Add RedlichKister tests and sample case for LiC6 electrode

See #293
Cantera · Feb 18, 2016 · 1183479 · 1183479
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diff --git a/samples/cxx/LiC6_electrode/LiC6_electrode.cpp b/samples/cxx/LiC6_electrode/LiC6_electrode.cpp
@@ -0,0 +1,72 @@
+#include "cantera/thermo.h"
+#include "cantera/thermo/RedlichKisterVPSSTP.h"
+#include <fstream>
+
+using namespace Cantera;
+
+void calc_potentials()
+{
+    suppress_deprecation_warnings();
+    double Tk = 273.15 + 25.0;
+
+    std::string filename = "LiC6_electrodebulk.xml";
+    std::string phasename = "LiC6_and_Vacancies";
+    std::unique_ptr<ThermoPhase> electrodebulk(newPhase(filename,phasename));
+    std::string intercalatingSpeciesName("Li(C6)");
+    size_t intercalatingSpeciesIdx = electrodebulk->speciesIndex(intercalatingSpeciesName);
+    size_t nsp_tot = electrodebulk->nSpecies();
+
+    std::ofstream fout("potentials_output.dat", std::ofstream::out);
+    fout << "x[LiC6] ChemPotential[LiC6] ChemPotential[C6] Uref ActCoeff[LiC6] ActCoeff[C6] dlnActCoeffdx[LiC6] dlnActCoeffdx[C6]" << std::endl;
+
+    vector_fp spvals(nsp_tot);
+    vector_fp actCoeff(nsp_tot);
+    vector_fp dlnActCoeffdlnX_diag(nsp_tot);
+    double xmin = 0.6;
+    double xmax = 0.9;
+
+    int numSteps = 9;
+    double dx = (xmax-xmin)/(numSteps-1);
+
+    size_t nsp_electrodeBulk = electrodebulk->nSpecies();
+    vector_fp xv(nsp_electrodeBulk, 0.0);
+
+    for (int i = 0; i < numSteps; ++i) {
+        double x = xmin + i*dx;
+
+        vector_fp xv(nsp_electrodeBulk, 0.0);
+        //Set the fraction of intercalted lithium
+        xv[intercalatingSpeciesIdx] = x;
+
+        //Set so that mole fractions sum to 1
+        for (size_t j = 0; j < nsp_electrodeBulk; ++j) {
+            if (j != intercalatingSpeciesIdx) {
+                xv[j] = (1.0 - xv[intercalatingSpeciesIdx]);
+            }
+        }
+
+        electrodebulk->setState_TX(Tk, &xv[0]);
+        electrodebulk->getChemPotentials(spvals.data());
+
+        //Calulate the open circuit potential
+        double Uref = (spvals[1] - spvals[0])/Faraday;
+
+        electrodebulk->getdlnActCoeffdlnX_diag(dlnActCoeffdlnX_diag.data());
+        electrodebulk->getActivityCoefficients(actCoeff.data());
+
+        fout << fmt::format("{} {} {} {} {} {} {} {}\n",
+            xv[0], spvals[0], spvals[1], Uref, actCoeff[0],
+            actCoeff[1], dlnActCoeffdlnX_diag[0], dlnActCoeffdlnX_diag[1]);
+    }
+}
+
+int main(int argc, char** argv)
+{
+    try {
+        calc_potentials();
+        return 0;
+    } catch (CanteraError& err) {
+        std::cout << err.what() << std::endl;
+        return 0;
+    }
+}
diff --git a/samples/cxx/LiC6_electrode/LiC6_electrodebulk.xml b/samples/cxx/LiC6_electrode/LiC6_electrodebulk.xml
@@ -0,0 +1,80 @@
+<?xml version="1.0"?>
+<ctml>
+  <validate reactions="yes" species="yes"/>
+
+  <!-- phase LiC6_and_Vacancies     -->
+  <phase dim="3" id="LiC6_and_Vacancies">
+    <elementArray datasrc="elements.xml"> Li C </elementArray>
+    <speciesArray datasrc="#species_data">Li(C6) V(C6)</speciesArray>
+    <state>
+      <temperature units="K">298.15</temperature>
