forked from antonpannekoek/sunbather
-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
1 changed file
with
121 additions
and
72 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,106 +1,155 @@ | ||
| import os | ||
| import sys | ||
|
|
||
| #sunbather imports | ||
| import sunbather.tools as tools | ||
| import sunbather.RT as RT | ||
|
|
||
| #other imports | ||
| # other imports | ||
| import pandas as pd | ||
| import numpy as np | ||
| from scipy.interpolate import interp1d | ||
| import shutil | ||
|
|
||
| # sunbather imports | ||
| from sunbather import tools, RT | ||
|
|
||
|
|
||
| print("\nWill perform installation check by running the three main sunbather modules and checking if the output is as expected. " \ | ||
| +"Expected total run-time: 10 to 60 minutes. Should print 'success' at the end.\n") | ||
| # the absolute path where this code lives | ||
| this_path = os.path.dirname(os.path.abspath(__file__)) | ||
| src_path = this_path.split('tests')[-2] + 'src/' | ||
|
|
||
| ### SETUP CHECKS ### | ||
| print( | ||
| "\nWill perform installation check by running the three main sunbather modules and checking if the output is as expected. " | ||
| + "Expected total run-time: 10 to 60 minutes. Should print 'success' at the end.\n" | ||
| ) | ||
|
|
||
| #make sure projectpath exists | ||
| assert os.path.isdir(tools.projectpath), "Please create the projectpath folder on your machine" | ||
| #make sure the planets.txt file exists | ||
| assert os.path.isfile(tools.projectpath+'/planets.txt'), "Please make sure the 'planets.txt' file is present in $SUNBATHER_PROJECT_PATH" | ||
| #make sure the SED we need for this test has been copied to Cloudy | ||
| assert os.path.isfile(tools.cloudypath+'/data/SED/eps_Eri_binned.spec'), "Please copy /sunbather/stellar_SEDs/eps_Eri_binned.spec into $CLOUDY_PATH/data/SED/" | ||
| # SETUP CHECKS | ||
|
|
||
| # make sure projectpath exists | ||
| assert os.path.isdir( | ||
| tools.projectpath | ||
| ), "Please create the projectpath folder on your machine" | ||
| # make sure the planets.txt file exists | ||
| assert os.path.isfile( | ||
| tools.projectpath + "/planets.txt" | ||
| ), "Please make sure the 'planets.txt' file is present in $SUNBATHER_PROJECT_PATH" | ||
| # make sure the SED we need for this test has been copied to Cloudy | ||
| assert os.path.isfile( | ||
| tools.cloudypath + "/data/SED/eps_Eri_binned.spec" | ||
| ), "Please copy /sunbather/stellar_SEDs/eps_Eri_binned.spec into $CLOUDY_PATH/data/SED/" | ||
|
|
||
|
|
||
| ### CHECK IF test.py HAS BEEN RAN BEFORE ### | ||
| # ## CHECK IF test.py HAS BEEN RAN BEFORE ### | ||
|
|
||
| parker_profile_file = tools.projectpath+"/parker_profiles/WASP52b/test/pprof_WASP52b_T=9000_M=11.000.txt" | ||
| simulation_folder = tools.projectpath+"/sims/1D/WASP52b/test/parker_9000_11.000/" | ||
| parker_profile_file = ( | ||
| tools.projectpath | ||
| + "/parker_profiles/WASP52b/test/pprof_WASP52b_T=9000_M=11.000.txt" | ||
| ) | ||
| simulation_folder = tools.projectpath + "/sims/1D/WASP52b/test/parker_9000_11.000/" | ||
|
|
||
| if os.path.exists(parker_profile_file) or os.path.exists(simulation_folder): | ||
| confirmation = input(f"It looks like test.py has been ran before, as {parker_profile_file} and/or {simulation_folder} already exist. Do you want to delete the previous output before continuing (recommended)? (y/n): ") | ||
| if confirmation.lower() == "y": | ||
| if os.path.exists(parker_profile_file): | ||
| os.remove(parker_profile_file) | ||
| if os.path.exists(simulation_folder): | ||
| shutil.rmtree(simulation_folder) | ||
| print("\nFile(s) deleted successfully.") | ||
| else: | ||
| print("\nDeletion cancelled.") | ||
|
|
||
|
|
||
|
|
||
| print("\nChecking construct_parker.py. A runtime for this module will follow when done...\n") | ||
