提取和处理两个字符串之间的信息，这些字符串沿着fi重复多次

LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - BOHR = 0.5291772083 ANGSTROM PRIMITIVE CELL - CENTRING CODE 7/0 VOLUME= 122.771603 - DENSITY 2.704 g/cm^3 A B C ALPHA BETA GAMMA 6.32540491 6.32540491 6.32540491 46.774144 46.774144 46.774144 ******************************************************************************* ATOMS IN THE ASYMMETRIC UNIT 3 - ATOMS IN THE UNIT CELL: 10 ATOM X/A Y/B Z/C ******************************************************************************* 1 T 20 CA 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2 F 20 CA -5.000000000000E-01 -5.000000000000E-01 -5.000000000000E-01 3 T 6 C 2.500000000000E-01 2.500000000000E-01 2.500000000000E-01 4 F 6 C -2.500000000000E-01 -2.500000000000E-01 -2.500000000000E-01 5 T 8 O -4.912600492192E-01 -8.739950780750E-03 2.500000000000E-01 6 F 8 O 2.500000000000E-01 -4.912600492193E-01 -8.739950780750E-03 7 F 8 O -8.739950780750E-03 2.500000000000E-01 -4.912600492193E-01 8 F 8 O 4.912600492193E-01 8.739950780750E-03 -2.500000000000E-01 9 F 8 O -2.500000000000E-01 4.912600492193E-01 8.739950780750E-03 10 F 8 O 8.739950780750E-03 -2.500000000000E-01 4.912600492193E-01 TRANSFORMATION MATRIX PRIMITIVE-CRYSTALLOGRAPHIC CELL 1.0000 0.0000 1.0000 -1.0000 1.0000 1.0000 0.0000 -1.0000 1.0000 ******************************************************************************* CRYSTALLOGRAPHIC CELL (VOLUME= 368.31480902) A B C ALPHA BETA GAMMA 5.02162261 5.02162261 16.86554607 90.000000 90.000000 120.000000 COORDINATES IN THE CRYSTALLOGRAPHIC CELL ATOM X/A Y/B Z/C ******************************************************************************* 1 T 20 CA 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2 F 20 CA 0.000000000000E+00 0.000000000000E+00 -5.000000000000E-01 3 T 6 C 3.333333333333E-01 -3.333333333333E-01 -8.333333333333E-02 4 F 6 C -3.333333333333E-01 3.333333333333E-01 8.333333333333E-02 5 T 8 O -4.079267158859E-01 -3.333333333333E-01 -8.333333333333E-02 6 F 8 O 3.333333333333E-01 -7.459338255258E-02 -8.333333333333E-02 7 F 8 O 7.459338255258E-02 4.079267158859E-01 -8.333333333333E-02 8 F 8 O 4.079267158859E-01 3.333333333333E-01 8.333333333333E-02 9 F 8 O -3.333333333333E-01 7.459338255258E-02 8.333333333333E-02 10 F 8 O -7.459338255258E-02 -4.079267158859E-01 8.333333333333E-02 T = ATOM BELONGING TO THE ASYMMETRIC UNIT more lines more lines more lines FINAL OPTIMIZED GEOMETRY - DIMENSIONALITY OF THE SYSTEM 3 (NON PERIODIC DIRECTION: LATTICE PARAMETER FORMALLY SET TO 500) ******************************************************************************* LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - BOHR = 0.5291772083 ANGSTROM PRIMITIVE CELL - CENTRING CODE 7/0 VOLUME= 119.823364 - DENSITY 2.770 g/cm^3 A B C ALPHA BETA GAMMA 6.28373604 6.28373604 6.28373604 46.646397 46.646397 46.646397 ******************************************************************************* ATOMS IN THE ASYMMETRIC UNIT 3 - ATOMS IN THE UNIT CELL: 10 ATOM X/A Y/B Z/C ******************************************************************************* 1 T 20 CA 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2 F 20 CA -5.000000000000E-01 -5.000000000000E-01 -5.000000000000E-01 3 T 6 C 2.500000000000E-01 2.500000000000E-01 2.500000000000E-01 4 F 6 C -2.500000000000E-01 -2.500000000000E-01 -2.500000000000E-01 5 T 8 O -4.924094276183E-01 -7.590572381674E-03 2.500000000000E-01 6 F 8 O 2.500000000000E-01 -4.924094276183E-01 -7.590572381674E-03 7 F 8 O -7.590572381674E-03 2.500000000000E-01 -4.924094276183E-01 8 F 8 O 4.924094276183E-01 7.590572381674E-03 -2.500000000000E-01 9 F 8 O -2.500000000000E-01 4.924094276183E-01 7.590572381674E-03 10 F 8 O 7.590572381674E-03 -2.500000000000E-01 4.924094276183E-01 TRANSFORMATION MATRIX PRIMITIVE-CRYSTALLOGRAPHIC CELL 1.0000 0.0000 