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Re: [lammps-users] Fwd:


From: Giacomo Fiorin <giacomo.fiorin@...24...>
Date: Sat, 12 Aug 2017 14:07:04 -0400

Hello Ialtu, please ask a specific question after reading the documentation relevant to what you are trying to do.

Giacomo

On Sat, Aug 12, 2017 at 8:47 AM, laltu dass <tanni222byc@...24...> wrote:

---------- Forwarded message ----------
From: laltu dass <tanni222byc@...24...>
Date: Sat, Aug 12, 2017 at 4:59 PM
Subject: Re:
To: Axel Kohlmeyer <akohlmey@...24...>


thanks a lot sir,

now its running and i got some files created but unable to sort out which one is giving me the angle information?as it is written in the manual that orientationProj ,The returned value is the cosine of the angle of rotation q between the current and the reference positions. The range of values is [-1:1].

this are the output files created

1.out.colvars.state
2.out.colvars.traj
3.out2.colvars.state
4.out2.colvars.traj


fix        2 all colvars orientation.in


fix 2 all colvars orientation.in input out.colvars.state output out2


On Sat, Aug 12, 2017 at 4:26 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Sat, Aug 12, 2017 at 2:31 AM, laltu dass <tanni222byc@...24...> wrote:
Respected sir,



i want to calculate Orientational ordering by calculating Legendre polynomial. i.e., P2(θ) )〈(3cos 2θ - 1)/2〉, in which θ is the angle between a direction vector and the surface normal

for that i am using lammps colvar


colvarsTrajFrequency 1
colvarsRestartFrequency 10
indexFile allindex.ndx

colvar {

    name one

    outputAppliedForce on

    width 0.5

  orientationProj {
        atoms {
            indexGroup cation
            centerReference yes
            rotateReference yes
            refPositionsGroup {
                indexGroup anion
            }
            refPositionsFile cation.xyz
        }
        refPositionsFile anion.xyz
    }
}

harmonic {
    colvars        one
    centers        (1.0, 0.0, 0.0, 0.0)
    forceConstant  0.001
}




but getting error everytime colvars: Error: in parsing "centers"

​from the manual:

​enters ⟨Initial harmonic restraint centers⟩
Context: harmonic
Acceptable values: space-separated list of colvar values 

 

​axel.​


help!!







--
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.



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--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD