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1、# MD simulation of Ar thermal conductivity # Initialization units lj dimension 3 newton on boundary p p p atom_style atomic neighbor 0.3 bin neigh_modify check yes lattice fcc 0.844 region box block -4 4 -4 4 -4 4 units lattice create_box 1 box create_atoms 1 box mass 1 1.0 velocity all create 0.71
2、458127641 mom yes rot yes dist gaussian units box # LJ potential * pair_style lj/cut 2.8 pair_coeff 1 1 1.0 1.0 # LJ parameters for Ar-Ar fix temp all temp/berendsen 0.71 0.71 0.000466 fix nve all nve thermo_style custom step temp etotal vol thermo_modify lost warn thermo 100 # Run timestep 0.000466
3、 run 200000 reset_timestep 0 # - Flux calculation in nve - compute myKE all ke/atom compute myPE all pe/atom compute myStress all stress/atom virial variable factor_ac equal 1.0 variable factor_tc equal 1.3806504e-23*sqrt(1.67e-21/6.633e-26)/3.405e-102 compute jflux all heat/flux myKE myPE myStress
4、compute tc all tc c_thermo_temp c_jflux v_factor_ac v_factor_tc iso first 10000 900000 100000 fix tc_out all ave/time 1 1 1 c_tc file tc_time.dat thermo_style custom step temp restart 100000 restart.* run 1000000 2. 用 fix thermal/conductivity command 得到温度梯度，进而得到热导名师资料总结 - - -精品资料欢迎下载 - - - - - - - -
5、 - - - - - - - - - - 名师精心整理 - - - - - - - 第 1 页，共 4 页 - - - - - - - - - 率(NEMD 方法 )# MD simulation of Ar thermal conductivity # Initialization units lj dimension 3 newton on boundary p p p atom_style atomic neighbor 0.3 bin neigh_modify check yes lattice fcc 0.844 region box block -4 4 -4 4 -4 4 uni
6、ts lattice create_box 1 box create_atoms 1 box region up1 block INF INF INF INF -0.5 -0.25 units lattice region up2 block INF INF INF INF 0.5 0.75 units lattice region up union 2 up1 up2 region down1 block INF INF INF INF -3.5 -3.25 units lattice region down2 block INF INF INF INF 3.5 3.75 units lat
7、tice region down union 2 down1 down2 mass 1 1.0 velocity all create 0.71 458127641 mom yes rot yes dist gaussian units box # Tersoff potential * pair_style lj/cut 2.8 pair_coeff 1 1 1.0 1.0 # LJ parameters for Ar-Ar fix temp all temp/berendsen 0.71 0.71 0.0466 fix nve all nve compute ke all ke/atom
8、variable temp atom c_ke/(1.5*1.0) fix temp_profile all ave/spatial 1 100000 100000 z lower 0.25 v_temp file temp.profile units lattice compute up_temp all temp/region up compute down_temp all temp/region down variable delta_temp equal c_up_temp-c_down_temp fix delta_out all ave/time 1 100000 100000
9、v_delta_temp file delta_temp.dat thermo_style custom step temp etotal vol thermo_modify lost warn thermo 100 # Run timestep 0.000466 名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 2 页，共 4 页 - - - - - - - - - run 100001 unfix temp fix heat_swap all thermal/conductivit
10、y 10 z 32 fix e_exchange all ave/time 10 10000 100000 f_heat_swap file e_exchange.dat variable thermal_conductivity equal f_e_exchange/(0.000466*10.0*4.0*f_delta_out)*1.3806504e-23/3.405e-10/3.405e-10*sqrt(1.67e-21/6.633e-26)*6.0/8.0 # 以上 variable 命令需要特别注意，因为我所模拟的系统，盒子边长Lx=Ly=Lz ，热导率计算公式经过推导变成为e_exc
11、hange/(4.0*t*L*delta_T)，# 为了不在in 文件里给L 赋值，我修改了fix_thermal_conductivity.cpp文件 (见附件 )，将e_exchange 修 改 成 了e_exchange += force-mvv2e * (all0.value - all1.value) / (domain-zprd); 同时在 end_of_step() 里添加了一句“ e_exchange = 0.0;“,详见附件中的fix_thermal_conductivity.cpp ， 这样所得的e_exchange曲线基本上是一条水平曲线，而不是用原来的fix therm
12、al/conductivity command所得到的斜向上的曲线，请注意！ ！# 所以才出现以上variable 的表达式。# 请看明白后再做计算，免得算出错误的结果！ ！fix thermal_conductivity_out all ave/time 100000 1 100000 v_thermal_conductivity file thermal_conductivity.dat # Run run 10000000 3. 用 fix heat command建立温度梯度， 进而得到热导率 （NEMD 方法）# MD simulation of Ar thermal conduct
13、ivity # Initialization units lj dimension 3 newton on boundary p p p atom_style atomic neighbor 0.3 bin neigh_modify check yes lattice fcc 0.844 region box block -4 4 -4 4 -4 4 units lattice create_box 1 box create_atoms 1 box region up1 block INF INF INF INF -0.5 -0.25 units lattice region up2 bloc
14、k INF INF INF INF 0.5 0.75 units lattice region up union 2 up1 up2 名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 3 页，共 4 页 - - - - - - - - - region down1 block INF INF INF INF -3.5 -3.25 units lattice region down2 block INF INF INF INF 3.5 3.75 units lattice region
15、down union 2 down1 down2 region hot block INF INF INF INF 0.0 0.25 units lattice group hot region hot region cold block INF INF INF INF -4.0 -3.75 units lattice group cold region cold mass 1 1.0 #mass0 6.633e-26 #epsilon0 1.67e-21 #sigma0 3.405e-10 velocity all create 0.71 458127641 mom yes rot yes
16、dist gaussian units box # Tersoff potential * pair_style lj/cut 2.8 pair_coeff 1 1 1.0 1.0 # LJ parameters for Ar-Ar fix temp all temp/berendsen 0.71 0.71 0.0466 fix nve all nve compute ke all ke/atom variable temp atom c_ke/(1.5*1.0) fix temp_profile all ave/spatial 1 100000 100000 z lower 0.25 v_t
17、emp file temp.profile units lattice compute up_temp all temp/region up compute down_temp all temp/region down variable delta_temp equal c_up_temp-c_down_temp fix delta_out all ave/time 1 100000 100000 v_delta_temp file delta_temp.dat thermo_style custom step temp etotal vol thermo_modify lost warn t
18、hermo 100 # Run timestep 0.000466 run 100001 unfix temp fix hot all heat 1 50 region hot fix cold all heat 1 -50 region cold variable thermal_conductivity equal 50.0*0.5*1.67e-21/3.405e-10/sqrt(6.633e-26/1.67e-21)/(4.0*8.0*8.0*8.0/0.844)(1.0/3.0)*3.405e-10*2.0*f_delta_out*1.67e-21/1.3806504e-23)*6.0/8.0 fix thermal_conductivity_out all ave/time 100000 1 100000 v_thermal_conductivity file thermal_conductivity.dat # Run run 10000000 名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 4 页，共 4 页 - - - - - - - - -