The atom with a constant speed does not move

LAMMPS LAMMPS Beginners
1

Hello, everyone. when simulateing tensile process, the boundary atoms don’t move in the later stage. What did I do wrong? I used the speed stretching method, and set the boundary atoms at a constant speed, which did not move in the later stage of stretching.
The script is the following.
#model

units metal
dimension 3
timestep 0.001
atom_modify map yes
read_data L4_L5_xyza.data
change_box all boundary fs p p

minimize-------------------------------

thermo 500
thermo_style custom step temp lx ly lz
thermo_modify lost ignore
dump 1 all custom 500 mini.fiber id type x y z vx vy vz fx fy fz
min_style cg
minimize 1e-12 1e-15 5000 5000
undump 1
reset_timestep 0

initialize temperature

reset_atom_ids sort yes
velocity move_group create 300 10000

fix boundary_group

fix 1 boundary_group setforce 0.0 0.0 0.0

relax in npt system

thermo 100
fix 2 all npt temp 300 298 (1000*v_timestep) y 1 1 (1000v_timestep) z 1 1 $(1000v_timestep)
thermo_modify lost ignore
dump 1 all atom 100 fiber_relax.1ammpstrj

run 5000

cancel fix, dump; clear timestep

unfix 2
undump 1
reset_timestep 0

define boundary of fix_group and move_group

variable length_0 equal bound(move_group,xmax)-bound(move_group,xmin)
variable length_start equal bound(move_group,xmin)
variable length_stop equal bound(move_group,xmax)
#set velocity in x direction
reset_atom_ids sort yes
velocity operate_group set ${tensile_rate} 0 0 sum yes units box
velocity fix_group set 0 0 0 units box

set temperature in tensile process

fix 2 all nvt temp 298 298 $(1000*v_timestep)

compute press

compute temp1 all temp
compute stress all pressure temp1
variable stressx equal -c_stress[1]/10000
variable stressy equal -c_stress[2]/10000
variable stressz equal -c_stress[3]/10000

compute stress of each atom

compute sigma_atom all stress/atom NULL

compute vol_atom all voronoi/atom
variable stressx_atom atom c_sigma_atom[1]/c_vol_atom[1]/10000
variable stressy_atom atom c_sigma_atom[2]/c_vol_atom[1]/10000
variable stressz_atom atom c_sigma_atom[3]/c_vol_atom[1]/10000

compute stress of move_group

compute 2 move_group reduce sum c_sigma_atom[1] c_sigma_atom[2] c_sigma_atom[3] c_vol_atom[1]

variable stres_x equal c_2[1]/c_2[4]/10000
variable stres_y equal c_2[2]/c_2[4]/10000
variable stres_z equal c_2[3]/c_2[4]/10000

print to file

thermo {num_step} thermo_style custom step temp v_stressx v_stressy v_stressz v_length_start v_length_stop v_stres_x v_stres_y v_stres_z c_2[1] c_2[2] c_2[3] c_2[4] thermo_modify lost ignore variable strain equal (v_length_stop-v_length_start)/{length_0}-1 # compute strain in x direct

#-------------------------save stress and strain to file---------------------------

fix stress_strain all print 800 “{stressx} {strain} {stres_x} {strain}” file stress_strain.dat screen no
dump 1 all custom ${num_step} fiber_tension.lammpstrj id type x y z vx vy vz v_stressx_atom v_stressy_atom v_stressz_atom c_vol_atom[1]

run 200000

2

please put quoted input files into triple backquotes “```” so they render properly with the forum. Otherwise the forum markup will interpret certain characters as formatting directives which make your input difficult or impossible to read (you should see this yourself).

which atoms are those?
your input file is hard to read (see above) and a bit convoluted to see what you intend to do.
if you want help, your chances to get good help and quickly depend crucially on how easy you make it to see and understand your issue.

just setting the speed is not sufficient, you also must zero the forces.
but why not simply use fix move on those atoms?

This setting is almost always a mistake. Unless you have a setup where you expect atoms to leave the system, you should not ignore lost atoms, as they may be a symptom of bad simulation settings and thus bogus results.

3

Thank you very much. I have solved this problem. In addition, can be temperature set when I use fix move?

4

Fix move will set the velocities of the atoms according to their prescribed motion.
You cannot have a “temperature” for such motions.

For clarity I should add then performing such simulations, the temperature displayed in the LAMMPS thermo output contains the information about the entire system. That usually has not much of a meaning, as it includes atoms that are immobilized or moved on an externally determined path (and that process is usually extremely rushed due to the time scale limitations of atomic scale MD and thus not adiabatic).