Use the fix deposit command to deposit a mixed system of atoms and molecules, where the atoms do not move

shuang · October 5, 2024, 11:35am

Here is my in-file：
restart 100000 restart..equil
#初始设置
dimension 3
units metal
atom_style atomic
boundary p p f
timestep 0.001
#区域划分
read_data CdTe-GaAs.data extra/atom/types 3
change_box all z final 0 5064 units box
read_data 1.data extra/atom/types 3
mass 1 69.72 # Cd
mass 2 74.92 # Te
mass 3 127.6 # Te
mass 4 127.6 # Te
mass 5 112.411 # Cd
region box block INF INF INF INF INF 65 units box
region bot block INF INF INF INF INF 13 units box
region top block INF INF INF INF 59 65 units box
region empty block INF INF INF INF 65.5 INF units box
group empty region empty
group box region box
group bot region bot
group top region top
group mobile1 subtract box bot
group mobile subtract mobile1 top
group mobile3 subtract box top
molecule Te2 Te2-1.data toff 2
group addatoms_Te type 3 4
group addatoms_Cd type 5
group addatoms union addatoms_Te addatoms_Cd
#力场设置
pair_style bop save
pair_coeff * * /share/home/e6a000187/test/CdTe-CdTe/CdTe.bop.table Cd Te Te Te Cd
comm_modify cutoff 15.7
#近邻列表参数设置
neighbor 0.3 bin
neigh_modify delay 1 check yes
neigh_modify exclude group bot bot check no
#neigh_modify exclude group mobile mobile check no
#neigh_modify exclude group empty top
#neigh_modify exclude group mobile top
#轨迹文件输出设置
#计算单个原子的动能
compute Ke_atom all ke/atom
#计算单个原子的势能
compute Pe_atom all pe/atom
#求和得到总能量
variable E_total atom c_Ke_atom+c_Pe_atom
dump 1 all custom 100 dump.sputter. id type mass x y z vx vy vz c_Ke_atom c_Pe_atom v_E_total
dump_modify 1 element Cd Te Te Te Cd
#屏幕输出信息设置
compute mobile1 mobile1 temp
compute mobile mobile temp
compute top top temp
compute bot bot temp
thermo 10
thermo_style custom step pe ke etotal c_mobile1 c_mobile c_top c_bot temp vol press lx ly lz
#固定底部原子，防止在沉积过程中移动
velocity bot set 0 0 0
fix s1 bot setforce 0 0 0
fix s2 mobile1 spring/self 10.0
#设置刚体
velocity mobile1 create 900 39849
#nvt弛豫
fix 11 addatoms_Cd nve
fix 12 addatoms_Te nve
fix 21 mobile1 langevin 900 900 0.1 98598
fix 31 mobile1 nve
run 50000
write_data final.data
#沉积过程
region sput block 1 79 1 90 65 75 units box
fix top1 all wall/reflect zhi 5000.0 units box
fix 1 addatoms_Cd deposit 1 5 2000 95485 region sput global 30 30 near 0.5 vz -3 -4 units box
run 2000
fix 3 addatoms_Cd deposit 1 5 2000 95485 region sput global 3 4 near 0.5 vz -3 -4 units box
run 2000
fix 2 addatoms_Te deposit 1 0 2000 12345 region sput global 3 4 near 0.5 vz -3 -4 mol Te2 units box
run 2000
variable i loop 638 # 循环10次
label loop
fix 30 addatoms_Cd deposit 1 5 2000 95485 region sput global 3 4 near 0.5 vz -3 -4 units box
run 2000
fix 100 addatoms_Cd deposit 1 5 2000 95485 region sput global 3 4 near 0.5 vz -3 -4 units box
run 2000
fix 20 addatoms_Te deposit 1 0 2000 12345 region sput global 3 4 near 0.5 vz -3 -4 mol Te2 units box
run 2000
next i
jump SELF loop
fix 301 addatoms_Cd deposit 1 5 2000 95485 region sput global 3 4 near 0.5 vz -3 -4 units box
run 2000
fix 101 addatoms_Cd deposit 1 5 2000 95485 region sput global 3 4 near 0.5 vz -3 -4 units box
run 2000
fix 201 addatoms_Te deposit 1 0 2000 12345 region sput global 3 4 near 0.5 vz -3 -4 mol Te2 units box
run 9562000
I’ve tried different ways to control the temperature. For example, NVT and NVE, due to the special system, NPT cannot be used, and no matter what the method is, the sedimentary atoms cannot move, which makes me confused.

simongravelle · October 5, 2024, 11:39am

Please take a look at the guidelines here, your post is impossible to read.

