# sample surface deposition script for atoms with fixed layer by zhuxuegang
# --------------- VARIABLE ------------------
label loop
suffix gpu
variable tp index 333.15 273.15 373.15 423.15 623.15
variable bxh equal 20
variable xn equal 14
variable yn equal 10
variable zn equal 10
variable btk equal 10
variable dpatomnum index 9
#substrate thickness 'btk' should larger than 3 for the fix, constant temp layer
variable vtk equal 10
# 'vtk' is the thickness of vacuum
variable rneq equal 50000
variable dag index 0 15 30 38 45 60
variable dae index 2 5 10 1 0.5 15 20
variable daed equal 0.0
variable numvl index 3 5 7 10 13 16 19 23 25
#first of all define the variable using in the follow context
#temperature tp,temperature low / high tpl / tph, boxs size and
variable tpl equal 10
variable tph equal 2000
#lattice constant lt
variable bxl equal 0
variable lt equal 3.21
variable mgmass equal 24.30500000
###timestep 'ts',run many timesteps to deposit atom'rneq',
###dump every many timesteps equilibrium 'dseq' and deposit 'dsdp'
###dpinter is the deposite time interval
variable ts equal 0.001
#variable rndp equal 10
variable dpinter equal 2000
variable rndp equal "v_dpn*v_dpinter+v_rneq"
variable dseq equal 20000
variable dsdp equal "ceil(v_dpinter*50+1500)"
#deposit atom number 'dpn', and every many timesteps to deposit 'dpts'
#variable dpn equal 4000
variable dpn equal "ceil(v_xn*v_yn*v_zn*16/v_dpatomnum)"
#deposit atom velocity basic vertical to surface with angle of 0 degree
#deposit atom degree dag, deposit atom energy dae
#for the symmetry system vx equal to vy so only one need to set daed is deposit energy deta
shell mkdir Mg_twin${numvl}_e${dae}_ag${dag}_temp${tp}_dpatom${dpatomnum}
shell cd Mg_twin${numvl}_e${dae}_ag${dag}_temp${tp}_dpatom${dpatomnum}
log log.Mg_twin${numvl}_e${dae}_ag${dag}_temp${tp}_dpatom${dpatomnum}.lammps
# --------------- INITIALIZATION ------------------
units metal
dimension 3
atom_style atomic
boundary p p p
# ------------------ ATOM DEFINITION -------------------
lattice hcp ${lt}
variable byl equal "ceil(v_bxl/(sqrt(3)))"
variable byh equal "ceil(v_bxh/(sqrt(3)))"
variable bzl equal "ceil(v_bxl/(sqrt(8/3)))"
variable bzh equal "v_btk+v_vtk"
#region box block ${bxl} ${bxh} ${byl} ${byh} ${bzl} ${bzh}
#create_box 4 box
read_data ../Mgpoly${numvl}.lmp
region bound block INF INF INF INF 0 0.6
region contemp block INF INF INF INF 0.6 1.6
region reltemp block INF INF INF INF 1.6 ${btk}
region substrate union 3 bound contemp reltemp
#create_atoms 1 region substrate
#variable chgz equal "v_bzh*1.568/1.632993"
#change_box all z final 0.0 ${chgz} remap
group bound region bound
group contemp region contemp
group reltemp region reltemp
group substrate region substrate
group addatoms type 2
set group bound type 3
set group contemp type 4
# -------------------- ATOM DEFINITION----------------------
pair_style eam/fs
pair_coeff * * ../Mg.eam.fs Mg Mg Mg Mg
#mass 1 ${mgmass}
#mass 2 ${mgmass}
#mass 3 ${mgmass}
#mass 4 ${mgmass}
#---------------------------Settings-equilibrium-------------
velocity all create ${tp} 28459
timestep ${ts}
thermo_style custom step elapsed atoms temp press ke pe etotal enthalpy vol density
thermo 100
thermo_modify lost ignore flush yes
velocity bound set 0.0 0.0 0.0
fix 1 bound setforce 0.0 0.0 0.0
fix 2 reltemp nve
#fix 3 contemp npt temp ${tp} ${tp} 0.01 iso 0.0 0.0 0.1
#run ${rneq}
#unfix 3
fix 3 contemp npt temp ${tp} ${tp} 0.01 iso 0.0 0.0 0.1
shell mkdir Mg_twin${numvl}eq_e${dae}_ag${dag}_temp${tp}_dpatom${dpatomnum}
shell cd Mg_twin${numvl}eq_e${dae}_ag${dag}_temp${tp}_dpatom${dpatomnum}
dump 1 all custom 100 Mg_mini_twin${numvl}_e${dae}_ag${dag}_temp${tp}_dpatom${dpatomnum}.* id type x y z fx fy fz vx vy vz
min_style cg
minimize 1e-25 1e-25 5000 10000
undump 1
dump 1 all custom ${dseq} Mg_twin${numvl}_eq_e${dae}_ag${dag}_temp${tp}_dpatom${dpatomnum}.* id type x y z fx fy fz vx vy vz
run ${rneq}
shell cd ..
