Dear lammps,
I am doing some surface adatom diffusion with MD, but then I have met the error “lost atoms” during the second run process which I have colored red! I want to know: how can I avoid this? And what should I care about during the next simulation?
I am looking forward to your reply!
Wish you happy every day!
Below is my in.txt
units metal
boundary p p s
atom_style atomic
#-------------------create simulation lattice-------------------#
lattice bcc 3.0737621 orient x 1 0 0 orient y 0 1 -1 orient z 0 1 1
region box block 0 8 0 8 0 16 #To define 5 lattice
create_box 1 box
create_atoms 1 box
#----------------to define the potential--------------#
pair_style meam
pair_coeff * * library.meam V V.meam V
#---------------define the top layers and construct the vacuum-----------#
region TopAtom block INF INF INF INF 8 INF #To define a delete region
group Top region TopAtom
delete_atoms group Top
#--------------define the bottom layers and fix them---------------#
region Bottom block INF INF INF INF INF 1 #To define a fix region
group Bottom region Bottom
fix BdCstr Bottom setforce 0.0 0.0 0.0 #To fix the 2 layers of bottom atoms
velocity Bottom set 0.0 0.0 0.0
#----------------add a adatom----------------#
create_atoms 1 single 12.295 17.388 34.7756 units box
region adAtom block 12.295 12.295 17.388 17.388 34.7756 34.7756 units box
group adAtom region adAtom
#--------------constraint the adatom diffuse in the surface-------------#
fix constraint adAtom setforce NULL NULL 0.0
velocity adAtom set NULL NULL 0.0
group surf subtract all Bottom
timestep 0.004
run 0
variable E equal pe
variable N equal atoms
print “the number of atoms & system energy now are $N $E”
neighbor 2 bin
neigh_modify every 20 delay 0 check yes
velocity surf create 500.0 4928459 rot yes dist gaussian
#---------------set the NVT resemble and relax ---------------#
min_style sd
minimize 1.0e-15 1.0e-10 1000 10000
fix myRelax surf nvt temp 300.0 500.0 0.4 drag 0.5
print “nvt performed, temperature down:$N atoms,total energy is $E”
compute 4 surf temp
thermo_style custom step temp etotal press
thermo_modify temp 4
thermo 100
run 5000
minimize 1.0e-20 1.0e-15 1000 10000
unfix myRelax
fix nextRelax surf nvt temp 500.0 700.0 0.4 drag 0.5
run 5000
minimize 1.0e-30 1.0e-20 1000 10000
unfix nextRelax
fix lastRelax surf nvt temp 700.0 700.0 0.4 drag 0.5
run 5000
unfix lastRelax
fix relax all nve
run 2500
unfix relax
#---------------start the MD run--------------#
fix dif surf nvt temp 700.00 700.00 0.4 drag 1
thermo 1000
compute 7 adAtom msd
compute 8 all ke/atom
dump id2 adAtom custom 500 xyz_adatom700K id type x y z
dump id4 adAtom xyz 500 snap_adatom700K.xyz
dump id3 all xyz 1000 snap_all700k.xyz
run 250000