wind_ae 2.0.0__tar.gz → 2.0.2__tar.gz

{wind_ae-2.0.0/wind_ae.egg-info → wind_ae-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: wind_ae
-Version: 2.0.0
+Version: 2.0.2
 Summary: 1D relaxation Parker wind model with metal and X-ray physics based on Murray-Clay et al. (2009)
 Author: Madelyn Broome, John McCann, Ruth Murray-Clay
 License-Expression: BSD-3-Clause
@@ -35,7 +35,7 @@ I <img src="docs/windae_logo_blue_light.png" alt="Wind-AE Logo" width="350"/>
 `Wind-AE` updates [Murray-Clay et al. (2009)](https://ui.adsabs.harvard.edu/abs/2009ApJ...693...23M/abstract) to allow for the modeling of atomic metals and multifrequency XUV stellar spectra (Broome et al. 2025). If you use `Wind-AE`, please cite [Broome et al. (2025)](https://ui.adsabs.harvard.edu/abs/2025ApJ...995..198B/abstract). 
 
 
-Take advantage of `Notebooks/Quickstart.ipynb` to get a quick orientation to `Wind-AE` and please report any bugs via [Github](https://github.com/mabroome/wind-ae/issues) or via email to broome.astro@gmail.com.
+Take advantage of `Notebooks/Quickstart.ipynb` to get a quick orientation to `Wind-AE` and please report any bugs via [Github](https://github.com/mibroome/wind-ae/issues) or via email to broome.astro@gmail.com.
 
 ![Build Status](https://github.com/mibroome/wind-ae/actions/workflows/python-pkg.yml/badge.svg)
 [![Coverage Status](https://coveralls.io/repos/github/mibroome/wind-ae/badge.svg?branch=main)](https://coveralls.io/github/mibroome/wind-ae?branch=main)
@@ -53,7 +53,7 @@ Take advantage of `Notebooks/Quickstart.ipynb` to get a quick orientation to `Wi
 
 Is Wind-AE the right tool for me?
 ----------------------
-`Wind-AE` is well-suited for users interested in **quickly estimating mass loss rates** or outflow structure. Outflow structure includes bulk temperature and per-species ionization fractions as a function of radius, so can be easily translated into approximating and **predicting observables and transits**, including metastable helium (He 10830$\AA$) transits, though a He transit module is not yet included. Precise modeling of lower atmosphere ($\lssim 100 \mu$bar) is considered necessary for highly accurate transit models, but Wind-AE can be easily coupled to lower atmosphere photochemistry models whose outputs can (e.g., radius, temperature, abundances, ionization fractions, etc. at 1 $\mu$bar) can be fed into Wind-AE as inputs.  
+`Wind-AE` is well-suited for users interested in **quickly estimating mass loss rates** or outflow structure. Outflow structure includes bulk temperature and per-species ionization fractions as a function of radius, so can be easily translated into approximating and **predicting observables and transits**, including metastable helium (He 10830 Å) transits, though a He transit module is not yet included. Precise modeling of lower atmosphere (< ~100 $\mu$bar) is considered necessary for highly accurate transit models, but Wind-AE can be easily coupled to lower atmosphere photochemistry models whose outputs can (e.g., radius, temperature, abundances, ionization fractions, etc. at 1 $\mu$bar) can be fed into Wind-AE as inputs.  
 
 >*If you are interested in outflow structure:* Past the Coriolis turning radius (a few planetary radii) 3D physics dominates, so `Wind-AE` does not integrate past that point. `Wind-AE` also makes simplifying assumptions about the region below the region below the wind-launch radius (~10 nanobars). 
 
@@ -64,11 +64,11 @@ Because `Wind-AE` runs on the order of seconds to minutes, it can be (and has be
 - Multiple ionization states of the same species (e.g., simultaneously tracking C I and C II as a linked ionization chain)
 - X-ray physics (secondary ionizations and K-shell ionization cross-sections for relevant metals)
 - Both low and high stellar XUV flux
-- **Heating & Cooling**: Ionization heating, bolometric heating & cooling (negligible in wind), PdV cooling (work done due to expansion of gas), radiative / atomic line cooling (Lyman-$\alpha$; O, C, Fe, Mg, Ca, and Ne lines), recombination cooling, free-free (bremsstrahlung) cooling, and, optionally, self-consistent conductive cooling (see note below)
+- **Heating & Cooling**: Ionization heating, bolometric heating & cooling (negligible in wind), PdV cooling (work done due to expansion of gas), radiative / atomic line cooling (Lyman-alpha; O, C, Fe, Mg, Ca, and Ne lines), recombination cooling, free-free (bremsstrahlung) cooling, and, optionally, self-consistent conductive cooling (see note below)
 #### `Wind-AE` does not (currently) include:
 - **Magnetic fields**
 - **Time dependence**
-- **Diffusion/drag** - the atomic species set by the user are assumed to be entrained in the outflow and in thermal equilibrium. This is an appropriate assumption for species below the [crossover mass](https://ui.adsabs.harvard.edu/abs/1987Icar...69..532H) and a warning will be raised.
+- **Fractionation/diffusion/drag** - the atomic species set by the user are assumed to be entrained in the outflow and in thermal equilibrium. This is an appropriate assumption for species below the [crossover mass](https://ui.adsabs.harvard.edu/abs/1987Icar...69..532H) and a warning will be raised.
 - **Heating & Cooling**: H3+ line cooling (not planned)
 
