Use identity reorder maps when reactions were not reordered

The reversible and pressure-dependent reorder maps were built by counting
Cantera's reactions, which do not correspond one-to-one with the generated
code's: a reaction written with an explicit collider is pressure-dependent
to Cantera, while the Chemkin reader folds the collider into the rate
expression. For h2o2 that produced a permutation of eleven indices applied
to the six entries the generated code writes.

The maps exist only to undo a reordering of the reactions, so where the
reactions were not reordered they are now identities sized from the
generated mechanism. This also covers the case where the species were
reordered but the reactions were not.

Author: kyleniemeyer

src/pyjac/functional_tester/test.py

@@ -395,6 +395,21 @@ def check_optimized(self, build_dir, gas, filename='mechanism.h'):
             [np.where(self.back_pdep_map == x)[0][0] for x in range(pdep_reacs)]
         )
 
+        # Those maps are built from Cantera's reactions, which do not always
+        # correspond one-to-one with the generated code's: a reaction written
+        # with an explicit collider is pressure-dependent to Cantera, while the
+        # Chemkin reader folds the collider into the rate expression and emits
+        # no pressure-modification entry for it. The maps exist only to undo a
+        # reordering of the reactions, so where the reactions were not
+        # reordered there is nothing to undo, and an identity sized from the
+        # generated mechanism is both correct and the right length.
+        if np.array_equal(self.fwd_rxn_map, np.arange(n_reac)):
+            counts = mechanism_counts(build_dir, filename)
+            self.fwd_rev_rxn_map = np.arange(counts['REV_RATES'])
+            self.back_rev_rxn_map = np.arange(counts['REV_RATES'])
+            self.fwd_pdep_map = np.arange(counts['PRES_MOD_RATES'])
+            self.back_pdep_map = np.arange(counts['PRES_MOD_RATES'])
+
         self.back_dydt_map = np.array([0] + [x + 1 for x in self.back_spec_map])
 
     def __init__(self, build_dir, gas, module_name='pyjacob', filename='mechanism.h'):