我在python中编写脚本，应该搜索数据文件，并将相关数据复制到单独的文件中。这是脚本：
#!/usr/bin/env python
import os
os.system("grep \"x \" dynamics.out | awk '{print $2}' > coord.dat")
os.system("grep \"Total\" dynamics.out | awk '{print $4}' > total.dat")
os.system("grep \"Kinetic\" dynamics.out | awk '{print $4}' > kinetic.dat")
问题是这部分使得coord.dat文件完全错误。 dynamics.out文件中的输出不是以此脚本中假定的方式排列的。 数据文件实际上是一长串数据块，如下所示：
time: 0.2fs
coordinates
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
velocities
0.000241908669 0.000039611121 -0.000250932377
-0.000163805243 -0.000115366290 -0.000017375326
-0.000047784448 0.000248119899 -0.000074616012
0.000272673498 -0.000017362735 0.000399681421
-0.000326634443 -0.000254296236 0.000120448584
-0.000094363714 0.000239927614 -0.000271069374
0.000122625277 0.000053803004 -0.000088144918
-0.000112099948 -0.000143815691 0.000140925518
-0.000020483349 -0.000161160777 0.000050721656
0.000277228119 0.000550968890 -0.000249788972
0.000308946542 0.000944826745 0.000083253008
-0.001453065687 0.000249483273 -0.000194390979
0.000370071103 0.000328142273 -0.000594811431
0.000983242907 -0.000247664001 -0.000337676641
0.000702749595 -0.000531050917 -0.000068247339
-0.000913913436 -0.000822599342 -0.000519543480
0.000657300149 -0.001239306947 0.000033192915
0.000763780031 0.000151892085 -0.000106941733
-0.000111349513 0.000591872099 0.000360147787
0.000283007739 0.000537032161 0.000183614425
-0.001766985000 0.001017499281 -0.000870068723
0.001560592306 -0.000636221326 0.001124910644
-0.000596019125 0.001094375746 0.000048984716
Kinetic energy : 0.030613110934
Electronic energy : -60.105483063648
Total energy : -60.074869952714
Conservation : -0.000000051487
self.forces:
-0.000751933584 -0.004126331042 -0.004033882094
-0.034302855990 0.029127675777 -0.007001211293
0.037731564948 -0.009915059812 0.020878531238
-0.109763802365 -0.102520873021 -0.034608644850
0.033373305433 0.018949006487 -0.015434320612
0.078807110369 0.101440274624 0.031960385836
0.027868883444 -0.012844760956 0.009625682828
0.011817203866 -0.011548503873 0.038027933611
-0.016951256413 -0.005848802217 -0.020755575427
0.002823354740 0.003214778324 -0.005974478408
-0.012101005124 -0.007850077809 0.000381372379
0.001958908572 -0.006446492464 0.003077496955
0.005728700900 -0.005220923285 -0.001710604936
-0.006358072353 -0.016410380723 -0.003938145281
0.000121143012 0.012930928986 -0.005592639661
0.008318475112 0.004530628154 0.009023640965
-0.010548513939 -0.005006070272 0.008756275583
-0.000601535778 -0.003075790288 -0.006209965764
-0.002729816846 -0.003390850759 -0.001421821138
-0.023967939963 0.000603482820 -0.016983439682
-0.006731466272 0.010586445711 -0.001984503303
0.009694983786 0.008555900046 0.002598629870
0.006564564487 0.004265795793 0.001319282998
state for next step: 1
所以我需要的是来自每个数据块（文件中有数千个）来获取位于“坐标”行和“速度”行之间的部分。我需要将其复制到一个文件中，该文件的编号为23（原子数），然后是空行，然后是这个数据，然后是23，空行，数据......
如何重写脚本来执行此操作？或者有人可以推荐一些我可以学习的文献。我不知道关于Python的第一件事，但我确实有一些C和C ++以及Matlab的经验，我理解编程的基本逻辑。 对于长篇文章感到抱歉，但我认为提供数据样本会很有用。 提前感谢您对此的任何帮助。
答案 0 :(得分：0)
您可以尝试这样的事情：
whole_data = []
grab_lines = False
with open('input','r') as atom_file:
molecule_data = ['23\n\n']
for line in atom_file:
if line.startswith('coordinates'):
grab_lines = True
continue
elif line.startswith('velocities'):
grab_lines = False
if molecule_data:
#just checks that we aren't appending an empty list.
molecule_data.append('\n')
whole_data.append(molecule_data)
molecule_data = ['23\n\n']
if grab_lines: #in python 'is True' is implicit for many types.