| confirmation = input( | ||
| f"It looks like test.py has been ran before, as {parker_profile_file} and/or {simulation_folder} already exist. Do you want to delete the previous output before continuing (recommended)? (y/n): " | ||
| ) | ||
| if confirmation.lower() == "y": | ||
| if os.path.exists(parker_profile_file): | ||
| os.remove(parker_profile_file) | ||
| if os.path.exists(simulation_folder): | ||
| shutil.rmtree(simulation_folder) | ||
| print("\nFile(s) deleted successfully.") | ||
| else: | ||
| print("\nDeletion cancelled.") | ||
|
|
||
|
|
||
| print( | ||
| "\nChecking construct_parker.py. A runtime for this module will follow when done...\n" | ||
| ) | ||
|
|
||
| ### CREATING PARKER PROFILE ### | ||
|
|
||
| #create a parker profile - we use the p-winds/Cloudy hybrid scheme | ||
| os.system(f"cd {tools.sunbatherpath} && python construct_parker.py -plname WASP52b -pdir test -Mdot 11.0 -T 9000 -z 10 -zelem Ca=0 -overwrite") | ||
| #load the created profile | ||
| pprof_created = pd.read_table(tools.projectpath+'/parker_profiles/WASP52b/test/pprof_WASP52b_T=9000_M=11.000.txt', | ||
| names=['alt', 'rho', 'v', 'mu'], dtype=np.float64, comment='#') | ||
| #load the expected output | ||
| pprof_expected = pd.read_table(this_path+'/materials/pprof_WASP52b_T=9000_M=11.000.txt', | ||
| names=['alt', 'rho', 'v', 'mu'], dtype=np.float64, comment='#') | ||
| #check if they are equal to within 1% in altitude and mu and 10% in rho and v. | ||
| assert np.isclose(pprof_created[['alt', 'mu']], pprof_expected[['alt', 'mu']], rtol=0.01).all().all(), "The profile created with the construct_parker.py module is not as expected" | ||
| assert np.isclose(pprof_created[['rho', 'v']], pprof_expected[['rho', 'v']], rtol=0.1).all().all(), "The profile created with the construct_parker.py module is not as expected" | ||
|
|
||
|
|
||
|
|
||
| print("\nChecking convergeT_parker.py. A runtime for this module will follow when done...\n") | ||
|
|
||
| ### CONVERGING TEMPERATURE STRUCTURE WITH CLOUDY ### | ||
|
|
||
| #run the created profile through Cloudy | ||
| os.system(f"cd {tools.sunbatherpath} && python convergeT_parker.py -plname WASP52b -pdir test -dir test -Mdot 11.0 -T 9000 -z 10 -zelem Ca=0 -overwrite") | ||
| #load the created simulation | ||
| sim_created = tools.Sim(tools.projectpath+'/sims/1D/WASP52b/test/parker_9000_11.000/converged') | ||
| #load the expected simulation | ||
| sim_expected = tools.Sim(this_path+'/materials/converged') | ||
| #interpolate them to a common altitude grid as Cloudy's internal depth-grid may vary between simulations | ||
| alt_grid = np.logspace(np.log10(max(sim_created.ovr.alt.iloc[-1], sim_expected.ovr.alt.iloc[-1])+1e4), | ||
| np.log10(min(sim_created.ovr.alt.iloc[0], sim_expected.ovr.alt.iloc[0])-1e4), num=100) | ||
| # create a parker profile - we use the p-winds/Cloudy hybrid scheme | ||
| os.system( | ||
| f"cd {tools.sunbatherpath} && python construct_parker.py -plname WASP52b -pdir test -Mdot 11.0 -T 9000 -z 10 -zelem Ca=0 -overwrite" | ||
| ) | ||
| # load the created profile | ||
| pprof_created = pd.read_table( | ||
| tools.projectpath | ||
| + "/parker_profiles/WASP52b/test/pprof_WASP52b_T=9000_M=11.000.txt", | ||
| names=["alt", "rho", "v", "mu"], | ||
| dtype=np.float64, | ||
| comment="#", | ||
| ) | ||
| # load the expected output | ||
| pprof_expected = pd.read_table( | ||
| this_path + "/materials/pprof_WASP52b_T=9000_M=11.000.txt", | ||
| names=["alt", "rho", "v", "mu"], | ||
| dtype=np.float64, | ||
| comment="#", | ||
| ) | ||
| # check if they are equal to within 1% in altitude and mu and 10% in rho and v. | ||
| assert ( | ||
| np.isclose(pprof_created[["alt", "mu"]], pprof_expected[["alt", "mu"]], rtol=0.01) | ||
| .all() | ||
| .all() | ||
| ), "The profile created with the construct_parker.py module is not as expected" | ||
