#==========模型基本设置==========
units           metal
dimension       3
newton          on
boundary        p p p
atom_style      atomic

neighbor        2.0 bin
neigh_modify    delay 0 every 1 check yes

variable        dt equal 0.0005
timestep        ${dt}

#==========读取文件==========
read_data       2.dat
mass            1 95.94
mass            2 32.066



pair_style      sw
pair_coeff      * * mos2.sw  Mo S

#==========分块参数==========
variable X1      equal xlo
variable X2      equal xhi
variable Nlay    equal 50
variable Dscale  equal 1/${Nlay}
variable Len     equal ${X2}-${X1}
variable Dz      equal ${Len}/${Nlay}


#==========修复：分离固定端和热源==========
# 左侧：固定端(0-2*Dz) + 热源(2*Dz-10*Dz)
variable BL1 equal ${X1}+0*${Dz}
variable BL2 equal ${X1}+2*${Dz}       # 固定端范围

variable HL1 equal ${X1}+2*${Dz}       # 热源起始
variable HL2 equal ${X1}+10*${Dz}      # 热源结束

# 右侧：冷源(40*Dz-48*Dz) + 固定端(48*Dz-50*Dz)
variable CR1 equal ${X2}-10*${Dz}      # 冷源起始
variable CR2 equal ${X2}-2*${Dz}       # 冷源结束

variable BR1 equal ${X2}-2*${Dz}
variable BR2 equal ${X2}+0*${Dz}       # 固定端范围


#==========区域定义==========
region fixed_L block INF ${BL2} INF INF INF INF units box
region fixed_R block ${BR1} INF INF INF INF INF units box

group fixed_L region fixed_L
group fixed_R region fixed_R

# 热源和冷源只在活动区域
region Hot  block ${HL1} ${HL2} INF INF INF INF units box
region Cold block ${CR1} ${CR2} INF INF INF INF units box

group Hot  region Hot
group Cold region Cold

group Mo  type 1
group S   type 2


group mobile subtract all fixed_L fixed_R



#==========能量最小化==========
thermo          1000
thermo_style    custom step temp pxx pyy pzz press vol

min_style       cg
minimize        1.0e-8 1.0e-8 10000 1000000
reset_timestep  0

#==========初始速度==========
velocity all create 300 898758 mom yes rot yes dist gaussian

#==========NVT弛豫==========
fix 1 all nvt temp 300 300 0.1
dump 1 all custom 2000 nvt.xyz id type x y z

thermo 2000
thermo_style custom step temp pe ke etotal vol pxx pyy pzz press

run 200000

unfix 1
undump 1
reset_timestep 0


#==========固定两端==========
velocity fixed_L set 0 0 0
velocity fixed_R set 0 0 0

fix fixL fixed_L setforce 0 0 0
fix fixR fixed_R setforce 0 0 0

#==========积分（只对活动原子）==========
fix 5 all nve

#==========冷热源（Langevin恒温器）==========

fix 3 Hot  langevin 325 325 0.1 14565 tally yes

fix 4 Cold langevin 275 275 0.1 16576 tally yes

#==========空间分块定义==========
compute chunk_T all chunk/atom bin/1d x lower ${Dscale} units reduced

#==========能量统计==========
variable Time equal step
variable EL equal f_3
variable ER equal f_4

fix E_out all print 2000 "${Time} ${EL} ${ER}" file Ener_equ.dat title "Time E1 E2" screen no

#==========第一阶段：建立稳态==========

thermo 2000
thermo_style custom step temp ke pe etotal press vol

run 2000000

reset_timestep 0

compute ke_atom all ke/atom
variable temp_atom atom c_ke_atom/1.5/8.625e-5

#==========第二阶段：统计==========

fix ave_T all ave/chunk 10 500 1500000 chunk_T temp file temp_profile.dat norm sample

#==========输出文件==========
dump 1 all custom 50000 nemd_stable.xyz id type x y z v_temp_atom

dump 2 all custom 200 voutput_all.lammpstrj id type vx vy vz
dump_modify 2 sort id

dump 3 S custom 200 voutput_S1.lammpstrj id type vx vy vz
dump_modify 3 sort id

dump 4 Mo custom 200 voutput_Mo1.lammpstrj id type vx vy vz
dump_modify 4 sort id




#==========热力学输出==========
thermo 2000
thermo_style custom step temp ke pe etotal press vol

run 2000000