#unfix 3
#fix 3 contemp npt temp ${tp} ${tp} 0.01 iso 0.0 0.0 0.1
#run ${rneq}
undump 1
write_restart restart.tem${tp}
#---------------------------deposit----------------------------
#compute add addatoms temp
#compute_modify add dynamic yes extra
variable x0 equal "xlo+0.01"
variable x4 equal "xhi-0.01"
variable y0 equal "ylo+0.01"
variable y4 equal "yhi-0.01"
variable z0 equal "zhi-v_lt*1.601*(v_vtk-9)"
variable z1 equal "zhi-v_lt*1.601*(v_vtk-9)"
variable x1 equal "v_x4/4"
variable y1 equal "v_y4/4"
variable x2 equal "v_x4/2"
variable y2 equal "v_y4/2"
variable x3 equal "v_x4*3/4"
variable y3 equal "v_y4*3/4"
variable x31 equal "v_x4/3"
variable y31 equal "v_y4/3"
variable x32 equal "v_x4*2/3"
variable y32 equal "v_y4*2/3"
lattice none 1.0
variable pi equal 3.14159265358979323846
variable dpvl equal "sqrt(2*v_dae*1.6021765314*10000/(v_mgmass*1.66053886))"
variable dpvh equal "sqrt(2*(v_dae+v_daed)*1.6021765314*10000/(v_mgmass*1.66053886))"
variable dpvzl equal "-v_dpvl*abs(cos(v_dag*v_pi/180))"
variable dpvzh equal "-v_dpvh*abs(cos(v_dag*v_pi/180))"
variable dpvyl equal "-v_dpvl*abs(sin(v_dag*v_pi/180))"
variable dpvyh equal "-v_dpvh*abs(sin(v_dag*v_pi/180))"
variable dpts equal "floor((v_rndp-v_rneq)/v_dpn)"
variable zdell equal "zhi-v_lt-0.5"
variable zdelh equal "zhi-v_lt+0.5"
region deletatom block ${x0} ${x4} ${y0} ${y4} ${zdell} ${zdelh}
fix 5 addatoms nve
run 0
compute addtp addatoms temp
compute_modify addtp dynamic yes extra 0
variable addtpc equal "c_addtp"
compute realtp reltemp temp
compute_modify realtp dynamic yes extra 0
variable realtpc equal "c_realtp"
compute addke addatoms ke
compute_modify addke dynamic yes extra 0
variable addkec equal "c_addke"
compute atallke all ke/atom
variable atallkec equal "c_atallke"
compute ctat all centro/atom fcc
variable ctatc equal "c_ctat"
compute atpe all pe/atom
variable atpec equal "c_atpe"
#compute allpe all reduce sum c_adpe
compute addpe addatoms pe/atom
compute_modify addpe dynamic yes extra 0
variable addpec equal "c_addpe"
compute adallpe addatoms reduce sum c_addpe
variable adallpec equal "c_adallpe"
variable dppz equal xcm(addatoms,z)
variable dppx equal xcm(addatoms,x)
variable dppy equal xcm(addatoms,y)
variable dpatn equal count(addatoms)
#fix pr addatoms print 1 " ${dppx} ${dppy} ${dppz} ${addtpc} ${addkec} ${adallpec} ${realtpc}" title "add_pos_x add_pos_y add_pos_z addtemp add_ke add_pe realtemp" append ke${dae}ag${dag}temp${tp}.txt screen no
#label loop
fix 7 all evaporate 1 100 deletatom 49892
shell mkdir Mg_twin${numvl}_dp_e${dae}_ag${dag}_temp${tp}_dpatom${dpatomnum}
shell cd Mg_twin${numvl}_dp_e${dae}_ag${dag}_temp${tp}_dpatom${dpatomnum}
if "${dpatomnum} ==1" then "jump SELF dpatom1"
if "${dpatomnum} ==4" then "jump SELF dpatom4"
if "${dpatomnum} ==8" then "jump SELF dpatom8"
if "${dpatomnum} ==9" then "jump SELF dpatom9"
if "${dpatomnum} ==16" then "jump SELF dpatom16"
label dpatom1
region deposit1 block ${x0} ${x4} ${y0} ${y4} ${z0} ${z1}
fix dp1 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit1 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
dump 1 all custom ${dsdp} Mg_twin${numvl}_dp_e${dae}_ag${dag}_temp${tp}.* id type x y z fx fy fz vx vy vz
run ${rndp}
shell cd ..