 > **Note (v2.0+):** Conductive, recombination, and free-free cooling are each independently toggleable via flags. Turning on conduction (`sim.turn_on_conduction()`) introduces numerically stiff ODEs and should only be done after all other ramping is complete. The temperature dependence of free-free and recombination cooling can make ramping to higher metallicities numerically unstable — if so, try ramping with them off and turning them back on afterwards.
@@ -85,7 +85,7 @@ See [Broome et al. (2025)](https://ui.adsabs.harvard.edu/abs/2025ApJ...995..198B
 - Just want a grid of mass loss rates for pure-Hydrogen, low-flux-EUV-irradiated planets? See [Kubyshkina & Fossati](https://ui.adsabs.harvard.edu/abs/2021RNAAS...5...74K/abstract) 
 - Want a grid of mass loss rates for pure-Hydrogen, high-flux-XUV-irradiated planets? See [Owen & Jackson (2012)](https://ui.adsabs.harvard.edu/abs/2012MNRAS.425.2931O/abstract)
 
->Want your model added to this list or to update the short bio? Email mabroome@ucsc.edu
+>Want your model added to this list or to update the short bio? Email broome.astro@gmail.com
 
 Requirements
 ------------
@@ -199,8 +199,8 @@ sim.ramp_molecular_erfc(v_drop=erf_loc, rate=erf_rate)
 - **(v2.0)** Ramping to high metallicity with recombination and/or free-free cooling on can be numerically unstable in some cases — see the cooling-flags note above.
 
 --------
-### Check out the [open issues](https://github.com/mabroome/wind-ae/issues).
+### Check out the [open issues](https://github.com/mibroome/wind-ae/issues).
 
 --------
 ## AI Use Statement
-We used Claude web (primarily model Sonnet 5.0) in `Wind-AE`'s v2.0 development to assist with refactoring `Wind-AE` for runtime improvements, with the implementation of the conductive cooling scheme in the code, and updating the docs for v2.0 release. All scientific content, methodology, and interpretations are the authors' own. The authors have reviewed and verified all code, outputs, and text, and take full responsibility for the integrity and accuracy of the work.
+Claude web (primarily model Sonnet 5.0) was used in `Wind-AE`'s v2.0 development to assist with refactoring `Wind-AE` for runtime improvements, with the implementation of the conductive cooling scheme in the code, and updating the docs for v2.0 release. All scientific content, methodology, and interpretations are the authors' own. The authors have reviewed and verified all code, outputs, and text, and take full responsibility for the integrity and accuracy of the work.

{wind_ae-2.0.0 → wind_ae-2.0.2}/README.md

@@ -8,7 +8,7 @@ I <img src="docs/windae_logo_blue_light.png" alt="Wind-AE Logo" width="350"/>
 `Wind-AE` updates [Murray-Clay et al. (2009)](https://ui.adsabs.harvard.edu/abs/2009ApJ...693...23M/abstract) to allow for the modeling of atomic metals and multifrequency XUV stellar spectra (Broome et al. 2025). If you use `Wind-AE`, please cite [Broome et al. (2025)](https://ui.adsabs.harvard.edu/abs/2025ApJ...995..198B/abstract). 
 
 
-Take advantage of `Notebooks/Quickstart.ipynb` to get a quick orientation to `Wind-AE` and please report any bugs via [Github](https://github.com/mabroome/wind-ae/issues) or via email to broome.astro@gmail.com.
+Take advantage of `Notebooks/Quickstart.ipynb` to get a quick orientation to `Wind-AE` and please report any bugs via [Github](https://github.com/mibroome/wind-ae/issues) or via email to broome.astro@gmail.com.
 