+      <pressure units="Pa">101325.0</pressure>
+      <moleFractions>Li(C6):0.6,V(C6):0.4</moleFractions>
+    </state>
+    <thermo model="Redlich-Kister">
+      <density units="kg/m3">2000.0</density>
+
+      <activityCoefficients model="Redlich-Kister">
+
+        <binaryNeutralSpeciesParameters speciesA="Li(C6)" speciesB="V(C6)">
+            <excessEnthalpy terms="15" units="J/kmol">
+	      -3.268E6,
+	       3.955E6,
+	      -4.573E6,
+	       6.147E6,
+	      -3.339E6,
+	       1.117E7,
+	       2.997E5,
+	      -4.866E7,
+	       1.362E5,
+	       1.373E8,
+	      -2.129E7,
+	      -1.722E8,
+	       3.956E7,
+	       9.302E7,
+	      -3.280E7
+            </excessEnthalpy>
+            <excessEntropy  terms="1" units="J/kmol/K">
+                 0.0
+            </excessEntropy>
+          </binaryNeutralSpeciesParameters>
+
+       </activityCoefficients>
+
+    </thermo>
+    <transport model="None"/>
+    <kinetics model="none"/>
+  </phase>
+
+
+  <!-- species definitions     -->
+  <speciesData id="species_data">
+
+    <!-- species Li(C6)    -->
+    <species name="Li(C6)">
+      <atomArray>C:6 Li:1 </atomArray>
+      <thermo>
+        <const_cp Tmax="5000.0" Tmin="100.0">
+           <t0 units="K">298.15</t0>
+           <h0 units="kJ/mol">-11.65</h0>
+           <s0 units="J/mol/K">0.0</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
+        </const_cp>
+      </thermo>
+    </species>
+
+    <!-- species V(C6)    -->
+    <species name="V(C6)">
+      <atomArray>C:6 </atomArray>
+      <thermo>
+        <const_cp Tmax="5000.0" Tmin="100.0">
+           <t0 units="K">298.15</t0>
+           <h0 units="kJ/mol">0.0</h0>
+           <s0 units="J/mol/K">0.0</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
+        </const_cp>
+      </thermo>
+    </species>
+  </speciesData>
+  <reactionData id="reaction_data"/>
+</ctml>
diff --git a/samples/cxx/LiC6_electrode/potentials_blessed.dat b/samples/cxx/LiC6_electrode/potentials_blessed.dat
@@ -0,0 +1,10 @@
+x[LiC6] ChemPotential[LiC6] ChemPotential[C6] Uref ActCoeff[LiC6] ActCoeff[C6] dlnActCoeffdx[LiC6] dlnActCoeffdx[C6]
+0.6 -1.27915e+07 -4.0265e+06 0.0908429 1.05164 0.492638 0.0907127 0.0907127
+0.6375 -1.26186e+07 -4.30768e+06 0.0861362 1.0613 0.48531 0.200612 0.200612
+0.675 -1.24454e+07 -4.63856e+06 0.0809124 1.07484 0.473671 0.229316 0.229316
+0.7125 -1.22826e+07 -5.00757e+06 0.0754005 1.08739 0.461396 0.193278 0.193278
+0.75 -1.21341e+07 -5.41192e+06 0.0696706 1.0968 0.450748 0.142257 0.142257
+0.7875 -1.19995e+07 -5.85996e+06 0.0636315 1.10287 0.442609 0.0766133 0.0766133
+0.825 -1.18827e+07 -6.34599e+06 0.0573836 1.10353 0.441766 -0.0712113 -0.0712113
+0.8625 -1.1793e+07 -6.82907e+06 0.0514475 1.09443 0.462697 -0.309379 -0.309379
+0.9 -1.17309e+07 -7.28939e+06 0.046033 1.07544 0.528389 -0.492206 -0.492206
diff --git a/test/data/RedlichKisterVPSSTP_valid.xml b/test/data/RedlichKisterVPSSTP_valid.xml
@@ -0,0 +1,80 @@
+<?xml version="1.0"?>
+<ctml>
+  <validate reactions="yes" species="yes"/>
+
+  <!-- phase LiC6_and_Vacancies     -->
+  <phase dim="3" id="LiC6_and_Vacancies">
+    <elementArray datasrc="elements.xml"> Li C </elementArray>
+    <speciesArray datasrc="#species_data">Li(C6) V(C6)</speciesArray>