shuang · October 5, 2024, 12:11pm

Sorry, I don’t see a solution.
Here is my in-file：
restart 100000 restart..equil
#初始设置
dimension 3
units metal
atom_style atomic
boundary p p f
timestep 0.001
#区域划分
read_data CdTe-GaAs.data extra/atom/types 3
change_box all z final 0 5064 units box
read_data 1.data extra/atom/types 3
mass 1 69.72 # Cd
mass 2 74.92 # Te
mass 3 127.6 # Te
mass 4 127.6 # Te
mass 5 112.411 # Cd
region box block INF INF INF INF INF 65 units box
region bot block INF INF INF INF INF 13 units box
region top block INF INF INF INF 59 65 units box
region empty block INF INF INF INF 65.5 INF units box
group empty region empty
group box region box
group bot region bot
group top region top
group mobile1 subtract box bot
group mobile subtract mobile1 top
group mobile3 subtract box top
molecule Te2 Te2-1.data toff 2
group addatoms_Te type 3 4
group addatoms_Cd type 5
group addatoms union addatoms_Te addatoms_Cd
#力场设置
pair_style bop save
pair_coeff * * /share/home/e6a000187/test/CdTe-CdTe/CdTe.bop.table Cd Te Te Te Cd
comm_modify cutoff 15.7
#近邻列表参数设置
neighbor 0.3 bin
neigh_modify delay 1 check yes
neigh_modify exclude group bot bot check no
#neigh_modify exclude group mobile mobile check no
#neigh_modify exclude group empty top
#neigh_modify exclude group mobile top
#轨迹文件输出设置
#计算单个原子的动能
compute Ke_atom all ke/atom
#计算单个原子的势能
compute Pe_atom all pe/atom
#求和得到总能量
variable E_total atom c_Ke_atom+c_Pe_atom
dump 1 all custom 100 dump.sputter. id type mass x y z vx vy vz c_Ke_atom c_Pe_atom v_E_total
dump_modify 1 element Cd Te Te Te Cd
#屏幕输出信息设置
compute mobile1 mobile1 temp
compute mobile mobile temp
compute top top temp
compute bot bot temp
thermo 10
thermo_style custom step pe ke etotal c_mobile1 c_mobile c_top c_bot temp vol press lx ly lz
#固定底部原子，防止在沉积过程中移动
velocity bot set 0 0 0
fix s1 bot setforce 0 0 0
fix s2 mobile1 spring/self 10.0
#设置刚体
velocity mobile1 create 900 39849
#nvt弛豫
fix 11 addatoms_Cd nve
fix 12 addatoms_Te nve
fix 21 mobile1 langevin 900 900 0.1 98598
fix 31 mobile1 nve
run 50000
write_data final.data
#沉积过程
region sput block 1 79 1 90 65 75 units box
fix top1 all wall/reflect zhi 5000.0 units box
fix 1 addatoms_Cd deposit 1 5 2000 95485 region sput global 30 30 near 0.5 vz -3 -4 units box
run 2000
fix 3 addatoms_Cd deposit 1 5 2000 95485 region sput global 3 4 near 0.5 vz -3 -4 units box
run 2000
fix 2 addatoms_Te deposit 1 0 2000 12345 region sput global 3 4 near 0.5 vz -3 -4 mol Te2 units box
run 2000
variable i loop 638 # 循环10次
label loop
fix 30 addatoms_Cd deposit 1 5 2000 95485 region sput global 3 4 near 0.5 vz -3 -4 units box
run 2000
fix 100 addatoms_Cd deposit 1 5 2000 95485 region sput global 3 4 near 0.5 vz -3 -4 units box
run 2000
fix 20 addatoms_Te deposit 1 0 2000 12345 region sput global 3 4 near 0.5 vz -3 -4 mol Te2 units box
run 2000
next i
jump SELF loop
fix 301 addatoms_Cd deposit 1 5 2000 95485 region sput global 3 4 near 0.5 vz -3 -4 units box
run 2000
fix 101 addatoms_Cd deposit 1 5 2000 95485 region sput global 3 4 near 0.5 vz -3 -4 units box
run 2000
fix 201 addatoms_Te deposit 1 0 2000 12345 region sput global 3 4 near 0.5 vz -3 -4 mol Te2 units box
run 9562000
I’ve tried different ways to control the temperature. For example, NVT and NVE, due to the special system, NPT cannot be used, and no matter what the method is, the sedimentary atoms cannot move, which makes me confused.

srtee · October 6, 2024, 9:51am

It is not obvious:

what the “sedimentary atoms” are
what makes your “system” “special”
what you expect your simulation to do
and what your simulation is actually doing instead.

Without that information, we cannot help you.