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上官七七

金虫 (小有名气)

应助: 1 (幼儿园)
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在线: 99.9小时
虫号: 1107113
注册: 2010-09-25
专业: 理论和计算化学

[求助] 请大家帮我看看，为什么不能增加原子

# 3d EAM V surface diffusion

units metal
boundary       p p s
atom_style atomic

#-------------------create simulation lattice-------------------#
lattice bcc 3.04139 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 2 box
create_atoms 1 box

#----------------to define the potential--------------#
pair_style meam
pair_coeff * * library.meam V V.meam V V

#---------------define the top layers and construct the vacuum-----------#
region       TopAtom block INF INF INF INF 16 INF #To define a delete region
group          Top region TopAtom
delete_atoms group Top

region       BotAtom block INF INF INF INF INF 0  #To define a delete region
group          Bot region BotAtom
delete_atoms group Bot

#--------------constraint the adatom diffuse in the surface-------------#
#fix          constraint1 adAtom1 setforce NULL NULL 0.0
#velocity       adAtom1 set NULL NULL 0.0

#fix          constraint2 adAtom2 setforce NULL NULL 0.0
#velocity       adAtom2 set NULL NULL 0.0

#group          surf subtract all Bottom

timestep       0.001

#dump          id1 all xyz 1 initial_coor.xyz
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 300.0 4928459 rot yes dist gaussian
print          "nvt performed, temperature up:$N atoms,total energy is $E"

compute       4 all temp
thermo_style custom step temp etotal press
thermo_modify temp 4
thermo       100

dump          id3 all xyz 1000 snap_all300k.xyz
#---------------set the NVT resemble and relax ---------------#
min_style    sd
minimize       1.0e-15 1.0e-10 1000 10000
fix          myRelax all nvt temp 10 100.0 0.1

run 10000
minimize 1.0e-20 1.0e-15 1000 10000
unfix          myRelax

fix          myRelax1 all nvt temp 100 100 0.1
run          5000
unfix          myRelax1

fix          nextRelax all nvt temp 100.0 300.0 0.1
run          10000
minimize       1.0e-30 1.0e-20 1000 10000
unfix          nextRelax

fix          nextRelax1 all nvt temp 300 300 0.1
run          20000
unfix          nextRelax1

fix          relax all nve
run          10000
unfix          relax

#----------------add  adatom----------------#
create_atoms 2 single 4 4 16 units lattice
region       adAtom1 block 4 4 4 4 16 16 units lattice
group          adAtom1 region adAtom1

create_atoms 2 single 4 4 0 units lattice
region       adAtom2 block 4 4 4 4 0 0 units lattice
group          adAtom2 region adAtom2
....

log文件中提示增加0个原子,  ???????

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