free electron additions

modules/geochemistry/include/utils/GeochemicalDatabaseReader.h

@@ -387,13 +387,15 @@ class GeochemicalDatabaseReader
    */
   const FileName & filename() const;
 
+  /// Returns true if name is a "secondary species" or "free electron" in the database
+  bool isSecondarySpecies(const std::string & name) const;
+
   /**
    * Checks if species is of given type
    * @param name species name
    * @return true iff species is of given type
    */
   bool isBasisSpecies(const std::string & name) const;
-  bool isSecondarySpecies(const std::string & name) const;
   bool isRedoxSpecies(const std::string & name) const;
   bool isGasSpecies(const std::string & name) const;
   bool isMineralSpecies(const std::string & name) const;
@@ -403,7 +405,7 @@ class GeochemicalDatabaseReader
   /// returns True iff name is the name of a sorbing mineral
   bool isSorbingMineral(const std::string & name) const;
 
-  /// Returns a list of all the names of the "secondary species" in the database
+  /// Returns a list of all the names of the "secondary species" and "free electron" in the database
   std::vector<std::string> secondarySpeciesNames() const;
 
   /// Returns a list of all the names of the "redox couples" in the database
@@ -441,7 +443,7 @@ class GeochemicalDatabaseReader
   std::map<std::string, GeochemistryElements> _elements;
   /// Basis species data read from the database
   std::map<std::string, GeochemistryBasisSpecies> _basis_species;
-  /// Secondary equilibrium species data read from the database
+  /// Secondary equilibrium species and free electron data read from the database
   std::map<std::string, GeochemistryEquilibriumSpecies> _equilibrium_species;
   /// Mineral species data read from the database
   std::map<std::string, GeochemistryMineralSpecies> _mineral_species;

modules/geochemistry/python/database_converter.py

@@ -82,6 +82,8 @@ def main():
         database['basis species'] = db.basis_species
     if db.secondary_species:
         database['secondary species'] = db.secondary_species
+    if db.free_electron:
+        database['free electron'] = db.free_electron
     if db.mineral_species:
         database['mineral species'] = db.mineral_species
     if db.gas_species:

modules/geochemistry/python/dbclass.py

@@ -25,6 +25,7 @@ def __init__(self):
         self._elements = None
         self._basis_species = None
         self._secondary_species = None
+        self._free_electron = None
         self._mineral_species = None
         self._gas_species = None
         self._redox_couples = None
@@ -117,6 +118,15 @@ def secondary_species(self):
     def secondary_species(self, secondary_species):
         self._secondary_species = secondary_species
 
+    # Free electron data
+    @property
+    def free_electron(self):
+        return self._free_electron
+
+    @free_electron.setter
+    def free_electron(self, free_electron):
+        self._free_electron = free_electron
+
     # Mineral species data
     @property
     def mineral_species(self):

modules/geochemistry/python/readers/gwb_reader.py

@@ -601,6 +601,7 @@ def readDatabase(dblist):
     db.elements = elements
     db.basis_species = basis_species
     db.secondary_species = secondary_species
+    db.free_electron = free_electron
     db.mineral_species = mineral_species
     db.sorbing_minerals = sorbing_minerals
     db.gas_species = gas_species

modules/geochemistry/python/tests/test_gwbreader.py

@@ -137,6 +137,18 @@ def testSecondarySpecies(self):
 
         self.assertDictEqual(self.db.secondary_species, gold)
 
+    def testFreeElectron(self):
+        """
+        Test that the free electron is correctly parsed
+        """
+        self.readDatabase()
+        gold = {'e-': {'charge': '-1', 'radius': '0.0', 'molecular weight': '0.0000',
+                         'species': {'H2O': '.500', 'O2(g)': '-.250', 'H+': '-1.000'},
+                         'logk': ['22.76135', '20.7757', '18.513025', '16.4658',
+                                  '14.473225', '12.92125', '11.68165', '10.67105']}}
+
+        self.assertDictEqual(self.db.free_electron, gold)
+
     def testMineralSpecies(self):
         """
         Test that the mineral species are correctly parsed

modules/geochemistry/python/tests/testdata/gwbtestdata.dat

@@ -132,3 +132,16 @@ Cu2O
        -2.000 H+              2.000 Cu+             1.000 H2O
 