| assert ( | ||
| np.isclose(pprof_created[["rho", "v"]], pprof_expected[["rho", "v"]], rtol=0.1) | ||
| .all() | ||
| .all() | ||
| ), "The profile created with the construct_parker.py module is not as expected" | ||
|
|
||
|
|
||
| print( | ||
| "\nChecking convergeT_parker.py. A runtime for this module will follow when done...\n" | ||
| ) | ||
|
|
||
| # ## CONVERGING TEMPERATURE STRUCTURE WITH CLOUDY ### | ||
|
|
||
| # run the created profile through Cloudy | ||
| os.system( | ||
| f"cd {tools.sunbatherpath} " | ||
| f"&& python convergeT_parker.py " | ||
| f"-plname WASP52b -pdir test -dir test " | ||
| f"-Mdot 11.0 -T 9000 -z 10 -zelem Ca=0 -overwrite" | ||
| ) | ||
| # load the created simulation | ||
| sim_created = tools.Sim( | ||
| tools.projectpath + "/sims/1D/WASP52b/test/parker_9000_11.000/converged" | ||
| ) | ||
| # load the expected simulation | ||
| sim_expected = tools.Sim(this_path + "/materials/converged") | ||
| # interpolate them to a common altitude grid as Cloudy's internal depth-grid may vary between simulations | ||
| alt_grid = np.logspace( | ||
| np.log10(max(sim_created.ovr.alt.iloc[-1], sim_expected.ovr.alt.iloc[-1]) + 1e4), | ||
| np.log10(min(sim_created.ovr.alt.iloc[0], sim_expected.ovr.alt.iloc[0]) - 1e4), | ||
| num=100, | ||
| ) | ||
| T_created = interp1d(sim_created.ovr.alt, sim_created.ovr.Te)(alt_grid) | ||
| T_expected = interp1d(sim_expected.ovr.alt, sim_expected.ovr.Te)(alt_grid) | ||
| #check if they are equal to within 10% | ||
| assert np.isclose(T_created, T_expected, rtol=0.1).all(), "The converged temperature profile of Cloudy is not as expected" | ||
|
|
||
| # check if they are equal to within 10% | ||
| assert np.isclose( | ||
| T_created, T_expected, rtol=0.1 | ||
| ).all(), "The converged temperature profile of Cloudy is not as expected" | ||
|
|
||
|
|
||
| print("\nChecking RT.py...\n") | ||
|
|
||
| ### MAKING TRANSIT SPECTRA ### | ||
|
|
||
| #make a helium spectrum | ||
| # make a helium spectrum | ||
| wavs = np.linspace(10830, 10836, num=300) | ||
| FinFout_created, found_lines, notfound_lines = RT.FinFout(sim_created, wavs, 'He') | ||
| #load the expected helium spectrum | ||
| FinFout_expected = np.genfromtxt(this_path+'/materials/FinFout_helium.txt')[:,1] | ||
| assert np.isclose(FinFout_created, FinFout_expected, rtol=0.05).all(), "The created helium spectrum is not as expected" | ||
| #make a magnesium+ spectrum | ||
| FinFout_created, found_lines, notfound_lines = RT.FinFout(sim_created, wavs, "He") | ||
| # load the expected helium spectrum | ||
| FinFout_expected = np.genfromtxt(this_path + "/materials/FinFout_helium.txt")[:, 1] | ||
| assert np.isclose( | ||
| FinFout_created, FinFout_expected, rtol=0.05 | ||
| ).all(), "The created helium spectrum is not as expected" | ||
| # make a magnesium+ spectrum | ||
| wavs = np.linspace(2795.5, 2797, num=300) | ||
| FinFout_created, found_lines, notfound_lines = RT.FinFout(sim_created, wavs, 'Mg+') | ||
| #load the expected magnesium+ spectrum | ||
| FinFout_expected = np.genfromtxt(this_path+'/materials/FinFout_magnesium+.txt')[:,1] | ||
| assert np.isclose(FinFout_created, FinFout_expected, rtol=0.05).all(), "The created magnesium+ spectrum is not as expected" | ||
|
|
||
| FinFout_created, found_lines, notfound_lines = RT.FinFout(sim_created, wavs, "Mg+") | ||
| # load the expected magnesium+ spectrum | ||
| FinFout_expected = np.genfromtxt(this_path + "/materials/FinFout_magnesium+.txt")[:, 1] | ||
| assert np.isclose( | ||
| FinFout_created, FinFout_expected, rtol=0.05 | ||
| ).all(), "The created magnesium+ spectrum is not as expected" | ||
|
|
||
|
|
||
| #if we made it past all the asserts, the code is correctly installed | ||
| # if we made it past all the asserts, the code is correctly installed | ||
| print("\nSuccess.") |