 ![Build Status](https://github.com/mibroome/wind-ae/actions/workflows/python-pkg.yml/badge.svg)
 [![Coverage Status](https://coveralls.io/repos/github/mibroome/wind-ae/badge.svg?branch=main)](https://coveralls.io/github/mibroome/wind-ae?branch=main)
@@ -26,7 +26,7 @@ Take advantage of `Notebooks/Quickstart.ipynb` to get a quick orientation to `Wi
 
 Is Wind-AE the right tool for me?
 ----------------------
-`Wind-AE` is well-suited for users interested in **quickly estimating mass loss rates** or outflow structure. Outflow structure includes bulk temperature and per-species ionization fractions as a function of radius, so can be easily translated into approximating and **predicting observables and transits**, including metastable helium (He 10830$\AA$) transits, though a He transit module is not yet included. Precise modeling of lower atmosphere ($\lssim 100 \mu$bar) is considered necessary for highly accurate transit models, but Wind-AE can be easily coupled to lower atmosphere photochemistry models whose outputs can (e.g., radius, temperature, abundances, ionization fractions, etc. at 1 $\mu$bar) can be fed into Wind-AE as inputs.  
+`Wind-AE` is well-suited for users interested in **quickly estimating mass loss rates** or outflow structure. Outflow structure includes bulk temperature and per-species ionization fractions as a function of radius, so can be easily translated into approximating and **predicting observables and transits**, including metastable helium (He 10830 Å) transits, though a He transit module is not yet included. Precise modeling of lower atmosphere (< ~100 $\mu$bar) is considered necessary for highly accurate transit models, but Wind-AE can be easily coupled to lower atmosphere photochemistry models whose outputs can (e.g., radius, temperature, abundances, ionization fractions, etc. at 1 $\mu$bar) can be fed into Wind-AE as inputs.  
 
 >*If you are interested in outflow structure:* Past the Coriolis turning radius (a few planetary radii) 3D physics dominates, so `Wind-AE` does not integrate past that point. `Wind-AE` also makes simplifying assumptions about the region below the region below the wind-launch radius (~10 nanobars). 
 
@@ -37,11 +37,11 @@ Because `Wind-AE` runs on the order of seconds to minutes, it can be (and has be
 - Multiple ionization states of the same species (e.g., simultaneously tracking C I and C II as a linked ionization chain)
 - X-ray physics (secondary ionizations and K-shell ionization cross-sections for relevant metals)
 - Both low and high stellar XUV flux
-- **Heating & Cooling**: Ionization heating, bolometric heating & cooling (negligible in wind), PdV cooling (work done due to expansion of gas), radiative / atomic line cooling (Lyman-$\alpha$; O, C, Fe, Mg, Ca, and Ne lines), recombination cooling, free-free (bremsstrahlung) cooling, and, optionally, self-consistent conductive cooling (see note below)
+- **Heating & Cooling**: Ionization heating, bolometric heating & cooling (negligible in wind), PdV cooling (work done due to expansion of gas), radiative / atomic line cooling (Lyman-alpha; O, C, Fe, Mg, Ca, and Ne lines), recombination cooling, free-free (bremsstrahlung) cooling, and, optionally, self-consistent conductive cooling (see note below)
 #### `Wind-AE` does not (currently) include:
 - **Magnetic fields**
 - **Time dependence**
-- **Diffusion/drag** - the atomic species set by the user are assumed to be entrained in the outflow and in thermal equilibrium. This is an appropriate assumption for species below the [crossover mass](https://ui.adsabs.harvard.edu/abs/1987Icar...69..532H) and a warning will be raised.
+- **Fractionation/diffusion/drag** - the atomic species set by the user are assumed to be entrained in the outflow and in thermal equilibrium. This is an appropriate assumption for species below the [crossover mass](https://ui.adsabs.harvard.edu/abs/1987Icar...69..532H) and a warning will be raised.
 - **Heating & Cooling**: H3+ line cooling (not planned)
 
 > **Note (v2.0+):** Conductive, recombination, and free-free cooling are each independently toggleable via flags. Turning on conduction (`sim.turn_on_conduction()`) introduces numerically stiff ODEs and should only be done after all other ramping is complete. The temperature dependence of free-free and recombination cooling can make ramping to higher metallicities numerically unstable — if so, try ramping with them off and turning them back on afterwards.
@@ -58,7 +58,7 @@ See [Broome et al. (2025)](https://ui.adsabs.harvard.edu/abs/2025ApJ...995..198B
 - Just want a grid of mass loss rates for pure-Hydrogen, low-flux-EUV-irradiated planets? See [Kubyshkina & Fossati](https://ui.adsabs.harvard.edu/abs/2021RNAAS...5...74K/abstract) 
 - Want a grid of mass loss rates for pure-Hydrogen, high-flux-XUV-irradiated planets? See [Owen & Jackson (2012)](https://ui.adsabs.harvard.edu/abs/2012MNRAS.425.2931O/abstract)
 
->Want your model added to this list or to update the short bio? Email mabroome@ucsc.edu
+>Want your model added to this list or to update the short bio? Email broome.astro@gmail.com
 
 Requirements
 ------------
@@ -172,8 +172,8 @@ sim.ramp_molecular_erfc(v_drop=erf_loc, rate=erf_rate)
 - **(v2.0)** Ramping to high metallicity with recombination and/or free-free cooling on can be numerically unstable in some cases — see the cooling-flags note above.
 
