[Transport] Automatically reinitialize after change in number of species

This makes it possible for GasTransport objects to work reasonably well with
ThermoPhase objects that have had species added to them. The main changes
required are to make the initialization functions idempotent.

interfaces/cython/cantera/test/test_transport.py

@@ -43,6 +43,51 @@ class TestTransport(utilities.CanteraTest):
         self.assertTrue(all(self.phase.multi_diff_coeffs.flat >= 0.0))
         self.assertTrue(all(self.phase.thermal_diff_coeffs.flat != 0.0))
 
+    def test_add_species_mix(self):
+        S = {s.name: s for s in ct.Species.listFromFile('gri30.xml')}
+
+        base = ['H', 'H2', 'OH', 'O2', 'AR']
+        extra = ['H2O', 'CH4']
+
+        state = 500, 2e5, 'H2:0.4, O2:0.29, CH4:0.01, H2O:0.3'
+
+        gas1 = ct.Solution(thermo='IdealGas', species=[S[s] for s in base+extra])
+        gas1.transport_model = 'Mix'
+        gas1.TPX = state
+
+        gas2 = ct.Solution(thermo='IdealGas', species=[S[s] for s in base])
+        gas2.transport_model = 'Mix'
+        for s in extra:
+            gas2.add_species(S[s])
+        gas2.TPX = state
+
+        self.assertNear(gas1.viscosity, gas2.viscosity)
+        self.assertNear(gas1.thermal_conductivity, gas2.thermal_conductivity)
+        self.assertArrayNear(gas1.binary_diff_coeffs, gas2.binary_diff_coeffs)
+        self.assertArrayNear(gas1.mix_diff_coeffs, gas2.mix_diff_coeffs)
+
+    def test_add_species_multi(self):
+        S = {s.name: s for s in ct.Species.listFromFile('gri30.xml')}
+
+        base = ['H', 'H2', 'OH', 'O2', 'AR', 'N2']
+        extra = ['H2O', 'CH4']
+
+        state = 500, 2e5, 'H2:0.3, O2:0.28, CH4:0.02, H2O:0.3, N2:0.1'
+
+        gas1 = ct.Solution(thermo='IdealGas', species=[S[s] for s in base+extra])
+        gas1.transport_model = 'Multi'
+        gas1.TPX = state
+
+        gas2 = ct.Solution(thermo='IdealGas', species=[S[s] for s in base])
+        gas2.transport_model = 'Multi'
+        for s in extra:
+            gas2.add_species(S[s])
+        gas2.TPX = state
+
+        self.assertNear(gas1.thermal_conductivity, gas2.thermal_conductivity)
+        self.assertArrayNear(gas1.multi_diff_coeffs, gas2.multi_diff_coeffs)
+
+
 class TestTransportGeometryFlags(utilities.CanteraTest):
     phase_data = """
 units(length="cm", time="s", quantity="mol", act_energy="cal/mol")

src/transport/GasTransport.cpp

@@ -101,6 +101,11 @@ GasTransport& GasTransport::operator=(const GasTransport& right)
 
 void GasTransport::update_T()
 {
+    if (m_thermo->nSpecies() != m_nsp) {
+        // Rebuild data structures if number of species has changed
+        init(m_thermo, m_mode, m_log_level);
+    }
+
     double T = m_thermo->temperature();
     if (T == m_temp) {
         return;
@@ -517,6 +522,10 @@ void GasTransport::fitCollisionIntegrals(MMCollisionInt& integrals)
         }
     }
     vector_fp fitlist;
+    m_omega22_poly.clear();
+    m_astar_poly.clear();
+    m_bstar_poly.clear();
+    m_cstar_poly.clear();
     for (size_t i = 0; i < m_nsp; i++) {
         for (size_t j = i; j < m_nsp; j++) {
             // Chemkin fits only delta* = 0
@@ -557,6 +566,9 @@ void GasTransport::fitProperties(MMCollisionInt& integrals)
     vector_fp tlog(np), spvisc(np), spcond(np);
     vector_fp w(np), w2(np);
 
+    m_visccoeffs.clear();
+    m_condcoeffs.clear();
+
     // generate array of log(t) values
     for (size_t n = 0; n < np; n++) {
         double t = m_thermo->minTemp() + dt*n;
@@ -715,6 +727,7 @@ void GasTransport::fitProperties(MMCollisionInt& integrals)
 
     mxerr = 0.0, mxrelerr = 0.0;
     vector_fp diff(np + 1);
+    m_diffcoeffs.clear();
     for (size_t k = 0; k < m_nsp; k++) {
         for (size_t j = k; j < m_nsp; j++) {
             for (size_t n = 0; n < np; n++) {

src/transport/MixTransport.cpp

@@ -123,7 +123,7 @@ void MixTransport::getSpeciesFluxes(size_t ndim, const doublereal* const grad_T,
 void MixTransport::update_T()
 {
     doublereal t = m_thermo->temperature();
-    if (t == m_temp) {
+    if (t == m_temp && m_nsp == m_thermo->nSpecies()) {
         return;
     }
     if (t < 0.0) {

src/transport/MultiTransport.cpp

@@ -388,7 +388,7 @@ void MultiTransport::getMultiDiffCoeffs(const size_t ld, doublereal* const d)
 
 void MultiTransport::update_T()
 {
-    if (m_temp == m_thermo->temperature()) {
+    if (m_temp == m_thermo->temperature() && m_nsp == m_thermo->nSpecies()) {
         return;
     }
     GasTransport::update_T();