[Tutor] building table from textfile

[Alan Gauld]

On 27/11/13 18:22, Ruben Guerrero wrote:
> Dear tutor.
>
> I am trying to build the matrix and get some other information from the
> following text files:
>
> file1:
> -O-
>                1          2          3          4          5          6
>       1  C    6.617775  -0.405794   0.371689  -0.212231   0.064402
> 0.064402
>       2  C   -0.405794   6.617775  -0.212231   0.371689  -0.010799
>   -0.010799
>       3  C    0.371689  -0.212231   4.887381  -0.005309   0.263318
> 0.263318
>       4  C   -0.212231   0.371689  -0.005309   4.887381  -0.005500
>   -0.005500

>                7          8          9         10
>       1  C    0.064402  -0.010799  -0.010799  -0.010799
>       2  C   -0.010799   0.064402   0.064402   0.064402
>       3  C    0.263318  -0.005500  -0.005500  -0.005500
>       4  C   -0.005500   0.263318   0.263318   0.263318
>
> file 2:
> -O-
>                1          2          3          4          5
>       1  C    5.898497   0.292009   0.177195   0.177195   0.177195
>       2  H    0.292009   0.686184  -0.099114  -0.099114  -0.099114
>       3  Cl   0.177195  -0.099114  17.045753  -0.129074  -0.129074
>       4  Cl   0.177195  -0.099114  -0.129074  17.045753  -0.129074
>
> using the following script:
>
> nombreInput=sys.argv[1]
>
> inputFile = open (nombreInput,"r")
> inputFileRead = inputFile.readlines()
> out = open (nombreInput+".out","w")
>
>
> mu = 0
> nu = 0
>
> countAtom = {
...
> }
> electrons = {
...
> }
>
> numberOfLines = len(inputFileRead)
>
> maxNumberOfOrbitals = 0
>
> # Contar el numero de orbitales
> for iline in range(0,numberOfLines) :
>      inputFileRead[iline] = inputFileRead[iline].replace("\n","")

You could do this more simply using

for line in inputFile:
     line = line.rstrip()

> if ( len(inputFileRead[iline].split()) == 6+2 ) :
>      numberOfOrbital =  int(inputFileRead[iline].split()[0])

And this becomes

line = line.split()
if len(line) == 8:   # 8 = 6+2 no point in extra math
    numberOfOrbital = int(line[0])


> if ( numberOfOrbital > maxNumberOfOrbitals ) :
> maxNumberOfOrbitals = numberOfOrbital
> # Contar los atomos
>
> for k in range(0,maxNumberOfOrbitals) :
>     atom = inputFileRead[k+2].split()[1]

This assumes you have 2 more lines than there are maxNumberofOrbitals.
I didn't check, but is it true?

Also it would be more efficient to store the split line in the first 
loop above.

I didn't go through the rest in detail but I suspect
the +2 thing may be to do with your error message:

> elif ( len(inputFileRead[l].split()) == maxNumberOfOrbitals%6+2 ) :
>    for j in range(0,maxNumberOfOrbitals%6) :
>       matrix[i][j+6*m] = float (inputFileRead[l].split()[j+2])

Notice the j+2 at the end?
Could that be the cause?

Or what about the j+6*m? I don't know where m is defined but
could it be busting your index?

> Traceback (most recent call last):
>    File "get_matrix.py", line 88, in <module>
>      matrix[i][j+6*m] = float (inputFileRead[l].split()[j+2])
> IndexError: index 10 is out of bounds for axis 0 with size 10

-- 
Alan G
Author of the Learn to Program web site
http://www.alan-g.me.uk/
http://www.flickr.com/photos/alangauldphotos