Greetings,
I am having difficulties pulling out a region to "move".
first, I select a region as a part of the data file then moving it
toward rest part and
pass through it.
my input file is at following.
when I executed run I always face with the following error even with
downsize timestep
ERROR on proc 45: Bond atoms 346 392 missing on proc 45 at step 66
(../ntopo_bond_all.cpp:63)
WARNING: Using 12-bit tables for long-range coul
one the other hand, my pair style must not change.
I would appreciate you helping out for this simulation.
regard
# ---------- Initialize Simulation ---------------------
clear
units real
dimension 3
boundary p p p
atom_style full
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
# ---------- Define Interatomic Potential ---------------------
pair_style lj/class2/coul/long 9.35 3.272
read_data hntpu.data
kspace_style pppm 1.0e-2
pair_modify mix arithmetic
neighbor 13.0 bin
neigh_modify delay 0 every 1 check yes page 500000 one 50000
special_bonds charmm
# ---------- define atoms in a small region---------------------
variable dx equal 0.003
group HNT id < 3304
set group HNT type 1
# ---------- Define Settings ---------------------
compute eng all pe/atom
compute peratom all pe/atom
compute pe all reduce sum c_peratom
# ---------- Compute stress information for Atomeye
visualization--------------------
compute s all stress/atom NULL
compute s1 all reduce sum c_s[1]
compute s2 all reduce sum c_s[2]
compute s3 all reduce sum c_s[3]
compute p all reduce sum c_s[1] c_s[2] c_s[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
# ------------ Equilibrate --------------------------
#Minimization
minimize 0.0 1.0e-4 10000 10000
# Equilibration
reset_timestep 0
velocity all create 0.0 1231 dist gaussian
fix 1 all nve
fix 2 all langevin 0 0 0.001 904297
thermo_style custom step etotal press vol temp density pxx pyy pzz
thermo 100
timestep 0.00001
run 20
unfix 1
unfix 2
write_restart hntnew811.data1
# ------------ moving piston region toward rest --------------------------
variable V equal 0.1
variable x equal vdisplace(0.0,$V)
fix 3 HNT move variable NULL v_x NULL NULL v_V NULL
dump d2 all image 100000 img-*.jpg type type zoom 1.2 adiam 0.6 size 1280 720
dump m1 all movie 1000 movie.avi type type zoom 1.2 adiam 0.6 size 1280 720
dump apf all custom 100000 atom_position.dat
id type x y z ix iy iz
dump trjfile all custom 100000 dump.lammpstrj id
mol type x y z ix iy iz
thermo_style custom step temp pxx pyy pzz lx ly lz epair ebond eangle
edihed press v_press c_s1 c_s2 c_s3
thermo 50
timestep 5.0e-11
reset_timestep 0
run 2000000
unfix 3
print "All done"