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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: Fri, 18 Aug 2017 14:21:56 -0400

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?


   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@...12...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.