Fixed issue with float type returned by likelihood function, fixed is…

…sue with np.inf in the likelihood that can not be handled by UltraNest, updated URLs in model_data.json
tomasstolker · Jan 31, 2024 · bc6a4d3 · bc6a4d3
1 parent 001aef6
commit bc6a4d3
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Showing 3 changed files with 28 additions and 20 deletions.
diff --git a/species/data/database.py b/species/data/database.py
@@ -271,7 +271,9 @@ def available_models(self, verbose: bool = False) -> Dict:
                     print(f"      - Reference: {model_dict['reference']}")
 
                 if "url" in model_dict:
-                    print(f"      - URL: {model_dict['url']}\n")
+                    print(f"      - URL: {model_dict['url']}")
+
+                print()
 
             else:
                 print(f"{model_dict['name']} -> label: {model_name}")

diff --git a/species/data/model_data/model_data.json b/species/data/model_data/model_data.json
@@ -23,7 +23,7 @@
         "resolution": 10000,
         "teff range": [200, 3000],
         "reference": "Phillips et al. (2020)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2020A%26A...637A..38P/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2020A%26A...637A..38P"
     },
     "atmo-ceq": {
         "parameters": ["teff", "logg"],
@@ -33,7 +33,7 @@
         "resolution": 10000,
         "teff range": [200, 3000],
         "reference": "Phillips et al. (2020)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2020A%26A...637A..38P/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2020A%26A...637A..38P"
     },
     "atmo-neq-weak": {
         "parameters": ["teff", "logg"],
@@ -43,7 +43,7 @@
         "resolution": 10000,
         "teff range": [200, 1800],
         "reference": "Phillips et al. (2020)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2020A%26A...637A..38P/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2020A%26A...637A..38P"
     },
     "atmo-neq-strong": {
         "parameters": ["teff", "logg"],
@@ -53,7 +53,7 @@
         "resolution": 10000,
         "teff range": [200, 1800],
         "reference": "Phillips et al. (2020)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2020A%26A...637A..38P/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2020A%26A...637A..38P"
     },
     "atmo-petrus2023": {
         "parameters": ["teff", "logg", "feh", "c_o_ratio", "ad_index"],
@@ -63,7 +63,7 @@
         "resolution": 3000,
         "teff range": [800, 3000],
         "reference": "Petrus et al. (2023)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2023A%26A...670L...9P/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2023A%26A...670L...9P"
     },
     "blackbody": {
         "parameters": ["teff"],
@@ -138,7 +138,7 @@
         "resolution": 4000,
         "teff range": [1000, 3000],
         "reference": "Helling et al. (2008)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2008ApJ...675L.105H/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2008ApJ...675L.105H"
     },
     "exo-rem": {
         "parameters": ["teff", "logg", "feh", "c_o_ratio"],
@@ -148,7 +148,7 @@
         "resolution": 500,
         "teff range": [400, 2000],
         "reference": "Charnay et al. (2018)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2018ApJ...854..172C/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2018ApJ...854..172C"
     },
     "exo-rem-highres": {
         "parameters": ["teff", "logg", "feh", "c_o_ratio"],
@@ -158,7 +158,7 @@
         "resolution": 20000,
         "teff range": [400, 2000],
         "reference": "Charnay et al. (2018)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2018ApJ...854..172C/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2018ApJ...854..172C"
     },
     "koester-wd": {
         "parameters": ["teff", "logg"],
@@ -168,7 +168,7 @@
         "resolution": 2000,
         "teff range": [5000, 80000],
         "reference": "Koester (2010)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2010MmSAI..81..921K/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2010MmSAI..81..921K"
     },
     "morley-2012": {
         "parameters": ["teff", "logg", "fsed"],
@@ -178,7 +178,7 @@
         "resolution": 10000,
         "teff range": [400, 1300],
         "reference": "Morley et al. (2012)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2012ApJ...756..172M/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2012ApJ...756..172M"
     },
     "petitcode-cool-clear": {
         "parameters": ["teff", "logg", "feh"],
@@ -188,7 +188,7 @@
         "resolution": 1000,
         "teff range": [500, 1000],
         "reference": "Mollière et al. (2015)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2015ApJ...813...47M/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2015ApJ...813...47M"
     },
     "petitcode-cool-cloudy": {
         "parameters": ["teff", "logg", "feh", "fsed"],
@@ -199,7 +199,7 @@
         "teff range": [500, 850],
         "information": "log(Kzz) = 7.5",
         "reference": "Mollière et al. (2015)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2015ApJ...813...47M/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2015ApJ...813...47M"
     },
     "petitcode-hot-clear": {
         "parameters": ["teff", "logg", "feh", "c_o_ratio"],
@@ -209,7 +209,7 @@
         "resolution": 1000,
         "teff range": [1000, 2000],
         "reference": "Mollière et al. (2015)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2015ApJ...813...47M/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2015ApJ...813...47M"
     },
     "petitcode-hot-cloudy": {
         "parameters": ["teff", "logg", "feh", "c_o_ratio", "fsed"],
@@ -219,7 +219,7 @@
         "resolution": 1000,
         "teff range": [1000, 2000],
         "reference": "Mollière et al. (2015)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2015ApJ...813...47M/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2015ApJ...813...47M"
     },
     "petitcode-linder2019-clear": {
         "parameters": ["teff", "logg", "feh"],
@@ -229,7 +229,7 @@
         "resolution": 1000,
         "teff range": [150, 1000],
         "reference": "Linder et al. (2019)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2019A%26A...623A..85L/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2019A%26A...623A..85L"
     },
     "petitcode-linder2019-cloudy": {
         "parameters": ["teff", "logg", "feh", "fsed"],
@@ -239,7 +239,7 @@
         "resolution": 1000,
         "teff range": [150, 1000],
         "reference": "Linder et al. (2019)",
-        "url": "https://ui.adsabs.harvard.edu/abs/2019A%26A...623A..85L/abstract"
+        "url": "https://ui.adsabs.harvard.edu/abs/2019A%26A...623A..85L"
     },
     "saumon2008-clear": {
         "parameters": ["teff", "logg"],

diff --git a/species/fit/fit_model.py b/species/fit/fit_model.py
@@ -1884,7 +1884,7 @@ def lnprior_multinest(cube, n_dim: int, n_param: int) -> None:
                     )
 
         @typechecked
-        def lnlike_multinest(params, n_dim: int, n_param: int) -> np.float64:
+        def lnlike_multinest(params, n_dim: int, n_param: int) -> Union[float, np.float64]:
             """
             Function for return the log-likelihood for the sampled parameter cube.
 
@@ -2119,7 +2119,7 @@ def lnprior_ultranest(cube: np.ndarray) -> np.ndarray:
             return params
 
         @typechecked
-        def lnlike_ultranest(params: np.ndarray) -> np.float64:
+        def lnlike_ultranest(params: np.ndarray) -> Union[float, np.float64]:
             """
             Function for returning the log-likelihood for the sampled parameter cube.
 
@@ -2134,7 +2134,13 @@ def lnlike_ultranest(params: np.ndarray) -> np.float64:
                 Log-likelihood.
             """
 
-            return self.lnlike_func(params, prior=prior)
+            ln_like = self.lnlike_func(params, prior=prior)
+
+            if not np.isfinite(ln_like):
+                # UltraNest can not handle np.inf in the likelihood
+                ln_like = -1e100
+
+            return ln_like
 
         sampler = ultranest.ReactiveNestedSampler(
             self.modelpar,