Commit 96177091 authored by Andrea Giannetti's avatar Andrea Giannetti
Browse files

Updated documentation and figures to demonstrate the relevance of the results.

parent a2fd4983

documentation/documentation.md

+8 −0
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@@ -172,6 +172,14 @@ The staging config file has three main categories: 
    * species_to_include: the list of molecular species to include in the RADMC postprocessing, e.g. ['e-ch3oh']

    * molecular_abundances: a dict-like parameter, containing the species name and the corresponding fractional

      abundance, e.g. {"e-ch3oh": 1e-8, "p-h2": 1}

    * hot_core_specs: a dict-like parameter, containing the threshold temperature for evaporation and the factor by which the abundance is increased, indexed by the species name, e.g.: 

     {

                        "e-ch3oh": {

                            "threshold": 90,

                            "abundance_jump": 1

                        }

     }



    * lines_mode: the line transfer mode. It can be 'lte', 'lvg', 'optically_thin_non_lte', 'user_defined_populations' (

      see the RADMC documentation if in doubt)

    * collision_partners: the list of collision partners to be used; it must appear in the correct order as in the

etl/prs/prs_analytical_representations.py

+5 −3
Original line number Diff line number Diff line
@@ -56,7 +56,7 @@ def main(ratios_to_fit: Union[List[str], None] = None): 
        _column_to_fit = f'ratio_{ratio_string}'

        data.sort_values(by=_column_to_fit, inplace=True)

        plt.clf()

        plt.scatter(data[_column_to_fit], data['avg_nh2'], marker='+', alpha=0.1)

        plt.scatter(data['avg_nh2'], data[_column_to_fit], marker='+', alpha=0.1)

        x_reg = np.linspace(min_ratio[ratio_string], max_ratio[ratio_string], 100)



        data_clean = data[[_column_to_fit, 'avg_nh2']].loc[data[_column_to_fit] <= max_ratio[ratio_string]].copy()
@@ -66,9 +66,11 @@ def main(ratios_to_fit: Union[List[str], None] = None): 
        rgi = RegularGridInterpolator((kde['y'] * bw[ratio_string], kde['x'] * 0.2), kde['values'].reshape(200, 200).T)

        density = rgi(data_clean[[_column_to_fit, 'avg_nh2']])

        data_clean = data_clean.loc[(density > density.mean() - density.std())]

        plt.scatter(data_clean[_column_to_fit], data_clean['avg_nh2'], marker='+', alpha=0.1, color='red')

        plt.scatter(data_clean['avg_nh2'], data_clean[_column_to_fit], marker='+', alpha=0.1, color='red')

        plt.xlabel('log(<n(H2)>)')

        plt.ylabel('Ratio')

        for components in x0[ratio_string]:

            plt.plot(x_reg, approx(x_reg, *components), color='cyan')

            plt.plot(approx(x_reg, *components),x_reg , color='cyan')

        plt.savefig(os.path.join('..',

        'publications',

        '6373bb408e4040043398e495',

etl/prs/prs_poc_latex_table.py

+2 −2
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@@ -104,8 +104,8 @@ table_cols = [ 
                                                                                                                                                         fwhm_units), ]

]

captions = [

    "Line properties of the lines in the $(2_K-1_K)$ methanol band. Only one FWHM is listed because the fit is performed forcing all lines to have the same width. The main-beam temperature of the lines is indicated as $T_{MB,J_K-J',_K'}$. A non-detection is indicated with three dots.",

    "Line properties of the lines in the $(5_K-4_K)$ and $(7_K-6_K)$ methanol bands. Only one FWHM is listed per band because the fit is performed forcing all lines to have the same width. The main-beam temperature of the lines is indicated as $T_{MB,J_K-J',_K'}$. A non-detection is indicated with three dots, while missing data are indicated with \'N/A\'.",

    "Line properties of the lines in the $(2_K-1_K)$ methanol band. Only one FWHM is listed because the fit is performed forcing all lines to have the same width. The main-beam temperature of the lines is indicated as $T_{MB,J_K-J^',_{K^'}}$. A non-detection is indicated with three dots.",

    "Line properties of the lines in the $(5_K-4_K)$ and $(7_K-6_K)$ methanol bands. Only one FWHM is listed per band because the fit is performed forcing all lines to have the same width. The main-beam temperature of the lines is indicated as $T_{MB,J_K-J^',_{K^'}}$. A non-detection is indicated with three dots, while missing data are indicated with \'N/A\'.",

]

labels = [

    'tab:poc_lines_3mm',