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
5 H 0.064402 -0.010799 0.263318 -0.005500 0.697750 -0.062986
6 H 0.064402 -0.010799 0.263318 -0.005500 -0.062986 0.697750
7 H 0.064402 -0.010799 0.263318 -0.005500 -0.062986 -0.062986
8 H -0.010799 0.064402 -0.005500 0.263318 0.003816 -0.001380
9 H -0.010799 0.064402 -0.005500 0.263318 -0.001380 -0.001380
10 H -0.010799 0.064402 -0.005500 0.263318 -0.001380 0.003816
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
5 H -0.062986 0.003816 -0.001380 -0.001380
6 H -0.062986 -0.001380 -0.001380 0.003816
7 H 0.697750 -0.001380 0.003816 -0.001380
8 H -0.001380 0.697750 -0.062986 -0.062986
9 H 0.003816 -0.062986 0.697750 -0.062986
10 H -0.001380 -0.062986 -0.062986 0.697750
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
5 Cl 0.177195 -0.099114 -0.129074 -0.129074 17.045753
using the following script:
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import os
import subprocess
import numpy as np
import time
import signal
nombreInput=sys.argv[1]
inputFile = open (nombreInput,"r")
inputFileRead = inputFile.readlines()
out = open (nombreInput+".out","w")
mu = 0
nu = 0
countAtom = {
'H': 0,
'Li': 0,
'C': 0,
'N': 0,
'O': 0,
'F': 0,
'Na': 0,
'Si': 0,
'P': 0,
'S': 0,
'Cl': 0,
}
electrons = {
'H': 1,
'Li': 3,
'C': 6,
'N': 7,
'O': 8,
'F': 9,
'Na': 11,
'Si': 14,
'P': 15,
'S': 16,
'Cl': 17,
}
numberOfLines = len(inputFileRead)
maxNumberOfOrbitals = 0
# Contar el numero de orbitales
for iline in range(0,numberOfLines) :
inputFileRead[iline] = inputFileRead[iline].replace("\n","") # Quitar los
saltos de linea
# print (inputFileRead[iline])
if ( len(inputFileRead[iline].split()) == 6+2 ) :
numberOfOrbital = int(inputFileRead[iline].split()[0])
if ( numberOfOrbital > maxNumberOfOrbitals ) :
maxNumberOfOrbitals = numberOfOrbital
# Contar los atomos
for k in range(0,maxNumberOfOrbitals) :
atom = inputFileRead[k+2].split()[1]
countAtom[atom] = countAtom[atom] + 1
# Imprimir la formula quimica
for k in countAtom :
if ( countAtom[k] > 0) :
out.write( k+"_{"+str(countAtom[k])+"}" )
out.write("\n")
# Imprimir el numero de electrones
numberOfElectrons = 0
for k in countAtom :
numberOfElectrons = numberOfElectrons + electrons[k]*countAtom[k]
out.write (str(numberOfElectrons) + "\n")
# Imprimir el numero de filas
out.write (str(maxNumberOfOrbitals) + "\n")
# Armar la matriz
matrix = np.zeros((maxNumberOfOrbitals,maxNumberOfOrbitals),dtype=float)
i = 0
m = 0
for l in range(0,numberOfLines) :
if ( len(inputFileRead[l].split()) == 6+2 ) :
for j in range(0,6) :
matrix[i][j+6*m] = float (inputFileRead[l].split()[j+2])
if ( i + 1 == maxNumberOfOrbitals) :
i = 0
m = m + 1
else:
i = i + 1
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])
i = i + 1
else :
i = 0
# Imprimir la matriz
for i in range(0,maxNumberOfOrbitals) :
for j in range(0,maxNumberOfOrbitals) :
out.write ("%.6f"%matrix[i][j]+" ")
out.write("\n")
#:::::::::::::::::::::::::::::::::::
# Cerrando los archivos
#:::::::::::::::::::::::::::::::::::
inputFile.close()
out.close()
but when I run teh script on file 1 I get the error:
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
And with file 2 I don't get errors but the information in the matrix in not
in the file.
so where is the error?
Thanks in advance,
-Ruben.
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