1.0000 -1.0000 1.0000 1.0000 0.0000 -1.0000 1.0000 ******************************************************************************* CRYSTALLOGRAPHIC CELL (VOLUME= 359.47009054) A B C ALPHA BETA GAMMA 4.97568007 4.97568007 16.76591397 90.000000 90.000000 120.000000 COORDINATES IN THE CRYSTALLOGRAPHIC CELL ATOM X/A Y/B Z/C ******************************************************************************* 1 T 20 CA 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2 F 20 CA -5.491739570355E-17 -2.745869785177E-17 -5.000000000000E-01 3 T 6 C 3.333333333333E-01 -3.333333333333E-01 -8.333333333333E-02 4 F 6 C -3.333333333333E-01 3.333333333333E-01 8.333333333333E-02 5 T 8 O -4.090760942850E-01 -3.333333333333E-01 -8.333333333333E-02 6 F 8 O 3.333333333333E-01 -7.574276095166E-02 -8.333333333333E-02 7 F 8 O 7.574276095166E-02 4.090760942850E-01 -8.333333333333E-02 8 F 8 O 4.090760942850E-01 3.333333333333E-01 8.333333333333E-02 9 F 8 O -3.333333333333E-01 7.574276095166E-02 8.333333333333E-02 10 F 8 O -7.574276095166E-02 -4.090760942850E-01 8.333333333333E-02 T = ATOM BELONGING TO THE ASYMMETRIC UNIT INFORMATION **** fort.34 **** GEOMETRY OUTPUT FILE more lines more lines more lines FINAL OPTIMIZED GEOMETRY - DIMENSIONALITY OF THE SYSTEM 3 (NON PERIODIC DIRECTION: LATTICE PARAMETER FORMALLY SET TO 500) ******************************************************************************* LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - BOHR = 0.5291772083 ANGSTROM PRIMITIVE CELL - CENTRING CODE 7/0 VOLUME= 121.143469 - DENSITY 2.740 g/cm^3 A B C ALPHA BETA GAMMA 6.32229536 6.32229536 6.32229536 46.436583 46.436583 46.436583 ******************************************************************************* ATOMS IN THE ASYMMETRIC UNIT 3 - ATOMS IN THE UNIT CELL: 10 ATOM X/A Y/B Z/C ******************************************************************************* 1 T 20 CA 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2 F 20 CA 5.000000000000E-01 -5.000000000000E-01 -5.000000000000E-01 3 T 6 C 2.500000000000E-01 2.500000000000E-01 2.500000000000E-01 4 F 6 C -2.500000000000E-01 -2.500000000000E-01 -2.500000000000E-01 5 T 8 O -4.927088991116E-01 -7.291100888437E-03 2.500000000000E-01 6 F 8 O 2.500000000000E-01 -4.927088991116E-01 -7.291100888437E-03 7 F 8 O -7.291100888437E-03 2.500000000000E-01 -4.927088991116E-01 8 F 8 O 4.927088991116E-01 7.291100888437E-03 -2.500000000000E-01 9 F 8 O -2.500000000000E-01 4.927088991116E-01 7.291100888437E-03 10 F 8 O 7.291100888437E-03 -2.500000000000E-01 4.927088991116E-01 TRANSFORMATION MATRIX PRIMITIVE-CRYSTALLOGRAPHIC CELL 1.0000 0.0000 1.0000 -1.0000 1.0000 1.0000 0.0000 -1.0000 1.0000 ******************************************************************************* CRYSTALLOGRAPHIC CELL (VOLUME= 363.43040599) A B C ALPHA BETA GAMMA 4.98494429 4.98494429 16.88768068 90.000000 90.000000 120.000000 COORDINATES IN THE CRYSTALLOGRAPHIC CELL ATOM X/A Y/B Z/C ******************************************************************************* 1 T 20 CA 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2 F 20 CA -5.471726358381E-17 -2.735863179191E-17 -5.000000000000E-01 3 T 6 C 3.333333333333E-01 -3.333333333333E-01 -8.333333333333E-02 4 F 6 C -3.333333333333E-01 3.333333333333E-01 8.333333333333E-02 5 T 8 O -4.093755657782E-01 -3.333333333333E-01 -8.333333333333E-02 6 F 8 O 3.333333333333E-01 -7.604223244490E-02 -8.333333333333E-02 7 F 8 O 7.604223244490E-02 4.093755657782E-01 -8.333333333333E-02 8 F 8 O 4.093755657782E-01 3.333333333333E-01 8.333333333333E-02 9 F 8 O -3.333333333333E-01 7.604223244490E-02 8.333333333333E-02 10 F 8 O -7.604223244490E-02 -4.093755657782E-01 8.333333333333E-02 T = ATOM BELONGING TO THE ASYMMETRIC UNIT INFORMATION **** fort.34 **** GEOMETRY OUTPUT FILE more lines more lines more lines

