revising Amanzi chem pks

src/pks/CMakeLists.txt

@@ -8,7 +8,7 @@ include_directories(${GEOCHEM_SOURCE_DIR})
 include_directories(${CHEMPK_SOURCE_DIR})
 
 set(ats_pks_src_files
-  pk_helpers.cc
+  chem_pk_helpers.cc
   pk_bdf_default.cc
   pk_physical_default.cc
   pk_physical_bdf_default.cc
@@ -17,7 +17,7 @@ set(ats_pks_src_files
   )
 
 set(ats_pks_inc_files
-  pk_helpers.hh
+  chem_pk_helpers.hh
   pk_bdf_default.hh
   pk_physical_default.hh
   pk_physical_bdf_default.hh

src/pks/chem_pk_helpers.cc

@@ -0,0 +1,74 @@
+/*
+  Copyright 2010-202x held jointly by participating institutions.
+  ATS is released under the three-clause BSD License.
+  The terms of use and "as is" disclaimer for this license are
+  provided in the top-level COPYRIGHT file.
+
+  Authors: Ethan Coon ([email protected])
+*/
+
+#include "chem_pk_helpers.hh"
+#include "Chemistry_PK.hh"
+
+namespace Amanzi {
+
+// -----------------------------------------------------------------------------
+// Helper functions for working with Amanzi's Chemistry PK
+// -----------------------------------------------------------------------------
+void
+convertConcentrationToAmanzi(const Epetra_MultiVector& mol_dens,
+                             int num_aqueous,
+                             const Epetra_MultiVector& tcc_ats,
+                             Epetra_MultiVector& tcc_amanzi)
+{
+  // convert from mole fraction [mol C / mol H20] to [mol C / L]
+  for (int k = 0; k != num_aqueous; ++k) {
+    for (int c = 0; c != tcc_ats.MyLength(); ++c) {
+      // 1.e-3 converts L to m^3
+      tcc_amanzi[k][c] = tcc_ats[k][c] * mol_dens[0][c] * 1.e-3;
+    }
+  }
+}
+
+void
+convertConcentrationToATS(const Epetra_MultiVector& mol_dens,
+                          int num_aqueous,
+                          const Epetra_MultiVector& tcc_amanzi,
+                          Epetra_MultiVector& tcc_ats)
+{
+  // convert from [mol C / L] to mol fraction [mol C / mol H20]
+  for (int k = 0; k != num_aqueous; ++k) {
+    for (int c = 0; c != tcc_amanzi.MyLength(); ++c) {
+      tcc_ats[k][c] = tcc_amanzi[k][c] / (mol_dens[0][c] * 1.e-3);
+    }
+  }
+}
+
+
+bool
+advanceChemistry(Teuchos::RCP<AmanziChemistry::Chemistry_PK> chem_pk,
+                 double t_old,
+                 double t_new,
+                 bool reinit,
+                 const Epetra_MultiVector& mol_dens,
+                 Teuchos::RCP<Epetra_MultiVector> tcc,
+                 Teuchos::Time& timer)
+{
+  bool fail = false;
+  int num_aqueous = chem_pk->num_aqueous_components();
+  convertConcentrationToAmanzi(mol_dens, num_aqueous, *tcc, *tcc);
+  chem_pk->set_aqueous_components(tcc);
+
+  {
+    auto monitor = Teuchos::rcp(new Teuchos::TimeMonitor(timer));
+    fail = chem_pk->AdvanceStep(t_old, t_new, reinit);
+  }
+  if (fail) return fail;
+
+  *tcc = *chem_pk->aqueous_components();
+  convertConcentrationToATS(mol_dens, num_aqueous, *tcc, *tcc);
+  return fail;
+}
+
+
+} //  namespace Amanzi

src/pks/chem_pk_helpers.hh

@@ -0,0 +1,46 @@
+/*
+  Copyright 2010-202x held jointly by participating institutions.
+  ATS is released under the three-clause BSD License.
+  The terms of use and "as is" disclaimer for this license are
+  provided in the top-level COPYRIGHT file.
+
+  Authors: Ethan Coon ([email protected])
+*/
+
+//! A set of helper functions for doing common things in PKs.
+#pragma once
+
+#include "Teuchos_TimeMonitor.hpp"
+#include "Epetra_MultiVector.hpp"
+
+namespace Amanzi {
+
+namespace AmanziChemistry {
+class Chemistry_PK;
+}
+
+// -----------------------------------------------------------------------------
+// Helper functions for working with Amanzi's Chemistry PK
+// -----------------------------------------------------------------------------
+void
+convertConcentrationToAmanzi(const Epetra_MultiVector& mol_den,
+                             int num_aqueous,
+                             const Epetra_MultiVector& tcc_ats,
+                             Epetra_MultiVector& tcc_amanzi);
+
+void
+convertConcentrationToATS(const Epetra_MultiVector& mol_den,
+                          int num_aqueous,
+                          const Epetra_MultiVector& tcc_ats,
+                          Epetra_MultiVector& tcc_amanzi);
+
+bool
+advanceChemistry(Teuchos::RCP<AmanziChemistry::Chemistry_PK> chem_pk,
+                 double t_old,
+                 double t_new,
+                 bool reinit,
+                 const Epetra_MultiVector& mol_dens,
+                 Teuchos::RCP<Epetra_MultiVector> tcc,
+                 Teuchos::Time& timer);
+
+} // namespace Amanzi