 --------
-### Check out the [open issues](https://github.com/mabroome/wind-ae/issues).
+### Check out the [open issues](https://github.com/mibroome/wind-ae/issues).
 
 --------
 ## AI Use Statement
-We used Claude web (primarily model Sonnet 5.0) in `Wind-AE`'s v2.0 development to assist with refactoring `Wind-AE` for runtime improvements, with the implementation of the conductive cooling scheme in the code, and updating the docs for v2.0 release. All scientific content, methodology, and interpretations are the authors' own. The authors have reviewed and verified all code, outputs, and text, and take full responsibility for the integrity and accuracy of the work.
+Claude web (primarily model Sonnet 5.0) was used in `Wind-AE`'s v2.0 development to assist with refactoring `Wind-AE` for runtime improvements, with the implementation of the conductive cooling scheme in the code, and updating the docs for v2.0 release. All scientific content, methodology, and interpretations are the authors' own. The authors have reviewed and verified all code, outputs, and text, and take full responsibility for the integrity and accuracy of the work.

{wind_ae-2.0.0 → wind_ae-2.0.2}/docs/conf.py

@@ -35,5 +35,6 @@ exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 
 html_theme = 'sphinx_rtd_theme'
 html_static_path = ['_static']
-html_logo = 'windae_logo_blue.png'
-html_favicon = 'windae_logo_blue_favicon_16.gif'
+html_css_files = ['custom.css',]
+html_logo = 'windae_logo_blue_light.png'
+html_favicon = 'windae_logo_blue_favicon_48x48.png'

{wind_ae-2.0.0 → wind_ae-2.0.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "wind_ae"
-version = "2.0.0"
+version = "2.0.2"
 authors = [
     { name = "Madelyn Broome" },
     { name = "John McCann" },

{wind_ae-2.0.0 → wind_ae-2.0.2}/wind_ae/setup.py

@@ -13,7 +13,7 @@ setup(
     name="wind_ae",
     version="1.0",
     author='Madelyn Broome',
-    author_email='mabroome@ucsc.edu',
+    author_email='broome.astro@gmail.com',
     description="1D relaxation Parker wind model based on Murray-Clay et al. (2009)",
     install_requires=[line.strip() for line in
                       open('requirements.txt', 'r').readlines()],

{wind_ae-2.0.0 → wind_ae-2.0.2}/wind_ae/wrapper/relax_wrapper.py

@@ -485,7 +485,7 @@ class wind_simulation:
         sub = Popen(self.path+'bin/relaxed_ae',cwd=self.workdir, stdout=PIPE, stderr=PIPE,bufsize=1, universal_newlines=True) 
         output, error_output = sub.communicate()
         if error_output:
-            if verbose:
+            if verbose is True:
                 print(output)
                 print(error_output)
             if error_output[0:55] == 'Numerical Recipes run-time error...\nstep size underflow':
@@ -573,7 +573,7 @@ class wind_simulation:
         return self.run_wind(expedite,calc_postfacto,verbose)
     
     def ramp_to(self, system=None, intermediate_converge_bcs=False, final_polish=False,
-                integrate_out=True, static_bcs=False, make_plot=False):
+                integrate_out=True, static_bcs=False, make_plot=False,verbose=False):
         """
         Ramps the current wind solution to a new system. Wrapper for ramp_Ftot(), ramp_grav(), ramp_star().
 
@@ -611,7 +611,7 @@ class wind_simulation:
                 result = self.ramp_var("Ftot", system.value("Ftot"),
                                     converge_bcs=intermediate_converge_bcs, make_plot=make_plot,
                                     expedite=True,static_bcs=static_bcs,
-                                    integrate_out=False)
+                                    integrate_out=False,verbose=verbose)
                 fail = result
                 
                 if (fail != 0) and (fail != 5):
@@ -620,7 +620,7 @@ class wind_simulation:
                 # Ramps Mp and Rp simultaneously, ~constant surface gravity
                 result = self.ramp_grav(system, converge_bcs=intermediate_converge_bcs,
                                     make_plot=make_plot, expedite=True,static_bcs=static_bcs,
-                                    integrate_out=False)
+                                    integrate_out=False,verbose=verbose)
                 fail = result 
                 
                 if (fail != 0) and (fail != 5):
@@ -629,7 +629,7 @@ class wind_simulation:
                 # Ramps Mstar and semimajor simultaneously, ~constant Hill radius
                 result = self.ramp_star(system, converge_bcs=intermediate_converge_bcs,
                                     make_plot=make_plot, expedite=True,static_bcs=static_bcs,
-                                    integrate_out=False)
+                                    integrate_out=False,verbose=verbose)
                 fail = result
 
         if final_polish == True:
@@ -666,7 +666,7 @@ class wind_simulation:
     
     def ramp_var(self, var, var_end, var_class=None, delta=0.02,
                  delta_additive=False, converge_bcs=False, make_plot=True,
-                 expedite=False, integrate_out=True, static_bcs=False):
+                 expedite=False, integrate_out=True, static_bcs=False,verbose=False):
         """
         Ramps a variable in the system or physics class to a target value with adaptive stepsizes.
 