+    <state>
+      <temperature units="K">298.15</temperature>
+      <pressure units="Pa">101325.0</pressure>
+      <moleFractions>Li(C6):0.6,V(C6):0.4</moleFractions>
+    </state>
+    <thermo model="Redlich-Kister">
+      <density units="kg/m3">2000.0</density>
+
+      <activityCoefficients model="Redlich-Kister">
+
+        <binaryNeutralSpeciesParameters speciesA="Li(C6)" speciesB="V(C6)">
+            <excessEnthalpy terms="15" units="J/kmol">
+	      -3.268E6,
+	       3.955E6,
+	      -4.573E6,
+	       6.147E6,
+	      -3.339E6,
+	       1.117E7,
+	       2.997E5,
+	      -4.866E7,
+	       1.362E5,
+	       1.373E8,
+	      -2.129E7,
+	      -1.722E8,
+	       3.956E7,
+	       9.302E7,
+	      -3.280E7
+            </excessEnthalpy>
+            <excessEntropy  terms="1" units="J/kmol/K">
+                 0.0
+            </excessEntropy>
+          </binaryNeutralSpeciesParameters>
+
+       </activityCoefficients>
+
+    </thermo>
+    <transport model="None"/>
+    <kinetics model="none"/>
+  </phase>
+
+
+  <!-- species definitions     -->
+  <speciesData id="species_data">
+
+    <!-- species Li(C6)    -->
+    <species name="Li(C6)">
+      <atomArray>C:6 Li:1 </atomArray>
+      <thermo>
+        <const_cp Tmax="5000.0" Tmin="100.0">
+           <t0 units="K">298.15</t0>
+           <h0 units="kJ/mol">-11.65</h0>
+           <s0 units="J/mol/K">0.0</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
+        </const_cp>
+      </thermo>
+    </species>
+
+    <!-- species V(C6)    -->
+    <species name="V(C6)">
+      <atomArray>C:6 </atomArray>
+      <thermo>
+        <const_cp Tmax="5000.0" Tmin="100.0">
+           <t0 units="K">298.15</t0>
+           <h0 units="kJ/mol">0.0</h0>
+           <s0 units="J/mol/K">0.0</s0>
+           <cp0 units="J/mol/K">0.0</cp0>
+        </const_cp>
+      </thermo>
+    </species>
+  </speciesData>
+  <reactionData id="reaction_data"/>
+</ctml>
diff --git a/test/thermo/RedlichKisterTest.cpp b/test/thermo/RedlichKisterTest.cpp
@@ -0,0 +1,147 @@
+#include "gtest/gtest.h"
+#include "cantera/thermo/RedlichKisterVPSSTP.h"
+#include "cantera/thermo/ThermoFactory.h"
+
+namespace Cantera
+{
+
+class RedlichKister_Test : public testing::Test
+{
+public:
+    RedlichKister_Test() {
+        test_phase.reset(newPhase("../data/RedlichKisterVPSSTP_valid.xml"));
+    }
+
+    void set_r(const double r) {
+        vector_fp moleFracs(2);
+        moleFracs[0] = r;
+        moleFracs[1] = 1-r;
+        test_phase->setMoleFractions(&moleFracs[0]);
+    }
+
+    std::unique_ptr<ThermoPhase> test_phase;
+};
+
+TEST_F(RedlichKister_Test, construct_from_xml)
+{
+    RedlichKisterVPSSTP* redlich_kister_phase = dynamic_cast<RedlichKisterVPSSTP*>(test_phase.get());
+    EXPECT_TRUE(redlich_kister_phase != NULL);
+}
+
+TEST_F(RedlichKister_Test, chem_potentials)
+{
+    test_phase->setState_TP(298.15, 101325.);
+
+    const double expected_result[9] = {
+        -1.2791500420236044e+007,
+        -1.2618554504124604e+007,
+        -1.2445418272766629e+007,
+        -1.2282611679165890e+007,
+        -1.2134110753109487e+007,
+        -1.1999465396970615e+007,
