Added the option to plot Teff and log(g) with the plot_cooling functi…

…on, added HIP99770b to companion_data.json

species/data/companion_data/companion_data.json

@@ -221,6 +221,37 @@
             "Stolker et al. 2020a"
         ]
     },
+    "HIP 99770 b": {
+        "simbad": "* b03 Cyg",
+        "parallax": [
+            24.5456,
+            0.0911
+        ],
+        "semi_major": [
+            16.9,
+            -1.8,
+            3.4
+        ],
+        "mass_star": [
+            1.85,
+            0.19
+        ],
+        "mass_companion": [
+            16.1,
+            -5.0,
+            5.4
+        ],
+        "accretion": false,
+        "age": [
+            45.0,
+            -5.0,
+            5.0
+        ],
+        "references": [
+            "Currie et al. 2023",
+            "Zuckerman 2019"
+        ]
+    },
     "51 Eri b": {
         "simbad": "51 Eri",
         "parallax": [
@@ -699,7 +730,7 @@
         "semi_major": [
             20.8,
             -0.7,
-            0.7
+            0.6
         ],
         "mass_star": [
             0.98,
@@ -720,10 +751,16 @@
                 2.3e-19
             ]
         },
+        "age": [
+            5.4,
+            -1.0,
+            1.0
+        ],
         "references": [
             "Gaia Early Data Release 3",
             "Haffert et al. 2019",
             "Hashimoto et al. 2020",
+            "Müller et al. 2018",
             "Stolker et al. 2020b",
             "Wang et al. 2020",
             "Wang et al. 2021"
@@ -747,7 +784,7 @@
         },
         "semi_major": [
             34.3,
-            -2.2,
+            -1.8,
             2.2
         ],
         "mass_star": [
@@ -759,9 +796,15 @@
             4.7
         ],
         "accretion": true,
+        "age": [
+            5.4,
+            -1.0,
+            1.0
+        ],
         "references": [
             "Gaia Early Data Release 3",
             "Haffert et al. 2019",
+            "Müller et al. 2018",
             "Stolker et al. 2020b",
             "Wang et al. 2020",
             "Wang et al. 2021"

species/fit/fit_evolution.py

@@ -359,14 +359,14 @@ def run_multinest(
         Function to run the ``PyMultiNest`` wrapper of the
         ``MultiNest`` sampler. While ``PyMultiNest`` can be
         installed with ``pip`` from the PyPI repository,
-        ``MultiNest`` has to to be build manually. See the
+        ``MultiNest`` has to be build manually. See the
         ``PyMultiNest`` documentation for details:
         http://johannesbuchner.github.io/PyMultiNest/install.html.
         Note that the library path of ``MultiNest`` should be set
         to the environmental variable ``LD_LIBRARY_PATH`` on a
         Linux machine and ``DYLD_LIBRARY_PATH`` on a Mac.
-        Alternatively, the variable can be set before importing
-        the ``species`` package, for example:
+        Alternatively, the variable can be set before
+        importing the ``species`` package, for example:
 
         .. code-block:: python
 

species/plot/plot_evolution.py

@@ -44,7 +44,7 @@ def plot_cooling(
         Number of randomly drawn cooling tracks that will be plotted.
     cooling_param : str
         Type of cooling parameter that will be plotted
-        ('luminosity' or 'radius').
+        ('luminosity', 'radius', 'teff', or 'logg').
     xlim : tuple(float, float), None
         Limits of the wavelength axis. Automatic limits are used if
         the argument is set to ``None``.
@@ -90,11 +90,11 @@ def plot_cooling(
 
     plt.close()
 
-    if cooling_param not in ["luminosity", "radius"]:
+    if cooling_param not in ["luminosity", "radius", "teff", "logg"]:
         raise ValueError(
             "The argument of 'cooling_parameter' is "
             "not valid and should be set to "
-            "'luminosity' or 'radius'."
+            "'luminosity', 'radius', 'teff', or 'logg'."
         )
 
     from species.data.database import Database
@@ -155,6 +155,12 @@ def plot_cooling(
                 radius_prior[i][0] + radius_prior[i][1],
             ]
 