@@ -880,7 +880,7 @@ class wind_simulation:
             self.inputs.write_flags(*expedite_flag_tuple,integrate_out) #user defined integrate out will override
         if integrate_out == True:
             self.inputs.write_flags(*self.windsoln.flags_tuple,integrate_out) 
-        result = self.run_wind(verbose=True,calc_postfacto=False)
+        result = self.run_wind(verbose=verbose,calc_postfacto=False)
 
         if result == 0:
             if converge_bcs:
@@ -901,6 +901,7 @@ class wind_simulation:
     
 
     def ramp_grav(self, system, delta=0.02, converge_bcs=False, make_plot=True,
+                  verbose=False,
                   expedite=False, integrate_out=True, static_bcs=False):
         """
         Ramps planet mass and radius along lines of constant surface gravity with adaptive stepsizes.
@@ -1140,7 +1141,7 @@ class wind_simulation:
             expedite_flag_tuple[3] = self.windsoln.bolo_heat_cool 
             expedite_flag_tuple[0] = 1
             self.inputs.write_flags(*expedite_flag_tuple,integrate_out) #user defined integrate out will override
-        result = self.run_wind(verbose=True,calc_postfacto=False)
+        result = self.run_wind(verbose=verbose,calc_postfacto=False)
 
         if result == 0:
             if converge_bcs:
@@ -1161,7 +1162,7 @@ class wind_simulation:
         
 
     def ramp_star(self, system, delta=0.02, converge_bcs=True, make_plot=True,
-                  expedite=False, integrate_out=True, static_bcs=False):
+                  expedite=False, integrate_out=True, static_bcs=False,verbose=False):
         """
         Ramps stellar mass (Mstar), semimajor axis (semimajor), and stellar bolometric luminosity (Lstar).
         If Mstar and semimajor axis change, ramps linearly along Hill radius rate of change.
@@ -1403,7 +1404,7 @@ class wind_simulation:
                 return 1
             # Write ramped variables to input file and try updating relaxation
             self.inputs.write_planet_params(*temp.system_tuple())
-            result = self.run_wind(expedite=True,verbose=True,calc_postfacto=False)
+            result = self.run_wind(expedite=True,verbose=verbose,calc_postfacto=False)
             fail=0
             while result == 4:
                 fail+=1
@@ -3594,7 +3595,7 @@ class wind_simulation:
     
 #Spectrum tools    
     def flux_norm(self,goal_flux_in_range,eV_range=[13.6,100],ramp=False,plot=True,
-                 integrate_out=True,converge_bcs=True):
+                 integrate_out=True,converge_bcs=True,verbose=False):
         """
         Computes the total flux (across the loaded spectrum range) necessary to achieve the goal_flux_in_range in the eV_range identified. If ramp=True, also ramps the solution to that Ftot.
 
@@ -3619,7 +3620,7 @@ class wind_simulation:
         if ramp == True:
             if abs(goal_total_flux-self.windsoln.Ftot)/self.windsoln.Ftot > 0.01:
                 return self.ramp_var("Ftot",goal_total_flux,make_plot=plot,
-                                    converge_bcs=converge_bcs,integrate_out=integrate_out)
+                                    converge_bcs=converge_bcs,integrate_out=integrate_out,verbose=verbose)
             else:
                 self._normal_print("  Flux ramping already done.")
                 return 0
@@ -3631,7 +3632,7 @@ class wind_simulation:
     def ramp_spectrum(self,Fnorm=0.0,norm_spec_range=[],
                       goal_spec_range=[],units='eV',normalize=True,plot=False):
         """
-        Ramps stellar spectrum wavelength/energy range to new wavelength/energy range. To change to a monofrequncy spectrum, e.g., at 20 eV, set goal_spec_range=[20] or [20,20] and kind='mono'. (Note: for numerical reason, a `monofrequency' spectrum is actually two wavelength bins with the same wavelength and the appropriately normalized wPhi_wl/Ftot.)
+        Ramps stellar spectrum wavelength/energy range to new wavelength/energy range. To change to a monofrequncy spectrum, e.g., at 20 eV, set goal_spec_range=[20] or [20,20] and kind='mono'. (Note: for numerical reason, a ``monofrequency`` spectrum is actually two wavelength bins with the same wavelength and the appropriately normalized wPhi_wl/Ftot.)
 
