Dear lammps developers and users;
I recently encountered a problem. I read the simulation of vacancy formation energy and migration energy in “influence of compositional complexity on species diffusion behavior in high entropy solid solution alloys” in this article, and carefully read the histogram of vacancy formation energy of alloys in this article. I wrote an in file for calculation of vacancy formation energy of each element as follows:
##定义变量##
variable a equal 2.0 ##定义原子模型截断半径
##模拟环境初始化##
units metal
atom_style atomic
boundary p p p
neighbor ${a} bin
neigh_modify every 1 delay 0 check yes
##建立单晶原子模型##
lattice fcc 3.56
region box block 0 30 0 30 0 30 units box
create_box 3 box
create_atoms 1 box
####将Ni原子进行替换##
set type 1 type/subset 2 818 666 ##替换成Cr
set type 1 type/subset 3 818 666 ##替换成Co
##定义相互作用势##
pair_style eam/alloy
pair_coeff * * NiCoCr.lammps.eam Ni Cr Co
##对原子进行分组
group Ni-1 type 1
group Cr-2 type 3
group Co-3 type 3
##计算各元素的总势能
compute 1 Ni-1 pe/atom
compute pe1 Ni-1 reduce sum c_1
compute 2 Cr-2 pe/atom
compute pe2 Cr-2 reduce sum c_2
compute 3 Co-3 pe/atom
compute pe3 Co-3 reduce sum c_3
#输出原子热力学信息和位置
thermo 100
thermo_style custom step lx ly lz c_pe1 c_pe2 c_pe3 temp vol dt time
###结构优化得到E_perfect能量
reset_timestep 0
minimize 1.0e-12 1.0e-12 10000 10000
###记录第一次优化后的能量和总原子数目
variable E1 equal c_pe1
variable E2 equal c_pe2
variable E3 equal c_pe3
variable E1_perfect equal ${E1}
variable E2_perfect equal ${E2}
variable E3_perfect equal ${E3}
variable N equal count(all)
variable N0 equal ${N}
##对原子模型进行删除形成缺陷
region 2 sphere 10.0 10.0 10.0 0.1 side in
delete_atoms region 2
write_data NiCrCo.data
##对删除原子之后进行分组
group Ni-4 type 1
group Cr-5 type 3
group Co-6 type 3
##计算各元素的总势能
compute 4 Ni-4 pe/atom
compute pe4 Ni-4 reduce sum c_4
compute 5 Cr-5 pe/atom
compute pe5 Cr-5 reduce sum c_5
compute 6 Co-6 pe/atom
compute pe6 Co-6 reduce sum c_6
##结构优化得到E_defect的能iang
reset_timestep 0
thermo 100
thermo_style custom step lx ly lz c_pe4 c_pe5 c_pe6 temp vol dt time
minimize 1.0e-12 1.0e-12 10000 10000
###记录第二次优化的能量值
variable E4_defect equal c_pe4
variable E5_defect equal c_pe5
variable E6_defect equal c_pe6
###通过公式分别计算元素Ni、Cr和Co的空位形成能
variable Ev_Ni equal ((1/${N0})*${E4_defect}-((${N0}-1)/${N0})*${E1_perfect})
variable Ev_Cr equal ((1/${N0})*${E5_defect}-((${N0}-1)/${N0})*${E2_perfect})
variable Ev_Co equal ((1/${N0})*${E6_defect}-((${N0}-1)/${N0})*${E3_perfect})
###导出直方图
fix 8 all ave/histo/weight 100 5 1000 -5 5 100 c_Ev_Ni mode vector file Ni.pe
fix 9 all ave/histo/weight 100 5 1000 -5 5 100 c_Ev_Cri mode vector file Cr.pe
fix 10 all ave/histo/weight 100 5 1000 -5 5 100 c_Ev_Co mode vector file Co.pe
timestep 0.001
run 0
I can’t define the calculation formula of the ordinate of this figure in the in file.The figure is as follows:
Uploading: image.png…
I wonder if any of you know the method of this drawing or the specific calculation formula for changing the ordinate of the drawing. I hope you can get your help!
xue bao shuai