Exojax

ExoJAX Version 1.2 allows modelings with a number of molecular lines (for instance, 100 million lines) using a new algorithm (but beta version), PreMODIT. Also, the I/O of the molecular databases were switched to a common api with the RADIS team from the original one. Several other improvements in a spin rotation, instrumental responses are include. 　

Major changes

- Moved on a common I/O of molecular/atomic database with [radis](https://github.com/radis).api for ExoMol/HITRAN/HITEMP #272
- Removed old moldb for ExoMol/HITRAN/HITEMP
- PreMODIT algorithm, applicable to a wide wavenumber range 265 287 288 307
- Memory saved version of spin rotation and instrumental response 295

Minor changes

- Solved unintended 4GB limit for MODIT 286
- Plotting tool to draw tau=1 height as a function of wavenumber 301
- molecular mass from HITRAN 269
- bug fixes 278 285 286 303 315
- refactoring...

gallery

Using PreMODIT, we can simulate an emission spectrum in wider wavenumber range (A100/80GB, x-axis wavelength AA):


Simpler new logo ;)

<img src="https://user-images.githubusercontent.com/15956904/206186134-c5100f28-790e-4e7b-b960-d83736fad0a0.JPG" width="100px">

The changes by this release are listed as below:

- patch to adopt [the recent JAX change of unsupport](https://github.com/google/jax/issues/10293) of `jax.ops.index ` #248 249
- setdgm for HITRAN/HITEMP 253
- doc updates, HITRAN, Krucz, jaxopt

This release includes a bug fix on ipgauss_sampling. See 238

New Contributors
* astrostevanus made their first contribution in https://github.com/HajimeKawahara/exojax/pull/195
* dcmvdbekerom made their first contribution in https://github.com/HajimeKawahara/exojax/pull/200
* erwanp made their first contribution in https://github.com/HajimeKawahara/exojax/pull/228

**Full Changelog**: https://github.com/HajimeKawahara/exojax/compare/v1.0.0...v1.1.0

New capabilities
- :atom: VALD3 reverse modeling and MODIT availability 218 See [this tutorial](http://secondearths.sakura.ne.jp/exojax/tutorials/retvald.html).

- :art: the reverse differentiation, which enables us to run an HMC in reverse mode 212

All of the following lines should work:
python
kernel = NUTS(model_c)
kernel = NUTS(model_c, forward_mode_differentiation=False)
kernel = NUTS(model_c, forward_mode_differentiation=True)


- :art: compatibility with [JAXopt](https://github.com/google/jaxopt) #212 See [this tutorial](http://secondearths.sakura.ne.jp/exojax/tutorials/optimize_spectrum_JAXopt.html). A demo:

https://user-images.githubusercontent.com/15956904/154577641-543397e1-6db5-4c16-b16f-4b7c7d688800.mp4

- :atom: moldb: HITEMP2010 multiple file load 216 220
- :atom: moldb: Line strength criterion is computed based on a typical temperature of the system. 223 See [this page](http://secondearths.sakura.ne.jp/exojax/userguide/moldb.html#masking-weak-lines)

Bug fix
- :electron: H minus opacity bug fixed 94
- several minor bugs

What's Changed
* Release by HajimeKawahara in https://github.com/HajimeKawahara/exojax/pull/192
* Refac/dynamics by HajimeKawahara in https://github.com/HajimeKawahara/exojax/pull/194
* Features/fastchem2 by astrostevanus in https://github.com/HajimeKawahara/exojax/pull/195
* sphinx completed by HajimeKawahara in https://github.com/HajimeKawahara/exojax/pull/197
* Updates on ditgrid() by dcmvdbekerom in https://github.com/HajimeKawahara/exojax/pull/200
* remove out-of-bounds check in jax function by dcmvdbekerom in https://github.com/HajimeKawahara/exojax/pull/201
* Bugfix/numpyro by HajimeKawahara in https://github.com/HajimeKawahara/exojax/pull/202
* update docs by HajimeKawahara in https://github.com/HajimeKawahara/exojax/pull/203
* Pyformat by HajimeKawahara in https://github.com/HajimeKawahara/exojax/pull/204
* Isodata refac by HajimeKawahara in https://github.com/HajimeKawahara/exojax/pull/205
* this is just test merge to develop by HajimeKawahara in https://github.com/HajimeKawahara/exojax/pull/209
* enable optimization and reverse mode by HajimeKawahara in https://github.com/HajimeKawahara/exojax/pull/212
* Refac1.1 1 by HajimeKawahara in https://github.com/HajimeKawahara/exojax/pull/214
* Refacv1.1 2 by HajimeKawahara in https://github.com/HajimeKawahara/exojax/pull/215
* Multi hitemp by ykawashima in https://github.com/HajimeKawahara/exojax/pull/216
* Multi hitemp (bug fix) by ykawashima in https://github.com/HajimeKawahara/exojax/pull/219
* MODIT+VALD by chonma0ctopus in https://github.com/HajimeKawahara/exojax/pull/218
* Refacv1.1 3 by HajimeKawahara in https://github.com/HajimeKawahara/exojax/pull/220
* Minor revisions to userguide and docstrings by chonma0ctopus in https://github.com/HajimeKawahara/exojax/pull/222
* bug about mask_needed parameter fixed by ykawashima in https://github.com/HajimeKawahara/exojax/pull/224
* Feature/sij0mask by ykawashima in https://github.com/HajimeKawahara/exojax/pull/223
* enabled masking based on Ttyp for HITRAN/HITEMP by ykawashima in https://github.com/HajimeKawahara/exojax/pull/226
* Improve minorthings by ykawashima in https://github.com/HajimeKawahara/exojax/pull/225
* auto create HitDB folders if missing by erwanp in https://github.com/HajimeKawahara/exojax/pull/228