wind_ae 0.2.0__tar.gz

wind_ae-0.2.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2025, Madelyn Broome
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

wind_ae-0.2.0/MANIFEST.in

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+include wind_ae/wrapper/wrapper_utils/*.dat
+include wind_ae/McAstro/atoms/Lodders.dat
+include wind_ae/McAstro/atoms/*.txt
+include wind_ae/McAstro/atoms/*.csv
+include wind_ae/saves/*.csv
+include wind_ae/inputs/*

wind_ae-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: wind_ae
+Version: 0.2.0
+Summary: 1D relaxation Parker wind model based on Murray-Clay et al. (2009)
+Author: Madelyn Broome, John McCann, Ruth Murray-Clay
+Requires-Python: >=3.13
+License-File: LICENSE
+Requires-Dist: scipy>1.6
+Requires-Dist: numpy
+Requires-Dist: astropy
+Requires-Dist: IPython
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: matplotlib
+Requires-Dist: datetime
+Requires-Dist: pyarrow
+Requires-Dist: fastparquet
+Requires-Dist: requests
+Requires-Dist: ChiantiPy
+Dynamic: license-file

wind_ae-0.2.0/README.md

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+# Wind-AE (BETA)
+
+`Wind-AE` (/windy/) stands for "wind atmospheric escape" and is a relatively fast 1D, steady-state, hydrodynamic, non-isothermal, Parker wind relaxation code for modeling atmospheric escape based on [Murray-Clay et al. (2009)](https://ui.adsabs.harvard.edu/abs/2009ApJ...693...23M/abstract). `Wind-AE` is a forward model that solves the energy conservation, momentum conservation, and ionization equilibrium equations at the substellar point using the ["Numerical Recipes in C"](https://ui.adsabs.harvard.edu/abs/1992nrca.book.....P/abstract) relaxation method. This allows `Wind-AE` to quickly compute the atmosphere mass loss rate as well as upper atmosphere (<~100 microbar) velocity, temperature, density, and ionization structure as a function of altitude. 
+
+`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. submitted). If you use `Wind-AE`, please consider citing Broome et al. (in prep). 
+
+
+We appreciate your patience while the docs are developed. In the meantime, 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 mabroome@ucsc.edu.
+
+[![A rectangular badge, half black half purple containing the text made at Code Astro](https://img.shields.io/badge/Made%20at-Code/Astro-blueviolet.svg)](https://semaphorep.github.io/codeastro/)
+
+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.  
+
+>*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). 
+
+Because `Wind-AE` runs on the order of seconds to minutes, it can be (and has been) used to **model planet evolution**.
+
+#### `Wind-AE` can model:
+- Multiple atomic species
+- 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-$\alpha$, OI, OII, OIII, CI, CII), recombination cooling
+#### `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.
+- **Heating & Cooling**: Conduction (warning raised if relevant, **planned**), H3+ line cooling (not planned), Fe & Ca  line cooling (relevant at high Z only, **planned**), free-free cooling (warning raised if relevant, not planned) 
+- Multiple ionization states of the same species (**planned**)
+See Broome et al. (submitted) for more details.
+
+- Want a rapid H/He model with power-law approximated XUV spectra? Check out [ATES](https://github.com/AndreaCaldiroli/ATES-Code) ([Caldiroli et al. 2021](https://ui.adsabs.harvard.edu/abs/2021A%26A...655A..30C/abstract))
+- Do you want to set the mass loss rate ($\dot{M}$) yourself or want an EUV isothermal Parker wind outflow model that runs in nanoseconds? Check out [p-winds](https://github.com/ladsantos/p-winds) ([Dos Santos et al. 2022](https://ui.adsabs.harvard.edu/abs/2022A%26A...659A..62D/abstract)).
+- Do you want to use p-winds and get transit models for metals via Cloudy? Check out [Sunbather](https://github.com/antonpannekoek/sunbather) ([Linssen et al. 2024](https://ui.adsabs.harvard.edu/abs/2024A%26A...688A..43L/abstract))
+- Want to leverage Cloudy and the hydrodynamic code PLUTO for more thorough XUV-irradiated, but slightly more expensive calculations? Check out TPCI ([Salz et al. 2015](https://ui.adsabs.harvard.edu/abs/2015A%26A...576A..21S/abstract))
+- That sound great, but you prefer to code in Python over C/C++? Check out pyTPCI [Riley, Zhang, & Bean 2025](https://ui.adsabs.harvard.edu/abs/2025ApJ...980...34R/abstract)
+- Do you care about diffusion throughout the wind? Check out [AIOLIS](https://github.com/Schulik/aiolos) ([Schulik & Booth, 2022](https://ui.adsabs.harvard.edu/abs/2023MNRAS.523..286S/abstract)).
+- Want to model the lower atmosphere in more detail? Check out CETIMB (Koskinen et al. 2022)
+- 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
+
+Requirements
+------------
+
+`Wind-AE` requires the following packages and will pip install them automatically by following the Installation guide below.
+
+* `python` 
+* `numpy` 
+* `scipy`
+* `astropy`
+* `pandas`>=2.2.3
+* `matplotlib` 
+* `datetime`
+* `pyarrow` 
+* `fastparquet`
+* `requests` 
+* `ChiantiPy`
+
+Installation
+------------
+### Compile from source (only available in beta)
+
+Clone the repository using
+```angular2html
+git clone https://github.com/mibroome/wind-ae/
+```
+or navigate to [github.com/mibroome/wind-ae/](https://github.com/mibroome/wind-ae/) and download and unzip the zip file.
+
+Until `Wind-AE` is dockerized, it is recommended to use a Python environment to avoid dependency issues. However, if your system meets the above requirements, there is no need to create an environment and you can skip to the compilation step.
+To create an environment use either
+```angular2html
+python3 -m venv venv_name.venv
+source venv_name.venv/bin/activate
+```
+or using `conda`
+```angular2html
+conda create -n venv_name
+conda activate venv_name
+conda install pip
+```
+
+To compile from the source,
+```angular2html
+python3 -m pip install -e .
+```
+
+REMEMBER to `make` the C code before running `Wind-AE` for the first time.
+```angular2html
+cd wind_ae/wind_ae/
+make
+```
+You can ignore any warnings that pop up.
+
+You can test the install by running
+```angular2html
+python -c "import wind_ae"
+```
+
+Now you can run `Wind-AE` from anywhere! As seen in the tutorial (`Notebooks/Quickstart.ipynb`), the following imports are helpful for most purposes. 
+```angular2html
+from wind_ae.wrapper.relax_wrapper import wind_simulation as wind_sim
+from wind_ae.wrapper.wrapper_utils.plots import energy_plot six_panel_plot quick_plot 
+from wind_ae.wrapper.wrapper_utils import constants as const
+from wind_ae.wrapper.wrapper_utils.system import system
+from wind_ae.wrapper.wrapper_utils.spectrum import spectrum
+```
+
+> **Note**: If you ever need to interface directly with the `C` code, it lives in `wind_ae/src/` and can be excecuted from within the `wind_ae/` folder via `./bin/relaxed_ae`. The solution generated will be for a planet with the parameters detailed in the input files in the `Inputs/` folder. There is generally no need to interface with the `C` code and most standard tasks can be accomplished by using the Python wrapper.
+
+Future features and known problems
+--------
+Check out the [open issues](https://github.com/mabroome/wind-ae/issues).