molecule_data.append(line)
with open('output','w') as out_file:
for molecule in whole_data:
out_file.write(''.join(molecule))
我复制/粘贴了几次输入数据，因此atom_file的内容如下所示：
time: 0.2fs
coordinates
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
velocities
0.000241908669 0.000039611121 -0.000250932377
-0.000163805243 -0.000115366290 -0.000017375326
-0.000047784448 0.000248119899 -0.000074616012
0.000272673498 -0.000017362735 0.000399681421
-0.000326634443 -0.000254296236 0.000120448584
-0.000094363714 0.000239927614 -0.000271069374
0.000122625277 0.000053803004 -0.000088144918
-0.000112099948 -0.000143815691 0.000140925518
-0.000020483349 -0.000161160777 0.000050721656
0.000277228119 0.000550968890 -0.000249788972
0.000308946542 0.000944826745 0.000083253008
-0.001453065687 0.000249483273 -0.000194390979
0.000370071103 0.000328142273 -0.000594811431
0.000983242907 -0.000247664001 -0.000337676641
0.000702749595 -0.000531050917 -0.000068247339
-0.000913913436 -0.000822599342 -0.000519543480
0.000657300149 -0.001239306947 0.000033192915
0.000763780031 0.000151892085 -0.000106941733
-0.000111349513 0.000591872099 0.000360147787
0.000283007739 0.000537032161 0.000183614425
-0.001766985000 0.001017499281 -0.000870068723
0.001560592306 -0.000636221326 0.001124910644
-0.000596019125 0.001094375746 0.000048984716
Kinetic energy : 0.030613110934
Electronic energy : -60.105483063648
Total energy : -60.074869952714
Conservation : -0.000000051487
self.forces:
-0.000751933584 -0.004126331042 -0.004033882094
-0.034302855990 0.029127675777 -0.007001211293
0.037731564948 -0.009915059812 0.020878531238
-0.109763802365 -0.102520873021 -0.034608644850
0.033373305433 0.018949006487 -0.015434320612
0.078807110369 0.101440274624 0.031960385836
0.027868883444 -0.012844760956 0.009625682828
0.011817203866 -0.011548503873 0.038027933611
-0.016951256413 -0.005848802217 -0.020755575427
0.002823354740 0.003214778324 -0.005974478408
-0.012101005124 -0.007850077809 0.000381372379
0.001958908572 -0.006446492464 0.003077496955
0.005728700900 -0.005220923285 -0.001710604936
-0.006358072353 -0.016410380723 -0.003938145281
0.000121143012 0.012930928986 -0.005592639661
0.008318475112 0.004530628154 0.009023640965
-0.010548513939 -0.005006070272 0.008756275583
-0.000601535778 -0.003075790288 -0.006209965764
-0.002729816846 -0.003390850759 -0.001421821138
-0.023967939963 0.000603482820 -0.016983439682
-0.006731466272 0.010586445711 -0.001984503303
0.009694983786 0.008555900046 0.002598629870
0.006564564487 0.004265795793 0.001319282998
state for next step: 1
time: 0.2fs
coordinates
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
velocities
0.000241908669 0.000039611121 -0.000250932377
-0.000163805243 -0.000115366290 -0.000017375326
-0.000047784448 0.000248119899 -0.000074616012
0.000272673498 -0.000017362735 0.000399681421
-0.000326634443 -0.000254296236 0.000120448584
-0.000094363714 0.000239927614 -0.000271069374
0.000122625277 0.000053803004 -0.000088144918
-0.000112099948 -0.000143815691 0.000140925518
-0.000020483349 -0.000161160777 0.000050721656
0.000277228119 0.000550968890 -0.000249788972
0.000308946542 0.000944826745 0.000083253008
-0.001453065687 0.000249483273 -0.000194390979
0.000370071103 0.000328142273 -0.000594811431
0.000983242907 -0.000247664001 -0.000337676641
0.000702749595 -0.000531050917 -0.000068247339
-0.000913913436 -0.000822599342 -0.000519543480
0.000657300149 -0.001239306947 0.000033192915
0.000763780031 0.000151892085 -0.000106941733
-0.000111349513 0.000591872099 0.000360147787
0.000283007739 0.000537032161 0.000183614425
-0.001766985000 0.001017499281 -0.000870068723
0.001560592306 -0.000636221326 0.001124910644
-0.000596019125 0.001094375746 0.000048984716
Kinetic energy : 0.030613110934
Electronic energy : -60.105483063648
Total energy : -60.074869952714
Conservation : -0.000000051487
self.forces:
-0.000751933584 -0.004126331042 -0.004033882094
-0.034302855990 0.029127675777 -0.007001211293
0.037731564948 -0.009915059812 0.020878531238
-0.109763802365 -0.102520873021 -0.034608644850
0.033373305433 0.018949006487 -0.015434320612
0.078807110369 0.101440274624 0.031960385836
0.027868883444 -0.012844760956 0.009625682828
0.011817203866 -0.011548503873 0.038027933611
