Package: acepython
ACEPython - An equilibrium chemistry codeIntroduction|Usage|TauREx 3|Citing ACEPythonIntroductionACEPython is a Python wrapper for the FORTRAN equilibrium chemistry code developed byAgúndez et al. 2012. It can rapidly compute the equilibirum chemical scheme for a given temperature and pressure.InstallationACEPython can be installed with prebuilt wheels using pip:pipinstallacepythonOr, if you prefer, you can build it from source which requires a FORTRAN and C compiler. The following commands will build and install ACEPython:gitclonehttps://github.com/ucl-exoplanets/acepython.gitcdacepython
pipinstall.UsageACEPython can be used to compute the equilibrium chemistry for a given temperature and pressure. Temperature and pressure must be created with astropy units. For pressure, any unit can be used (Pa, bar etc). The following example shows how to compute the equilibrium chemistry for a column of atmosphere:fromacepythonimportrun_acefromastropyimportunitsasuimportnumpyasnpimportmatplotlib.pyplotasplttemperature=np.linspace(3000,1000,100)<<u.Kpressure=np.logspace(6,-2,100)<<u.barspecies,mix_profile,mu_profile=run_ace(temperature,pressure,)species_to_see=["H2","H20","CH4","NH3","C2H2","CO","CO2","H2CO"]fig,(ax1,ax2)=plt.subplots(1,2,figsize=(10,5))fori,specinenumerate(species):ifspecinspecies_to_see:ax1.plot(mix_profile[i],pressure,label=spec)ax1.set_yscale("log")ax1.set_xscale("log")ax1.invert_yaxis()ax1.set_ylabel("Pressure (bar)")ax1.set_xlabel("VMR")ax1.legend()ax2.plot(mu_profile,pressure)ax2.set_yscale("log")ax2.invert_yaxis()ax2.set_ylabel("Pressure (bar)")ax2.set_xlabel("Mean molecular weight (au)")plt.show()Should produce the following figure:Custom chemical schemeBy default the elements in the chemical scheme are H, He, C, N, O at log abundances 12, 10.93, 8.39, 7.86, 8.73 respectively. The abundances can be changed by passing the elements and corresponding abundances to therun_acefunction:species,mix_profile,mu_profile=run_ace(temperature,pressure,elements=["H","He","C","N","O"],abundances=[12,10.93,8.39,7.86,7.73],)where we have changedOto have a log abundance of7.73.You can customize the species included by passing in thermochemical and species data files.For example, if we have a custom thermochemical data file calledcustom_thermochemical_data.datand a custom species data file calledcustom_species_data.datthat includes sulphur we can run ACEPython with:species,mix_profile,mu_profile=run_ace(temperature,pressure,elements=["H","He","C","N","O","S"],abundances=[12,10.93,8.39,7.86,7.73,7.0],thermochemical_data="custom_thermochemical_data_w_S.dat",species_data="custom_species_data_w_S.dat",)TauREx3ACEPython also includes a plugin forTauREx 3.1that allows you to use ACEPython as a chemistry scheme. In the input file you can select it in theChemistrysection using acepython with arguments:[Chemistry]chemistry=acepython# He/H ratio (optional)he_h_ratio=0.83# Elements excluding H, He (optional)elements=C,N,O# log abundances (optional)abundances=8.39,7.86,8.73# Custom species data file (optional)spec_file=custom_species_data.dat# Custom thermochemical data file (optional)thermo_file=custom_thermochemical_data.datCiting ACEPythonIf you use ACEPython in your research, please cite the following papers:@ARTICLE{Agundez2012,author={{Ag{\'u}ndez}, M. and {Venot}, O. and {Iro}, N. and {Selsis}, F. and{Hersant}, F. and {H{'e}brard}, E. and {Dobrijevic}, M.},title="{The impact of atmospheric circulation on the chemistry of the hot Jupiter HD 209458b}",journal={A\&A},keywords={astrochemistry, planets and satellites: atmospheres, planets and satellites: individual: HD 209458b, Astrophysics - Earth and Planetary Astrophysics},year="2012",month="Dec",volume={548},eid={A73},pages={A73},doi={10.1051/0004-6361/201220365},archivePrefix={arXiv},eprint={1210.6627},primaryClass={astro-ph.EP},adsurl={https://ui.adsabs.harvard.edu/abs/2012A&A...548A..73A},adsnote={Provided by the SAO/NASA Astrophysics Data System}}@ARTICLE{2021ApJ...917...37A,author={{Al-Refaie}, A.~F. and {Changeat}, Q. and {Waldmann}, I.~P. and {Tinetti}, G.},title="{TauREx 3: A Fast, Dynamic, and Extendable Framework for Retrievals}",journal={\apj},keywords={Open source software, Astronomy software, Exoplanet atmospheres, Radiative transfer, Bayesian statistics, Planetary atmospheres, Planetary science, 1866, 1855, 487, 1335, 1900, 1244, 1255, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics},year=2021,month=aug,volume={917},number={1},eid={37},pages={37},doi={10.3847/1538-4357/ac0252},archivePrefix={arXiv},eprint={1912.07759},primaryClass={astro-ph.IM},adsurl={https://ui.adsabs.harvard.edu/abs/2021ApJ...917...37A},adsnote={Provided by the SAO/NASA Astrophysics Data System}}@ARTICLE{2022ApJ...932..123A,author={{Al-Refaie}, A.~F. and {Changeat}, Q. and {Venot}, O. and {Waldmann}, I.~P. and {Tinetti}, G.},title="{A Comparison of Chemical Models of Exoplanet Atmospheres Enabled by TauREx 3.1}",journal={\apj},keywords={Open source software, Publicly available software, Chemical abundances, Bayesian statistics, Exoplanet atmospheres, Exoplanet astronomy, Exoplanet atmospheric composition, Exoplanets, Radiative transfer, 1866, 1864, 224, 1900, 487, 486, 2021, 498, 1335, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics},year=2022,month=jun,volume={932},number={2},eid={123},pages={123},doi={10.3847/1538-4357/ac6dcd},archivePrefix={arXiv},eprint={2110.01271},primaryClass={astro-ph.EP},adsurl={https://ui.adsabs.harvard.edu/abs/2022ApJ...932..123A},adsnote={Provided by the SAO/NASA Astrophysics Data System}}