wind_ae-0.2.0/docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../wind_ae/'))
+sys.path.insert(0, os.path.abspath('../wind_ae/wrapper/'))
+sys.path.insert(0, os.path.abspath('../wind_ae/wrapper/wrapper_utils/'))
+
+
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'Wind-AE'
+copyright = '2025, Madelyn Broome, John McCann, Ruth Murray-Clay'
+author = 'Madelyn Broome, John McCann, Ruth Murray-Clay'
+release = '0.2.0'
+root_doc = 'index'
+autodoc_member_order = 'bysource'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.napoleon", "nbsphinx"]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']

wind_ae-0.2.0/pyproject.toml

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+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "wind_ae"
+version = "0.2.0"
+description = "1D relaxation Parker wind model based on Murray-Clay et al. (2009)"
+authors = [
+    { name = "Madelyn Broome" },
+    { name = "John McCann" },
+    { name = "Ruth Murray-Clay" }
+]
+requires-python = ">=3.13"
+
+dependencies = [
+    "scipy>1.6",
+    "numpy", 
+    "astropy",
+    "IPython",
+    "pandas>=2.2.3",
+    "matplotlib", 
+    "datetime", 
+    "pyarrow", 
+    "fastparquet",
+    "requests",
+    "ChiantiPy",
+]
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages]
+find = {}

wind_ae-0.2.0/saves/setup.py

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+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+import sys
+
+try:
+    from setuptools import setup, find_packages
+except ImportError:
+    from distutils.core import setup
+
+setup(
+    name="wind_ae",
+    version="1.0",
+    author='Madelyn Broome, John McCann, Ruth Murray-Clay',
+    author_email='mabroome@ucsc.edu',
+    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()],
+    packages=find_packages(),
+    package_data={
+        'wind_ae': ['wind_ae/wrapper/wrapper_utils/*.dat',
+                    'wind_ae/saves/*.csv',
+                    'wind_ae/inputs/*', 
+                    'wind_ae/McAstro/atoms/*.csv',
+                    'wind_ae/McAstro/atoms/*.txt',
+                    'wind_ae/McAstro/atoms/Lodders.dat'],  # include all .txt files in the data folder
+    },
+    include_package_data=True,
+)