VOLUMES = [] with open('g.out') as file: passed_mid_point = False for line in file: if re.match(initial_pattern, line): passed_mid_point = False print file.next() print file.next() print file.next() volume_line = file.next() print volume_line aux = volume_line.split() each_volume = aux[7] print each_volume VOLUMES.append(each_volume) print 'VOLUMES = ', VOLUMES

if re.match(middle_pattern, line): passed_mid_point = True print line print file.next() parameters_line = file.next() aux = parameters_line.split() p0 = aux[0] p1 = aux[1] p2 = aux[2] p3 = aux[3] p4 = aux[4] p5 = aux[5] # print p0 print p2 P0.append(p0) P2.append(p2) print file.next() print file.next() print file.next() print file.next() if re.match(end_pattern, line): passed_mid_point = False elif passed_mid_point: # parse the coordinates print 'line2 =', line terms = line.split() print 'terms =', terms # print 'terms[1] =', terms[1] if terms and terms[1] == 'T': print terms[1] atomic_number = terms[2] print 'atomic_number = ', atomic_number ATOMIC_NUMBERS.append(atomic_number) x = terms[4] print 'x =', x Xs.append(x) y = terms[5] print 'y = ', y Ys.append(y) z = terms[6] print 'z = ', z Zs.append(z) print 'VOLUMES = ', VOLUMES print 'P0 = ', P0 print 'P2 = ', P2 print 'Xs = ', Xs print 'Ys = ', Ys print 'Zs = ', Zs print 'ATOMIC_NUMBERS = ', ATOMIC_NUMBERS

Xs = ['0.000000000000E+00', '3.333333333333E-01', '-4.079267158859E-01', '0.000000000000E+00', '3.333333333333E-01', '-4.090760942850E-01', '0.000000000000E+00', '3.333333333333E-01', '-4.093755657782E-01'] Ys = ['0.000000000000E+00', '-3.333333333333E-01', '-3.333333333333E-01', '0.000000000000E+00', '-3.333333333333E-01', '-3.333333333333E-01', '0.000000000000E+00', '-3.333333333333E-01', '-3.333333333333E-01'] Zs = ['0.000000000000E+00', '-8.333333333333E-02', '-8.333333333333E-02', '0.000000000000E+00', '-8.333333333333E-02', '-8.333333333333E-02', '0.000000000000E+00', '-8.333333333333E-02', '-8.333333333333E-02'] ATOMIC_NUMBERS = ['20', '6', '8', '20', '6', '8', '20', '6', '8']

VOLUMES = ['119.823364', '121.143469'] P0 = ['4.97568007', '4.98494429'] P1 = [16.76591397, '16.88768068'] Xs = ['0.000000000000E+00', '3.333333333333E-01', '-4.090760942850E-01', '0.000000000000E+00', '3.333333333333E-01', '-4.093755657782E-01'] Ys = ['0.000000000000E+00', '-3.333333333333E-01', '-3.333333333333E-01', '0.000000000000E+00', '-3.333333333333E-01', '-3.333333333333E-01'] Zs = ['0.000000000000E+00', '-8.333333333333E-02', '-8.333333333333E-02', '0.000000000000E+00', '-8.333333333333E-02', '-8.333333333333E-02'] ATOMIC_NUMBERS = ['20', '6', '8', '20', '6', '8']

