Merge pull request #709 from bobmyhill/n_moles

Add number_of_moles property and extensive thermodynamic properties to Material

Author: bobmyhill

burnman/classes/anisotropicsolution.py

@@ -178,8 +178,10 @@ def set_composition(self, molar_fractions):
         )
         # Calculate all other required properties
         Solution.set_composition(self, molar_fractions)
-        if self._scalar_solution.pressure is not None:
+        try:  # if pressure and temperature are already set, compute base properties
             self.compute_base_properties()
+        except AttributeError:
+            pass
 
     @cached_property
     def ones(self):
@@ -349,9 +351,12 @@ def set_state(self, pressure, temperature, relaxed=True):
         """
         self.unrelaxed.set_state(pressure, temperature)
 
-        if hasattr(self.unrelaxed, "molar_fractions") and relaxed:
-            self._relax_at_PTX()
-            AnisotropicSolution.set_state(self, pressure, temperature)
+        if relaxed:
+            try:  # relax the structure if composition has been set
+                self._relax_at_PTX()
+                AnisotropicSolution.set_state(self, pressure, temperature)
+            except AttributeError:
+                pass
 
     def set_composition(self, molar_fractions, q_initial=None, relaxed=True):
         """
@@ -383,11 +388,14 @@ def set_composition(self, molar_fractions, q_initial=None, relaxed=True):
 
         self.unrelaxed.set_composition(n)
 
-        if self.unrelaxed.pressure is not None and relaxed:
-            AnisotropicSolution.set_composition(self, n)
-            self._relax_at_PTX()
-            self.unrelaxed._scalar_solution.set_composition(self.molar_fractions)
-            self.unrelaxed.set_composition(self.molar_fractions)
+        if relaxed:
+            try:  # relax the structure if state has been set
+                AnisotropicSolution.set_composition(self, n)
+                self._relax_at_PTX()
+                self.unrelaxed._scalar_solution.set_composition(self.molar_fractions)
+                self.unrelaxed.set_composition(self.molar_fractions)
+            except AttributeError:
+                pass
 
     def _relax_at_PTX(self):
         """

burnman/classes/composite.py

@@ -214,7 +214,7 @@ def phase_volumes(self):
         """
         volumes = np.array(
             [
-                phase.molar_volume * molar_fraction
+                phase.volume * molar_fraction * self.number_of_moles
                 for (phase, molar_fraction) in zip(self.phases, self.molar_fractions)
             ]
         )
@@ -227,7 +227,7 @@ def phase_masses(self):
         """
         masses = np.array(
             [
-                phase.molar_mass * molar_fraction
+                phase.mass * molar_fraction * self.number_of_moles
                 for (phase, molar_fraction) in zip(self.phases, self.molar_fractions)
             ]
         )
@@ -236,9 +236,10 @@ def phase_masses(self):
     @material_property
     def formula(self):
         """
-        Returns molar chemical formula of the composite
+        Returns extensive chemical formula of the composite
         """
-        return sum_formulae([ph.formula for ph in self.phases], self.molar_fractions)
+        molar_amounts = self.molar_fractions * self.number_of_moles
+        return sum_formulae([ph.formula for ph in self.phases], molar_amounts)
 
     @material_property
     def molar_internal_energy(self):
@@ -282,14 +283,14 @@ def molar_volume(self):
         Returns molar volume of the composite [m^3/mol]
         Aliased with self.V
         """
-        return np.sum(self.phase_volumes)
+        return np.sum(self.phase_volumes) / self.number_of_moles
 
     @material_property
     def molar_mass(self):
         """
         Returns molar mass of the composite [kg/mol]
         """
-        return sum(self.phase_masses)
+        return sum(self.phase_masses) / self.number_of_moles
 
     @material_property
     def density(self):
@@ -438,7 +439,7 @@ def effective_isentropic_bulk_modulus(self):
         Returns the effective isotropic, isentropic bulk modulus of the composite [Pa]
         Aliased with self.K_eff
         """
-        V_frac = self.phase_volumes
+        V_frac = self.phase_volumes / sum(self.phase_volumes)
         K_ph = np.array([phase.isentropic_bulk_modulus_reuss for phase in self.phases])
         G_ph = np.array([phase.shear_modulus for phase in self.phases])
 
@@ -450,7 +451,7 @@ def effective_shear_modulus(self):
         Returns the effective isotropic shear modulus of the mineral [Pa]
         Aliased with self.G_eff
         """
-        V_frac = self.phase_volumes
+        V_frac = self.phase_volumes / sum(self.phase_volumes)
         K_ph = np.array([phase.isentropic_bulk_modulus_reuss for phase in self.phases])
         G_ph = np.array([phase.shear_modulus for phase in self.phases])
 

burnman/classes/elasticsolution.py

@@ -111,8 +111,10 @@ def set_composition(self, molar_fractions):
         self.reset()
         self.molar_fractions = np.array(molar_fractions)
 
-        if self.temperature is not None:
+        try:  # set the volume if pressure and temperature are already set
             _ = self.molar_volume
+        except AttributeError:
+            pass
 
     def set_method(self, method):
         for i in range(self.n_endmembers):