+        -1.1882669410525253e+007,
+        -1.1792994839484975e+007,
+        -1.1730895987035934e+007
+    };
+
+    double xmin = 0.6;
+    double xmax = 0.9;
+    int numSteps = 9;
+    double dx = (xmax-xmin)/(numSteps-1);
+    vector_fp chemPotentials(2);
+    for(int i=0; i < 9; ++i)
+    {
+        set_r(xmin + i*dx);
+        test_phase->getChemPotentials(&chemPotentials[0]);
+        EXPECT_NEAR(expected_result[i], chemPotentials[0], 1.e-6);
+    }
+}
+
+TEST_F(RedlichKister_Test, dlnActivities)
+{
+    test_phase->setState_TP(298.15, 101325.);
+
+    const double expected_result[9] = {
+        0.0907127,
+        0.200612,
+        0.229316,
+        0.193278,
+        0.142257,
+        0.0766133,
+        -0.0712113,
+        -0.309379,
+        -0.492206
+    };
+
+    double xmin = 0.6;
+    double xmax = 0.9;
+    int numSteps = 9;
+    double dx = (xmax-xmin)/(numSteps-1);
+    vector_fp dlnActCoeffdx(2);
+    for(int i=0; i < 9; ++i)
+    {
+        const double r = xmin + i*dx;
+        set_r(r);
+        test_phase->getdlnActCoeffdlnX_diag(&dlnActCoeffdx[0]);
+        EXPECT_NEAR(expected_result[i], dlnActCoeffdx[0], 1.e-6);
+    }
+}
+
+TEST_F(RedlichKister_Test, activityCoeffs)
+{
+    test_phase->setState_TP(298., 1.);
+
+    // Test that mu0 + RT log(activityCoeff * MoleFrac) == mu
+    const double RT = GasConstant * 298.;
+    vector_fp mu0(2);
+    vector_fp activityCoeffs(2);
+    vector_fp chemPotentials(2);
+    double xmin = 0.6;
+    double xmax = 0.9;
+    int numSteps = 9;
+    double dx = (xmax-xmin)/(numSteps-1);
+
+    for(int i=0; i < numSteps; ++i)
+    {
+        const double r = xmin + i*dx;
+        set_r(r);
+        test_phase->getChemPotentials(&chemPotentials[0]);
+        test_phase->getActivityCoefficients(&activityCoeffs[0]);
+        test_phase->getStandardChemPotentials(&mu0[0]);
+        EXPECT_NEAR(chemPotentials[0], mu0[0] + RT*std::log(activityCoeffs[0] * r), 1.e-6);
+        EXPECT_NEAR(chemPotentials[1], mu0[1] + RT*std::log(activityCoeffs[1] * (1-r)), 1.e-6);
+    }
+}
+
+TEST_F(RedlichKister_Test, standardConcentrations)
+{
+    EXPECT_DOUBLE_EQ(1.0, test_phase->standardConcentration(0));
+    EXPECT_DOUBLE_EQ(1.0, test_phase->standardConcentration(1));
+}
+
+TEST_F(RedlichKister_Test, activityConcentrations)
+{
+    // Check to make sure activityConcentration_i == standardConcentration_i * gamma_i * X_i
+    vector_fp standardConcs(2);
+    vector_fp activityCoeffs(2);
+    vector_fp activityConcentrations(2);
+    double xmin = 0.6;
+    double xmax = 0.9;
+    int numSteps = 9;
+    double dx = (xmax-xmin)/(numSteps-1);
+
+    for(int i=0; i < 9; ++i)
+    {
+        const double r = xmin + i*dx;
+        set_r(r);
+        test_phase->getActivityCoefficients(&activityCoeffs[0]);
+        standardConcs[0] = test_phase->standardConcentration(0);
+        standardConcs[1] = test_phase->standardConcentration(1);
+        test_phase->getActivityConcentrations(&activityConcentrations[0]);
+
+        EXPECT_NEAR(standardConcs[0] * r * activityCoeffs[0], activityConcentrations[0], 1.e-6);
+        EXPECT_NEAR(standardConcs[1] * (1-r) * activityCoeffs[1], activityConcentrations[1], 1.e-6);
+    }
+}
+
+};