 -end-
+
+   1 free electron
+
+e-
+     charge= -1      ion size=  0.0 A      mole wt.=    0.0000 g
+     3 species in reaction
+         .500 H2O             -.250 O2(g)          -1.000 H+
+       22.76135     20.7757   18.513025     16.4658
+      14.473225    12.92125    11.68165    10.67105
+
+-end-
+
+

modules/geochemistry/src/utils/GeochemicalDatabaseReader.C

@@ -159,11 +159,13 @@ GeochemicalDatabaseReader::getEquilibriumSpecies(const std::vector<std::string>
 {
   // Parse the secondary species specified in names
   for (const auto & species : names)
-    if (_root["secondary species"].isMember(species))
+    if (_root["secondary species"].isMember(species) or _root["free electron"].isMember(species))
     {
       GeochemistryEquilibriumSpecies dbs;
 
-      auto sec_species = _root["secondary species"][species];
+      auto sec_species = _root["secondary species"].isMember(species)
+                             ? _root["secondary species"][species]
+                             : _root["free electron"][species];
       dbs.name = species;
       dbs.radius = MooseUtils::convert<Real>(sec_species["radius"].asString());
       dbs.charge = MooseUtils::convert<Real>(sec_species["charge"].asString());
@@ -610,6 +612,8 @@ std::vector<std::string>
 GeochemicalDatabaseReader::secondarySpeciesNames() const
 {
   std::vector<std::string> names(_root["secondary species"].getMemberNames());
+  for (const auto nm : _root["free electron"].getMemberNames())
+    names.push_back(nm);
   return names;
 }
 
@@ -654,7 +658,7 @@ GeochemicalDatabaseReader::isSorbingMineral(const std::string & name) const
 bool
 GeochemicalDatabaseReader::isSecondarySpecies(const std::string & name) const
 {
-  return _root["secondary species"].isMember(name);
+  return _root["secondary species"].isMember(name) || _root["free electron"].isMember(name);
 }
 
 bool

modules/geochemistry/unit/data/moose_testdb.json

@@ -584,5 +584,27 @@
       "log K": "1.7200",
       "dlogK/dT": "0.0000"
     }
+  },
+  "free electron": {
+    "e-": {
+      "species": {
+        "H2O": ".500",
+        "O2(g)": "-.250",
+        "H+": "-1.000"
+      },
+      "charge": "-1",
+      "radius": "0.0",
+      "molecular weight": "0.0000",
+      "logk": [
+        "22.76135",
+        "20.7757",
+        "18.513025",
+        "16.4658",
+        "14.473225",
+        "12.92125",
+        "11.68165",
+        "10.67105"
+      ]
+    }
   }
 }

modules/geochemistry/unit/src/GeochemicalDatabaseReaderTest.C

@@ -478,6 +478,7 @@ TEST(GeochemicalDatabaseReaderTest, isBasisSpecies)
   EXPECT_FALSE(database.isBasisSpecies("Fe+++"));
   EXPECT_FALSE(database.isBasisSpecies("Cu2O"));
   EXPECT_FALSE(database.isBasisSpecies(">(s)FeO-"));
+  EXPECT_FALSE(database.isBasisSpecies("e-"));
 }
 
 TEST(GeochemicalDatabaseReaderTest, isSecondarySpecies)
@@ -496,6 +497,7 @@ TEST(GeochemicalDatabaseReaderTest, isSecondarySpecies)
   EXPECT_FALSE(database.isSecondarySpecies("Fe+++"));
   EXPECT_FALSE(database.isSecondarySpecies("Cu2O"));
   EXPECT_FALSE(database.isSecondarySpecies(">(s)FeO-"));
+  EXPECT_TRUE(database.isSecondarySpecies("e-"));
 }
 
