in relative to the very latest released
version just yesterday that seems related.

if you have a compatible OS, you may save the effort to compile by
downloading a precompiled (serial) binary rpm from rpm.lammps.org
(just updated them) and then extracting the executable with rpm2cpio
lammps-latest.x86_64.rpm | cpio -ivd

if the issue persists, i suggest you better report the issue on the
github issue tracker and attach example inputs to reproduce it.

axel.

On Wed, Dec 10, 2014 at 2:59 PM, K. Michael Salerno
<ksalerno@...15...> wrote:
> Hi All,
> I am new to using the colvars package/fix.
>
> I would like to apply two constraints to a pair of atoms.
>
> First, I would like to apply a harmonic potential between the two atoms,
> based on their distance from one another.  This seems to work fine.
>
> I would also like to apply a constraint to keep the two particles parallel
> to a single axis.
> The relevant block for defining this angle in the .colvars file is below:
>
> colvar {
>   name angle
>
>   orientationangle {
>     atoms {
>       atomnumbers 1 9022
>     }
>       refpositions (0, 0, 0) (10, 0, 0)
>
>   }
> }
>
> This block produces output that makes sense most of the time, but
> intermittently has values that are wrong.  The output from the .traj file is
> below:
>
>
> # step         one                   fa_one                 angle
> E_h_pot               x0_one                W_h_pot
>            0    2.63443126732797e+01  4.96706198016085e+00
> 7.10991472947676e+00   4.11195078579324e+00  2.80000000000000e+01
> -2.15239352473637e+00
>            1    2.63445235947703e+01  4.96642921568898e+00
> 7.10980348107483e+00   4.11090319240818e+00  2.80000000000000e+01
> -4.30451285153493e+00
>            2    2.63447172415882e+01  4.96584827523553e+00
> 7.10970573171377e+00   4.10994151544328e+00  2.80000000000000e+01
> -6.45638043747032e+00
>            3    2.63448937414113e+01  4.96531877576597e+00
> 7.10962199287174e+00   4.10906509082901e+00  2.80000000000000e+01
> -8.60801857363558e+00
>            4    2.63450534150514e+01  4.96483975484581e+00
> 7.10955270220001e+00   4.10827229854957e+00  2.80000000000000e+01
> -1.07594491340688e+01
>            5    2.63451967319910e+01  4.96440980402706e+00
> 7.10949824538948e+00   4.10756078371999e+00  2.80000000000000e+01
> -1.29106933824805e+01
>            6    2.63453243392690e+01  4.96402698219292e+00
> 1.79979388626225e+02   4.10692731332322e+00  2.80000000000000e+01
> -1.50617717414308e+01
>            7    2.63454369997417e+01  4.96368900077495e+00
> 7.10943484838600e+00   4.10636808273571e+00  2.80000000000000e+01
> -1.72127036417666e+01
>            8    2.63455356106389e+01  4.96339316808321e+00
> 7.10942624765969e+00   4.10587862349585e+00  2.80000000000000e+01
> -1.93635073479360e+01
>            9    2.63456211470618e+01  4.96313655881467e+00
> 7.10943305980519e+00   4.10545408357378e+00  2.80000000000000e+01
> -2.15141998567556e+01
>           10    2.63456946650961e+01  4.96291600471174e+00
> 7.10984839588891e+00   4.10508921163732e+00  2.80000000000000e+01
> -2.36647967921307e+01
>           11    2.63457572996944e+01  4.96272810091666e+00
> 1.79304379628549e+02   4.10477836727131e+00  2.80000000000000e+01
> -2.58153123025279e+01
>           12    2.63458102315154e+01  4.96256930545368e+00
> 7.10954396489181e+00   4.10451568523850e+00  2.80000000000000e+01
> -2.79657590015579e+01
>
> The value of 7.1 for the angle is correct, based on the positions of the
> particles, but at random times the value jumps to ~ 180 as it does at steps
> # 6 and 11.  This produces warning messages:
> colvars:     Warning: one molecular orientation has changed by more than
> 0.01: discontinuous rotation ?
>
> It seems this could be because I've done something incorrectly, but then the
> correct values confuse me.  Is this a bug or have I done something wrong?
> The problem seems consistent between LAMMPS versions 9 Dec 2014 and 14 Jun
> 2014.
>
> Thanks,
> Mike
>
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
> _______________________________________________
> lammps-users mailing list
> lammps-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>



-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.