Added support for clear and cloudy petitCODE grid from Linder et al. …

…(2019)
tomasstolker · Oct 15, 2023 · 04d84c3 · 04d84c3
1 parent 87ebe56
commit 04d84c3
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Showing 4 changed files with 67 additions and 6 deletions.
diff --git a/species/data/model_data.json b/species/data/model_data.json
@@ -55,7 +55,7 @@
         "reference": "Phillips et al. (2020)",
         "url": "https://ui.adsabs.harvard.edu/abs/2020A%26A...637A..38P/abstract"
     },
-    "petrus2023": {
+    "atmo-petrus2023": {
         "parameters": ["teff", "logg", "feh", "c_o_ratio", "ad_index"],
         "name": "ATMO (Petrus et al. 2023)",
         "file size": "2.1 GB",
@@ -212,6 +212,26 @@
         "reference": "Mollière et al. (2015)",
         "url": "https://ui.adsabs.harvard.edu/abs/2015ApJ...813...47M/abstract"
     },
+    "petitcode-linder2019-clear": {
+        "parameters": ["teff", "logg", "feh"],
+        "name": "petitCODE (Linder et al. 2019)",
+        "file size": "225 MB",
+        "wavelength range": [0.1, 250],
+        "resolution": 1000,
+        "teff range": [150, 1000],
+        "reference": "Linder et al. (2019)",
+        "url": "https://ui.adsabs.harvard.edu/abs/2019A%26A...623A..85L/abstract"
+    },
+    "petitcode-linder2019-cloudy": {
+        "parameters": ["teff", "logg", "feh", "fsed"],
+        "name": "petitCODE hot cloudy",
+        "file size": "1.4 GB",
+        "wavelength range": [0.1, 250],
+        "resolution": 1000,
+        "teff range": [150, 1000],
+        "reference": "Linder et al. (2019)",
+        "url": "https://ui.adsabs.harvard.edu/abs/2019A%26A...623A..85L/abstract"
+    },
     "saumon2008-clear": {
         "parameters": ["teff", "logg"],
         "name": "Saumon & Marley (2008) clear",

diff --git a/species/read/read_isochrone.py b/species/read/read_isochrone.py
@@ -133,11 +133,40 @@ def __init__(
             "atmo-neq-strong": "atmo-neq-strong",
             "atmo-neq-weak": "atmo-neq-weak",
             "bt-settl": "bt-settl",
+            "linder2019-petitCODE-metal_-0.4": "petitcode-linder2019-clear",
+            "linder2019-petitCODE-metal_0.0": "petitcode-linder2019-clear",
+            "linder2019-petitCODE-metal_0.4": "petitcode-linder2019-clear",
+            "linder2019-petitCODE-metal_0.8": "petitcode-linder2019-clear",
+            "linder2019-petitCODE-metal_1.2": "petitcode-linder2019-clear",
+            "linder2019-petitCODE-metal_-0.4-fsed_1.0": "petitcode-linder2019-cloudy",
+            "linder2019-petitCODE-metal_0.0-fsed_1.0": "petitcode-linder2019-cloudy",
+            "linder2019-petitCODE-metal_0.4-fsed_1.0": "petitcode-linder2019-cloudy",
+            "linder2019-petitCODE-metal_0.8-fsed_1.0": "petitcode-linder2019-cloudy",
+            "linder2019-petitCODE-metal_1.2-fsed_1.0": "petitcode-linder2019-cloudy",
             "saumon2008-nc_solar": "saumon2008-clear",
             "saumon2008-f2_solar": "saumon2008-cloudy",
             "sonora+0.0": "sonora-bobcat",
         }
 
+        # Set attribute with extra parameters
+        # The attribute will be overwritten by any of
+        # the methods that have the extra_param parameter
+
+        self.extra_param = None
+
+        if self.tag.split("-")[0] == "linder2019":
+            self.extra_param = {}
+            tag_split = self.tag.split("_")
+
+            if len(tag_split) == 2:
+                self.extra_param['feh'] = float(tag_split[1])
+
+            elif len(tag_split) == 3:
+                self.extra_param['feh'] = float(tag_split[1][:-5])
+                self.extra_param['fsed'] = float(tag_split[2])
+
+            print(f"Setting 'extra_param' attribute: {self.extra_param}")
+
     @typechecked
     def _read_data(
         self,
@@ -385,6 +414,9 @@ def _update_param(
             the evolutionary model.
         """
 
+        if len(extra_param) == 0 and self.extra_param is not None:
+            extra_param = self.extra_param.copy()
+
         for key, value in param_bounds.items():
             if key not in model_param:
                 if key in extra_param:

diff --git a/species/read/read_model.py b/species/read/read_model.py
@@ -148,7 +148,7 @@ def open_database(self) -> h5py._hl.files.File:
                 "If this does not work (e.g. currently without an "
                 "internet connection) then please use the "
                 "'add_model' method of 'Database' to add the "
-                "grid of spectra yourself."
+                "grid of spectra at a later moment."
             )
 
             species_db = database.Database()

diff --git a/species/util/plot_util.py b/species/util/plot_util.py
@@ -879,6 +879,9 @@ def convert_model_name(in_name: str) -> str:
     elif in_name == "petrus2023":
         out_name = "ATMO (Petrus et al. 2023)"
 
+    elif in_name == "atmo-petrus2023":
+        out_name = "ATMO (Petrus et al. 2023)"
+
     elif in_name == "bt-cond":
         out_name = "BT-Cond"
 
@@ -895,16 +898,22 @@ def convert_model_name(in_name: str) -> str:
         out_name = "BT-NextGen"
 
     elif in_name == "petitcode-cool-clear":
-        out_name = "petitCODE"
+        out_name = "petitCODE clear"
 
     elif in_name == "petitcode-cool-cloudy":
-        out_name = "petitCODE"
+        out_name = "petitCODE cloudy"
 
     elif in_name == "petitcode-hot-clear":
-        out_name = "petitCODE"
+        out_name = "petitCODE clear"
 
     elif in_name == "petitcode-hot-cloudy":
-        out_name = "petitCODE"
+        out_name = "petitCODE cloudy"
+
+    elif in_name == "petitcode-linder2019-clear":
+        out_name = "petitCODE clear (Linder et al. 2019)"
+
+    elif in_name == "petitcode-linder2019-cloudy":
+        out_name = "petitCODE cloudy (Linder et al. 2019)"
 
     elif in_name == "exo-rem":
         out_name = "Exo-REM"