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

From: "Zheng, Xuechen" <xuechen_zheng@...802...>
Date: Fri, 18 Aug 2017 13:48:44 -0400

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.
   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