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Atomic/atomic symbols #69

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merged 4 commits into from
Jan 10, 2014
Merged

Atomic/atomic symbols #69

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cc61d95
added atomic symbol reader
wkerzendorf Jan 10, 2014
56dd277
added atomic_symbols data file
wkerzendorf Jan 10, 2014
727c83a
added reader and file
wkerzendorf Jan 10, 2014
aedcbe6
added tests for atomic2symbol dicts
wkerzendorf Jan 10, 2014
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10 changes: 10 additions & 0 deletions tardis/atomic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,16 @@

default_atom_h5_path = os.path.join(os.path.dirname(__file__), 'data', 'atom_data.h5')

def data_path(fname):
data_dir = os.path.join(os.path.dirname(__file__), 'data')
return os.path.join(data_dir, fname)

atomic_symbols_data = np.recfromtxt(data_path('atomic_symbols.dat'),
names=['atomic_number', 'symbol'])

symbol2atomic_number = OrderedDict(zip(atomic_symbols_data['symbol'], atomic_symbols_data['atomic_number']))
atomic_number2symbol = OrderedDict(atomic_symbols_data)


@PendingDeprecationWarning
def read_atomic_data(fname=None):
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118 changes: 118 additions & 0 deletions tardis/data/atomic_symbols.dat
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Original file line number Diff line number Diff line change
@@ -0,0 +1,118 @@
1 H
2 He
3 Li
4 Be
5 B
6 C
7 N
8 O
9 F
10 Ne
11 Na
12 Mg
13 Al
14 Si
15 P
16 S
17 Cl
18 Ar
19 K
20 Ca
21 Sc
22 Ti
23 V
24 Cr
25 Mn
26 Fe
27 Co
28 Ni
29 Cu
30 Zn
31 Ga
32 Ge
33 As
34 Se
35 Br
36 Kr
37 Rb
38 Sr
39 Y
40 Zr
41 Nb
42 Mo
43 Tc
44 Ru
45 Rh
46 Pd
47 Ag
48 Cd
49 In
50 Sn
51 Sb
52 Te
53 I
54 Xe
55 Cs
56 Ba
57 La
58 Ce
59 Pr
60 Nd
61 Pm
62 Sm
63 Eu
64 Gd
65 Tb
66 Dy
67 Ho
68 Er
69 Tm
70 Yb
71 Lu
72 Hf
73 Ta
74 W
75 Re
76 Os
77 Ir
78 Pt
79 Au
80 Hg
81 Tl
82 Pb
83 Bi
84 Po
85 At
86 Rn
87 Fr
88 Ra
89 Ac
90 Th
91 Pa
92 U
93 Np
94 Pu
95 Am
96 Cm
97 Bk
98 Cf
99 Es
100 Fm
101 Md
102 No
103 Lr
104 Rf
105 Db
106 Sg
107 Bh
108 Hs
109 Mt
110 Ds
111 Rg
112 Cn
113 Uut
114 Fl
115 Uup
116 Lv
117 Uus
118 Uuo
6 changes: 6 additions & 0 deletions tardis/tests/test_atomic.py
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Expand Up @@ -20,3 +20,9 @@ def test_atom_levels():
atom_data = atomic.AtomData.from_hdf5(atomic.default_atom_h5_path)
with pytest.raises(Exception):
raise Exception('test the atom_data thoroughly')

def test_atomic_symbol():
assert atomic.atomic_number2symbol[14] == 'Si'

def test_atomic_symbol_reverse():
assert atomic.symbol2atomic_number['Si'] == 14