         Args:
             Fnorm (float, optional): Flux in ergs/s/cm2 AT SEMIMAJOR AXIS OF PLANET. If 0.0, flux is normalized to the current value in norm_spec_range. Otherwise, ramps to given Fnorm. Defaults to 0.0.

{wind_ae-2.0.0 → wind_ae-2.0.2}/wind_ae/wrapper/wrapper_utils/plots.py

@@ -605,13 +605,17 @@ def energy_plot(windsoln, ax=None, alpha=1, plot_dom_lines=True, N_top_lines=2,
         r = windsoln.soln_norm['r']
 
         profiles = {}
-        for species in ['OI', 'OII', 'CI', 'CII', 'FeI', 'MgI','CaII', 'NeII']:
+        for species in ['OI', 'OII', 'CI', 'CII', 'FeI','FeII', 'MgI','MgII','CaI','CaII','NeII','NeIII']:
             if species in windsoln.species_list_unspaced:
                 species_spaced = McAtom.formatting_species_list([species])[0]
                 element_name, lowest_state = species_spaced.split()
                 highest_state = McAtom.arabic_to_roman(McAtom.roman_to_arabic(lowest_state) + 1)
-                ion_name = element_name + highest_state
-
+                lower_ion = element_name + lowest_state
+                higher_ion = element_name + highest_state
+                if lower_ion in coeff_table['Species'].values:
+                    ion_name = lower_ion
+                else:
+                    ion_name = higher_ion
                 lines = coeff_table.loc[coeff_table['Species'] == ion_name, 'Line'].astype(int).tolist()
                 for line_num in lines:
                     key = f'cool_{ion_name}_{line_num:.0f}A'

{wind_ae-2.0.0 → wind_ae-2.0.2}/wind_ae/wrapper/wrapper_utils/windsoln.py

@@ -368,7 +368,7 @@ class wind_solution:
         self.R_exo = np.nan
         # Skip unnecessary calculations when users is expediting windsoln
         if calc_postfacto:
-            self.add_user_vars(expedite = expedite_postfacto)
+            self.add_user_vars(expedite = expedite_postfacto, print_warnings=print_warnings)
             
 
     def _rate_coeff_interpolater(self,species):
@@ -881,8 +881,12 @@ class wind_solution:
                 highest_state = McAtom.arabic_to_roman(
                     McAtom.roman_to_arabic(lowest_state) + 1
                 )
-
-                ion_name = element_name + highest_state
+                lower_ion = element_name + lowest_state
+                higher_ion = element_name + highest_state
+                if lower_ion in coeff_table['Species'].values:
+                    ion_name = lower_ion
+                else:
+                    ion_name = higher_ion
                 mask = (coeff_table['Species'] == ion_name)
                 line, A, T_line, nc = (
                     coeff_table[mask]["Line"],
@@ -892,6 +896,7 @@ class wind_solution:
                 )
                 nIONj = self.soln["n_"+ion_name]
                 for idx in range(len(A.T)):
+                    # print(ion_name)
                     line_cool_cols[f'cool_{ion_name}_{line.iloc[idx]:.0f}A'] = (
                         -nIONj
                         * n_e
@@ -900,8 +905,9 @@ class wind_solution:
                         / (n_e * (1 + nc.iloc[idx] / n_e))
                     )
 
-            for species in ['OI', 'OII', 'CI', 'CII', 'FeI', 'MgI', 'CaI', 'NeII']:
+            for species in ['OI', 'OII', 'CI', 'CII', 'FeI', 'FeII', 'MgI', 'MgII', 'CaI', 'CaII', 'NeII', 'NeIII']:
                 if species in self.species_list_unspaced:
+                    # print(f"Computing line cooling for species: {species}")
                     compute_line_cool(species)
                 
             _assign_soln_cols(line_cool_cols)
@@ -1212,9 +1218,12 @@ class wind_solution:
     def calc_mu(self):
         '''Calculates mean molecular weight (mu in physical units, grams).
 
