[1D/Python] Fix range of components used when settings species tolerances

Boundaries do not necessarily have species variables, so setting species
tolerances will now raise an exception. This approach also avoids making
the assumption that the index of the first species equation is 4 in flow
domains.

interfaces/cython/cantera/_cantera.pxd

@@ -957,10 +957,10 @@ cdef class ReactorNet:
 
 cdef class Domain1D:
     cdef CxxDomain1D* domain
+    cdef _SolutionBase gas
 
 cdef class Boundary1D(Domain1D):
     cdef CxxBdry1D* boundary
-    cdef _SolutionBase phase
 
 cdef class Inlet1D(Boundary1D):
     cdef CxxInlet1D* inlet
@@ -982,7 +982,6 @@ cdef class ReactingSurface1D(Boundary1D):
 
 cdef class _FlowBase(Domain1D):
     cdef CxxStFlow* flow
-    cdef _SolutionBase gas
 
 cdef class FreeFlow(_FlowBase):
     pass

interfaces/cython/cantera/onedim.pyx

@@ -5,13 +5,15 @@ cdef class Domain1D:
         self.domain = NULL
 
     # The signature of this function causes warnings for Sphinx documentation
-    def __init__(self, *args, name=None, **kwargs):
+    def __init__(self, _SolutionBase phase, *args, name=None, **kwargs):
         if self.domain is NULL:
             raise TypeError("Can't instantiate abstract class Domain1D.")
 
         if name is not None:
             self.name = name
 
+        self.gas = phase
+
     property index:
         """
         Index of this domain in a stack. Returns -1 if this domain is not part
@@ -60,7 +62,8 @@ cdef class Domain1D:
                 self.domain.setBounds(n, default[0], default[1])
 
         if Y is not None:
-            for n in range(4, self.n_components):
+            k0 = self.component_index(self.gas.species_name(0))
+            for n in range(k0, k0 + self.gas.n_species):
                 self.domain.setBounds(n, Y[0], Y[1])
 
         for name,(lower,upper) in kwargs.items():
@@ -80,7 +83,8 @@ cdef class Domain1D:
             self.domain.setSteadyTolerances(default[0], default[1])
 
         if Y is not None:
-            for n in range(4, self.n_components):
+            k0 = self.component_index(self.gas.species_name(0))
+            for n in range(k0, k0 + self.gas.n_species):
                 self.domain.setSteadyTolerances(Y[0], Y[1], n)
 
         for name,(lower,upper) in kwargs.items():
@@ -100,7 +104,8 @@ cdef class Domain1D:
             self.domain.setTransientTolerances(default[0], default[1])
 
         if Y is not None:
-            for n in range(4, self.n_components):
+            k0 = self.component_index(self.gas.species_name(0))
+            for n in range(k0, k0 + self.gas.n_species):
                 self.domain.setTransientTolerances(Y[0], Y[1], n)
 
         for name,(lower,upper) in kwargs.items():
@@ -171,12 +176,10 @@ cdef class Boundary1D(Domain1D):
         self.boundary = NULL
 
     # The signature of this function causes warnings for Sphinx documentation
-    def __init__(self, *args, _SolutionBase phase, **kwargs):
+    def __init__(self, *args, **kwargs):
         if self.boundary is NULL:
             raise TypeError("Can't instantiate abstract class Boundary1D.")
         self.domain = <CxxDomain1D*>(self.boundary)
-        self.phase = phase
-
         Domain1D.__init__(self, *args, **kwargs)
 
     property T:
@@ -199,12 +202,12 @@ cdef class Boundary1D(Domain1D):
         or as an array.
         """
         def __get__(self):
-            self.phase.TPY = self.phase.T, self.phase.P, self.Y
-            return self.phase.X
+            self.gas.TPY = self.gas.T, self.gas.P, self.Y
+            return self.gas.X
 
         def __set__(self, X):
-            self.phase.TPX = None, None, X
-            cdef np.ndarray[np.double_t, ndim=1] data = self.phase.X
+            self.gas.TPX = None, None, X
+            cdef np.ndarray[np.double_t, ndim=1] data = self.gas.X
             self.boundary.setMoleFractions(&data[0])
 
     property Y:
@@ -221,8 +224,8 @@ cdef class Boundary1D(Domain1D):
             return Y
 
         def __set__(self, Y):
-            self.phase.TPY = self.phase.T, self.phase.P, Y
-            self.X = self.phase.X
+            self.gas.TPY = self.gas.T, self.gas.P, Y
+            self.X = self.gas.X
 
 
 cdef class Inlet1D(Boundary1D):
@@ -321,12 +324,11 @@ cdef class _FlowBase(Domain1D):
     def __cinit__(self, *args, **kwargs):
         self.flow = NULL
 
-    def __init__(self, _SolutionBase thermo, *args, **kwargs):
+    def __init__(self, *args, **kwargs):
         self.domain = <CxxDomain1D*>(self.flow)
         super().__init__(*args, **kwargs)
-        if not thermo.transport_model:
-            thermo.transport_model = 'Mix'
-        self.gas = thermo
+        if not self.gas.transport_model:
+            self.gas.transport_model = 'Mix'
         self.flow.setKinetics(deref(self.gas.kinetics))
         self.flow.setTransport(deref(self.gas.transport))
         self.P = self.gas.P