unfix dp1
jump SELF break
label dpatom4
region deposit1 block ${x0} ${x2} ${y0} ${y2} ${z0} ${z1}
region deposit2 block ${x2} ${x4} ${y0} ${y2} ${z0} ${z1}
region deposit3 block ${x0} ${x2} ${y2} ${y4} ${z0} ${z1}
region deposit4 block ${x2} ${x4} ${y2} ${y4} ${z0} ${z1}
fix dp1 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit1 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp2 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit2 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp3 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit3 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp4 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit4 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
dump 1 all custom ${dsdp} Mg_twin${numvl}_dp_e${dae}_ag${dag}_temp${tp}.* id type x y z fx fy fz vx vy vz
run ${rndp}
shell cd ..
unfix dp1
unfix dp2
unfix dp3
unfix dp4
jump SELF break
label dpatom8
region deposit1 block ${x0} ${x1} ${y0} ${y2} ${z0} ${z1}
region deposit2 block ${x1} ${x2} ${y0} ${y2} ${z0} ${z1}
region deposit3 block ${x2} ${x3} ${y0} ${y2} ${z0} ${z1}
region deposit4 block ${x3} ${x4} ${y0} ${y2} ${z0} ${z1}
region deposit5 block ${x0} ${x1} ${y2} ${y4} ${z0} ${z1}
region deposit6 block ${x1} ${x2} ${y2} ${y4} ${z0} ${z1}
region deposit7 block ${x2} ${x3} ${y2} ${y4} ${z0} ${z1}
region deposit8 block ${x3} ${x4} ${y2} ${y4} ${z0} ${z1}
fix dp1 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit1 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp2 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit2 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp3 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit3 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp4 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit4 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp5 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit5 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp6 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit6 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp7 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit7 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp8 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit8 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
dump 1 all custom ${dsdp} Mg_twin${numvl}_dp_e${dae}_ag${dag}_temp${tp}.* id type x y z fx fy fz vx vy vz
run ${rndp}
shell cd ..
unfix dp1
unfix dp2
unfix dp3
unfix dp4
unfix dp5
unfix dp6
unfix dp7
unfix dp8
jump SELF break
label dpatom9
region deposit1 block ${x0} ${x31} ${y0} ${y31} ${z0} ${z1}
region deposit2 block ${x31} ${x32} ${y0} ${y31} ${z0} ${z1}
region deposit3 block ${x32} ${x4} ${y0} ${y31} ${z0} ${z1}
region deposit4 block ${x0} ${x31} ${y31} ${y32} ${z0} ${z1}
region deposit5 block ${x31} ${x32} ${y31} ${y32} ${z0} ${z1}
region deposit6 block ${x32} ${x4} ${y31} ${y32} ${z0} ${z1}
region deposit7 block ${x0} ${x31} ${y32} ${y4} ${z0} ${z1}
region deposit8 block ${x31} ${x32} ${y32} ${y4} ${z0} ${z1}
region deposit9 block ${x32} ${x4} ${y32} ${y4} ${z0} ${z1}
fix dp1 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit1 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp2 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit2 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp3 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit3 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp4 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit4 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp5 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit5 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp6 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit6 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp7 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit7 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp8 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit8 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp9 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit9 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
dump 1 all custom ${dsdp} Mg_twin${numvl}_dp_e${dae}_ag${dag}_temp${tp}.* id type x y z fx fy fz vx vy vz
run ${rndp}
shell cd ..
