GeochemicalDatabaseReaderTest.C File Reference

Go to the source code of this file.

Functions
	TEST (GeochemicalDatabaseReaderTest, filename)
	TEST (GeochemicalDatabaseReaderTest, faultyDB)
	TEST (GeochemicalDatabaseReaderTest, getActivityModel)
	TEST (GeochemicalDatabaseReaderTest, getFugacityModel)
	TEST (GeochemicalDatabaseReaderTest, getLogKModel)
	TEST (GeochemicalDatabaseReaderTest, getTemperatures)
	TEST (GeochemicalDatabaseReaderTest, getPressures)
	TEST (GeochemicalDatabaseReaderTest, getDebyeHuckel)
	TEST (GeochemicalDatabaseReaderTest, getNeutralSpeciesActivity)
	TEST (GeochemicalDatabaseReaderTest, getElements)
	TEST (GeochemicalDatabaseReaderTest, getBasisSpecies)
	TEST (GeochemicalDatabaseReaderTest, getEquilibriumSpecies)
	TEST (GeochemicalDatabaseReaderTest, getMineralSpecies)
	TEST (GeochemicalDatabaseReaderTest, getGasSpecies)
	TEST (GeochemicalDatabaseReaderTest, getRedoxSpecies)
	TEST (GeochemicalDatabaseReaderTest, getOxideSpecies)
	TEST (GeochemicalDatabaseReaderTest, getSurfaceSpecies)
	TEST (GeochemicalDatabaseReaderTest, equilibriumReactions)
	TEST (GeochemicalDatabaseReaderTest, mineralReactions)
	TEST (GeochemicalDatabaseReaderTest, gasReactions)
	TEST (GeochemicalDatabaseReaderTest, redoxReactions)
	TEST (GeochemicalDatabaseReaderTest, oxideReactions)
	TEST (GeochemicalDatabaseReaderTest, isBasisSpecies)
	TEST (GeochemicalDatabaseReaderTest, isSecondarySpecies)
	TEST (GeochemicalDatabaseReaderTest, isMineralSpecies)
	TEST (GeochemicalDatabaseReaderTest, isRedoxSpecies)
	TEST (GeochemicalDatabaseReaderTest, isGasSpecies)
	TEST (GeochemicalDatabaseReaderTest, isSorbingMineral)
	TEST (GeochemicalDatabaseReaderTest, isOxideSpecies)
	TEST (GeochemicalDatabaseReaderTest, isSurfaceSpecies)
	TEST (GeochemicalDatabaseReaderTest, mineralSpeciesNames)
	TEST (GeochemicalDatabaseReaderTest, secondarySpeciesNames)
	TEST (GeochemicalDatabaseReaderTest, redoxCoupleNames)
	TEST (GeochemicalDatabaseReaderTest, surfaceSpeciesNames)
	TEST (GeochemicalDatabaseReaderTest, getSpeciesData)
	TEST (GeochemicalDatabaseReaderTest, freeElectron)
	Test the reexpression of the free electron in terms of O2(aq) More...
	TEST (GeochemicalDatabaseReaderTest, freeElectronNoReexpress)
	Test that the free electron can be determined in terms of O2(g) More...
	TEST (GeochemicalDatabaseReaderTest, isSecondarySpecies_noextrap)
	Test the DatabaseReader when the secondary species that contain extrapolated logK are removed. More...

Function Documentation

TEST() [1/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		filename
	)

Definition at line 15 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  EXPECT_EQ(database.filename(), "database/moose_testdb.json");
}

TEST() [2/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		faultyDB
	)

Definition at line 22 of file GeochemicalDatabaseReaderTest.C.

{
  // Test that the database validator throws an error when a faulty
  // database is read (the full range of validation errors are tested
  // in GeochemicalDatabaseValidatorTest.C)
  try
  {
    GeochemicalDatabaseReader database("database/faultydbs/missing_header.json");
  }
  catch (const std::exception & err)
  {
    const std::string msg = "The MOOSE database database/faultydbs/missing_header.json does not "
                            "have a required \"Header\" field";

    std::size_t pos = std::string(err.what()).find(msg);
    ASSERT_TRUE(pos != std::string::npos);
  }
}

TEST() [3/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getActivityModel
	)

Definition at line 41 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  EXPECT_EQ(database.getActivityModel(), "debye-huckel");
}

TEST() [4/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getFugacityModel
	)

Definition at line 48 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  EXPECT_EQ(database.getFugacityModel(), "tsonopoulos");
}

TEST() [5/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getLogKModel
	)

Definition at line 55 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  EXPECT_EQ(database.getLogKModel(), "fourth-order");

  GeochemicalDatabaseReader database2("database/moose_testdb.json", true);

  EXPECT_EQ(database2.getLogKModel(), "fourth-order");

  GeochemicalDatabaseReader database3("database/moose_testdb.json", false, true);

  EXPECT_EQ(database3.getLogKModel(), "piecewise-linear");
}

TEST() [6/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getTemperatures
	)