 TEST(GeochemicalDatabaseReaderTest, isMineralSpecies)
@@ -514,6 +516,7 @@ TEST(GeochemicalDatabaseReaderTest, isMineralSpecies)
   EXPECT_FALSE(database.isMineralSpecies("Fe+++"));
   EXPECT_FALSE(database.isMineralSpecies("Cu2O"));
   EXPECT_FALSE(database.isMineralSpecies(">(s)FeO-"));
+  EXPECT_FALSE(database.isMineralSpecies("e-"));
 }
 
 TEST(GeochemicalDatabaseReaderTest, isRedoxSpecies)
@@ -532,6 +535,7 @@ TEST(GeochemicalDatabaseReaderTest, isRedoxSpecies)
   EXPECT_TRUE(database.isRedoxSpecies("Fe+++"));
   EXPECT_FALSE(database.isRedoxSpecies("Cu2O"));
   EXPECT_FALSE(database.isRedoxSpecies(">(s)FeO-"));
+  EXPECT_FALSE(database.isRedoxSpecies("e-"));
 }
 
 TEST(GeochemicalDatabaseReaderTest, isGasSpecies)
@@ -550,6 +554,7 @@ TEST(GeochemicalDatabaseReaderTest, isGasSpecies)
   EXPECT_FALSE(database.isGasSpecies("Fe+++"));
   EXPECT_FALSE(database.isGasSpecies("Cu2O"));
   EXPECT_FALSE(database.isGasSpecies(">(s)FeO-"));
+  EXPECT_FALSE(database.isGasSpecies("e-"));
 }
 
 TEST(GeochemicalDatabaseReaderTest, isSorbingMineral)
@@ -568,6 +573,7 @@ TEST(GeochemicalDatabaseReaderTest, isSorbingMineral)
   EXPECT_FALSE(database.isSorbingMineral("Fe+++"));
   EXPECT_FALSE(database.isSorbingMineral("Cu2O"));
   EXPECT_FALSE(database.isSorbingMineral(">(s)FeO-"));
+  EXPECT_FALSE(database.isSorbingMineral("e-"));
 }
 
 TEST(GeochemicalDatabaseReaderTest, isOxideSpecies)
@@ -586,6 +592,7 @@ TEST(GeochemicalDatabaseReaderTest, isOxideSpecies)
   EXPECT_FALSE(database.isOxideSpecies("Fe+++"));
   EXPECT_TRUE(database.isOxideSpecies("Cu2O"));
   EXPECT_FALSE(database.isOxideSpecies(">(s)FeO-"));
+  EXPECT_FALSE(database.isOxideSpecies("e-"));
 }
 
 TEST(GeochemicalDatabaseReaderTest, isSurfaceSpecies)
@@ -604,16 +611,17 @@ TEST(GeochemicalDatabaseReaderTest, isSurfaceSpecies)
   EXPECT_FALSE(database.isSurfaceSpecies("Fe+++"));
   EXPECT_FALSE(database.isSurfaceSpecies("Cu2O"));
   EXPECT_TRUE(database.isSurfaceSpecies(">(s)FeO-"));
+  EXPECT_FALSE(database.isSurfaceSpecies("e-"));
 }
 
 TEST(GeochemicalDatabaseReaderTest, secondarySpeciesNames)
 {
   GeochemicalDatabaseReader database("data/moose_testdb.json");
 
   std::vector<std::string> names = database.secondarySpeciesNames();
-  for (const auto & n : {"CO2(aq)", "CO3--", "CaCO3", "CaOH+", "OH-"})
+  for (const auto & n : {"CO2(aq)", "CO3--", "CaCO3", "CaOH+", "OH-", "e-"})
     EXPECT_TRUE(std::find(names.begin(), names.end(), n) != names.end());
-  EXPECT_EQ(names.size(), 5);
+  EXPECT_EQ(names.size(), 6);
 }
 
 TEST(GeochemicalDatabaseReaderTest, redoxCoupleNames)