unfix dp1
unfix dp2
unfix dp3
unfix dp4
unfix dp5
unfix dp6
unfix dp7
unfix dp8
unfix dp9
jump SELF break
label dpatom16
region deposit1 block ${x0} ${x1} ${y0} ${y1} ${z0} ${z1}
region deposit2 block ${x1} ${x2} ${y0} ${y1} ${z0} ${z1}
region deposit3 block ${x2} ${x3} ${y0} ${y1} ${z0} ${z1}
region deposit4 block ${x3} ${x4} ${y0} ${y1} ${z0} ${z1}
region deposit5 block ${x0} ${x1} ${y1} ${y2} ${z0} ${z1}
region deposit6 block ${x1} ${x2} ${y1} ${y2} ${z0} ${z1}
region deposit7 block ${x2} ${x3} ${y1} ${y2} ${z0} ${z1}
region deposit8 block ${x3} ${x4} ${y1} ${y2} ${z0} ${z1}
region deposit9 block ${x0} ${x1} ${y2} ${y3} ${z0} ${z1}
region deposit10 block ${x1} ${x2} ${y2} ${y3} ${z0} ${z1}
region deposit11 block ${x2} ${x3} ${y2} ${y3} ${z0} ${z1}
region deposit12 block ${x3} ${x4} ${y2} ${y3} ${z0} ${z1}
region deposit13 block ${x0} ${x1} ${y3} ${y4} ${z0} ${z1}
region deposit14 block ${x1} ${x2} ${y3} ${y4} ${z0} ${z1}
region deposit15 block ${x2} ${x3} ${y3} ${y4} ${z0} ${z1}
region deposit16 block ${x3} ${x4} ${y3} ${y4} ${z0} ${z1}
fix dp1 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit1 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp2 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit2 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp3 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit3 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp4 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit4 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp5 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit5 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp6 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit6 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp7 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit7 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp8 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit8 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp9 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit9 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp10 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit10 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp11 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit11 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp12 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit12 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp13 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit13 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp14 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit14 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp15 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit15 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
fix dp16 addatoms deposit ${dpn} 2 ${dpts} 12345 region deposit16 near ${lt} vz ${dpvzl} ${dpvzh} vy ${dpvyl} ${dpvyh}
dump 1 all custom ${dsdp} Mg_twin${numvl}_dp_e${dae}_ag${dag}_temp${tp}.* id type x y z fx fy fz vx vy vz
#run 20000
#unfix pr
run ${rndp}
shell cd ..
unfix dp1
unfix dp2
unfix dp3
unfix dp4
unfix dp5
unfix dp6
unfix dp7
unfix dp8
unfix dp9
unfix dp10
unfix dp11
unfix dp12
unfix dp13
unfix dp14
unfix dp15
unfix dp16
jump SELF break
label break
#unfix 7
#if "${dpatn} >= ${dpn}" then "jump SELF break"
#jump SELF loop
#label break
run ${rneq}
write_restart restart.tem300.deposit
undump 1
unfix 7
shell cd ..
clear
next tp
jump SELF loop
clear
next dag
jump SELF loop
clear
next dae
jump SELF loop
clear
next numvl
jump SELF loop
clear
#next dpatomnum
#jump SELF loop
#clear
print "All done"
简化版本的input，去掉变量，循环等
# exsample surface deposition script for atoms with fixed layer by xuegang emal xuegangzhu@qq.com
# --------------- INITIALIZATION ------------------
units metal
dimension 3
atom_style atomic
boundary p p p
# ------------------ ATOM DEFINITION -------------------
lattice hcp 2.2856
read_data /home/zxg/BeCu/STRU/Be/lmp_file/Be128_surface.lmp
region bound block INF INF INF INF 0 0.6
region contemp block INF INF INF INF 0.6 1.6
region reltemp block INF INF INF INF 1.6 16.6
region substrate union 3 bound contemp reltemp
group bound region bound
group contemp region contemp
group reltemp region reltemp
group substrate region substrate
group addatoms type 1
pair_style deepmd /home/zxg/BeCu/dpgennew/dp_potential/inter09/000/frozen_model.pb
pair_coeff * *
mass 1 9.012182
mass 2 63.55
#---------------------------Settings-equilibrium-------------
velocity all create 250 28459
timestep 0.001
thermo_style custom step elapsed atoms temp press ke pe etotal
thermo 100
thermo_modify lost ignore flush yes
velocity bound set 0.0 0.0 0.0
fix 1 bound setforce 0.0 0.0 0.0
fix 2 reltemp nve
fix 3 contemp npt temp 250 250 0.01 iso 0.0 0.0 0.1
shell mkdir Be_equlibrum
shell cd Be_equlibrum
dump 1 all custom 100 Be_mini.* id type x y z fx fy fz vx vy vz
min_style cg
minimize 1e-25 1e-25 5000 10000
undump 1
dump 1 all custom 200 Be_equlibrum.* id type x y z fx fy fz vx vy vz
run 200000
undump 1
shell cd ..
