Python调用shell脚本命令的方法

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本文基于Python和shell脚本语法编写了根据CONTCAR/POSCAR文件批量计算键长的脚本。

Python调用shell脚本命令的方法：

  1. os.system
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    os.system("rm atom_* extract.sh")  # 删除以atom_开头的文件和extract.sh文件
    os.system("bash extract.sh")  # 执行无外参的extract.sh脚本文件
    os.system("bash extract.sh tonny")  # 执行extract.sh文件，并将tonny字符串传给extract.sh脚本
    os.system("python test.py tonny")  #执行test.py文件，并将tonny字符串传给test.py
  2. os.popen 可以将执行结果返回给一个对象
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    files = os.popen('bash -c "find -type f -name CONTCAR"')  # 列出当前目录下所有含有CONTCAR文件的文件路径，并返回files对象
    file_path = files.read().split()  # 读取files对象中的内容，并切割字符串
  3. subprocess库
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    cmd1 = "sed -n 6p " + CONTCAR + " > atom_names"
    subprocess.call(cmd1,shell=True)
    subprocess.run("rm atom_* vect",shell=True)  # delete temporary files
    # find folders containing CONTCAR file and save file path into a list
    files = subprocess.Popen('bash -c "find -type f -name CONTCAR"',stdout=subprocess.PIPE).stdout.read().decode(encoding="utf-8").split()
  4. envy模块

脚本内容

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#########################################################################################
#### usage:   python dist_in_CONTCAR.py Atom1 Atom2 [Atom3 [Atom4]]                  ####
#### example: python dist_in_CONTCAR.py Pt1 O1                                       ####
####          python dist_in_CONTCAR.py Pt1 O1 O2                                    ####
####          python dist_in_CONTCAR.py N1 Pt1 O1 O2                                 ####
#### The Atom Names are specified same with those Atom Names shown in VESTA software ####
#########################################################################################
import subprocess
import numpy as np
import sys


def dist(a,b):
    """ read coordinates of two points and return distance of two points"""
    """vector module -->  |A - B|"""
    # distance = np.sqrt(np.dot(a - b, a - b))
    distance = np.linalg.norm(a-b)
    return distance
    

def angle(a,b,c):
    """read coordinates of three points and return angle of <a_b_c"""
    """cos_AB = A * B / (|A| * |B|)"""
    cos_abc = np.dot(a-b, c-b) / (np.linalg.norm(a-b) * np.linalg.norm(c-b))
    angle_abc = np.arccos(cos_abc) * 180 / np.pi
    return angle_abc

    
def diheral_angle(a,b,c,d):
    """read coordinates of four points and return diheral angle of plane abc and bcd"""
    NormVect_abc = np.cross(b-a,c-a)  # NormalVector = A X B
    NormVect_bcd = np.cross(b-c,d-c)
    cosA = np.dot(NormVect_abc,NormVect_bcd) / (np.linalg.norm(NormVect_abc) * np.linalg.norm(NormVect_bcd))
    angle_A = np.arccos(cosA) * 180 / np.pi
    if angle_A > 90:
        return 180 - angle_A
    else:
        return angle_A


def file_process(CONTCAR):
    """read data from CONTCAR file and return the distance between ATOM1 and Atom2"""
    
    #1. use bash script to extract atom coordinate, atom name and cell parameter into temporary files
    cmd1 = "sed -n 6p " + CONTCAR + " > atom_names"
    cmd2 = "sed -n 7p " + CONTCAR + " > atom_nums"
    cmd3 = "sed -n 3,5p " + CONTCAR + " > vect"
    cmd4 = "sed 1,8d " + CONTCAR + " | grep -v E > atom_coors"
    subprocess.call(cmd1,shell=True)
    subprocess.call(cmd2,shell=True)
    subprocess.call(cmd3,shell=True)
    subprocess.call(cmd4,shell=True)
    
    #2. data process
    matrix_trans = np.loadtxt('vect')  # read cell parameters into an array
    atom_nums = np.loadtxt('atom_nums').astype(int)  # read atom nums into an array
    coor = np.loadtxt('atom_coors')  # read atom coordinates into an array
    with open('atom_names','r') as f:
        atom_names = f.readline().split()  # read atom names into a list
        name = []
        for i in range(len(atom_names)):
            for j in range(atom_nums[i]):
                name.append(atom_names[i]+str(j+1))  # add nums on atoms and save into name list
                
    subprocess.run("rm atom_* vect",shell=True)  # delete temporary files
    return matrix_trans,coor,name


def distAB(CONTCAR,Atom1,Atom2):    
    matrix_trans,coor,name = file_process(CONTCAR) 
    a = np.dot(matrix_trans.T,coor[name.index(Atom1)])
    b = np.dot(matrix_trans.T,coor[name.index(Atom2)])                      
    dist_value = dist(a,b)    
    return dist_value
    
    
def angleABC(CONTCAR,Atom1,Atom2,Atom3):
    matrix_trans,coor,name = file_process(CONTCAR)
    a = np.dot(matrix_trans.T,coor[name.index(Atom1)])
    b = np.dot(matrix_trans.T,coor[name.index(Atom2)])
    c = np.dot(matrix_trans.T,coor[name.index(Atom3)])             
    angle_value = angle(a,b,c)    
    return angle_value
    

def diheralABCD(CONTCAR,Atom1,Atom2,Atom3,Atom4):
    matrix_trans,coor,name = file_process(CONTCAR)          
    a = np.dot(matrix_trans.T,coor[name.index(Atom1)])
    b = np.dot(matrix_trans.T,coor[name.index(Atom2)])
    c = np.dot(matrix_trans.T,coor[name.index(Atom3)])
    d = np.dot(matrix_trans.T,coor[name.index(Atom4)])
    angle_value = diheral_angle(a,b,c,d)    
    return angle_value
    

#1. find folders containing CONTCAR file and save file path into a list
ArgvNum = len(sys.argv)
Atom = []
for i in range(ArgvNum):
    Atom.append(sys.argv[i])
cmd5 = 'bash -c "find -type f -name CONTCAR"'
files = subprocess.Popen(cmd5,stdout=subprocess.PIPE).stdout.read().decode(encoding="utf-8").split()
#2. for each CONTCAR file, calculate the distance between two atoms
value_list = []
file_name_list = []
for CONTCAR in files:
    file_name_list.append(CONTCAR.lstrip('./').rstrip('CONTCAR').replace('/','__'))
    if ArgvNum == 3:
        value = distAB(CONTCAR,Atom[1],Atom[2])
    elif ArgvNum == 4:
        value = angleABC(CONTCAR,Atom[1],Atom[2],Atom[3])
    elif ArgvNum == 5:
        value = diheralABCD(CONTCAR,Atom[1],Atom[2],Atom[3],Atom[4])
    else:
        break
    value_list.append(value)
#3. write the file name and distance value into a file 'dist_between_Atom1_and_Atom2.dat'
with open('output.dat', 'w') as file:
    file.write("species"+" " * 13 + "values\n")
    for i in range(len(files)):
        file.write("{:<20}{:>.3f}\n".format(file_name_list[i],value_list[i]))