+        param_idx = samples_box.parameters.index(f"teff_{i}")
+        teff_tmp = np.percentile(samples[:, param_idx], [50.0, 16.0, 84.0])
+
+        param_idx = samples_box.parameters.index(f"logg_{i}")
+        logg_tmp = np.percentile(samples[:, param_idx], [50.0, 16.0, 84.0])
+
         ax[i].set_xscale(xscale)
         ax[i].set_yscale(yscale)
 
@@ -199,10 +205,16 @@ def plot_cooling(
             ax[i].set_xlabel("Age (Myr)", fontsize=13)
 
         if cooling_param == "luminosity":
-            ax[i].set_ylabel("$\\log(L/L_\\odot)$", fontsize=13)
+            ax[i].set_ylabel("$\log(L/L_\odot)$", fontsize=13)
 
         elif cooling_param == "radius":
-            ax[i].set_ylabel("Radius ($R_\\mathrm{J}$)", fontsize=13)
+            ax[i].set_ylabel("Radius ($R_\mathrm{J}$)", fontsize=13)
+
+        elif cooling_param == "teff":
+            ax[i].set_ylabel("$T_\mathrm{eff}$ (K)", fontsize=13)
+
+        elif cooling_param == "logg":
+            ax[i].set_ylabel("$\log\,g$", fontsize=13)
 
         if xlim is not None:
             ax[i].set_xlim(xlim[0], xlim[1])
@@ -228,6 +240,12 @@ def plot_cooling(
                 elif cooling_param == "radius":
                     cool_tracks[planet_idx].append([cool_box.age, cool_box.radius])
 
+                elif cooling_param == "teff":
+                    cool_tracks[planet_idx].append([cool_box.age, cool_box.teff])
+
+                elif cooling_param == "logg":
+                    cool_tracks[planet_idx].append([cool_box.age, cool_box.logg])
+
                 ax[planet_idx].plot(
                     cool_tracks[planet_idx][-1][0],
                     cool_tracks[planet_idx][-1][1],
@@ -261,6 +279,30 @@ def plot_cooling(
                 color="tab:orange",
             )
 
+        elif cooling_param == "teff":
+            ax[i].errorbar(
+                [age_prior[0]],
+                [teff_tmp[0]],
+                xerr=[
+                    [age_prior[0] - np.abs(age_prior[1])],
+                    [age_prior[2] - age_prior[0]],
+                ],
+                yerr=[[teff_tmp[0] - teff_tmp[1]], [teff_tmp[2] - teff_tmp[0]]],
+                color="tab:orange",
+            )
+
+        elif cooling_param == "logg":
+            ax[i].errorbar(
+                [age_prior[0]],
+                [logg_tmp[0]],
+                xerr=[
+                    [age_prior[0] - np.abs(age_prior[1])],
+                    [age_prior[2] - age_prior[0]],
+                ],
+                yerr=[[logg_tmp[0] - logg_tmp[1]], [logg_tmp[2] - logg_tmp[0]]],
+                color="tab:orange",
+            )
+
     if title is not None:
         ax[0].set_title(title, fontsize=18.0)
 

species/read/read_model.py

@@ -1853,7 +1853,7 @@ def integrate_spectrum(self, model_param: Dict[str, float]) -> float:
         extinct luminosity and not the intrinsic luminosity. Without
         applying extinction, the integrated luminosity should in
         principle be the same as the luminosity calculated directly
-        from the :math:`T_\\mathrm{eff}` and radius parameters. Unless
+        from the :math:`T_\\mathrm{eff}` and radius parameters, unless
         the radiative-convective model had not fully converged for a
         particular set of input parameters. It can thus be useful
         to check if the integrated luminosity is indeed consistent