Inherit test_tolerances to MoleReactors

MoleReactors have varying orders of magnitude in comparsion to mass fraction
based Reactors. Tolerances that are too tight based on the state vector
cause test failures. This commit inherits the test and modifies tolerances
appropriately.

src/zeroD/IdealGasConstPressureMoleReactor.cpp

@@ -135,9 +135,9 @@ Eigen::SparseMatrix<double> IdealGasConstPressureMoleReactor::jacobian()
     m_kin->getNetProductionRates(netProductionRates.data()); // "omega dot"
     Eigen::SparseMatrix<double> dnk_dnj = m_kin->netProductionRates_ddN();
     double molarVolume = m_thermo->molarVolume();
-    // Calculate ROP derivatives, excluding the term
-    // molarVolume * (wdot(j) - sum_k(X_k * dwdot_j/dX_k))
-    // which is small and would completely destroy the sparsity of the Jacobian
+    // Calculate ROP derivatives, excluding the terms where dnk/dnj is zero but
+    // molarVolume * wdot is not, as it reduces matrix sparsity and diminishes
+    // performance.
     for (int k = 0; k < dnk_dnj.outerSize(); k++) {
         for (Eigen::SparseMatrix<double>::InnerIterator it(dnk_dnj, k); it; ++it) {
             it.valueRef() = it.value() + netProductionRates[it.row()] * molarVolume;

src/zeroD/MoleReactor.cpp

@@ -193,7 +193,6 @@ void MoleReactor::getState(double* y)
     getSurfaceInitialConditions(y+m_nsp+m_sidx);
 }
 
-
 void MoleReactor::updateState(double* y)
 {
     // The components of y are [0] total internal energy, [1] the total volume, and

test/python/test_reactor.py

@@ -235,7 +235,7 @@ def test_equalize_pressure(self):
         self.assertNear(self.gas1.P, self.gas2.P)
         self.assertNotAlmostEqual(self.r1.T, self.r2.T)
 
-    def test_tolerances(self):
+    def test_tolerances(self, rtol_lim=1e-10, atol_lim=1e-20):
         def integrate(atol, rtol):
             P0 = 10 * ct.one_atm
             T0 = 1100
@@ -257,9 +257,9 @@ def integrate(atol, rtol):
 
             return nSteps
 
-        n_baseline = integrate(1e-10, 1e-20)
-        n_rtol = integrate(5e-7, 1e-20)
-        n_atol = integrate(1e-10, 1e-5)
+        n_baseline = integrate(rtol_lim, atol_lim)
+        n_rtol = integrate(rtol_lim * 1e2, atol_lim)
+        n_atol = integrate(rtol_lim, atol_lim * 1e15)
         assert n_baseline > n_rtol
         assert n_baseline > n_atol
 
@@ -873,6 +873,8 @@ def test_mole_reactor_surface_chem(self):
             self.assertArrayNear(rsurf1.coverages, rsurf2.coverages, rtol=1e-4,
                 atol=1e-8)
 
+    def test_tolerances(self, rtol_lim=1e-8, atol_lim=1e-18):
+        super().test_tolerances(rtol_lim, atol_lim)
 
 class TestIdealGasReactor(TestReactor):
     reactorClass = ct.IdealGasReactor