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Re: [lammps-users] problem with special_bonds
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Re: [lammps-users] problem with special_bonds


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 30 Apr 2018 11:54:12 -0400

On Mon, Apr 30, 2018 at 11:20 AM, Juan Antonio Seijas Bellido
<juaseibel@...24...> wrote:
> Hello, I am working with the buck/coul/long/cs potential and a core-shell
> model, so I want to remove the Coulomb interaction between all the cores and
> their own shells. To do that, I am using the command:  special_bonds coul
> 0.0 1.0 1.0
> but if I print the forces over each atom of the system there is no
> difference between using the command or not.

that is because the default setting is: special_bonds lj/coul 0.0 0.0 0.0

so if your system only has the core-shell bonds, then what you see is
the expected behavior.

axel.

> I think I am doing something
> wrong but I don't know what. Can you tell me what I have to do? I leave here
> my input and the file with the coordinates, which is the groung state with a
> shell displaced by me to not have zero force. In both cases (with and
> without the special_bonds command) I obtain this force for the first shell
> (second atom): 2 3 -2.20213 -3.37996 -6.88967
>
>
> Thank you very much for your attention.
> Juan
>
> input file
> ------------
>  units        metal
>  boundary     p p p
>  atom_style   full
>
>  read_data    coord.dat
>
>  kspace_style ewald 1.0e-5
>  pair_style   buck/coul/long/cs 8.5
>  pair_coeff * *      0.0  1.0      0.0
>  pair_coeff 3 4    499.6  0.3595   0.0
>  pair_coeff 4 4  22764.0  0.1490  27.88
>
>  bond_style harmonic
>  bond_coeff 1 4.385 0.0
>  bond_coeff 2 7.760 0.0
>  special_bonds coul 0.0 1.0 1.0
>
>  dump name_dump all custom 1 forces_LAMMPS id type fx fy fz
>  dump_modify name_dump sort id
>
> run 1
>
>
> coord.dat
> -------------
> LAMMPS empty line
>
>     16 atoms    # core and shell atoms
>      8 bonds    # number of core/shell springs
>
>  4 atom types   # 2 cores and 2 shells for Zn and O
>  2 bond types
>
>  0.00000000   3.2328763 xlo xhi
>  0.00000000   5.5994991 ylo yhi
>  0.00000000   5.1807427 zlo zhi
>
>  Masses
>
>  1 58.842    # Zn core
>  2 14.39946  #  O core
>  3 6.538     # Zn shell
>  4 1.59994   #  O shell
>
>  Atoms
>
>  1 1 1  -0.05 0.000000000000000000   0.000000000000000000
> 0.000000000000000000
>  2 1 3   2.05 0.200000000000000000   0.200000000000000000
> 0.200000000000000000
>  3 2 1  -0.05 3.232473748343905218   1.928674177488681973
> 2.469640121135010524
>  4 2 3   2.05 3.232473748343905218   1.928674177488681973
> 2.469640121135010524
>  5 3 1  -0.05 1.616038132398342819   2.861891922558703616
> 5.060007410266783801
>  6 3 3   2.05 1.616038132398342819   2.861891922558703616
> 5.060007410266783801
>  7 4 1  -0.05 1.616038258394003835   4.728419338484792789
> 2.469640121238056096
>  8 4 3   2.05 1.616038258394003835   4.728419338484792789
> 2.469640121238056096
>  9 5 2   0.00 3.232473874375850986   0.062146505458974266
> 1.880772821867820355
> 10 5 4  -2.00 3.232473874375850986   0.062146505458974266
> 1.880772821867820355
> 11 6 2   0.00 3.232473748346172737   1.928674433776235375
> 4.471140110972311454
> 12 6 4  -2.00 3.232473748346172737   1.928674433776235375
> 4.471140110972311454
> 13 7 2   0.00 1.616038132335708477   2.861891666290283798
> 1.880772821859789889
> 14 7 4  -2.00 1.616038132335708477   2.861891666290283798
> 1.880772821859789889
> 15 8 2   0.00 1.616038258417267226   4.728419594758751288
> 4.471140110974821447
> 16 8 4  -2.00 1.616038258417267226   4.728419594758751288
> 4.471140110974821447
>
>  Bonds
>
> 1 1 1 2
> 2 1 3 4
> 3 1 5 6
> 4 1 7 8
> 5 2 9 10
> 6 2 11 12
> 7 2 13 14
> 8 2 15 16
>
>
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-- 
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.