Definition at line 70 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Get the temperature points from the database and compare with the expected
  // valules
  auto temperature_points = database.getTemperatures();

  std::vector<Real> temperature_points_gold{0.0, 25.0, 60.0, 100.0, 150.0, 200.0, 250.0, 300.0};
  EXPECT_EQ(temperature_points, temperature_points_gold);
}

TEST() [7/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getPressures
	)

Definition at line 82 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Get the pressure points from the database and compare with the expected
  // valules
  auto pressure_points = database.getPressures();

  std::vector<Real> pressure_points_gold{
      1.0134, 1.0134, 1.0134, 1.0134, 4.7600, 15.5490, 39.7760, 85.9270};
  EXPECT_EQ(pressure_points, pressure_points_gold);
}

TEST() [8/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getDebyeHuckel
	)

Definition at line 95 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Get the Debye-Huckel from the database and compare with the expected
  // valules
  auto dh = database.getDebyeHuckel();

  std::vector<Real> adh_gold{.4913, .5092, .5450, .5998, .6898, .8099, .9785, 1.2555};
  std::vector<Real> bdh_gold{.3247, .3283, .3343, .3422, .3533, .3655, .3792, .3965};
  std::vector<Real> bdot_gold{.0174, .0410, .0440, .0460, .0470, .0470, .0340, 0.0000};

  EXPECT_EQ(dh.adh, adh_gold);
  EXPECT_EQ(dh.bdh, bdh_gold);
  EXPECT_EQ(dh.bdot, bdot_gold);
}

TEST() [9/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getNeutralSpeciesActivity
	)

Definition at line 112 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Get the neutral species activity coefficients from the database
  // and compare with the expected values
  auto nsa = database.getNeutralSpeciesActivity();

  auto ns = nsa["co2"];
  std::vector<Real> a_gold{.1224, .1127, .09341, .08018, .08427, .09892, .1371, .1967};
  std::vector<Real> b_gold{-.004679, -.01049, -.0036, -.001503, -.01184, -.0104, -.007086, -.01809};
  std::vector<Real> c_gold{
      -0.0004114, 0.001545, 9.609e-05, 0.0005009, 0.003118, 0.001386, -0.002887, -0.002497};
  std::vector<Real> d_gold(8);

  EXPECT_EQ(ns.a, a_gold);
  EXPECT_EQ(ns.b, b_gold);
  EXPECT_EQ(ns.c, c_gold);
  EXPECT_TRUE(ns.d.empty());

  ns = nsa["h2o"];
  a_gold = {1.4203, 1.45397, 1.5012, 1.5551, 1.6225, 1.6899, 1.7573, 1.8247};
  b_gold = {0.0177, 0.022357, 0.0289, 0.036478, 0.045891, 0.0553, 0.0647, 0.0741};
  c_gold = {0.0103, 0.0093804, 0.008, 0.0064366, 0.0045221, 0.0026, 0.0006, -0.0013};
  d_gold = {-0.0005, -0.0005362, -0.0006, -0.0007132, -0.0008312, -0.0009, -0.0011, -0.0012};

  EXPECT_EQ(ns.a, a_gold);
  EXPECT_EQ(ns.b, b_gold);
  EXPECT_EQ(ns.c, c_gold);
  EXPECT_EQ(ns.d, d_gold);

  // check error is thrown if database has no neutral species
  GeochemicalDatabaseReader database_non("database/faultydbs/no_neutral_species.json");
  try
  {
    auto nsa = database_non.getNeutralSpeciesActivity();
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("No neutral species activity coefficients in database") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [10/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getElements
	)

Definition at line 159 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Get the elements from the database and compare with the expected
  // valules
  auto els = database.getElements();
  auto el = els["Ag"];

  EXPECT_EQ(el.name, "Silver");
  EXPECT_EQ(el.molecular_weight, 107.8680);

  el = els["Al"];

  EXPECT_EQ(el.name, "Aluminum");
  EXPECT_EQ(el.molecular_weight, 26.9815);
}

TEST() [11/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getBasisSpecies
	)

Definition at line 177 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Vector of primary species
  std::vector<std::string> bs_names{"Ca++", "HCO3-", "H+"};

  // Check the basis species
  auto bs = database.getBasisSpecies(bs_names);

  // Check that only the species in bs_names are returned
  std::vector<std::string> bs_names_returned;
  for (auto b : bs)
    bs_names_returned.push_back(b.first);

  std::sort(bs_names_returned.begin(), bs_names_returned.end());
  std::sort(bs_names.begin(), bs_names.end());
  EXPECT_EQ(bs_names_returned, bs_names);

