keflavich/pyradex — pull request #4 by keflavich (2014-11-04 06:43:15+00:00)
Title: Add Fujun Du's myRadex

This PR adds Fujun Du's myRadex as a submodule and adds an object-oriented wrapper with identical call signatures to RADEX. It includes some comparison scripts too. The two are now *nearly* identical, with only subtle differences. Example:

```
In [1]: import pyradex.fjdu, pyradex

In [2]: FF = pyradex.fjdu.Fjdu(species='co', column=1e15, density=1e3, temperature=30)

In [3]: RR = pyradex.Radex(species='co', column=1e15, density=1e3, temperature=30)

In [4]: FF(species='ph2co-h2', deltav=5, density={'oH2':1e5, 'pH2':1e5,}, column=1e14, temperature=30)[np.array((2,9,12))].pprint()
! 1.0000E+05 = pH2
! 1.0000E+05 = oH2
Tex tau frequency upperstateenergy upperlevel lowerlevel upperlevelpop lowerlevelpop brightness T_B
K GHz K erg / (cm2 Hz s sr) K
------------- -------------- ------------- ---------------- ---------- ---------- --------------- --------------- ------------------- --------------
10.9850266643 1.32179129864 218.221928103 20.9564811133 3.0 2.0 0.151766825553 0.281254720835 6.79892676587e-14 4.64698536225
8.05053084523 0.15678636984 218.476751692 68.0940679574 8.0 6.0 0.019292274524 0.0506864308309 7.83989913836e-15 0.534598497514
8.03698214519 0.154534224046 218.761554527 68.1111893831 9.0 7.0 0.0189155655708 0.0498907178498 7.72394242942e-15 0.525320979097

In [5]: RR(species='ph2co-h2', deltav=5, density={'oH2':1e5, 'pH2':1e5,}, column=1e14, temperature=30)[np.array((2,9,12))].pprint()
pyradex/core.py:806: RuntimeWarning: invalid value encountered in divide
frac_level_diff = level_diff/self.level_population
Tex tau frequency upperstateenergy upperlevel lowerlevel upperlevelpop lowerlevelpop brightness T_B
K GHz K erg / (cm2 Hz s sr) K
------------- -------------- ---------- ---------------- ---------- ---------- --------------- --------------- ------------------- --------------
10.8725461875 1.333141597 218.222192 21.0 3_0_3 2_0_2 0.150645903772 0.281945353464 6.86054393918e-14 4.68909371872
7.80402367318 0.161072242648 218.475632 68.1 3_2_2 2_2_1 0.0187394568895 0.0513020999616 8.07559238671e-15 0.550676535796
7.79197678094 0.158774743839 218.760066 68.1 3_2_1 2_2_0 0.018378137173 0.0505058504318 7.95918249474e-15 0.541328087558
```