-        1/mu = sum_roots[mr_root * HX_root]  (one atom per atom, roots only)
-               + n_e * m_H / rho             (one entry per free electron)
-        Mirrors the refactored get_mu() in soe.c exactly.
+            ::
+
+                1/mu = sum_roots[mr_root * HX_root]  (one atom per atom, roots only)
+                    + n_e * m_H / rho             (one entry per free electron)
+
+            Mirrors the refactored ``get_mu()`` in ``soe.c`` exactly.
         '''
         if (self.species_list[0]).replace(" ", "") != "HI":
             if self.print_warnings is True:
@@ -1472,20 +1481,21 @@ class wind_solution:
 
 
     def calc_R_exo(self, Kn="Kn_mx_HI"):
-        '''Calculating exosphere radius in Rp and index. 
-        DEPRECATED, requires updated Knudsen number calculations for all species. 
-        
+        '''Calculating exosphere radius in Rp and index.
+        DEPRECATED, requires updated Knudsen number calculations for all species.
+
         Args:
-            Kn (str): Knudsen collision number for a given species. 
-                      Default: "Kn_mx_HI", which is a weighted mix of hardbody and Coulomb Kn for HI.
-                      Where a Kn > 1 indicates that the flow is collisionless for that species and a 
-                      fluid solution is no longer valid.
+            Kn (str): Knudsen collision number for a given species.
+                Default: "Kn_mx_HI", which is a weighted mix of hardbody and Coulomb
+                Kn for HI. A Kn > 1 indicates that the flow is collisionless for
+                that species and a fluid solution is no longer valid.
 
         Returns:
-            float: R_exo: exosphere radius in Rp. 
-                If Kn always < 1, then R_exo = NaN (R_exo is outside of the range of the simulation).
-                If R_exo > R_sp, then R_exo = Rmax
-            int: exo_index: index of exosphere radius in soln
+            float: R_exo: exosphere radius in Rp.
+                If Kn always < 1, then R_exo = NaN (R_exo is outside of the range
+                of the simulation).
+                If R_exo > R_sp, then R_exo = Rmax.
+            int: exo_index: index of exosphere radius in soln.
         '''
         try:
             index = self.soln[self.soln[Kn] > 1].index[0]

{wind_ae-2.0.0 → wind_ae-2.0.2/wind_ae.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: wind_ae
-Version: 2.0.0
+Version: 2.0.2
 Summary: 1D relaxation Parker wind model with metal and X-ray physics based on Murray-Clay et al. (2009)
 Author: Madelyn Broome, John McCann, Ruth Murray-Clay
 License-Expression: BSD-3-Clause
@@ -35,7 +35,7 @@ I <img src="docs/windae_logo_blue_light.png" alt="Wind-AE Logo" width="350"/>
 `Wind-AE` updates [Murray-Clay et al. (2009)](https://ui.adsabs.harvard.edu/abs/2009ApJ...693...23M/abstract) to allow for the modeling of atomic metals and multifrequency XUV stellar spectra (Broome et al. 2025). If you use `Wind-AE`, please cite [Broome et al. (2025)](https://ui.adsabs.harvard.edu/abs/2025ApJ...995..198B/abstract). 
 
 
-Take advantage of `Notebooks/Quickstart.ipynb` to get a quick orientation to `Wind-AE` and please report any bugs via [Github](https://github.com/mabroome/wind-ae/issues) or via email to broome.astro@gmail.com.
+Take advantage of `Notebooks/Quickstart.ipynb` to get a quick orientation to `Wind-AE` and please report any bugs via [Github](https://github.com/mibroome/wind-ae/issues) or via email to broome.astro@gmail.com.
 
 ![Build Status](https://github.com/mibroome/wind-ae/actions/workflows/python-pkg.yml/badge.svg)
 [![Coverage Status](https://coveralls.io/repos/github/mibroome/wind-ae/badge.svg?branch=main)](https://coveralls.io/github/mibroome/wind-ae?branch=main)
@@ -53,7 +53,7 @@ Take advantage of `Notebooks/Quickstart.ipynb` to get a quick orientation to `Wi
 
 Is Wind-AE the right tool for me?
 ----------------------
-`Wind-AE` is well-suited for users interested in **quickly estimating mass loss rates** or outflow structure. Outflow structure includes bulk temperature and per-species ionization fractions as a function of radius, so can be easily translated into approximating and **predicting observables and transits**, including metastable helium (He 10830$\AA$) transits, though a He transit module is not yet included. Precise modeling of lower atmosphere ($\lssim 100 \mu$bar) is considered necessary for highly accurate transit models, but Wind-AE can be easily coupled to lower atmosphere photochemistry models whose outputs can (e.g., radius, temperature, abundances, ionization fractions, etc. at 1 $\mu$bar) can be fed into Wind-AE as inputs.  
+`Wind-AE` is well-suited for users interested in **quickly estimating mass loss rates** or outflow structure. Outflow structure includes bulk temperature and per-species ionization fractions as a function of radius, so can be easily translated into approximating and **predicting observables and transits**, including metastable helium (He 10830 Å) transits, though a He transit module is not yet included. Precise modeling of lower atmosphere (< ~100 $\mu$bar) is considered necessary for highly accurate transit models, but Wind-AE can be easily coupled to lower atmosphere photochemistry models whose outputs can (e.g., radius, temperature, abundances, ionization fractions, etc. at 1 $\mu$bar) can be fed into Wind-AE as inputs.  
 
