I got error message : ERROR on proc 2: Bond atom missing in image check (…/domain.cpp:658)
ERROR on proc 1: Bond atom missing in image check (…/domain.cpp:658)
ERROR on proc 0: Bond atom missing in image check (…/domain.cpp:658)
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This is my input file.
variable strain equal 0.001
variable repx equal 1
variable repz equal 1
variable strain2 equal "1+v_strain"
variable deldist equal 50
variable fixdist equal 45
######################################
# INITIALIZATION
units real
dimension 3
boundary p p p
atom_style full
pair_style lj/class2/coul/long 9.5 9.5
dielectric 1.0
pair_modify tail yes
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
read_data mC12o-DSB-303K3.data
kspace_style pppm 0.00000001
#variable minlength equal 100
variable xlen equal lx
variable ylen equal ly
variable zlen equal lz
print "lx: ${xlen}"
print "ly: ${ylen}"
print "lz: ${zlen}"
# Compute stress information for Atomeye visualization
compute stress all stress/atom NULL
compute stress1 all reduce sum c_stress[1]
compute stress2 all reduce sum c_stress[2]
compute stress3 all reduce sum c_stress[3]
compute stress4 all reduce sum c_stress[4]
compute stress5 all reduce sum c_stress[5]
compute stress6 all reduce sum c_stress[6]
# Compute distance for each side of the grain boundary to displace
#variable ly1 equal ly
compute ly1low all reduce min y
compute ly1hi all reduce max y
variable Temp_target equal 300.0
variable Temp_anneal equal 300.0
variable Press equal 1.0
#velocity all create ${Temp_anneal} 38951 dist gaussian
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
special_bonds lj/coul 0.0 0.0 1.0
replicate 20 20 4
# Minimize first
timestep 0.5
thermo 10000
thermo_style custom step lx ly lz press pxx pyy pzz pe c_ly1low c_ly1hi
write_data data.mindone
min_style sd
fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001
minimize 1.0e-2 1.0e-2 1000 1000
velocity all create ${Temp_anneal} 38951 dist gaussian
unfix 1
fix Mynvt1 all nvt temp ${Temp_anneal} ${Temp_anneal} 100.0 drag 0.01
dump Myatom1 all atom 1000 1_NVT_${Temp_anneal}K.pos
dump_modify Myatom1 image yes scale yes
restart 10000 1_NVT_${Temp_anneal}K.restart
run_style verlet
run 5000
unfix Mynvt1
undump Myatom1
# CREATE REGIONS FOR BOUNDARY CONDITIONS
# lx, ly, lz are fixed for the rest
thermo_style custom step lx ly lz press pxx pyy pzz pe c_ly1low c_ly1hi
# Delete groups of atoms far from boundary
region rlow block 0 INF -10 25 0 INF units box
region rhigh block 0 INF 75 110 0 INF units box
group glow region rlow
group ghigh region rhigh
delete_atoms group glow
delete_atoms group ghigh
# Create groups to fix and displace
region rgblow block 0 INF -10 30 0 INF units box
region rgbhigh block 0 INF 70 110 0 INF units box
group gbhigh region rgbhigh
group gblow region rgblow
# Put fixed boundary condition on edge atoms by setting forces to zero
fix 2 gbhigh setforce 0 0 0
fix 3 gblow setforce 0 0 0
run 0
variable ly1 equal "c_ly1hi - c_ly1low"
variable ly0 equal ${ly1}
variable lydelta equal "v_strain*v_ly0/2"
print "Length of box w/ GB: ${ly0}"
print "y Strain increments: ${lydelta}"
##########################################
# MS Deformation loop
variable a loop ${nloop}
label loop
# Displace the atoms and minimize again
# displace_atoms group-ID style args keyword value
displace_atoms gblow move 0 INF -10 25 0 INF units box
displace_atoms gbhigh move 0 INF 75 110 0 INF units box
minimize 1.0e-2 1.0e-2 1000 1000
# Create cfg files with stress in y direction for AtomEye viewing
reset_timestep ${a}
dump 1 all cfg 1000 dump. mC12o-DSB-303K3_*.cfg mass type xs ys zs c_stress[2]
dump_modify 1 element mC12o-DSB-303K3
dump_modify 1 first yes
dump_modify 1 pad 3
run 0
undump 1
next a
jump mC12o-DSB-303K3.txt loop
unfix gb_fracture
######################################
# SIMULATION DONE
print "All done"
Give me a advise please.
