fix abundance converstion between sme<->, kuruca<->H=12.

docs/index.rst

@@ -4,6 +4,8 @@ PySME documentation
 More than two decades ago `Valenti & Piskunov (1996) <https://ui.adsabs.harvard.edu/abs/1996A&AS..118..595V>`_ developed SME – Spectroscopy Made Easy, a high-precision stellar-spectra synthesis/analysis engine that has powered hundreds of studies.
 PySME is its modern Python front-end: a wrapper around the original C++/Fortran core that lets you (1) compute accurate, high-resolution synthetic spectra from a linelist + model atmosphere, (2) invert observed spectra to derive stellar parameters, and (3) explore NLTE corrections — all from an interactive notebook or scripted pipeline. The same capabilities make PySME invaluable for exoplanet work, where characterising the host star is essential for understanding its planets.
 
+🎉 PySME (version 0.6.14+) is now fully compatible with the arm64 MacOS! Feel free to try it out. 🎉
+
 .. admonition:: Key features
 
    * Plane-parallel and spherical radiative-transfer engine  

src/pysme/abund.py

@@ -556,12 +556,19 @@ def fromtype(pattern, fromtype, raw=False):
         if np.isnan(abund[0]):
             raise ValueError("Pattern must define abundance of H")
 
+        # print(abund)
+
         type = fromtype.lower()
         if type == "h=12":
             pass
         elif type == "sme":
+            # sme -> H=12
+            abund[1:] += 12 - np.log10(abund[0])
+            abund[0] = 12
+        elif type == "kurucz":
+            # kurucz -> H=12
+            abund[2:] = abund[2:] + np.log10(abund[1] / abund[0] + 1) + 12
             abund[1] = np.log10(abund[1]/abund[0]) + 12
-            abund[2:] += 12 - np.log10(abund[0])
             abund[0] = 12
         elif type == "n/ntot":
             abund /= abund[0]
@@ -580,16 +587,17 @@ def fromtype(pattern, fromtype, raw=False):
                 "got abundance type '{}',".format(type)
                 + " should be 'H=12', 'n/nH', 'n/nTot', 'n/nFe', 'Fe=12', or 'sme'"
             )
+
         if raw:
             return abund
         else:
             return {el: abund[elements_dict[el]] for el in elements}
-
+        
     @staticmethod
-    def totype(pattern, totype, raw=False, copy=True):
+    def totype(pattern, totype, raw=False, copy=True, X=None):
         """Return a copy of the input abundance pattern, transformed from
         the 'H=12' type to the output type. Valid abundance pattern types
-        are 'sme', 'n/nTot', 'n/nH', and 'H=12'.
+        are 'sme', 'kurucz', 'n/nTot', 'n/nH', and 'H=12'.
         """
         if isinstance(pattern, dict):
             abund = [pattern[el] if el in pattern.keys() else np.nan for el in elements]
@@ -604,12 +612,13 @@ def totype(pattern, totype, raw=False, copy=True):
         if type == "h=12":
             pass
         elif type == "sme":
-            abund2 = 10 ** (abund - 12)
-            abund[0] = 1 / np.nansum(abund2)
-            abund[1] = 10**(abund[1] - 12) * abund[0]
-            abund[2:] = abund[2:] - 12 + np.log10(abund[0])
-            # abund /= np.sum(abund)
-            # abund[1:] = np.log10(abund[1:])
+            abund[0] = 1 / (1 + np.nansum(10**(abund[1:]-12)))
+            abund[1:] = np.log10(abund[0] * 10**(abund[1:] - 12))
+        elif type == "kurucz":
+            # H=12 -> kurucz
+            abund[0] = 1 / (1 + np.nansum(10**(abund[1:] - 12)))
+            abund[1] = 1 / (10**(12-abund[1]) + 1 + 10**(12-abund[1]) * np.nansum(10**(abund[2:]-12)))
+            abund[2:] = abund[2:] - 12 - np.log10(1 + 10**(abund[1]-12))
         elif type == "n/ntot":
             abund = 10 ** (abund - 12)
             abund /= np.nansum(abund)
@@ -627,7 +636,7 @@ def totype(pattern, totype, raw=False, copy=True):
         else:
             raise ValueError(
                 "got abundance type '{}',".format(type)
-                + " should be 'H=12', 'n/nH', 'n/nTot', 'n/nFe', 'Fe=12', or 'sme'"
+                + " should be 'H=12', 'kurucz', 'n/nH', 'n/nTot', 'n/nFe', 'Fe=12', or 'sme'"
             )
 
         if raw:

src/pysme/atmosphere/krzfile.py

@@ -107,7 +107,7 @@ def load(self, filename):
 
         # parse abundance
         pattern = abun[:, 1]
-        self.abund = Abund(monh=self.monh, pattern=pattern, type="sme")
+        self.abund = Abund(monh=self.monh, pattern=pattern, type="kurucz")
 
         # parse table
         self.table = model_lines

src/pysme/synthesize.py

@@ -957,6 +957,7 @@ def update_cdr(self, sme, cdr_database=None, cdr_create=False, cdr_grid_overwrit
             raise ValueError
 
         if cdr_database is not None:
+            # cdr_database is provided, use it to update the central depth and line range
             self._interpolate_or_compute_and_update_linelist(sme, cdr_database, cdr_create=cdr_create, cdr_grid_overwrite=cdr_grid_overwrite, mode=mode, dims=dims)
             return sme
 
@@ -1022,7 +1023,7 @@ def update_cdr(self, sme, cdr_database=None, cdr_create=False, cdr_grid_overwrit
         return sme
 
     def _interpolate_or_compute_and_update_linelist(
-        self, sme, cdr_database, cdepth_decimals=4, cdepth_thres=0.0001,
+        self, sme, cdr_database, cdepth_decimals=4, cdepth_thres=0,
         range_decimals=2, cdr_create=False, cdr_grid_overwrite=False,
         mode='linear', dims=['teff', 'logg', 'monh']
     ):