Dear Users,
I want to simulate a liquid crystal composed of ellipsoidal particles that interact through the Gay-Berne potential. The system has periodic boundary conditions except on the axis-z, the limits in this dimension are walls that interact with the particles through lj93 potential. The problem is that the system lose atoms (ERROR: Lost atoms: original 256 current 238 (…/thermo.cpp441)) Can anyone sort out what is my mistake? I attach the input.
input ------------------------------------------
units lj
atom_style ellipsoid
dimension 3
boundary p p f
lattice fcc 1.88
region simbox2 block 0 4 0 4 8 12
region simbox3 block 0 20 0 20 0 20
create_box 1 simbox2
create_atoms 1 box
fix zwalls all wall/lj93 zlo 2.0 1.0 1.0 2.5 zhi 18.0 1.0 1.0 2.5
#set group all type/fraction 2 0.1 73263
#set type 1 mass 1.0
set type 1 shape 1 1 0.5
set group all quat/random 27193
compute rot all temp/asphere
group spheroid type 1
variable dof equal count(spheroid)
compute_modify rot extra ${dof}
compute kerot all erotate/asphere
velocity all create 1.607 348943 loop geom
pair_style gayberne 1.0 1.0 2.0 4.0
pair_coeff * * 1.0 1.0 1 1 1 1 1 1
neighbor 0.3 bin
neigh_modify every 10 delay 0 check no
restart 2500 restart # punto de salvado
thermo_style custom step c_rot temp ke c_kerot pe etotal press vol
thermo 10
compute orient all property/atom quati quatj quatk quatw
compute shape all property/atom shapex shapey shapez
dump 1 all custom 10 dump.lammpatrj id type x y z vx vy vz &
c_orient[1] c_orient[2] c_orient[3] c_orient[4] &
c_shape[1] c_shape[2] c_shape[3]
timestep 0.0002
fix 1 all nvt/asphere temp 0.5 0.5 0.01
compute_modify 1_temp extra ${dof}
#fix 1 all nve/asphere
run 1000
write_restart restart.end
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Pablo.