wind_ae-0.2.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

wind_ae-0.2.0/wind_ae/McAstro/__init__.py

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+import os
+import importlib
+
+__version__ = "0.1"
+
+class McAstroIS:
+    """
+    McAstro import status
+    """
+    def __init__(self):
+        """
+        Try to import all packages contained in self.packages and save status.
+        """
+        self.packages = []
+        self.findpackages()
+        self.importStatus = {}
+        for m in self.packages:
+            try:
+                importlib.import_module("." + m, "McAstro")
+                self.importStatus[m] = True
+            except Exception:
+                self.importStatus[m] = False
+            
+    def findpackages(self):
+        for root, dirs, fns in os.walk(__path__[0]):
+            for dir_ in dirs:
+                if os.path.isfile(os.path.join(__path__[0], dir_,
+                                               "__init__.py")):
+                    self.packages.append(dir_)
+            break;
+    
+    def showStatus(self):
+        print() 
+        print("               McAstro import status")
+        print("--------------------------------------------------")
+        print("{:41s} | {:6s}".format("Package", "Loaded"))
+        print("--------------------------------------------------")
+        for m, v in sorted(self.importStatus.items()):
+            print("{:41s} | {}".format(m, v))
+        
+
+def importCheck():
+    m = McAstroIS()
+    m.showStatus()

wind_ae-0.2.0/wind_ae/McAstro/atoms/Lodders.dat

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+#Lodders 2009
+Z name source N_per_Si err A err2
+1 H s 2.93E+10 0 12.00 0
+2 He s 2.47E+09 0.12E+09 10.93 0.02
+3 Li m 55.6 7.2 3.28 0.05
+4 Be m 0.612 0.043 1.32 0.03
+5 B m 18.8 1.9 2.81 0.04
+6 C s 7.19E+06 0.69E+06 8.39 0.04
+7 N s 2.12E+06 0.68E+06 7.86 0.12
+8 O s 1.57E+07 0.28E+07 8.73 0.07
+9 F m 804 121 4.44 0.06
+10 Ne s 3.29E+06 0.85E+06 8.05 0.10
+11 Na a 57700 5100 6.29 0.04
+12 Mg a 1.03E+06 0.15E+06 7.54 0.06
+13 Al a 84600 15300 6.46 0.07
+14 Si m 1.00E+06 0.03E+06 7.53 0.01
+15 P a 8300 1100 5.45 0.05
+16 S a 4.21E+05 0.24E+05 7.16 0.02
+17 Cl m 5170 780 5.25 0.06
+18 Ar s 92700 24000 6.50 0.10
+19 K a 3760 330 5.11 0.04
+20 Ca m 60400 3000 6.31 0.02
+21 Sc m 34.4 1.7 3.07 0.02
+22 Ti m 2470 200 4.93 0.03
+23 V a 286 20 3.99 0.03
+24 Cr a 13100 500 5.65 0.02
+25 Mn m 9220 280 5.50 0.01
+26 Fe a 8.48E+05 1.69E+05 7.46 0.08
+27 Co a 2350 500 4.90 0.08
+28 Ni a 49000 5000 6.22 0.04
+29 Cu m 541 54 4.27 0.04
+30 Zn m 1300 130 4.65 0.04
+31 Ga m 36.6 1.8 3.10 0.02
+32 Ge a 115 18 3.59 0.06
+33 As m 6.10 0.55 2.32 0.04
+34 Se m 67.5 4.7 3.36 0.03
+35 Br m 10.7 1.6 2.56 0.06
+36 Kr t 55.8 11.3 3.28 0.08
+37 Rb m 7.10 0.50 2.38 0.03
+38 Sr m 23.4 1.6 2.90 0.03
+39 Y a 4.63 0.50 2.20 0.04
+40 Zr a 10.8 1.2 2.57 0.04
+41 Nb a 0.780 0.139 1.42 0.07
+42 Mo a 2.55 0.40 1.94 0.06
+44 Ru m 1.78 0.11 1.78 0.03
+45 Rh a 0.370 0.128 1.10 0.13
+46 Pd a 1.36 0.15 1.67 0.04
+47 Ag m 0.489 0.024 1.22 0.02
+48 Cd m 1.57 0.11 1.73 0.03
+49 In m 0.178 0.012 0.78 0.03
+50 Sn m 3.60 0.54 2.09 0.06
+51 Sb m 0.313 0.047 1.03 0.06
+52 Te m 4.69 0.33 2.20 0.03
+53 I m 1.10 0.22 1.57 0.08
+54 Xe t 5.46 1.10 2.27 0.08
+55 Cs m 0.371 0.019 1.10 0.02
+56 Ba a 4.47 0.81 2.18 0.07
+57 La m 0.457 0.023 1.19 0.02
+58 Ce a 1.18 0.19 1.60 0.06
+59 Pr a 0.172 0.020 0.77 0.05
+60 Nd m 0.857 0.043 1.47 0.02
+62 Sm m 0.265 0.013 0.96 0.02
+63 Eu a 0.0984 0.0106 0.53 0.04
+64 Gd a 0.360 0.049 1.09 0.06
+65 Tb m 0.0634 0.0044 0.34 0.03
+66 Dy a 0.404 0.062 1.14 0.06
+67 Ho m 0.0910 0.0064 0.49 0.03
+68 Er a 0.262 0.042 0.95 0.06
+69 Tm m 0.0406 0.0028 0.14 0.03
+70 Yb m 0.256 0.013 0.94 0.02
+71 Lu m 0.0380 0.0019 0.11 0.02
+72 Hf m 0.156 0.008 0.73 0.02
+73 Ta m 0.0210 0.0021 -0.14 0.04
+74 W m 0.137 0.014 0.67 0.04
+75 Re m 0.0554 0.0055 0.28 0.04
+76 Os m 0.680 0.054 1.37 0.03
+77 Ir a 0.672 0.092 1.36 0.06
+78 Pt m 1.27 0.10 1.64 0.03
+79 Au m 0.195 0.019 0.82 0.04
+80 Hg m 0.458 0.092 1.19 0.08
+81 Tl m 0.182 0.015 0.79 0.03
+82 Pb m 3.33 0.23 2.06 0.03
+83 Bi m 0.138 0.012 0.67 0.04
+90 Th m 0.0351 0.0028 0.08 0.03
+92 U m 0.00893 0.00071 -0.52 0.03

