StackOverflow2013

Note that there are some explanatory texts on larger screens.

plurals

POPython3: writing info from a text file to a csv file
text
Body
copied!<p>I have multiple directories each with multiple files in:</p> <pre><code>Ce +---top.txt +---X0.0 | | | +---Y0.0 | | | | | +---X0.0Y0.0Z0.0.dat | | +---X0.0Y0.0Z0.0.out | | +---X0.0Y0.0Z0.05.dat | | +---X0.0Y0.0Z0.05.out | +---Y0.05 | | | +---X0.0Y0.05Z0.0.dat | | +---X0.0Y0.0Z0.05.out | +---X0.0Y0.05Z0.05.dat | +---X0.0Y0.05Z0.05.out +---X0.05 | +---Y0.0 | | | +---X0.0Y0.0Z0.0.dat | +---X0.0Y0.0Z0.0.out | +---X0.0Y0.0Z0.05.dat | +---X0.0Y0.0Z0.05.out +---Y0.05 | +---X0.0Y0.05Z0.0.dat +---X0.0Y0.05Z0.0.out +---X0.0Y0.05Z0.05.dat +---X0.0Y0.05Z0.05.out </code></pre> <p>I am attempting to extract the relevant information from the '.out' files and write it to a csv file. For this I have devised the following code:</p> <pre><code>import os import csv with open('results.csv', 'a', newline='') as f: writer=csv.writer(f) writer.writerow(['Filename', 'Optimisation Achieved?', 'Final Energy', 'Number of Defects', 'Defect Charge', 'M-L Centre X', 'M-L Centre Y', 'M-L Centre Z', 'Defect X', 'Defect Y', 'Defect Z', 'Defect Energy']) for root, dirs, files in os.walk('.'): for filename in files: if filename.endswith('.out'): file = os.path.join(root, filename) with open(file, 'r') as reader: opt_cnt=0 for line in reader: s=line.strip() if s=='**** Optimisation achieved ****': opt_cnt+=1 if opt_cnt==1: opt1='Y' + str(opt_cnt) if opt_cnt==2: opt2='Y' + str(opt_cnt) else: opt2='N' elif s.startswith('Final energy='): Final=s[18:31] elif s.startswith('Total Number of Defects'): Number=s[31] elif s.startswith('Total charge on defect'): Q=s[-4:] elif s.startswith('Defect centre'): centrex=s[21:28] centrey=s[31:37] centrez=s[40:46] elif s.startswith('Atom/Fractional'): coordx=s[40:49] coordy=s[51:60] coordz=s[62:71] elif s.startswith('Final defect energy'): Defect_Energy=s[-13:] writer.writerow([filename, opt1, Final, Number, centrex, centrey, centrez, coordx, coordy, coordz, Defect_Energy]) </code></pre> <p>However, this produces the following error:</p> <p><strong>Traceback (most recent call last):<br> File "C:\Users\Rebecca\Dropbox\Brannerite\Published Potentials\interstitials\Grid\Ce\results.py", line 39, in <br> writer.writerow([filename, opt1, Final, Number, centrex, centrey, centrez, coordx, coordy, coordz, Defect_Energy])<br> NameError: name 'Final' is not defined</strong> </p> <p>[Altering the amount of indentation of the the last line in my code alters which of the variables comes up in the nameError: as the code is there are 16 indents (the same is NameError is given with 20 indents); altering this to 8, 12 or 24 gives '<strong>NameError: name 'opt1' is not defined</strong>]</p> <p>I should say that much of this code [remove the lines relating to os.walk] has been used successfully for a different set of files (that were all in one directory). </p> <p>Can anyone suggest where the error is coming from in the above code and how it can be corrected?</p>

Querying!

Guidance

An individual column

Larger individual text columns get their own page to allow for proper reading.

SQuiL has stopped working due to an internal error.

If you are curious you may find further information in the browser console, which is accessible through the devtools (F12).

Reload