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[lammps-users] Particles outside surface of region
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[lammps-users] Particles outside surface of region

From: Jagroop Kaur <jagroopk610@...24...>
Date: Fri, 6 Oct 2017 00:48:42 +0530

Hi all,

I am using lammps version 31 March, 2016. I want to simulate an isotropic liquid with gay berne interaction in a box (p p f) with periodic boundaries along x and y axes and non periodic boundary along z axis. I am using fix wall/region command. I am also changing the box's z dimension. Also, I have used displace_atoms command to displace atoms so that they remain in box. But still I am getting the error 'Particle outside surface of region used in fix wall/region'. Is still the problem in particle's displacement or in the values of sigma and epsilon for wall-particle interaction or something else? My input script is provided below.

Thank you in advance.

units                  lj
atom_style         ellipsoid
dimension          3
boundary           p p p
lattice               sc 0.05

region               box block 0 15 0 15 0 24    
create_box        1 box
create_atoms      1 box

set               type 1 mass 1.0
set               type 1 shape 3 1 1
set              group all quat/random 18238

compute              rot all temp/asphere

variable          dof equal 2
compute_modify    rot extra/dof ${dof}

velocity          all create 2.4 87287 loop geom

pair_style        gayberne 1.0 3.0 1.0 5.5
pair_coeff        1 1 3.0 1.0 1 1 1 1 1 1 5.0

neighbor          1.0 bin

variable          step equal step
variable          density equal density
variable          temp equal temp
variable          etotal equal etotal
variable          pxx equal pxx
variable          pyy equal pyy
variable          pzz equal pzz
variable         lx equal lx
variable         ly equal ly
variable         lz equal lz
variable          zlo equal zlo
variable          zhi equal zhi
variable          xlo equal xlo
variable          xhi equal xhi
variable          ylo equal ylo
variable          yhi equal yhi
variable          pe equal pe

thermo_style      custom temp press pe step xlo xhi lx ylo yhi ly zlo zhi lz
thermo              10

timestep          0.002

compute              q all property/atom quatw quati quatj quatk

fix               1 all npt/asphere temp 1.0 1.0 0.1 iso 3.2 3.2 0.1 &
               mtk no pchain 0 tchain 1
compute_modify    1_temp extra/dof ${dof}

fix               2 all print 10 "${step} ${density} ${temp} ${etotal} ${pxx} ${pyy} ${pzz} ${lx} ${ly} ${lz} ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}" file output1e.txt screen no title "step density temp etotal pxx pyy pzz lx ly lz xlo xhi ylo yhi zlo zhi"
run               20

unfix             2
unfix             1

fix                1 all nve

fix               2 all print 10 "${step} ${density} ${temp} ${etotal} ${pxx} ${pyy} ${pzz} ${lx} ${ly} ${lz} ${xlo} ${xhi} ${ylo} ${yhi} ${zlo}  ${zhi}" file output2e.txt screen no title "step density temp etotal pxx pyy pzz lx ly lz xlo xhi ylo yhi zlo zhi"               

run               20

unfix             2

variable          rljmin equal (2^(1.0/6.0))
variable          delz atom -${zlo}+${rljmin}
variable          z1hi equal (${zhi}-${zlo}+${rljmin})
variable          z1lo equal 0.0
variable           N equal count(all)
displace_atoms    all move 0.0 0.0 v_delz units box

dump                 1 all custom 10 dump.ellipse.gayberne    id type x y z

thermo_style      custom step temp press pe xlo xhi lx ylo yhi ly zlo zhi lz v_N

change_box        all z final ${z1lo} ${z1hi} boundary p p f remap units box
region            zlowall plane 0 0 0 0 0 1 units box
region            zhiwall plane 0 0 ${z1hi} 0 0 -1 units box
fix               lw all wall/region zlowall lj126 1.0 1.0 ${rljmin}
fix_modify        lw energy yes
fix               rw all wall/region zhiwall lj126 1.0 1.0 ${rljmin}
fix_modify        rw energy yes

fix               2 all print 10 "${step} ${density} ${temp} ${pe} ${etotal} ${pxx} ${pyy} ${pzz} ${lx} ${ly} ${lz} ${xlo} ${xhi} ${ylo} ${yhi} ${zlo}  ${zhi} " file output3e.txt screen no title "step density temp etotal pxx pyy pzz lx ly lz xlo xhi ylo yhi zlo zhi"              
run               50  

Thanks and best regards,
Jagroop Kaur
Research Scholar,
Thapar University, Patiala.