  // Check each species
  auto species = bs["Ca++"];

  std::map<std::string, Real> els_gold = {{"Ca", 1}};
  EXPECT_EQ(species.radius, 6);
  EXPECT_EQ(species.charge, 2);
  EXPECT_EQ(species.molecular_weight, 40.08);
  EXPECT_EQ(species.elements, els_gold);

  species = bs["HCO3-"];

  els_gold = {{"C", 1}, {"H", 1}, {"O", 3}};
  EXPECT_EQ(species.radius, 4.5);
  EXPECT_EQ(species.charge, -1);
  EXPECT_EQ(species.molecular_weight, 61.0171);
  EXPECT_EQ(species.elements, els_gold);

  species = bs["H+"];

  els_gold = {{"H", 1}};
  EXPECT_EQ(species.radius, 9);
  EXPECT_EQ(species.charge, 1);
  EXPECT_EQ(species.molecular_weight, 1.0079);
  EXPECT_EQ(species.elements, els_gold);

  // check that an error is thrown if the species does not exist
  try
  {
    auto bs_not = database.getBasisSpecies({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [12/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getEquilibriumSpecies
	)

Definition at line 236 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Vector of secondary species
  std::vector<std::string> ss_names{"CO2(aq)", "CO3--", "CaCO3", "CaOH+", "OH-"};

  // Check the secondary species
  auto ss = database.getEquilibriumSpecies(ss_names);

  // Check that only the species in ss_names are returned
  std::vector<std::string> ss_names_returned;
  for (auto s : ss)
    ss_names_returned.push_back(s.first);

  std::sort(ss_names_returned.begin(), ss_names_returned.end());
  std::sort(ss_names.begin(), ss_names.end());
  EXPECT_EQ(ss_names_returned, ss_names);

  // Check each species
  auto sspecies = ss["CO2(aq)"];
  std::vector<Real> logk_gold{
      -6.5570, -6.3660, -6.3325, -6.4330, -6.7420, -7.1880, -7.7630, -8.4650};
  std::map<std::string, Real> bs_gold = {{"H2O", -1}, {"H+", 1}, {"HCO3-", 1}};

  EXPECT_EQ(sspecies.radius, 4);
  EXPECT_EQ(sspecies.charge, 0);
  EXPECT_EQ(sspecies.molecular_weight, 44.0098);
  EXPECT_EQ(sspecies.basis_species, bs_gold);
  EXPECT_EQ(sspecies.equilibrium_const, logk_gold);

  sspecies = ss["CO3--"];
  logk_gold = {10.6169, 10.3439, 10.2092, 10.2793, 10.5131, 10.8637, 11.2860, 11.6319};
  bs_gold = {{"H+", -1}, {"HCO3-", 1}};

  EXPECT_EQ(sspecies.radius, 4.5);
  EXPECT_EQ(sspecies.charge, -2);
  EXPECT_EQ(sspecies.molecular_weight, 60.0092);
  EXPECT_EQ(sspecies.basis_species, bs_gold);
  EXPECT_EQ(sspecies.equilibrium_const, logk_gold);

  sspecies = ss["CaCO3"];
  logk_gold = {7.5520, 7.1280, 6.7340, 6.4350, 6.1810, 5.9320, 5.5640, 4.7890};
  bs_gold = {{"Ca++", 1}, {"HCO3-", 1}, {"H+", -1}};

  EXPECT_EQ(sspecies.radius, 4);
  EXPECT_EQ(sspecies.charge, 0);
  EXPECT_EQ(sspecies.molecular_weight, 100.0892);
  EXPECT_EQ(sspecies.basis_species, bs_gold);
  EXPECT_EQ(sspecies.equilibrium_const, logk_gold);

  sspecies = ss["CaOH+"];
  logk_gold = {13.7095, 12.6887, 11.5069, 10.4366, 9.3958, 8.5583, 7.8155, 7.0306};
  bs_gold = {{"Ca++", 1}, {"H2O", 1}, {"H+", -1}};

  EXPECT_EQ(sspecies.radius, 4);
  EXPECT_EQ(sspecies.charge, 1);
  EXPECT_EQ(sspecies.molecular_weight, 57.0873);
  EXPECT_EQ(sspecies.basis_species, bs_gold);
  EXPECT_EQ(sspecies.equilibrium_const, logk_gold);

  sspecies = ss["OH-"];
  logk_gold = {14.9325, 13.9868, 13.0199, 12.2403, 11.5940, 11.2191, 11.0880, 1001.2844};
  bs_gold = {{"H2O", 1}, {"H+", -1}};

  EXPECT_EQ(sspecies.radius, 3.5);
  EXPECT_EQ(sspecies.charge, -1);
  EXPECT_EQ(sspecies.molecular_weight, 17.0073);
  EXPECT_EQ(sspecies.basis_species, bs_gold);
  EXPECT_EQ(sspecies.equilibrium_const, logk_gold);

  // check that an error is thrown if the species does not exist
  try
  {
    auto bs_not = database.getEquilibriumSpecies({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [13/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getMineralSpecies
	)

Definition at line 322 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Vector of mineral species to be read
  std::vector<std::string> ms_names{"Calcite", "Fe(OH)3(ppd)"};

  // Check the mineral species
  auto ms = database.getMineralSpecies(ms_names);

