diff --git a/documentation/documentation.md b/documentation/documentation.md index 9ac3996532e6d66cb1fa1402d021991d9ecc7e17..1872ad29a17230e55632799a4e267a8a448b1365 100644 --- a/documentation/documentation.md +++ b/documentation/documentation.md @@ -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 diff --git a/etl/prs/prs_analytical_representations.py b/etl/prs/prs_analytical_representations.py index 942e1e64a6ebf65569eed275530cac50e8c548ad..09ce4d998a4ffd964be92fb1423850789d4af662 100644 --- a/etl/prs/prs_analytical_representations.py +++ b/etl/prs/prs_analytical_representations.py @@ -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', diff --git a/etl/prs/prs_poc_latex_table.py b/etl/prs/prs_poc_latex_table.py index 30dcdf04156a7b93cce8b7063b23f1e6a74e4b5f..857e8e69b632ae340ed16674de7485ff84a6d0c7 100644 --- a/etl/prs/prs_poc_latex_table.py +++ b/etl/prs/prs_poc_latex_table.py @@ -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',