LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] periodic molecule COM moving with fix momentum
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [lammps-users] periodic molecule COM moving with fix momentum


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 20 Sep 2017 10:02:09 -0400

On Wed, Sep 20, 2017 at 5:27 AM, Ali Shomali <ali.shomali111@...24...> wrote:
> Hello all Dear lammps useres
>
> I'm facing an odd problem with my simulation. I'm modeling an infinite CNT
> and another modified-functionalized CNT  that are  co-centered , thus the
> outer CNT is moving on the inner one with smaller diameter. the problem is
> no matter how many time steps I eliminate my infinite cnt center of mass
> momentum using fix momentum command, it moves! I managed to solve this
> problem by fix recenter but I'm not sure why this happened in fix momentum
> command, I've checked the control parameters and log file and every thing
> seems normal.

your description is very confusing. it is impossible to follow what
you are doing.
please note, that fix recenter do *nothing* to change the dynamics or
actually immobilize the object it is attached to.
it simply translates the frame of reference. this way, you will not
see, if you have a center of mass drift, yet - unlike with fix
momentum - that drift will remain. even in the most extreme case, the
so called "flying icecube syndrome", you would just see your system
spontaneously freeze, but not notice the massive COM drift that would
happen at the same time, even though the COM momentum will remain
(just output the COM velocity  vcm()).

> by the way I've used OPLS forcefield so I defined the extra angles and bonds
> and dihedrals which across the boundaries in data file.

fix momentum will not perfectly immobilize the atoms in question, it
will just regularly remove any residual COM momentum. if your setup
has a systematic force pushing that system into a preferred direction,
it will keep - very slowly - creeping in that direction. for a typical
periodic system, the COM actually is supposed to oscillate around its
average.

a (tiny!) residual creep can result from your choice of origin and
choice of interactions. in your input, the choice of a cutoff coulomb
is rather questionable. that can lead to an unphysical shape of the
total potential. have you tried with a well converged (i.e. 10-6)
long-range coulomb solver.
also, you only apply fix momentum to a part of your system. how can
you be sure, there is not systematic residual force cause by the rest?

axel.

> Thanks for your kind help
>
>
> this is my input file:
> #processors 1 1 10
> units                    real
> dimension                3
> boundary                 p p p
> atom_style               full
> read_data                pucnthimproper.data extra/atom/types 1
> extra/bond/types 1 extra/angle/types 1 extra/dihedral/types 1
> read_data                innerperiodic.data add append offset 2 2 2 3 1
> neighbor                 2.0 bin
> neigh_modify             delay 2 every 1
> region bottom block INF INF INF INF INF 5
> region top block INF INF INF INF 355 INF
> group pucnt type 1 2
> group                    nanotube type 3
> group                    cm id 536
> #********************************************************** force-field
> *********************************************
>
> pair_style               lj/cut/coul/cut 10 10
> bond_style               harmonic
> angle_style              harmonic
> dihedral_style           opls
> improper_style           harmonic
> special_bonds            lj/coul 0.0 0.0 0.5
>
> ################set parameters#####################
>
> ## argon and PUCNTH  opls
>
> pair_coeff               1 1 0.070    3.55000
> pair_coeff               2 2 0.030000 2.4200
> pair_coeff     3 3 0.070    3.55000 # carbon 2 = nanotube inner
> pair_modify              mix geometric
> bond_coeff               1 469.00     1.4000
> bond_coeff               2 367.00     1.0800
> bond_coeff               3 469.00     1.4000
> angle_coeff              1  63.00     120.00
> angle_coeff              2  35.00     120.00
> angle_coeff              3  63.00     120.00
>
> dihedral_coeff           1 0.0 7.250 0.0 0.0
> dihedral_coeff           2 0.0 7.250 0.0 0.0
> dihedral_coeff           3 0.0 7.250 0.0 0.0
> dihedral_coeff           4 0.0 7.250 0.0 0.0
> improper_coeff            1 0.55 180
>
> ################simualtion#####################
> #kspace_style            pppm 1e-4
> compute                  com pucnt com
> timestep                 1
> minimize                 0.001 0.001 1000 10000
> velocity                 pucnt create 300 1234 dist gaussian
> velocity                 nanotube create 300 1234 dist gaussian
> #delete_atoms             overlap 1 argon nanotube mol yes
> fix                      1 nanotube nvt temp 300 300 100
> fix                      2 pucnt nve
> compute                  1 pucnt chunk/atom molecule
> compute                  msd pucnt msd/chunk 1
> fix                      3 pucnt ave/time 1000 1 1000 c_msd file msd.out
> mode vector
> dump                     t all xyz 1000 dumpt.xyz
> thermo_style             custom step temp press ke pe etotal c_com[1]
> c_com[2] c_com[3]
> thermo                   1000
> fix      momcnt nanotube momentum 100 linear 0 0 0 angular
> run                      1000000
> undump t
> write_data               cocenterrealxed.data
> dump                     1 all xyz 1000 dump.xyz
> dump                     2 pucnt xyz 1000 dump_pucnt.xyz
> dump                     3 cm xyz 10000 dumpcm_pucnt.xyz
> restart 1000000 poly.restart
> run                      10000000
> write_data               final.data
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> 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.