  // Check that only the species in ms_names are returned
  std::vector<std::string> ms_names_returned;
  for (auto s : ms)
    ms_names_returned.push_back(s.first);

  std::sort(ms_names_returned.begin(), ms_names_returned.end());
  std::sort(ms_names.begin(), ms_names.end());
  EXPECT_EQ(ms_names_returned, ms_names);

  auto mspecies = ms["Calcite"];
  std::vector<Real> logk_gold = {2.0683, 1.7130, 1.2133, .6871, .0762, -.5349, -1.2301, -2.2107};
  std::map<std::string, Real> bs_gold = {{"Ca++", 1}, {"H+", -1}, {"HCO3-", 1}};

  EXPECT_EQ(mspecies.molecular_volume, 36.934);
  EXPECT_EQ(mspecies.molecular_weight, 100.0892);
  EXPECT_EQ(mspecies.basis_species, bs_gold);
  EXPECT_EQ(mspecies.equilibrium_const, logk_gold);
  EXPECT_EQ(mspecies.surface_area, 0.0);

  mspecies = ms["Fe(OH)3(ppd)"];
  logk_gold = {6.1946, 4.8890, 3.4608, 2.2392, 1.1150, .2446, -.5504, -1.5398};
  bs_gold = {{"H+", -3}, {"Fe+++", 1}, {"H2O", 3}};

  EXPECT_EQ(mspecies.molecular_volume, 34.32);
  EXPECT_EQ(mspecies.molecular_weight, 106.8689);
  EXPECT_EQ(mspecies.basis_species, bs_gold);
  EXPECT_EQ(mspecies.equilibrium_const, logk_gold);
  EXPECT_EQ(mspecies.surface_area, 600.0);
  bs_gold = {{">(s)FeOH", 0.005}, {">(w)FeOH", 0.2}};
  EXPECT_EQ(mspecies.sorption_sites, bs_gold);

  // check that an error is thrown if the species does not exist
  try
  {
    auto bs_not = database.getMineralSpecies({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [14/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getGasSpecies
	)

Definition at line 378 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Vector of gas species to be read
  std::vector<std::string> gs_names{"N2(g)", "CH4(g)"};

  // Check the gas species
  auto gs = database.getGasSpecies(gs_names);

  // Check that only the species in gs_names are returned
  std::vector<std::string> gs_names_returned;
  for (auto s : gs)
    gs_names_returned.push_back(s.first);

  std::sort(gs_names_returned.begin(), gs_names_returned.end());
  std::sort(gs_names.begin(), gs_names.end());
  EXPECT_EQ(gs_names_returned, gs_names);

  auto gspecies = gs["N2(g)"];
  std::vector<Real> logk_gold = {
      -2.9620, -3.1848, -3.3320, -3.2902, -3.1631, -2.9499, -2.7827, -2.3699};
  std::map<std::string, Real> bs_gold = {{"N2(aq)", 1}};

  EXPECT_EQ(gspecies.molecular_weight, 28.0134);
  EXPECT_EQ(gspecies.basis_species, bs_gold);
  EXPECT_EQ(gspecies.equilibrium_const, logk_gold);
  EXPECT_TRUE(gspecies.chi.empty());
  EXPECT_EQ(gspecies.Pcrit, 33.9);
  EXPECT_EQ(gspecies.Tcrit, 126.2);
  EXPECT_EQ(gspecies.omega, .039);

  gspecies = gs["CH4(g)"];
  logk_gold = {-2.6487, -2.8202, -2.9329, -2.9446, -2.9163, -2.7253, -2.4643, -2.1569};
  bs_gold = {{"CH4(aq)", 1}};
  std::vector<Real> chi_gold = {-537.779, 1.54946, -.000927827, 1.20861, -.00370814, 3.33804e-6};

  EXPECT_EQ(gspecies.molecular_weight, 16.0426);
  EXPECT_EQ(gspecies.basis_species, bs_gold);
  EXPECT_EQ(gspecies.equilibrium_const, logk_gold);
  EXPECT_EQ(gspecies.chi, chi_gold);
  EXPECT_EQ(gspecies.Pcrit, 46.0);
  EXPECT_EQ(gspecies.Tcrit, 190.4);
  EXPECT_EQ(gspecies.omega, .011);

  // check that an error is thrown if the species does not exist
  try
  {
    auto bs_not = database.getGasSpecies({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [15/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getRedoxSpecies
	)

Definition at line 438 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Vector of redox species
  std::vector<std::string> rs_names{"Am++++"};

  // Check the secondary species
  auto rs = database.getRedoxSpecies(rs_names);

  // Check that only the species in ss_names are returned
  std::vector<std::string> rs_names_returned;
  for (auto s : rs)
    rs_names_returned.push_back(s.first);

  std::sort(rs_names_returned.begin(), rs_names_returned.end());
  std::sort(rs_names.begin(), rs_names.end());
  EXPECT_EQ(rs_names_returned, rs_names);

  auto rspecies = rs["Am++++"];
  std::vector<Real> logk_gold = {
      18.7967, 18.0815, 17.2698, 16.5278, 15.8024, 15.2312, 14.7898, 14.4250};
  std::map<std::string, Real> bs_gold = {{"H2O", -0.5}, {"H+", 1}, {"Am+++", 1}, {"O2(aq)", 0.250}};

