"""
chemsitry object
"""
print "chemistry solver setup..."
chemistry_obj = Chemistry(mechanism_path,composition,uniform_grid,atol,rtol)
print "Number of species:", chemistry_obj.gas.n_species, "Number of reactions:",chemistry_obj.gas.n_reactions
print "The absolute error is", chemistry_obj.network.atol, "The relative error is", chemistry_obj.network.rtol
"""
time evolution
"""
print "Initialize the composition..."
if restart == 0:
# a new run, start from equilibrium abundances
y = chemistry_obj.equilibrate()
# write equilibrium values into files
np.savetxt('./output/y_equilibrium.txt',y)
t_0 = 0
else:
# restart
# read the starting time from file
f=open('./output/time.txt','r')
t_0=int(f.read())
f.close()
# read the array from file
y = np.loadtxt('./output/y_t.txt')
print "start time evolution..."
t_start = time.time()
n_species = chemistry_obj.gas.n_species
