CK and LBL RT working (#6)

-fixed LBL rt
-added functionality to generate and use correlated k RT
-added surface class and new functions, but not well organized yet

doc/README-opacity.md

@@ -0,0 +1,71 @@
+# Instruction on generating opacity
+
+## Files required
+1. atmospheric profile, e.g. `jupiter.atm` 
+2. opacity definition file, e.g. `jupiter.yaml`
+
+## Atmospheric profile
+The atmospheric profile is a text file with named columns. The particular order of the columns is not important,
+except for the first column, which is assumed to be an index of the vertical levels.
+The vertical level index starts from 1 at the bottom of the atmosphere and progresses upwards. 
+The rest of the columns are altitude, pressure, temperature, and gas mole fractions.
+The following names are required to be present in the file:
+
+- 'IDX': index of the layer
+- 'ALT': altitude (km)
+- 'PRE': pressure (mbar)
+- 'TEM': temperature (K)
+
+If no units are provided, the code assumes `km` for altitude, `mbar` for pressure, and `K` for temperature.
+It is possible to use different units by specifying them after the name of the column
+(without spaces), and enclosed in square brackets, e.g. 'ALT[km]'. The code will convert the units automatically to SI units.
+The recognized units are: `km`, `m`, `cm`, `bar`, `Pa`, `hPa`, `mbar`, `pa`, `hpa`, `K`
+
+Following the required columns, the file can contain any number of additional columns with gas mole fractions.
+The names of the columns should correspond to the names of the gases in the opacity definition file.
+The units of the mole fractions are by default in `ppmv` (parts per million by volume), but it is possible to specify
+different units by enclosing them in square brackets, e.g. 'H2[ppbv]' or `H2[1]`, where `1` is the unitless mole fraction.
+The recognized units are: `ppmv`, `ppbv`, `ppm`, `ppb`, `mol/mol`, `1`
+
+It is required that the atmospheric profile file contains all the gases that are defined in the opacity definition file.
+The gases that are not present in the atmospheric profile are assumed to be radiatively inactive.
+The mean molecular weight of the atmosphere is calculated based on the pressure and
+altitude levels in the atmospheric profile.
+
+Here is an example of an atmospheric profile file for Jupiter:
+```text
+# Sample atmospheric profile for Jupiter
+IDX ALT[km] PRE[mbar] TEM[K] H2[ppmv] He[ppmv] CH4[ppmv]
+1 -315.8 6289.6 294.2 861993 136001 1809
+2 -310.2 5501.5 282.4 861993 136001 1809
+```
+
+You may add comments to the file by starting the line with `#`.
+Any text after the `#` symbol wil be ignored.
+
+We provide a python script `atm_profile_utils.py` that parses the atmospheric profile file and returns the data in a dictionary.
+The dictionary contains the following keys:
+- 'IDX': index of the layer
+- 'ALT': altitude (m)
+- 'PRE': pressure (Pa)
+- 'TEM': temperature (K)
+and additional keys for the names of the gases present in the file.
+The entries are numpy arrays with the column data in SI units.
+The script checks the units of the columns and converts them to SI units if necessary.
+It will raise an error if the units are not recognized or the file format is incorrect.
+
+The script can be used as follows:
+```python
+from atm_profile_utils import read_atm_profile
+data = read_atm_profile('jupiter.atm')
+```
+
+Or you can use the script as a command line tool:
+```bash
+python3 atm_profile_utils.py -i [input_file] -o [output_file] -u [units]
+```
+where `[input_file]` is the name of the input atmospheric profile file, `[output_file]` is the name of the output file,
+The format of the input file is determined by the extension of the file name.
+Currently, the script supports `.atm`, `.txt` and `.nc` file formats.
+
+## Generate line-by-line opacity using RFM

examples/2024-CMetz-amars/amars.inp

@@ -36,15 +36,15 @@ dt          = 5.E1
 
 <time>
 cfl_number  = 0.9           # The Courant, Friedrichs, & Lewy (CFL) Number
-nlim        = -1            # cycle limit
+nlim        = 1            # cycle limit
 tlim        = 1.E7         # time limit
 xorder      = 5             # horizontal reconstruction order
 integrator  = rk3           # integration method
 
 <mesh>
 nx1         = 128           # Number of zones in X1-direction
 x1min       = 0.            # minimum value of X1
-x1max       = 50.E3         # maximum value of X1
+x1max       = 20.E3         # maximum value of X1
 ix1_bc      = reflecting    # inner-X1 boundary flag
 ox1_bc      = reflecting    # outer-X1 boundary flag
 

