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Re: [lammps-users] Can lammps run single atom at NVE?
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Re: [lammps-users] Can lammps run single atom at NVE?

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sat, 19 Aug 2017 09:18:29 -0400


On Sat, Aug 19, 2017 at 9:15 AM, Steve Plimpton <sjplimp@...24...> wrote:
You can use the velocity command with its "set"
option to set the velocity of a single atom.
Then it will move when you use fix nve.

There will be no "energy" of the system, other
than kinetic, because there is no potential
energy for a single atom.

​but it is pointless to run an MD for this.
the atom will just keep moving with the given velocity and nothing will change it, since there are no interactions (well, with a large enough cutoff the atom would interact with periodic images of itself, but those forces would cancel out).​

axel.


 

Steve

On Fri, Aug 18, 2017 at 1:22 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Fri, Aug 18, 2017 at 3:17 PM, Zheng, Xuechen <xuechen_zheng@...802...> wrote:
Dear Mr or Mrs,
   
    Thank you for your reply. The problem is the "velocity", and when I comment out it , then the kinetic  energy, potential energy  and temperature will all be 0 and will never change.

​this is not a problem of the velocity command. it is a problem of you asking for something that doesn't make sense.

as mentioned already, you cannot compute a temperature for a single atom via Sum_i(1/2*m*v^2)*​k_B/n_DOF, since your system is considered invariant to translation, i.e. the number of degrees of freedom is zero. please keep in mind, that the velocity command acts only on and knows only about point particles. so the rotational DOFs of your particles do not factor in here.  LAMMPS is behaving as one should expect.

​axel.​


 

Sincerely,
Xuechen

On Fri, Aug 18, 2017 at 2:21 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Fri, Aug 18, 2017 at 1:48 PM, Zheng, Xuechen <xuechen_zheng@...802...> wrote:
Dear Mr or Mrs,

   I would like to simulate only single atom at NVE without the thermostatting. But it will say "Attempting to rescale a 0.0 temperature". And after I create the second atom, then it will run in a right way. Therefore, I wonder whether lammps can simulate single atom at NVE. If so , How to do that?My input file is attached.

​yes, you can run an MD for a single atom, but it will have limited utility and meaning, especially in an environment without any other interactions.
you cannot assign a temperature (since the system considered to be invariant to translation) or compute one for translation of the atoms.
if you watch very closely, you should see at which command LAMMPS fails and i will bet a large sum of money, it is not the "run" command.​
if you comment out the failing list, what happens?

axel.

 
  
   Thank you!

  # 3D Gay Berne on Surface simulation

units                real
atom_style           ellipsoid
dimension            3
boundary             p p p
atom_modify          id yes

atom_modify          map array


atom_modify          sort 100 25
lattice              fcc 5.0
region               box block 0.0 5.0 0.0 5.0 0.0 5.0
create_box           1 box
#create_atoms         1 region substrate
create_atoms         1 single 2 2 2 
#create_atoms         1 single 3 3 3 
compute_modify       extra 0
set                  type 1 mass 16.04
set                  type 1 shape 1 1 1
velocity             all create 300.0 4928459 rot yes dist gaussian

set                  group all quat/random 18238


compute              rot all temp/asphere
compute_modify       extra 0
group                spheroid type 1
variable             dof equal count(spheroid)+2

compute_modify       rot extra ${dof}



neigh_modify     delay 0 every 1

timestep             0.0002

variable             z_atom atom z

variable             x_atom atom x

variable             y_atom atom y



# Get Constants of the Energy That Don't Change Upon Taking Directional Derivatives

variable         energy_x atom (1.47025e-06*v_x_atom^4+-0.000598126*v_x_atom^2+0.0156679+0.00012389*v_x_atom^3+-0.0128309*v_x_atom)*sin(1.04344*v_x_atom)+-1098.47+sin(-10.7193*v_x_atom+0.464616)*0.000818385+0.24923*cos(0.0319159*v_x_atom+0.106606)

variable         energy_y atom (1.47025e-06*v_y_atom^4+-0.000598126*v_y_atom^2+0.0156679+0.00012389*v_y_atom^3+-0.0128309*v_y_atom)*sin(1.04344*v_y_atom)+-1098.47+sin(-10.7193*v_y_atom+0.464616)*0.000818385+0.24923*cos(0.0319159*v_y_atom+0.106606)

variable         energy_z atom 6602.67*exp(-2.41063*v_z_atom)-176.047*v_z_atom^(-3)-1829.08*v_z_atom^(-6)+2866.59*v_z_atom^(-8)    

variable         energy_total atom v_energy_x*v_energy_y*v_energy_z



#Trans Forces

variable        fx_2 atom v_energy_y*v_energy_z*(-5.881*10^(-6)*v_x_atom^3+1.19624*10^(-3)*v_x_atom-3.7167*10^(-4)*v_x_atom^2+.0128309)*sin(1.04344*v_x_atom)+(-1.47025*10^(-6)*v_x_atom^(4)+.00059812*v_x_atom^2-.0156679-.00012399*v_x_atom^3+.0128309*v_x_atom)*1.04344*cos(1.04344*v_x_atom)+8.772139*10^(-3)*cos(-10.713*v_x_atom+.464616)+7.954399*10^(-3)*sin(.0319159*v_x_atom+.106606)    


variable        fy_2 atom v_energy_x*v_energy_z*(-5.881*10^(-6)*v_y_atom^3+1.19624*10^(-3)*v_y_atom-3.7167*10^(-4)*v_y_atom^2+.0128309)*sin(1.04344*v_y_atom)+(-1.47025*10^(-6)*v_y_atom^(4)+.00059812*v_y_atom^2-.0156679-.00012399*v_y_atom^3+.0128309*v_y_atom)*1.04344*cos(1.04344*v_y_atom)+8.772139*10^(-3)*cos(-10.7193*v_y_atom+.464616)+7.954399*10^(-3)*sin(.0319159*v_y_atom+.106606)


variable         fz_2 atom  v_energy_x*v_energy_y*15917.0*exp(-2.41063*v_z_atom)-528.14*v_z_atom^(-4)+10974*v_z_atom^(-7)+22932.7*v_z_atom^(-9)
 



compute          q all property/atom quatw quati quatj quatk



fix              1 all nve    
#fix  1 all nvt temp 300.0 300.0 1.0        

dump             1 all custom 100000 dump.ellipse.gayberne &
             id type x y z c_q[1] c_q[2] c_q[3] c_q[4]


dump 2 all image 100000 image.*.jpg type type adiam 1.2

dump_modify 2 pad 5


dump             4 all custom 100000 dump.force.test &
             id v_fx_2 v_fy_2 v_fz_2 v_energy_x v_energy_y v_energy_z 

dump             5 all custom 100000 dump.x.test &
             id x 
                  


thermo 10000

thermo_style     custom step temp ke pe etotal press vol


run 50000000



--
Xuechen Zheng


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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.



--
Xuechen Zheng




--
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.

------------------------------------------------------------------------------
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@...655....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.