import sys import re import os initial_pattern = '^ FINAL OPTIMIZED GEOMETRY - DIMENSIONALITY OF THE SYSTEM 3$' middle_pattern = '^ CRYSTALLOGRAPHIC CELL ' end_pattern = '^ T = ATOM BELONGING TO THE ASYMMETRIC UNIT$' global N_atom_irreducible_unit N_atom_irreducible_unit = 3 VOLUMES = [] P0 = [] P2 = [] ATOMIC_NUMBERS = [] Xs = [] Ys = [] Zs = [] with open('g.out') as file: passed_mid_point = False for line in file: if re.match(initial_pattern, line): passed_mid_point = False print file.next() print file.next() print file.next() volume_line = file.next() print volume_line aux = volume_line.split() each_volume = aux[7] print each_volume VOLUMES.append(each_volume) if re.match(middle_pattern, line): passed_mid_point = True print line print file.next() parameters_line = file.next() aux = parameters_line.split() p0 = aux[0] p1 = aux[1] p2 = aux[2] p3 = aux[3] p4 = aux[4] p5 = aux[5] # print p0 print p2 P0.append(p0) P2.append(p2) print file.next() print file.next() print file.next() print file.next() if re.match(end_pattern, line): passed_mid_point = False elif passed_mid_point: # parse the coordinates print 'line2 =', line terms = line.split() print 'terms =', terms # print 'terms[1] =', terms[1] if terms and terms[1] == 'T': print terms[1] atomic_number = terms[2] print 'atomic_number = ', atomic_number ATOMIC_NUMBERS.append(atomic_number) x = terms[4] print 'x =', x Xs.append(x) y = terms[5] print 'y = ', y Ys.append(y) z = terms[6] print 'z = ', z Zs.append(z) print 'VOLUMES = ', VOLUMES print 'P0 = ', P0 print 'P2 = ', P2 print 'Xs = ', Xs print 'Ys = ', Ys print 'Zs = ', Zs print 'ATOMIC_NUMBERS = ', ATOMIC_NUMBERS

2条回答

网友

1楼 · 编辑于 2024-05-20 00:00:28

我写了你的剧本的简化版，看起来不错。我希望这可以作为你最后剧本的起点：

#!/usr/bin/env python
# -*- coding: utf-8 -*-

VOLUMES = []
P0 = []
P2 = []
ATOMIC_NUMBERS = []
Xs = []
Ys = []
Zs = []

with open('g.out') as gout:
    final_optimized_geometry = False
    for line in gout:
        if 'FINAL OPTIMIZED GEOMETRY' in line:
            final_optimized_geometry = True
        elif 'PRIMITIVE CELL' in line:
            if not final_optimized_geometry:
                continue
            volume = line.split()[7]
            VOLUMES.append(volume)
        elif 'CRYSTALLOGRAPHIC CELL (VOLUME=' in line:
            if not final_optimized_geometry:
                continue
            gout.readline()
            line = gout.readline()
            p0, p2 = line.split()[0:3:2]

            P0.append(p0)
            P2.append(p2)
        elif 'COORDINATES IN THE CRYSTALLOGRAPHIC CELL' in line:
            if not final_optimized_geometry:
                continue
            gout.readline()
            gout.readline()
            while 'T = ATOM BELONGING TO THE ASYMMETRIC UNIT' not in line:
                line = gout.readline()
                atomdata = line.split()
                if not atomdata or atomdata[1] != 'T':
                    continue
                atomicnumber = atomdata[2]
                x, y, z = atomdata[4:7]
                ATOMIC_NUMBERS.append(atomicnumber)
                Xs.append(x)
                Ys.append(y)
                Zs.append(z)
            final_optimized_geometry = False


print(VOLUMES)
print(P0)
print(P2)
print(ATOMIC_NUMBERS)
print(Xs)
print(Ys)
print(Zs)

这将生成以下输出：

['119.823364', '121.143469']
['4.97568007', '4.98494429']
['16.76591397', '16.88768068']
['20', '6', '8', '20', '6', '8']
['0.000000000000E+00', '3.333333333333E-01', '-4.090760942850E-01', '0.000000000000E+00', '3.333333333333E-01', '-4.093755657782E-01']
['0.000000000000E+00', '-3.333333333333E-01', '-3.333333333333E-01', '0.000000000000E+00', '-3.333333333333E-01', '-3.333333333333E-01']
['0.000000000000E+00', '-8.333333333333E-02', '-8.333333333333E-02', '0.000000000000E+00', '-8.333333333333E-02', '-8.333333333333E-02']

