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LAMMPS计算Cu体积模量
《计算材料学》组队共读
《计算材料学》组队共读
1310819006@qq.com
发布于 2024-03-15
推荐镜像 :Basic Image:ubuntu:22.04-py3.10-cuda12.1
推荐机型 :c2_m4_cpu
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写入Cu体积模量计算脚本

代码
文本
[39]
%%writefile in.Cu_lj_module
units metal
boundary p p p
atom_style atomic

variable i loop 40
variable x equal 3.40+0.01*$i
lattice fcc $x
region box block 0 1 0 1 0 1
create_box 1 box
create_atoms 1 box
mass 1 64

#使用LJ势函数
pair_style lj/cut 10.0
pair_coeff 1 1 0.40933 2.338 #Σ和伊布西龙 使用金属单位

variable v equal ($x)^3
variable n equal count(all)
variable P equal pe

#######运行########
run 0

print "Cohesive Energy of Cu v = $v x = $x E = $P"

clear
next i
jump SELF #重新开始运行程序
Overwriting in.Cu_lj_module
代码
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[40]
%%capture #capture命令禁止屏幕输出
!OMP_NUM_THREADS=2 lmp -i in.Cu_lj_module
代码
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[41]
!vi log.lammps
7t;4;2m="log.lammps" 3284L, 112692B▽  Pzz\           t;c]10;?]11;?LAMMPS (2 Aug 2023)
  using 2 OpenMP thread(s) per MPI taskLoaded 1 plugins from /opt/deepmd-kit-3.0.0/lib/deepmd_lmpunits metal
boundary p p p
atom_style atomic

variable i loop 40
variable x equal 3.40+0.01*$i
variable x equal 3.40+0.01*1
lattice fcc $x
lattice fcc 3.41
Lattice spacing in x,y,z = 3.41 3.41 3.41
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (3.41 3.41 3.41)
  1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4 atoms
  using lattice units in orthogonal box = (0 0 0) to (3.41 3.41 3.41)
  create_atoms CPU = 0.001 seconds
mass 1 641,1TopType  :qa  and press <Enter> to exit Vim1,1Top
代码
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[42]
!grep "Cohesive" log.lammps
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 39.651821 x = 3.41 E = -11.6743276227989
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 40.001688 x = 3.42 E = -11.9405476050061
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 40.353607 x = 3.43 E = -12.1595640975458
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 40.707584 x = 3.44 E = -12.3842526979336
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 41.063625 x = 3.45 E = -12.5895372366665
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 41.421736 x = 3.46 E = -12.7764125325894
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 41.781923 x = 3.47 E = -12.9458260014581
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 42.144192 x = 3.48 E = -13.0986799313477
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 42.508549 x = 3.49 E = -13.2358336452587
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 42.875 x = 3.5 E = -13.3581055567528
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 43.243551 x = 3.51 E = -13.4662751241234
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 43.614208 x = 3.52 E = -13.5610847083218
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 43.986977 x = 3.53 E = -13.6432413395693
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 44.361864 x = 3.54 E = -13.7070496808943
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 44.738875 x = 3.55 E = -13.7659953596674
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 45.118016 x = 3.56 E = -13.8142114984977
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 45.499293 x = 3.57 E = -13.852279849293
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 45.882712 x = 3.58 E = -13.8807544504762
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 46.268279 x = 3.59 E = -13.9001629355792
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 46.656 x = 3.6 E = -13.9110077784364
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 47.045881 x = 3.61 E = -13.9137674781707
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 47.437928 x = 3.62 E = -13.9088976869966
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 47.832147 x = 3.63 E = -13.8968322836988
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 48.228544 x = 3.64 E = -13.8779843955076
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 48.627125 x = 3.65 E = -13.8527473709409
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 49.027896 x = 3.66 E = -13.7961834075309
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 49.430863 x = 3.67 E = -13.759684579032
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 49.836032 x = 3.68 E = -13.7178592687278
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 50.243409 x = 3.69 E = -13.6710307078911
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 50.653 x = 3.7 E = -13.6195065548619
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 51.064811 x = 3.71 E = -13.5635796208348
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 51.478848 x = 3.72 E = -13.5035285612586
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 51.895117 x = 3.73 E = -13.4396185345301
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 52.313624 x = 3.74 E = -13.3721018295858
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 52.734375 x = 3.75 E = -13.3012184639042
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 53.157376 x = 3.76 E = -13.2271967533648
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 53.582633 x = 3.77 E = -13.1502538553272
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 54.010152 x = 3.78 E = -13.0705962862321
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 54.439939 x = 3.79 E = -12.9884204149546
print "Cohesive  Energy of Cu v = $v x = $x E = $P"
Cohesive  Energy of Cu v = 54.872 x = 3.8 E = -12.9039129330838
代码
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[45]
import re
data = []
pattern = re.compile(r"Cohesive Energy of Cu v = ([\d\.-]+)\s+x = ([\d\.-]+)+\s+E = ([\d\.-]+)")

