moves when the chem engine is set, which allows transport parseParame…

…terList to use specie names

src/pks/mpc/mpc_coupled_reactivetransport.cc

@@ -37,7 +37,20 @@ MPCCoupledReactiveTransport::MPCCoupledReactiveTransport(
 void
 MPCCoupledReactiveTransport::parseParameterList()
 {
-  WeakMPC::parseParameterList();
+  cast_sub_pks_();
+  coupled_chemistry_pk_->parseParameterList();
+
+  // communicate chemistry engine to transport.
+#ifdef ALQUIMIA_ENABLED
+  transport_pk_->setChemEngine(
+    Teuchos::rcp_static_cast<AmanziChemistry::Alquimia_PK>(chemistry_pk_),
+    chemistry_pk_->chem_engine());
+  transport_pk_surf_->setChemEngine(
+    Teuchos::rcp_static_cast<AmanziChemistry::Alquimia_PK>(chemistry_pk_surf_),
+    chemistry_pk_surf_->chem_engine());
+#endif
+
+  coupled_transport_pk_->parseParameterList();
 
   domain_ = Keys::readDomain(*plist_, "domain", "domain");
   domain_surf_ = Keys::readDomainHint(*plist_, domain_, "domain", "surface");
@@ -57,8 +70,6 @@ MPCCoupledReactiveTransport::parseParameterList()
 void
 MPCCoupledReactiveTransport::Setup()
 {
-  cast_sub_pks_();
-
   // must Setup transport first to get alias for saturation, etc set up correctly
   coupled_transport_pk_->Setup();
   coupled_chemistry_pk_->Setup();
@@ -106,27 +117,11 @@ MPCCoupledReactiveTransport::cast_sub_pks_()
     Teuchos::rcp_dynamic_cast<Transport::Transport_ATS>(coupled_transport_pk_->get_subpk(1));
   AMANZI_ASSERT(transport_pk_surf_ != Teuchos::null);
 
-  chemistry_pk_ =
-    Teuchos::rcp_dynamic_cast<AmanziChemistry::Chemistry_PK>(coupled_chemistry_pk_->get_subpk(0));
-  AMANZI_ASSERT(chemistry_pk_ != Teuchos::null);
-  chemistry_pk_surf_ =
-    Teuchos::rcp_dynamic_cast<AmanziChemistry::Chemistry_PK>(coupled_chemistry_pk_->get_subpk(1));
-  AMANZI_ASSERT(chemistry_pk_surf_ != Teuchos::null);
-
   AMANZI_ASSERT(transport_pk_->domain() == chemistry_pk_->domain());
   AMANZI_ASSERT(transport_pk_surf_->domain() == chemistry_pk_surf_->domain());
-
-// communicate chemistry engine to transport.
-#ifdef ALQUIMIA_ENABLED
-  transport_pk_->SetupAlquimia(
-    Teuchos::rcp_static_cast<AmanziChemistry::Alquimia_PK>(chemistry_pk_),
-    chemistry_pk_->chem_engine());
-  transport_pk_surf_->SetupAlquimia(
-    Teuchos::rcp_static_cast<AmanziChemistry::Alquimia_PK>(chemistry_pk_surf_),
-    chemistry_pk_surf_->chem_engine());
-#endif
 }
 
+
 // -----------------------------------------------------------------------------
 //
 // -----------------------------------------------------------------------------

src/pks/mpc/mpc_reactivetransport.cc

@@ -39,21 +39,34 @@ MPCReactiveTransport::MPCReactiveTransport(Teuchos::ParameterList& pk_tree,
 
 
 void
-MPCReactiveTransport::Setup()
+MPCReactiveTransport::parseParameterList()
 {
   cast_sub_pks_();
+  chemistry_pk_->parseParameterList();
+
+#ifdef ALQUIMIA_ENABLED
+  transport_pk_->setChemEngine(
+    Teuchos::rcp_static_cast<AmanziChemistry::Alquimia_PK>(chemistry_pk_),
+    chemistry_pk_->chem_engine());
+#endif
 
+  // now transport can be parse with knowledge of names
+  transport_pk_->parseParameterList();
+}
+
+
+void
+MPCReactiveTransport::Setup()
+{
   transport_pk_->Setup();
   chemistry_pk_->Setup();
 