-0.016951256413 -0.005848802217 -0.020755575427
0.002823354740 0.003214778324 -0.005974478408
-0.012101005124 -0.007850077809 0.000381372379
0.001958908572 -0.006446492464 0.003077496955
0.005728700900 -0.005220923285 -0.001710604936
-0.006358072353 -0.016410380723 -0.003938145281
0.000121143012 0.012930928986 -0.005592639661
0.008318475112 0.004530628154 0.009023640965
-0.010548513939 -0.005006070272 0.008756275583
-0.000601535778 -0.003075790288 -0.006209965764
-0.002729816846 -0.003390850759 -0.001421821138
-0.023967939963 0.000603482820 -0.016983439682
-0.006731466272 0.010586445711 -0.001984503303
0.009694983786 0.008555900046 0.002598629870
0.006564564487 0.004265795793 0.001319282998
state for next step: 1
time: 0.2fs
coordinates
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
velocities
0.000241908669 0.000039611121 -0.000250932377
-0.000163805243 -0.000115366290 -0.000017375326
-0.000047784448 0.000248119899 -0.000074616012
0.000272673498 -0.000017362735 0.000399681421
-0.000326634443 -0.000254296236 0.000120448584
-0.000094363714 0.000239927614 -0.000271069374
0.000122625277 0.000053803004 -0.000088144918
-0.000112099948 -0.000143815691 0.000140925518
-0.000020483349 -0.000161160777 0.000050721656
0.000277228119 0.000550968890 -0.000249788972
0.000308946542 0.000944826745 0.000083253008
-0.001453065687 0.000249483273 -0.000194390979
0.000370071103 0.000328142273 -0.000594811431
0.000983242907 -0.000247664001 -0.000337676641
0.000702749595 -0.000531050917 -0.000068247339
-0.000913913436 -0.000822599342 -0.000519543480
0.000657300149 -0.001239306947 0.000033192915
0.000763780031 0.000151892085 -0.000106941733
-0.000111349513 0.000591872099 0.000360147787
0.000283007739 0.000537032161 0.000183614425
-0.001766985000 0.001017499281 -0.000870068723
0.001560592306 -0.000636221326 0.001124910644
-0.000596019125 0.001094375746 0.000048984716
Kinetic energy : 0.030613110934
Electronic energy : -60.105483063648
Total energy : -60.074869952714
Conservation : -0.000000051487
self.forces:
-0.000751933584 -0.004126331042 -0.004033882094
-0.034302855990 0.029127675777 -0.007001211293
0.037731564948 -0.009915059812 0.020878531238
-0.109763802365 -0.102520873021 -0.034608644850
0.033373305433 0.018949006487 -0.015434320612
0.078807110369 0.101440274624 0.031960385836
0.027868883444 -0.012844760956 0.009625682828
0.011817203866 -0.011548503873 0.038027933611
-0.016951256413 -0.005848802217 -0.020755575427
0.002823354740 0.003214778324 -0.005974478408
-0.012101005124 -0.007850077809 0.000381372379
0.001958908572 -0.006446492464 0.003077496955
0.005728700900 -0.005220923285 -0.001710604936
-0.006358072353 -0.016410380723 -0.003938145281
0.000121143012 0.012930928986 -0.005592639661
0.008318475112 0.004530628154 0.009023640965
-0.010548513939 -0.005006070272 0.008756275583
-0.000601535778 -0.003075790288 -0.006209965764
-0.002729816846 -0.003390850759 -0.001421821138
-0.023967939963 0.000603482820 -0.016983439682
-0.006731466272 0.010586445711 -0.001984503303
0.009694983786 0.008555900046 0.002598629870
0.006564564487 0.004265795793 0.001319282998
state for next step: 1
我out_file的内容如下：
23
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
23
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
23
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
修改：您可以将if grab_lines语句替换为：
if grab_lines: #in python 'is True' is implicit for many types.
line = [line.split()[0]]+[str(float(element)*.529) for element in line.split()[1:]]+['\n']
molecule_data.append('\t'.join(line))
line的中间部分称为list comprehension。如果其中任何一个真的不清楚，请问。
答案 1 :(得分：0)
grab_lines = False
with open('input','r') as atom_file:
molecule_data = ['23\n\n']
for line in atom_file:
if line.startswith('coordinates'):
grab_lines = True
continue
elif line.startswith('velocities'):
grab_lines = False
#if molecule_data:
#just checks that we aren't appending an empty list.
#molecule_data.append('\n')
#whole_data.append(molecule_data)
#molecule_data = ['23\n\n']
if grab_lines: #in python 'is True' is implicit for many types.
new_line = molecule_data.append(line)
with open('output','w') as out_file:
for molecule in molecule_data:
out_file.write(molecule)
#out_file.write(''.join(molecule))