  EXPECT_EQ(rspecies.radius, 11);
  EXPECT_EQ(rspecies.charge, 4);
  EXPECT_EQ(rspecies.molecular_weight, 241.0600);
  EXPECT_EQ(rspecies.basis_species, bs_gold);
  EXPECT_EQ(rspecies.equilibrium_const, logk_gold);

  // check that an error is thrown if the species does not exist
  try
  {
    auto bs_not = database.getRedoxSpecies({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [16/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getOxideSpecies
	)

Definition at line 483 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Vector of gas species to be read
  std::vector<std::string> os_names{"Cu2O"};

  // Check the oxide species
  auto os = database.getOxideSpecies(os_names);

  // Check that only the species in gs_names are returned
  std::vector<std::string> os_names_returned;
  for (auto s : os)
    os_names_returned.push_back(s.first);

  EXPECT_EQ(os_names_returned, os_names);

  auto ospecies = os["Cu2O"];
  std::map<std::string, Real> bs_gold = {{"H+", -2}, {"Cu+", 2}, {"H2O", 1}};

  EXPECT_EQ(ospecies.molecular_weight, 143.0929);
  EXPECT_EQ(ospecies.basis_species, bs_gold);

  // check that an error is thrown if the species does not exist
  try
  {
    auto bs_not = database.getOxideSpecies({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [17/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getSurfaceSpecies
	)

Definition at line 521 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  std::vector<std::string> ss_names{">(s)FeO-"};

  auto ss = database.getSurfaceSpecies(ss_names);

  // Check that only the species in ss_names are returned
  std::vector<std::string> ss_names_returned;
  for (auto s : ss)
    ss_names_returned.push_back(s.first);

  EXPECT_EQ(ss_names_returned, ss_names);

  auto sspecies = ss[">(s)FeO-"];
  std::map<std::string, Real> ss_gold = {{">(s)FeOH", 1}, {"H+", -1}};

  EXPECT_EQ(sspecies.basis_species, ss_gold);

  // check that an error is thrown if the species does not exist
  try
  {
    auto bs_not = database.getSurfaceSpecies({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [18/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		equilibriumReactions
	)

Definition at line 556 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Secondary equilibrium species
  std::vector<std::string> names{"CO2(aq)", "CO3--", "CaCO3", "CaOH+", "OH-"};

  auto reactions = database.equilibriumReactions(names);

  EXPECT_EQ(reactions[0], "CO2(aq) = H+ - H2O + HCO3-");
  EXPECT_EQ(reactions[1], "CO3-- = - H+ + HCO3-");
  EXPECT_EQ(reactions[2], "CaCO3 = Ca++ - H+ + HCO3-");
  EXPECT_EQ(reactions[3], "CaOH+ = Ca++ - H+ + H2O");
  EXPECT_EQ(reactions[4], "OH- = - H+ + H2O");

  // check that an error is thrown if the species does not exist
  try
  {
    auto reactions_not = database.equilibriumReactions({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [19/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		mineralReactions
	)

Definition at line 586 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Secondary mineral species
  std::vector<std::string> names{"Calcite"};

  auto reactions = database.mineralReactions(names);

  EXPECT_EQ(reactions[0], "Calcite = Ca++ - H+ + HCO3-");

  // check that an error is thrown if the species does not exist
  try
  {
    auto reactions_not = database.mineralReactions({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [20/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		gasReactions
	)

Definition at line 612 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Secondary gas species
  std::vector<std::string> names{"CH4(g)", "N2(g)"};

  auto reactions = database.gasReactions(names);

  EXPECT_EQ(reactions[0], "CH4(g) = CH4(aq)");
  EXPECT_EQ(reactions[1], "N2(g) = N2(aq)");

  // check that an error is thrown if the species does not exist
  try
  {
    auto reactions_not = database.gasReactions({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [21/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		redoxReactions
	)

Definition at line 639 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Secondary redox couples
  std::vector<std::string> names{"(O-phth)--", "Am++++"};

  auto reactions = database.redoxReactions(names);

  EXPECT_EQ(reactions[0], "(O-phth)-- = 6H+ -5H2O + 8HCO3- -7.5O2(aq)");
  EXPECT_EQ(reactions[1], "Am++++ = Am+++ + H+ -0.5H2O + 0.25O2(aq)");

  // check that an error is thrown if the species does not exist
  try
  {
    auto reactions_not = database.redoxReactions({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [22/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		oxideReactions
	)

Definition at line 666 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  // Secondary oxide species
  std::vector<std::string> names{"Cu2O"};

  auto reactions = database.oxideReactions(names);

  EXPECT_EQ(reactions[0], "Cu2O = 2Cu+ -2H+ + H2O");