-
   S_->Require<CompositeVector, CompositeVectorSpace>(tcc_key_, tag_next_, "state")
     .SetMesh(S_->GetMesh(domain_))
     ->SetGhosted()
     ->AddComponent("cell", AmanziMesh::Entity_kind::CELL, chemistry_pk_->num_aqueous_components());
   S_->RequireEvaluator(tcc_key_, tag_next_);
 
-
   S_->Require<CompositeVector, CompositeVectorSpace>(mol_dens_key_, tag_next_)
     .SetMesh(S_->GetMesh(domain_))
     ->SetGhosted()
@@ -64,18 +77,13 @@ MPCReactiveTransport::Setup()
 void
 MPCReactiveTransport::cast_sub_pks_()
 {
-  transport_pk_ = Teuchos::rcp_dynamic_cast<Transport::Transport_ATS>(sub_pks_[1]);
-  AMANZI_ASSERT(transport_pk_ != Teuchos::null);
-
+  // cast and call parse on chemistry
   chemistry_pk_ = Teuchos::rcp_dynamic_cast<AmanziChemistry::Chemistry_PK>(sub_pks_[0]);
   AMANZI_ASSERT(chemistry_pk_ != Teuchos::null);
 
-  // communicate chemistry engine to transport.
-#ifdef ALQUIMIA_ENABLED
-  transport_pk_->SetupAlquimia(
-    Teuchos::rcp_static_cast<AmanziChemistry::Alquimia_PK>(chemistry_pk_),
-    chemistry_pk_->chem_engine());
-#endif
+  // now chem engine is set and we can hand it to transport
+  transport_pk_ = Teuchos::rcp_dynamic_cast<Transport::Transport_ATS>(sub_pks_[1]);
+  AMANZI_ASSERT(transport_pk_ != Teuchos::null);
 }
 
 // -----------------------------------------------------------------------------

src/pks/mpc/mpc_reactivetransport.hh

@@ -35,6 +35,9 @@ class MPCReactiveTransport : public WeakMPC {
 
   // PK methods
   virtual double get_dt() override;
+
+  virtual void parseParameterList() override;
+
   virtual void Setup() override;
   virtual void Initialize() override;
   virtual bool AdvanceStep(double t_old, double t_new, bool reinit = false) override;

src/pks/transport/transport_ats.hh

@@ -311,7 +311,7 @@ class Transport_ATS : public PK_PhysicalExplicit<Epetra_Vector> {
 
   // coupling with chemistry
 #ifdef ALQUIMIA_ENABLED
-  void SetupAlquimia(Teuchos::RCP<AmanziChemistry::Alquimia_PK> chem_pk,
+  void setChemEngine(Teuchos::RCP<AmanziChemistry::Alquimia_PK> chem_pk,
                      Teuchos::RCP<AmanziChemistry::ChemistryEngine> chem_engine);
 #endif
 

src/pks/transport/transport_ats_pk.cc

@@ -152,7 +152,7 @@ Transport_ATS::set_tags(const Tag& current, const Tag& next)
 ****************************************************************** */
 #ifdef ALQUIMIA_ENABLED
 void
-Transport_ATS::SetupAlquimia(Teuchos::RCP<AmanziChemistry::Alquimia_PK> chem_pk,
+Transport_ATS::setChemEngine(Teuchos::RCP<AmanziChemistry::Alquimia_PK> chem_pk,
                              Teuchos::RCP<AmanziChemistry::ChemistryEngine> chem_engine)
 {
   chem_pk_ = chem_pk;
@@ -985,6 +985,7 @@ Transport_ATS ::Advance_Dispersion_Diffusion_(double t_old, double t_new)
     // Disperse and diffuse aqueous components
     for (int i = 0; i < num_aqueous_; i++) {
       FindDiffusionValue_(component_names_[i], &md_new, &phase);
+      AMANZI_ASSERT(phase == 0);
       md_change = md_new - md_old;
       md_old = md_new;
 
@@ -1055,8 +1056,9 @@ Transport_ATS ::Advance_Dispersion_Diffusion_(double t_old, double t_new)
     // are treated with a hack of the accumulation term.
     D_.clear();
     md_old = 0.0;
-    for (int i = num_aqueous_; i < num_components_; i++) {
+    for (int i = num_aqueous_; i < (num_aqueous_ + num_gaseous_); i++) {
       FindDiffusionValue_(component_names_[i], &md_new, &phase);
+      AMANZI_ASSERT(phase == 1);
       md_change = md_new - md_old;
       md_old = md_new;