Question sur un exemple de script en python

En effet j'ai déjà essayé des choses qui ne fonctionnent pas . Voici le programme (il est un peu long):
s0 = [[],[]]
f=open('compute_biochem.in')
for line in f.readlines():
if line[0]!='#':
if ":" in line:
li=line.split(":")
if li[0].split()[0] == 'SPECIES':
lis=li[1].split(';')
s0[0].append(lis[0].split()[0])
s0[1].append(lis[1].split('\n')[0].split()[0])
elif li[0].split()[0] == 'XMLFILE':
INPUTFILE = li[1].split('\n')[0].split()[0]
f.close()

print('Biochemistry read from ',INPUTFILE)
print(' ')


#
# Compute source from chemistry
#
def source_biochem(concentration,time, reac_rate, index_in, index_out):
number_of_species = len(concentration)
number_of_reactions = len(reac_rate)
source = [0 for s in range(number_of_species)]
for r in range(number_of_reactions):
ind_in = index_in[r]
ind_out = index_out[r]
for spec in ind_in:
source[spec] = source[spec] - reac_rate[r] * reduce(mul,[concentration[s] for s in ind_in])
for spec in ind_out:
source[spec] = source[spec] + reac_rate[r] * reduce(mul,[concentration[s] for s in ind_in])
return source


#
# Read an .xml file for biochemistry
#
tree = etree.parse(INPUTFILE)

#
# Read the species from .xml and check consistency with initial conditions in compute_biochem.in
#
for spec in tree.xpath("species"):
rr=spec.findall("name")
spec_name = [rr[n].text for n in range(len(rr))]
number_of_species = len(spec_name)

#
# Check if the list of species is correct
#
if spec_name != sorted(s0[0]):
print('Species list not valid')
print('From .xml file: ',spec_name)
print('From .in file: ',sorted(s0[0]))
quit()

#
# if list of species is correct, reorder the initial concentrations and generate y0
# y0 contains the initial conditions of the species in the same order as in spec_name
#
s0t=[[x[i] for x in s0] for i in range(len(s0[0]))]
s0tsorted=sorted(s0t,key=lambda col: col[0])
s0sorted=[[x[i] for x in s0tsorted] for i in range(len(s0tsorted[0]))]
y0 = [float(data) for data in s0sorted[1]]

#
# Read the reactions and deduce species indices for computing the source terms
#
for reac in tree.xpath("reactions"):
rr=reac.findall("reaction")
reac_name = [rr[n].text for n in range(len(rr))]
rr=reac.findall("reaction_rate")
reac_rate = [rr[n].text for n in range(len(rr))]
number_of_reactions = len(reac_name)

specs_in=[[] for r in range(number_of_reactions)]
specs_out=[[] for r in range(number_of_reactions)]
index_in=[[] for r in range(number_of_reactions)]
index_out=[[] for r in range(number_of_reactions)]
for reac in reac_name:
all_in = reac[:reac.index("--")].split("+")
specs_in[reac_name.index(reac)] = [spec.split() for spec in all_in][0]
index_in[reac_name.index(reac)] = [spec_name.index(spec.split()[0]) for spec in all_in]

all_out = reac[reac.index("--")+2:].split("+")
specs_out[reac_name.index(reac)] = [spec.split() for spec in all_out][0]
index_out[reac_name.index(reac)] = [spec_name.index(spec.split()[0]) for spec in all_out]


fichier = open("reactions2.in", "r")
line=fichier.readline()
while line:
print(line)
print(("reac_rate"))
line=fichier.readline()
fichier.close()


#
# Print case
#

print("Species :")
print(spec_name)
print(" ")
print('Initial conditions: ',y0)
print(" ")
print("Reactions :")
print(reac_name)
print(" ")
print("Reactions rates:")
print(reac_rate)
print(" ")
print("Indices in / out:")
print(index_in)
print(index_out)

j'ai voulu ouvrir un fichier "reactions2.in" pour que le programme puisse aller là bas car c'est là bas où se trouvent les fichiers.in et xml des reactions biochimiques. Du coup le programme me dit :"I/O operation on closed file"