  // check that an error is thrown if the species does not exist
  try
  {
    auto reactions_not = database.oxideReactions({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist does not exist in database database/moose_testdb.json") !=
                std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [23/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		isBasisSpecies
	)

Definition at line 692 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  EXPECT_TRUE(database.isBasisSpecies("Ca++"));
  EXPECT_TRUE(database.isBasisSpecies("H2O"));
  EXPECT_FALSE(database.isBasisSpecies("Ag"));
  EXPECT_FALSE(database.isBasisSpecies("CO2(aq)"));
  EXPECT_FALSE(database.isBasisSpecies("CO3--"));
  EXPECT_FALSE(database.isBasisSpecies("Calcite"));
  EXPECT_FALSE(database.isBasisSpecies("Fe(OH)3(ppd)"));
  EXPECT_FALSE(database.isBasisSpecies("CH4(g)"));
  EXPECT_FALSE(database.isBasisSpecies("(O-phth)--"));
  EXPECT_FALSE(database.isBasisSpecies("Fe+++"));
  EXPECT_FALSE(database.isBasisSpecies("Cu2O"));
  EXPECT_FALSE(database.isBasisSpecies(">(s)FeO-"));
  EXPECT_FALSE(database.isBasisSpecies("e-"));
}

TEST() [24/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		isSecondarySpecies
	)

Definition at line 711 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  EXPECT_FALSE(database.isSecondarySpecies("Ca++"));
  EXPECT_FALSE(database.isSecondarySpecies("H2O"));
  EXPECT_FALSE(database.isSecondarySpecies("Ag"));
  EXPECT_TRUE(database.isSecondarySpecies("CO2(aq)"));
  EXPECT_TRUE(database.isSecondarySpecies("CO3--"));
  EXPECT_TRUE(database.isSecondarySpecies("OH-"));
  EXPECT_FALSE(database.isSecondarySpecies("Calcite"));
  EXPECT_FALSE(database.isSecondarySpecies("Fe(OH)3(ppd)"));
  EXPECT_FALSE(database.isSecondarySpecies("CH4(g)"));
  EXPECT_FALSE(database.isSecondarySpecies("(O-phth)--"));
  EXPECT_FALSE(database.isSecondarySpecies("Fe+++"));
  EXPECT_FALSE(database.isSecondarySpecies("Cu2O"));
  EXPECT_FALSE(database.isSecondarySpecies(">(s)FeO-"));
  EXPECT_TRUE(database.isSecondarySpecies("e-"));
}

TEST() [25/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		isMineralSpecies
	)

Definition at line 731 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  EXPECT_FALSE(database.isMineralSpecies("Ca++"));
  EXPECT_FALSE(database.isMineralSpecies("H2O"));
  EXPECT_FALSE(database.isMineralSpecies("Ag"));
  EXPECT_FALSE(database.isMineralSpecies("CO2(aq)"));
  EXPECT_FALSE(database.isMineralSpecies("CO3--"));
  EXPECT_TRUE(database.isMineralSpecies("Calcite"));
  EXPECT_TRUE(database.isMineralSpecies("Fe(OH)3(ppd)"));
  EXPECT_FALSE(database.isMineralSpecies("CH4(g)"));
  EXPECT_FALSE(database.isMineralSpecies("(O-phth)--"));
  EXPECT_FALSE(database.isMineralSpecies("Fe+++"));
  EXPECT_FALSE(database.isMineralSpecies("Cu2O"));
  EXPECT_FALSE(database.isMineralSpecies(">(s)FeO-"));
  EXPECT_FALSE(database.isMineralSpecies("e-"));
}

TEST() [26/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		isRedoxSpecies
	)

Definition at line 750 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  EXPECT_FALSE(database.isRedoxSpecies("Ca++"));
  EXPECT_FALSE(database.isRedoxSpecies("H2O"));
  EXPECT_FALSE(database.isRedoxSpecies("Ag"));
  EXPECT_FALSE(database.isRedoxSpecies("CO2(aq)"));
  EXPECT_FALSE(database.isRedoxSpecies("CO3--"));
  EXPECT_FALSE(database.isRedoxSpecies("Calcite"));
  EXPECT_FALSE(database.isRedoxSpecies("Fe(OH)3(ppd)"));
  EXPECT_FALSE(database.isRedoxSpecies("CH4(g)"));
  EXPECT_TRUE(database.isRedoxSpecies("(O-phth)--"));
  EXPECT_TRUE(database.isRedoxSpecies("Fe+++"));
  EXPECT_FALSE(database.isRedoxSpecies("Cu2O"));
  EXPECT_FALSE(database.isRedoxSpecies(">(s)FeO-"));
  EXPECT_FALSE(database.isRedoxSpecies("e-"));
}

TEST() [27/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		isGasSpecies
	)

