def read_topbase(self, filename, mode="Top"):
'''
read in XS info from Topbase XS data in Python format
:INPUT:
filename string
atomic data filename e.g. topbase_h1_phot.py
:OUTPUT:
top topbase class instance
topbase class instance containing information
for this filename
'''
# read in summary records
Z,ion,islp,l, E0, num_records = sum_records = np.loadtxt( filename,
dtype={'names': ('Z', 'ion', 'islp', 'l', 'E0', 'np'),
'formats': ('i4', 'i4', 'i4', 'i4', 'float', 'i4')},
comments='Phot%s ' % mode , delimiter=None, converters=None,
skiprows=0, usecols=(1,2,3,4,5,6), unpack=True, ndmin=0)
# then read the actual cross sections
energy, XS = np.loadtxt(filename, dtype='float',
comments='Phot%sS' % mode, delimiter=None, converters=None,
skiprows=0, usecols=(1,2), unpack=True, ndmin=0)
#ion = int(Z) - int(ne) +1
# create blank array to store topbase class instances
top = np.ndarray( len(Z),dtype=np.object)
sr = np.transpose(sum_records)
nline = 0
for i in range(len(top)):
n_p = int(num_records[i])
nmax = nline + n_p
#ion = int(Z[i]) - int(ne[i]) + 1
top[i] = cls.top_photo(Z[i], int(ion[i]), int(islp[i]), int(l[i]), E0[i], n_p, energy[nline:nmax], XS[nline:nmax])
#if ion[i] == 2 and int(islp[i]) / 100 != 2:
# print "Error, non doublet in He II! ion %i islp[i] %i" % (ion, int(islp[i]))
# print sr[i]
# print ne[i], ion[i]
nline = nmax
# top is an array of class instances like the topbase_ptr in PYTHONRT
return top
def read_original_topbase_xs(self, filename, suffix="Mac"): '''this needs to be done manually, annoyingly, as format of topbase has no PhotTop or PhotMac string''' f = open(filename, "r") i = -1 top = [] for line in f: data = line.split() if len(data) == 2: top_dummy.energy[j] = float(data[0]) * RYDBERG top_dummy.XS[j] = 1e-18 * float(data[1]) if j > top_dummy.np: print "error, j > top[i].np" j += 1 elif len(data) == 7: i += 1 j = 0 if i>0: top.append(top_dummy) Z = int(data[1]) ion = Z - int(data[2]) + 1 islp = int(data[3]) l = int(data[4]) E = -1 * float(data[5]) * RYDBERG num = int(data[6]) top_dummy = cls.top_photo (Z, ion, islp, l, E, num, np.ndarray( num, dtype=np.object), np.ndarray( num, dtype=np.object)) elif data[0]!="#": print "Didn't understand data, exiting" print line sys.exit() top = np.array(top) return top