rename formulas to site_formulae

Author: bobmyhill

burnman/classes/elasticsolutionmodel.py

@@ -227,7 +227,7 @@ class ElasticMechanicalSolution(ElasticSolutionModel):
     def __init__(self, endmembers):
         self.endmembers = endmembers
         self.n_endmembers = len(endmembers)
-        self.formulas = [e[1] for e in endmembers]
+        self.site_formulae = [e[1] for e in endmembers]
 
     def excess_helmholtz_energy(self, volume, temperature, molar_fractions):
         return 0.0
@@ -263,7 +263,7 @@ class ElasticIdealSolution(ElasticSolutionModel):
     def __init__(self, endmembers):
         self.endmembers = endmembers
         self.n_endmembers = len(endmembers)
-        self.formulas = [e[1] for e in endmembers]
+        self.site_formulae = [e[1] for e in endmembers]
 
         # Process solution chemistry
         process_solution_chemistry(self)

burnman/classes/solutionmodel.py

@@ -374,7 +374,7 @@ class MechanicalSolution(SolutionModel):
     def __init__(self, endmembers):
         self.endmembers = endmembers
         self.n_endmembers = len(endmembers)
-        self.formulas = [e[1] for e in endmembers]
+        self.site_formulae = [e[1] for e in endmembers]
 
     def excess_gibbs_free_energy(self, pressure, temperature, molar_fractions):
         return 0.0
@@ -421,7 +421,7 @@ class IdealSolution(SolutionModel):
     def __init__(self, endmembers):
         self.endmembers = endmembers
         self.n_endmembers = len(endmembers)
-        self.formulas = [e[1] for e in endmembers]
+        self.site_formulae = [e[1] for e in endmembers]
 
         # Process solution chemistry
         process_solution_chemistry(self)

burnman/optimize/composition_fitting.py

@@ -36,7 +36,7 @@ def __init__(self, endmember_element_formulae, endmember_site_formulae):
             dictionarize_formula(f) for f in endmember_element_formulae
         ]
         self.solution_model = type(
-            "Dimension", (object,), {"formulas": endmember_site_formulae}
+            "Dimension", (object,), {"site_formulae": endmember_site_formulae}
         )()
         self.solution_model.endmembers = [None for f in endmember_site_formulae]
         process_solution_chemistry(self.solution_model)

burnman/utils/chemistry.py

@@ -284,7 +284,7 @@ def convert_formula(formula, to_type="mass", normalize=False):
 
 def process_solution_chemistry(solution_model):
     """
-    This function parses a class instance with a "formulas"
+    This function parses a class instance with a "site_formulae"
     attribute containing site information, e.g.
 
         [ '[Mg]3[Al]2Si3O12', '[Mg]3[Mg1/2Si1/2]2Si3O12' ]
@@ -297,7 +297,7 @@ def process_solution_chemistry(solution_model):
     molar fractions of the phases and pressure
     and temperature where necessary.
 
-    :param solution_model: Class must have a "formulas" attribute,
+    :param solution_model: Class must have a "site_formulae" attribute,
         containing a list of chemical formulae with site information
     :type solution model: instance of class
 
@@ -341,7 +341,7 @@ def process_solution_chemistry(solution_model):
             containing the number of atoms of each species on each site
             per mole of endmember.
     """
-    formulae = solution_model.formulas
+    formulae = solution_model.site_formulae
     n_sites = formulae[0].count("[")
     n_endmembers = len(formulae)
 
@@ -424,7 +424,7 @@ def process_solution_chemistry(solution_model):
     )
 
     solution_model.empty_formula = re.sub(
-        "([\\[]).*?([\\]])", "\\g<1>\\g<2>", solution_model.formulas[0]
+        "([\\[]).*?([\\]])", "\\g<1>\\g<2>", solution_model.site_formulae[0]
     )
     split_empty = solution_model.empty_formula.split("[")
     solution_model.general_formula = split_empty[0]