with open("./log.lammps", "r") as file:
for line in file:
match = pattern.search(line)
if match:
v_value = float(match.group(1))
x_value = float(match.group(2))
E_value = float(match.group(3))
data.append((v_value,x_value, E_value))
len(data)
40
代码
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[46]
with open ("Cu_fcc.csv","w") as f:
f.write("v, x, E\n")
for v,x,E in data:
f.write(f"{v},{x},{E}\n")
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
file_name = "Cu_fcc.csv"
data_frame = pd.read_csv(file_name)
data_frame
v x E
0 39.651821 3.41 -11.674328
1 40.001688 3.42 -11.940548
2 40.353607 3.43 -12.159564
3 40.707584 3.44 -12.384253
4 41.063625 3.45 -12.589537
5 41.421736 3.46 -12.776413
6 41.781923 3.47 -12.945826
7 42.144192 3.48 -13.098680
8 42.508549 3.49 -13.235834
9 42.875000 3.50 -13.358106
10 43.243551 3.51 -13.466275
11 43.614208 3.52 -13.561085
12 43.986977 3.53 -13.643241
13 44.361864 3.54 -13.707050
14 44.738875 3.55 -13.765995
15 45.118016 3.56 -13.814211
16 45.499293 3.57 -13.852280
17 45.882712 3.58 -13.880754
18 46.268279 3.59 -13.900163
19 46.656000 3.60 -13.911008
20 47.045881 3.61 -13.913767
21 47.437928 3.62 -13.908898
22 47.832147 3.63 -13.896832
23 48.228544 3.64 -13.877984
24 48.627125 3.65 -13.852747
25 49.027896 3.66 -13.796183
26 49.430863 3.67 -13.759685
27 49.836032 3.68 -13.717859
28 50.243409 3.69 -13.671031
29 50.653000 3.70 -13.619507
30 51.064811 3.71 -13.563580
31 51.478848 3.72 -13.503529
32 51.895117 3.73 -13.439619
33 52.313624 3.74 -13.372102
34 52.734375 3.75 -13.301218
35 53.157376 3.76 -13.227197
36 53.582633 3.77 -13.150254
37 54.010152 3.78 -13.070596
38 54.439939 3.79 -12.988420
39 54.872000 3.80 -12.903913
代码
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[55]
lat = np.array(data_frame['v'])
ene = np.array(data_frame[' E'])

a, b, c = np.polyfit(lat, ene, 2)
mesh = np.linspace(np.min(lat),np.max(lat),1000)

opt_lat = -b/(2*a)

Emin = np.polyval([a,b,c], opt_lat)
print("a,b,c=", a, b, c )
print("Emin = ", Emin, "opt_lat = ", opt_lat)

plt.scatter(lat, ene, 10)
plt.plot(mesh, a*mesh**2+b*mesh +c)
plt.xlabel("volume")
plt.ylabel("Energy")
plt.show()
a,b,c= 0.027859136511323872 -2.677008042125913 50.35779796262389
Emin =  -13.951195019749292 opt_lat =  48.04542382420561
代码
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二次多项式拟合效果较差选用BM方程进行拟合

代码
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[63]
v = np.array(data_frame['v'])
e = np.array(data_frame[' E'])
a, b, c = np.polyfit(v, e, 2)
v0 = -b/(2*a)
b0 = 2*a*v0
e0 = a*v0**2 +b*v0+c
bp =3.5
x0 = [e0, b0, bp, v0]

def Murnaghan(parameters ,vol):
E0 = parameters[0]
B0 = parameters[1]
BP = parameters[2]
V0 = parameters[3]
E = E0+ B0*vol/BP*(((v0/vol)**BP)/(BP-1)+1)-V0*B0/(BP-1.)
return E
def residual(pars, y, x):
err = y - Murnaghan(pars,x)
return err
from scipy.optimize import leastsq
murnpars, ier = leastsq(residual, x0, args=(e,v))
v_mesh = np.linspace(np.min(v),np.max(v),1000)

#输出结果
print("Bulk Modulus :"+ str(murnpars[1]))

#print("Lattice constant: "+ murnpars[3]**(1/3))
plt.scatter(v, e, 10)

plt.plot(v_mesh, Murnaghan(murnpars, v_mesh))

plt.ylabel("Energy")
plt.xlabel("Volume")
plt.show()
Bulk Modulus :2.43855493304413
代码
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[64]
%%bash
## 这行命令可以下载 lammps安装包中，potentials文件夹下的所有势函数，用于后续eam势函数的导入
wget https://bohrium-api.dp.tech/ds-dl/lammps-potentials-8snt-v1.zip
unzip -o ./lammps-potentials-8snt-v1.zip
已隐藏输出
代码
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居然和二次函数一样

代码
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[65]
%%bash

## 查看 potentials 文件夹中自带的势函数
cd potentials && ls
已隐藏输出
代码
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[ ]

代码
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《计算材料学》组队共读
《计算材料学》组队共读
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