examples/2024-CMetz-amars/amarsw-ck.yaml

@@ -0,0 +1,62 @@
+opacity-sources:
+  - name: H2O
+    class: HitranCK
+    data: amarsw-ck-B1.nc
+    dependent-species: [vapor.H2O]
+
+  - name: CO2
+    class: HitranCK
+    data: amarsw-ck-B2.nc
+    dependent-species: [vapor.dry]
+
+  - name: H2O
+    class: HitranCK
+    data: amarsw-ck-B3.nc
+    dependent-species: [vapor.H2O]
+
+bands: [B1, B2, B3]
+
+B1:
+  units: cm-1
+  grid-type: cktable
+  wavenumber-range: [1., 500.]
+  opacity: [H2O]
+  rt-solver: Disort
+  flags: [thermal_emission]
+  albedo: 0.01
+
+B2:
+  units: cm-1
+  grid-type: cktable
+  wavenumber-range: [500., 1200.]
+  opacity: [CO2]
+  rt-solver: Disort
+  flags: [thermal_emission]
+  albedo: 0.01
+
+B3:
+  units: cm-1
+  grid-type: cktable
+  wavenumber-range: [1200., 2000.]
+  opacity: [H2O]
+  rt-solver: Disort
+  flags: [thermal_emission]
+  albedo: 0.01
+
+Disort-flags:
+  ibcnd: false
+  usrtau: false
+  usrang: false
+  lamber: true
+  onlyfl: true
+  spher: false
+  intensity_correction: true
+  old_intensity_correction: false
+  general_source: false
+  output_uum: false
+  quiet: true
+  print-input: false
+  print-fluxes: false
+  print-intensity: false
+  print-transmissivity: false
+  print-phase-function: true

examples/2024-CMetz-amars/amarsw-lbl.yaml

@@ -0,0 +1,65 @@
+opacity-sources:
+  - name: H2O
+    class: Hitran
+    data: amarsw-lbl-B1.nc
+    dependent-species: [vapor.H2O]
+
+  - name: CO2
+    class: Hitran
+    data: amarsw-lbl-B2.nc
+    dependent-species: [vapor.dry]
+
+  - name: H2O
+    class: Hitran
+    data: amarsw-lbl-B3.nc
+    dependent-species: [vapor.H2O]
+
+bands: [B1, B2, B3]
+
+B1:
+  units: cm-1
+  grid-type: regular
+  wavenumber-range: [1., 500.]
+  resolution: 0.1
+  opacity: [H2O]
+  rt-solver: Disort
+  flags: [thermal_emission]
+  albedo: 0.01
+
+B2:
+  units: cm-1
+  grid-type: regular
+  wavenumber-range: [500., 1200.]
+  resolution: 0.1
+  opacity: [CO2]
+  rt-solver: Disort
+  flags: [thermal_emission]
+  albedo: 0.01
+
+B3:
+  units: cm-1
+  grid-type: regular
+  wavenumber-range: [1200., 2000.]
+  resolution: 0.1
+  opacity: [H2O]
+  rt-solver: Disort
+  flags: [thermal_emission]
+  albedo: 0.01
+
+Disort-flags:
+  ibcnd: false
+  usrtau: false
+  usrang: false
+  lamber: true
+  onlyfl: true
+  spher: false
+  intensity_correction: true
+  old_intensity_correction: false
+  general_source: false
+  output_uum: false
+  quiet: true
+  print-input: false
+  print-fluxes: false
+  print-intensity: false
+  print-transmissivity: false
+  print-phase-function: true

examples/2024-CMetz-amars/amarsw-mp.yaml

@@ -0,0 +1,38 @@
+microphysics:
+  - H2O-system
+
+H2O-system:
+  scheme: Kessler94
+  dependent-species: [vapor.H2O, cloud.H2O(c), cloud.H2O(p)]
+  parameters:
+    autoconversion: 1.e-4
+    accretion: 0.0
+    evaporation: 3.e-1
+    sedimentation: -20.
+
+CO2-system:
+  scheme: Kessler94
+  dependent-species: [vapor.CO2, cloud.CO2(c), cloud.CO2(p)]
+  parameters:
+    autoconversion: 1.e-4
+    accretion: 0.0
+    evaporation: 3.e-1
+    sedimentation: -20.
+
+H2S-system:
+  scheme: Kessler94
+  dependent-species: [vapor.H2S, cloud.H2S(c), cloud.H2S(p)]
+  parameters:
+    autoconversion: 1.e-4
+    accretion: 0.0
+    evaporation: 3.e-1
+    sedimentation: -20.
+
+SO2-system:
+  scheme: Kessler94
+  dependent-species: [vapor.SO2, cloud.SO2(c), cloud.SO2(p)]
+  parameters:
+    autoconversion: 1.e-4
+    accretion: 0.0
+    evaporation: 3.e-1
+    sedimentation: -20.

examples/2024-CMetz-amars/amarsw-op.yaml

@@ -0,0 +1,29 @@
+opacity-sources:
+  - name: H2O
+    class: Hitran
+
+  - name: CO2
+    class: Hitran
+
+bands: [B1, B2, B3]
+
+B1:
+  units: cm-1
+  grid-type: regular
+  wavenumber-range: [1., 500.]
+  resolution: 0.1
+  opacity: [H2O, CO2]
+
+B2:
+  units: cm-1
+  grid-type: regular
+  wavenumber-range: [500., 1200.]
+  resolution: 0.1
+  opacity: [H2O, CO2]
+
+B3:
+  units: cm-1
+  grid-type: regular
+  wavenumber-range: [1200., 2000.]
+  resolution: 0.1
+  opacity: [H2O, CO2]