 >*If you are interested in outflow structure:* Past the Coriolis turning radius (a few planetary radii) 3D physics dominates, so `Wind-AE` does not integrate past that point. `Wind-AE` also makes simplifying assumptions about the region below the region below the wind-launch radius (~10 nanobars). 
 
@@ -64,11 +64,11 @@ Because `Wind-AE` runs on the order of seconds to minutes, it can be (and has be
 - Multiple ionization states of the same species (e.g., simultaneously tracking C I and C II as a linked ionization chain)
 - X-ray physics (secondary ionizations and K-shell ionization cross-sections for relevant metals)
 - Both low and high stellar XUV flux
-- **Heating & Cooling**: Ionization heating, bolometric heating & cooling (negligible in wind), PdV cooling (work done due to expansion of gas), radiative / atomic line cooling (Lyman-$\alpha$; O, C, Fe, Mg, Ca, and Ne lines), recombination cooling, free-free (bremsstrahlung) cooling, and, optionally, self-consistent conductive cooling (see note below)
+- **Heating & Cooling**: Ionization heating, bolometric heating & cooling (negligible in wind), PdV cooling (work done due to expansion of gas), radiative / atomic line cooling (Lyman-alpha; O, C, Fe, Mg, Ca, and Ne lines), recombination cooling, free-free (bremsstrahlung) cooling, and, optionally, self-consistent conductive cooling (see note below)
 #### `Wind-AE` does not (currently) include:
 - **Magnetic fields**
 - **Time dependence**
-- **Diffusion/drag** - the atomic species set by the user are assumed to be entrained in the outflow and in thermal equilibrium. This is an appropriate assumption for species below the [crossover mass](https://ui.adsabs.harvard.edu/abs/1987Icar...69..532H) and a warning will be raised.
+- **Fractionation/diffusion/drag** - the atomic species set by the user are assumed to be entrained in the outflow and in thermal equilibrium. This is an appropriate assumption for species below the [crossover mass](https://ui.adsabs.harvard.edu/abs/1987Icar...69..532H) and a warning will be raised.
 - **Heating & Cooling**: H3+ line cooling (not planned)
 
 > **Note (v2.0+):** Conductive, recombination, and free-free cooling are each independently toggleable via flags. Turning on conduction (`sim.turn_on_conduction()`) introduces numerically stiff ODEs and should only be done after all other ramping is complete. The temperature dependence of free-free and recombination cooling can make ramping to higher metallicities numerically unstable — if so, try ramping with them off and turning them back on afterwards.
@@ -85,7 +85,7 @@ See [Broome et al. (2025)](https://ui.adsabs.harvard.edu/abs/2025ApJ...995..198B
 - Just want a grid of mass loss rates for pure-Hydrogen, low-flux-EUV-irradiated planets? See [Kubyshkina & Fossati](https://ui.adsabs.harvard.edu/abs/2021RNAAS...5...74K/abstract) 
 - Want a grid of mass loss rates for pure-Hydrogen, high-flux-XUV-irradiated planets? See [Owen & Jackson (2012)](https://ui.adsabs.harvard.edu/abs/2012MNRAS.425.2931O/abstract)
 
->Want your model added to this list or to update the short bio? Email mabroome@ucsc.edu
+>Want your model added to this list or to update the short bio? Email broome.astro@gmail.com
 
 Requirements
 ------------
@@ -199,8 +199,8 @@ sim.ramp_molecular_erfc(v_drop=erf_loc, rate=erf_rate)
 - **(v2.0)** Ramping to high metallicity with recombination and/or free-free cooling on can be numerically unstable in some cases — see the cooling-flags note above.
 
 --------
-### Check out the [open issues](https://github.com/mabroome/wind-ae/issues).
+### Check out the [open issues](https://github.com/mibroome/wind-ae/issues).
 
 --------
 ## AI Use Statement
-We used Claude web (primarily model Sonnet 5.0) in `Wind-AE`'s v2.0 development to assist with refactoring `Wind-AE` for runtime improvements, with the implementation of the conductive cooling scheme in the code, and updating the docs for v2.0 release. All scientific content, methodology, and interpretations are the authors' own. The authors have reviewed and verified all code, outputs, and text, and take full responsibility for the integrity and accuracy of the work.
+Claude web (primarily model Sonnet 5.0) was used in `Wind-AE`'s v2.0 development to assist with refactoring `Wind-AE` for runtime improvements, with the implementation of the conductive cooling scheme in the code, and updating the docs for v2.0 release. All scientific content, methodology, and interpretations are the authors' own. The authors have reviewed and verified all code, outputs, and text, and take full responsibility for the integrity and accuracy of the work.