实际上，它是一个非常简单的有限状态机，只有两个状态。警告：如果在一个最终优化的几何结构中有多个晶体学单元，它将不起作用。在这种情况下，它将只捕获第一个单元格的信息。你知道吗

代码还对文件进行了其他假设，当然，这些假设可能需要验证。你知道吗

我避免使用正则表达式。你知道吗

此代码将仅在Python3中运行（针对Python3.6.2进行了测试）。Python2.7将在文件迭代块中使用readline()（这是有意义的，但是看到Python3可以使用它是很好的）。我们使用readline()作为一个小技巧来跳过输入文件中的行，我们知道必须跳过这些行，而不必再次遍历整个循环（这将需要更多的标志变量）。你知道吗

顺便说一下，如果您的唯一任务是解析文本文件，那么查看专用语言（例如Lex）可能会很有趣。而且，Perl的设计目的是做类似的事情，而不是Python。你知道吗

希望这有帮助！你知道吗

网友

2楼 · 编辑于 2024-05-20 00:00:28

感谢所有@Bart Van Loon的帮助，更简单的代码版本是：

#!/usr/bin/env python
# -*- coding: utf-8 -*-

global N_atom_irreducible_unit
N_atom_irreducible_unit = 3

filename = 'g.out'

VOLUMES = []
P0 = []
P2 = []
ATOMIC_NUMBERS = []
Xs = []
Ys = []
Zs = []

with open(filename) as gout:
    final_optimized_geometry = False
    for line in gout:
        if 'FINAL OPTIMIZED GEOMETRY' in line:
            final_optimized_geometry = True
        elif 'PRIMITIVE CELL - CENTRING CODE' in line:
            if final_optimized_geometry:
                volume = line.split()
                print volume
                print volume[7]
                volume = line.split()[7]
                VOLUMES.append(volume)

        elif ' CRYSTALLOGRAPHIC CELL (V' in line:
            if final_optimized_geometry:
                print 'gout.next() =', gout.next()
                done = gout.next()
                print 'done =', done
                p0 = done.split()[0]
                p2 = done.split()[2]

#               p0, p2 = done.split()[0:3:2]

                P0.append(p0)
                P2.append(p2)
        elif 'COORDINATES IN THE CRYSTALLOGRAPHIC CELL' in line:
            if final_optimized_geometry:
                gout.next()
                gout.next()
                while True:
                    line = gout.next()
                    atomdata = line.split()
                    if not atomdata:
                        break
                    if atomdata[1] != 'T':
                        continue
                    atomicnumber = atomdata[2]
                    x, y, z = atomdata[4:7]
                    ATOMIC_NUMBERS.append(atomicnumber)
                    Xs.append(x)
                    Ys.append(y)
                    Zs.append(z)
                final_optimized_geometry = False



print 'VOLUMES = ', VOLUMES
print 'P0 = ', P0
print 'P2 = ', P2
print 'Xs = ', Xs
print 'Ys = ', Ys
print 'Zs = ', Zs
print 'ATOMIC_NUMBERS = ', ATOMIC_NUMBERS

其中：

1）因为最后一个原子（本例中为第10个原子）后面的下一行是空行

                    if not atomdata:
                        break

当atomdata为空时，将始终停止。换言之，当空行时，即原子列表结束时，这将始终停止。因此，这将允许避免while 'T = ATOM BELONGING TO THE ASYMMETRIC UNIT' not in line:语句。你知道吗

类似的说法是：

                    if  atomdata:   
                        continue

然而，由于某种原因，我不明白，这不能解释非空行作为唯一要分析的。为什么？你知道吗

2）这部分代码：

                if atomdata[1] != 'T':
                    continue
                atomicnumber = atomdata[2]
                x, y, z = atomdata[4:7]
                ATOMIC_NUMBERS.append(atomicnumber)
                Xs.append(x)
                Ys.append(y)
                Zs.append(z)

也可以说：

              if atomdata[1] == 'T':
                  atomicnumber = atomdata[2]
                  x, y, z = atomdata[4:7]
                  ATOMIC_NUMBERS.append(atomicnumber)
                  Xs.append(x)
                  Ys.append(y)
                  Zs.append(z)

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