Definition at line 769 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  EXPECT_FALSE(database.isGasSpecies("Ca++"));
  EXPECT_FALSE(database.isGasSpecies("H2O"));
  EXPECT_FALSE(database.isGasSpecies("Ag"));
  EXPECT_FALSE(database.isGasSpecies("CO2(aq)"));
  EXPECT_FALSE(database.isGasSpecies("CO3--"));
  EXPECT_FALSE(database.isGasSpecies("Calcite"));
  EXPECT_FALSE(database.isGasSpecies("Fe(OH)3(ppd)"));
  EXPECT_TRUE(database.isGasSpecies("CH4(g)"));
  EXPECT_FALSE(database.isGasSpecies("(O-phth)--"));
  EXPECT_FALSE(database.isGasSpecies("Fe+++"));
  EXPECT_FALSE(database.isGasSpecies("Cu2O"));
  EXPECT_FALSE(database.isGasSpecies(">(s)FeO-"));
  EXPECT_FALSE(database.isGasSpecies("e-"));
}

TEST() [28/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		isSorbingMineral
	)

Definition at line 788 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  EXPECT_FALSE(database.isSorbingMineral("Ca++"));
  EXPECT_FALSE(database.isSorbingMineral("H2O"));
  EXPECT_FALSE(database.isSorbingMineral("Ag"));
  EXPECT_FALSE(database.isSorbingMineral("CO2(aq)"));
  EXPECT_FALSE(database.isSorbingMineral("CO3--"));
  EXPECT_FALSE(database.isSorbingMineral("Calcite"));
  EXPECT_TRUE(database.isSorbingMineral("Fe(OH)3(ppd)"));
  EXPECT_FALSE(database.isSorbingMineral("CH4(g)"));
  EXPECT_FALSE(database.isSorbingMineral("(O-phth)--"));
  EXPECT_FALSE(database.isSorbingMineral("Fe+++"));
  EXPECT_FALSE(database.isSorbingMineral("Cu2O"));
  EXPECT_FALSE(database.isSorbingMineral(">(s)FeO-"));
  EXPECT_FALSE(database.isSorbingMineral("e-"));
}

TEST() [29/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		isOxideSpecies
	)

Definition at line 807 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  EXPECT_FALSE(database.isOxideSpecies("Ca++"));
  EXPECT_FALSE(database.isOxideSpecies("H2O"));
  EXPECT_FALSE(database.isOxideSpecies("Ag"));
  EXPECT_FALSE(database.isOxideSpecies("CO2(aq)"));
  EXPECT_FALSE(database.isOxideSpecies("CO3--"));
  EXPECT_FALSE(database.isOxideSpecies("Calcite"));
  EXPECT_FALSE(database.isOxideSpecies("Fe(OH)3(ppd)"));
  EXPECT_FALSE(database.isOxideSpecies("CH4(g)"));
  EXPECT_FALSE(database.isOxideSpecies("(O-phth)--"));
  EXPECT_FALSE(database.isOxideSpecies("Fe+++"));
  EXPECT_TRUE(database.isOxideSpecies("Cu2O"));
  EXPECT_FALSE(database.isOxideSpecies(">(s)FeO-"));
  EXPECT_FALSE(database.isOxideSpecies("e-"));
}

TEST() [30/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		isSurfaceSpecies
	)

Definition at line 826 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  EXPECT_FALSE(database.isSurfaceSpecies("Ca++"));
  EXPECT_FALSE(database.isSurfaceSpecies("H2O"));
  EXPECT_FALSE(database.isSurfaceSpecies("Ag"));
  EXPECT_FALSE(database.isSurfaceSpecies("CO2(aq)"));
  EXPECT_FALSE(database.isSurfaceSpecies("CO3--"));
  EXPECT_FALSE(database.isSurfaceSpecies("Calcite"));
  EXPECT_FALSE(database.isSurfaceSpecies("Fe(OH)3(ppd)"));
  EXPECT_FALSE(database.isSurfaceSpecies("CH4(g)"));
  EXPECT_FALSE(database.isSurfaceSpecies("(O-phth)--"));
  EXPECT_FALSE(database.isSurfaceSpecies("Fe+++"));
  EXPECT_FALSE(database.isSurfaceSpecies("Cu2O"));
  EXPECT_TRUE(database.isSurfaceSpecies(">(s)FeO-"));
  EXPECT_FALSE(database.isSurfaceSpecies("e-"));
}

TEST() [31/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		mineralSpeciesNames
	)

Definition at line 845 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  std::vector<std::string> names = database.mineralSpeciesNames();
  for (const auto & n : {"Calcite",
                         "Calcite_asdf",
                         "Fe(OH)3(ppd)",
                         "Fe(OH)3(ppd)fake",
                         "Goethite",
                         "Something",
                         "problematic_sorber"})
    EXPECT_TRUE(std::find(names.begin(), names.end(), n) != names.end());
  EXPECT_EQ(names.size(), (std::size_t)7);
}

TEST() [32/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		secondarySpeciesNames
	)

Definition at line 861 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  std::vector<std::string> names = database.secondarySpeciesNames();
  for (const auto & n : {"CO2(aq)", "CO3--", "CaCO3", "CaOH+", "OH-", "e-", "seq_radius_neg1"})
    EXPECT_TRUE(std::find(names.begin(), names.end(), n) != names.end());
  EXPECT_EQ(names.size(), (std::size_t)8);
}