write_restart restart.temp250
#---------------------------deposit----------------------------
lattice none 1.0
fix 5 addatoms nve
run 0
shell mkdir Be_deposite
shell cd Be_deposite
region deposit1 block 2 6 2 6 40 41
fix dp1 addatoms deposit 2 1 500 12345 region deposit1 near 0.5 vz -1 -1 vy -1 -1
dump 1 all custom 100 Be_dp_growth.* id type x y z fx fy fz vx vy vz
run 10000000
undump 1
shell cd ..
unfix dp1
dump 1 all custom 100 Be_final.* id type x y z fx fy fz vx vy vz
run 200000
undump 1
print "All done"
结构文件，基底模型
结构文件准备
将Be的hcp晶体构型的LAMMPS文件进行修改，把z轴的最高值由16.6手动增加到46.6（相当于手动添加了真空层）
用ovitio打开可看到图片形式
运行LAMMPS
激活conda环境然后用dpmd版本的lmp运行
conda activate deepmd
lmp -in in.Be_dp_deposit
结果分析
运行完成后生成了对应的文件和文件夹如下
(deepmd) [root@87_gpu grwoth]# tree
.
├── Be_deposite
│ ├── Be_dp_growth.2100
│ ├── Be_dp_growth.2200
│ ├── Be_dp_growth.2300
│ ├── Be_dp_growth.2400
│ ├── Be_dp_growth.2500
│ ├── Be_dp_growth.2600
│ ├── Be_dp_growth.2700
│ ├── Be_dp_growth.2800
│ ├── Be_dp_growth.2900
│ └── Be_dp_growth.3000
├── Be_equlibrum
│ ├── Be_equlibrum.1000
│ ├── Be_equlibrum.1200
│ ├── Be_equlibrum.1400
│ ├── Be_equlibrum.1600
│ ├── Be_equlibrum.1800
│ ├── Be_equlibrum.200
│ ├── Be_equlibrum.2000
│ ├── Be_equlibrum.400
│ ├── Be_equlibrum.600
│ ├── Be_equlibrum.800
│ ├── Be_mini.0
│ └── Be_mini.26
├── Be_final.3100
├── Be_final.3200
├── in.Be_dp_deposit
├── in.Mg_deposit_9atom
├── log.lammps
└── restart.temp250
2 directories, 28 files
其中平衡结构在equlibrum文件夹中，生长结构在deposite文件夹中。
用ovitio对deposite文件夹下的LAMMPS输出进行薄膜生长可视化，以及其他分析等，可参考我以前发表的文章，分析晶界，表面等内容。
Symmetric tilt grain boundary evolution during the growth of copper thin films: Molecular dynamics simulation | Xuegang Zhu，Xinlu Cheng | 论文 | Physica B: Physics of Condensed Matter | 2019.11 |
由于我是访问之后才接触python因此后续薄膜生长的python脚本待详细做薄膜生长时再补充。
注意：势函数不准问题 由于势函数拟合时并无表面，且只有平衡结构，并不适用于薄膜生长模拟，且在模拟过程中出现模拟原子散掉模拟盒子增大等势函数不准导致的情况出现，因此需要增加数据集提高势函数的准确性和适用性。
作者：朱雪刚 邮箱:xuegangzhu@qq.com； 工作单位：石家庄学院 理学院/北京科学智能研究院（AISI）访问学者2023.07-2024.09，访问导师北京大学陈默涵; 徐张满仓 邮箱: xuzhangmancang@dp.tech