wind_ae-0.2.0/wind_ae/McAstro/atoms/Verner.csv

@@ -0,0 +1,191 @@
+# Z: number of protons
+# Ne: number of electrons
+# E_th: Ionization potential (in eV)
+# E_max: Value which cross-section should not be extrapolated past
+# sigma_0 (in MB), E_0 (in eV), y_a, P, y_w, y_0, y_1: fitted parameters
+Z,Ne,E_th,E_max,E_0,sigma_0,y_a,P,y_w,y_0,y_1
+1,1,1.360E+01,5.000E+04,4.298E-01,5.475E+04,3.288E+01,2.963E+00,0.000E+00,0.000E+00,0.000E+00
+2,2,2.459E+01,5.000E+04,1.361E+01,9.492E+02,1.469E+00,3.188E+00,2.039E+00,4.434E-01,2.136E+00
+2,1,5.442E+01,5.000E+04,1.720E+00,1.369E+04,3.288E+01,2.963E+00,0.000E+00,0.000E+00,0.000E+00
+3,3,5.392E+00,6.439E+01,3.107E+00,6.245E+01,1.501E+01,4.895E+00,0.000E+00,0.000E+00,0.000E+00
+3,2,7.564E+01,5.000E+04,2.006E+01,3.201E+02,7.391E+00,2.916E+00,0.000E+00,0.000E+00,0.000E+00
+3,1,1.225E+02,5.000E+04,3.871E+00,6.083E+03,3.288E+01,2.963E+00,0.000E+00,0.000E+00,0.000E+00
+4,4,9.323E+00,1.193E+02,9.539E+00,2.932E+05,4.301E-01,1.052E+01,3.655E-01,8.278E-04,1.269E-02
+4,3,1.821E+01,1.299E+02,1.181E+00,2.678E+02,5.645E+00,1.170E+01,0.000E+00,0.000E+00,0.000E+00
+4,2,1.539E+02,5.000E+04,1.760E+01,5.458E+02,1.719E+01,3.157E+00,0.000E+00,0.000E+00,0.000E+00
+4,1,2.177E+02,5.000E+04,6.879E+00,3.422E+03,3.288E+01,2.963E+00,0.000E+00,0.000E+00,0.000E+00
+5,5,8.298E+00,1.940E+02,5.213E-01,5.466E+00,8.618E+00,1.728E+01,1.887E+01,1.319E+01,4.556E+00
+5,4,2.516E+01,2.098E+02,2.869E+00,1.859E+04,1.783E+00,1.618E+01,3.503E+00,4.960E-03,3.400E-02
+5,3,3.793E+01,2.274E+02,1.041E+00,5.393E+01,1.767E+01,9.540E+00,0.000E+00,0.000E+00,0.000E+00
+5,2,2.594E+02,5.000E+04,3.336E+01,2.846E+02,2.163E+01,2.624E+00,0.000E+00,0.000E+00,0.000E+00
+5,1,3.402E+02,5.000E+04,1.075E+01,2.190E+03,3.288E+01,2.963E+00,0.000E+00,0.000E+00,0.000E+00
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