Refactor opacity and 1D RT

.gitignore

@@ -75,3 +75,7 @@ output
 
 # cache
 *__pycache__*
+
+# release/debug
+*.release
+*.debug

README.md

@@ -110,9 +110,9 @@ written on `(del_temperature, pressure, wavenumber)`, include a
 `pressure` coordinate in Pa, and still retain
 degenerate `del_temperature` and `pressure` dimensions when only one state is
 requested.
-Across `pyharp.spectra`, wavenumber ranges are interpreted as
-lower-inclusive and upper-exclusive: `--wn-range=20,22` with `1 cm^-1`
-resolution samples `20` and `21`, not `22`.
+Across `pyharp.spectra`, wavenumber ranges are interpreted as inclusive at
+both ends: `--wn-range=20,22` with `1 cm^-1` resolution samples `20`, `21`,
+and `22`.
 See the [pyharp-dump CLI documentation](https://pyharp.readthedocs.io/en/latest/dump_cli.html)
 for the full command reference, output naming conventions, and NetCDF schema.
 
@@ -133,10 +133,11 @@ pyharp-plot overview --species H2O CO2 --temperature-k 300 --pressure-bar 1 --wn
 Use `--pair` for CIA pairs, `--species` for molecules, and `--composition`
 for gas mixtures such as `H2O:0.1,H2:0.9`. All plot commands accept
 `--wn-range=min,max`; `overview` accepts multiple `--wn-range` values for
-multi-page PDFs. These ranges are lower-inclusive and upper-exclusive. Use
-`--output` to choose the output path. Without `--output`, plots are written
-under `--output-dir` (default `output/`) with names derived from the target,
-plot type, temperature, pressure, and wavenumber range.
+multi-page PDFs. These ranges include both endpoints, so adjacent repeated
+ranges such as `20,2500` and `2500,10000` both include `2500`. Use `--output`
+to choose the output path. Without `--output`, plots are written under
+`--output-dir` (default `output/`) with names derived from the target, plot
+type, temperature, pressure, and wavenumber range.
 For plot commands that use pressure, `--temperature-k` and `--pressure-bar`
 also accept matched comma-separated vectors such as
 `--temperature-k 300,400 --pressure-bar 1,10`. `pyharp-plot` then runs one

docs/source/builtin_opacities.rst

@@ -51,6 +51,16 @@ The following functions have been used to process the legacy CIA data files:
    :undoc-members:
    :imported-members:
 
+NetCDF dump-backed molecular opacities
+--------------------------------------
+
+Pyharp also supports NetCDF dump-backed molecular absorption through the
+``molecule-line`` and ``cia`` opacity types. These readers consume
+cross-section fields on ``(del_temperature, pressure, wavenumber)`` or any
+equivalent variable-dimension ordering, convert them into the runtime units
+used by the C++ radiative-transfer core, and interpolate on the requested
+band grid.
+
 References
 ----------
 .. [1] Lupu, R., et al. "Correlated k coefficients for H2-He atmospheres; 196 spectral windows and 1460 pressure-temperature points." Zenodo, doi 0.5281/zenodo.5590988 (2021).

docs/source/dump_cli.rst

@@ -75,8 +75,8 @@ Shared Options
     Wavenumber bounds in ``cm^-1``. Repeat this option to write one NetCDF
     file per band. When ``--output`` is provided with multiple ranges,
     pyharp appends ``_<wnmin>_<wnmax>`` to the requested stem. Ranges are
-    lower-inclusive and upper-exclusive, so ``--wn-range=20,22`` with
-    ``--resolution 1`` samples ``20`` and ``21``.
+    inclusive at both ends, so ``--wn-range=20,22`` with ``--resolution 1``
+    samples ``20``, ``21``, and ``22``.
 
 ``--resolution value``
     Wavenumber spacing in ``cm^-1``. The default is ``1``.
@@ -177,8 +177,8 @@ Repeat ``--wn-range`` to compute multiple bands in one run:
    pyharp-dump xsection --species H2O --temperature-k 300 --pressure-bar 1 \
        --wn-range=20,2500 --wn-range=2500,10000
 
-This writes one file for ``[20, 2500)`` and one file for ``[2500, 10000)``.
-Adjacent repeated ranges do not duplicate the boundary sample. If
+This writes one file for ``[20, 2500]`` and one file for ``[2500, 10000]``.
+Adjacent repeated ranges duplicate the shared boundary sample. If
 ``--output output/h2o.nc`` is provided, the generated files are
 ``output/h2o_20_2500.nc`` and ``output/h2o_2500_10000.nc``.
 

docs/source/opacity.rst

@@ -23,12 +23,12 @@ A complete list of built-in opacity types is given in the table below.
   * - 'jit'
     - '.pt' (saved by :func:`torch.jit.save` or :func:`pyharp.compile`)
     - Just-In-Time scripted opacity model
-  * - 'rfm-lbl'
+  * - 'molecule-line'
     - NetCDF
-    - Line-by-line absorption data computed by RFM
-  * - 'rfm-ck'
+    - Molecular line cross sections on ``(wavenumber, pressure, del_temperature)`` with optional same-species continuum fields
+  * - 'molecule-cia'
     - NetCDF
-    - Correlated-k absorption computed from line-by-line data
+    - Collision-induced absorption binary coefficients on ``(wavenumber, pressure, del_temperature)``
   * - 'multiband-ck'
     - '.pt' (saved by :func:`torch.jit.save`)
     - Three-dimensional correlated-k opacity lookup table. The axis are
@@ -52,6 +52,13 @@ A complete list of built-in opacity types is given in the table below.
 
 We give a few examples showing how to use these opacity class to load and compute optical properties.
 
+The NetCDF dump-backed molecular opacities expect the coordinate variables
+``wavenumber``, ``pressure``, ``del_temperature``, and ``temperature``.
+Line opacity variables follow the naming convention ``sigma_line_<species>``.
+Optional same-species continuum terms use ``sigma_continuum_<species>_*`` and
+are summed into the line attenuation automatically. CIA variables use
+``binary_absorption_coefficient_<species_a>_<species_b>``.
+
 .. _example_sonora:
 
 Example 1. Compute Sonora2020 molecular opacities

docs/source/opacity_classes.rst

@@ -15,7 +15,10 @@ Opacity Classes
 .. autoclass:: pyharp.opacity.WaveTemp
    :members: __init__, forward
 
-.. autoclass:: pyharp.opacity.RFM
+.. autoclass:: pyharp.opacity.MoleculeLine
+   :members: __init__, forward
+
+.. autoclass:: pyharp.opacity.MoleculeCIA
    :members: __init__, forward
 
 .. autoclass:: pyharp.opacity.JITOpacity

docs/source/plot_cli.rst

@@ -116,8 +116,8 @@ Shared Options
     Wavenumber bounds in ``cm^-1``. CIA plots default to ``20,10000`` when it
     is omitted. Molecular and mixture plots default to ``20,2500``. The
     ``overview`` subcommand accepts this option more than once. Ranges are
-    lower-inclusive and upper-exclusive, so ``--wn-range=20,22`` with
-    ``--resolution 1`` samples ``20`` and ``21``.
+    inclusive at both ends, so ``--wn-range=20,22`` with ``--resolution 1``
+    samples ``20``, ``21``, and ``22``.
 
 ``--resolution value``
     Wavenumber grid spacing in ``cm^-1``. The default is ``1``.