TEST() [33/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		redoxCoupleNames
	)

Definition at line 871 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  std::vector<std::string> names = database.redoxCoupleNames();
  for (const auto & n : {"(O-phth)--", "Am++++", "CH4(aq)", "Fe+++", "StoiCheckRedox"})
    EXPECT_TRUE(std::find(names.begin(), names.end(), n) != names.end());
  EXPECT_EQ(names.size(), (std::size_t)5);
}

TEST() [34/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		surfaceSpeciesNames
	)

Definition at line 881 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  std::vector<std::string> names = database.surfaceSpeciesNames();
  for (const auto & n : {">(s)FeO-", ">(s)FeOCa+"})
    EXPECT_TRUE(std::find(names.begin(), names.end(), n) != names.end());
  EXPECT_EQ(names.size(), (std::size_t)2);
}

TEST() [35/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		getSpeciesData
	)

Definition at line 891 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  std::string data = database.getSpeciesData("Ca++");
  std::string gold = "Ca++:\n{\n    \"charge\": 2,\n    \"elements\": {\n        \"Ca\": 1.0\n    "
                     "},\n    \"molecular weight\": 40.08,\n    \"radius\": 6.0\n}";
  EXPECT_EQ(data, gold);

  // check that an error is thrown if the species does not exist
  try
  {
    auto reactions_not = database.getSpeciesData({"does_not_exist"});
    FAIL() << "Missing expected exception.";
  }
  catch (const std::exception & e)
  {
    std::string msg(e.what());
    ASSERT_TRUE(msg.find("does_not_exist is not a species in the database") != std::string::npos)
        << "Failed with unexpected error message: " << msg;
  }
}

TEST() [36/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		freeElectron
	)

Test the reexpression of the free electron in terms of O2(aq)

Definition at line 915 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json");

  auto fe = database.getEquilibriumSpecies({"e-"})["e-"];

  std::vector<Real> logk_gold{
      23.4266, 21.50045, 19.277525, 17.24705, 15.238975, 13.64975, 12.34665, 11.27355};
  std::map<std::string, Real> bs_gold = {{"H2O", 0.5}, {"H+", -1}, {"O2(aq)", -0.25}};
  EXPECT_EQ(fe.charge, -1.0);
  EXPECT_EQ(fe.radius, 0.0);
  EXPECT_EQ(fe.molecular_weight, 0.0);
  EXPECT_EQ(fe.basis_species, bs_gold);
  EXPECT_EQ(fe.equilibrium_const, logk_gold);
}

TEST() [37/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		freeElectronNoReexpress
	)

Test that the free electron can be determined in terms of O2(g)

Definition at line 932 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json", false);

  auto fe = database.getEquilibriumSpecies({"e-"})["e-"];

  std::vector<Real> logk_gold{
      22.76135, 20.7757, 18.513025, 16.4658, 14.473225, 12.92125, 11.68165, 10.67105};
  std::map<std::string, Real> bs_gold = {{"H2O", 0.5}, {"H+", -1}, {"O2(g)", -0.25}};
  EXPECT_EQ(fe.charge, -1.0);
  EXPECT_EQ(fe.radius, 0.0);
  EXPECT_EQ(fe.molecular_weight, 0.0);
  EXPECT_EQ(fe.basis_species, bs_gold);
  EXPECT_EQ(fe.equilibrium_const, logk_gold);
}

TEST() [38/38]

TEST	(	GeochemicalDatabaseReaderTest	,
		isSecondarySpecies_noextrap
	)

Test the DatabaseReader when the secondary species that contain extrapolated logK are removed.

Definition at line 949 of file GeochemicalDatabaseReaderTest.C.

{
  GeochemicalDatabaseReader database("database/moose_testdb.json", true, false, true);

  EXPECT_FALSE(database.isSecondarySpecies("Ca++"));
  EXPECT_FALSE(database.isSecondarySpecies("H2O"));
  EXPECT_FALSE(database.isSecondarySpecies("Ag"));
  EXPECT_TRUE(database.isSecondarySpecies("CO2(aq)"));
  EXPECT_TRUE(database.isSecondarySpecies("CO3--"));
  EXPECT_FALSE(database.isSecondarySpecies("OH-"));
  EXPECT_FALSE(database.isSecondarySpecies("Calcite"));
  EXPECT_FALSE(database.isSecondarySpecies("Fe(OH)3(ppd)"));
  EXPECT_FALSE(database.isSecondarySpecies("CH4(g)"));
  EXPECT_FALSE(database.isSecondarySpecies("(O-phth)--"));
  EXPECT_FALSE(database.isSecondarySpecies("Fe+++"));
  EXPECT_FALSE(database.isSecondarySpecies("Cu2O"));
  EXPECT_FALSE(database.isSecondarySpecies(">(s)FeO-"));
  EXPECT_TRUE(database.isSecondarySpecies("e-"));
}