pyEQL 0.5.2__py3-none-any.whl → 1.0.3__py3-none-any.whl

pyEQL/tests/test_activity.py

@@ -1,578 +0,0 @@
-"""
-pyEQL activity correction methods test suite
-============================================
-
-This file contains tests for some of the activity correction methods
-employed by pyEQL.
-
-NOTE: generally, these tests check the module output against experimental
-data rather than the theoretical result of the respective functions. In some
-cases, the output is also tested against a well-established model published
-by USGS(PHREEQC)
-"""
-
-import pyEQL
-import unittest
-
-
-class Test_activity_pitzer_nacl(unittest.TestCase, pyEQL.CustomAssertions):
-    """
-    test Pitzer model for activity of NaCl
-    ------------------------------------------------
-    """
-
-    def setUp(self):
-        self.s1 = pyEQL.Solution([["Na+", "0.1 mol/L"], ["Cl-", "0.1 mol/L"]])
-
-        # relative error tolerance for assertWithinExperimentalError
-        self.tol = 0.05
-
-    def test_activity_pitzer_coeff_units(self):
-        # the activity coefficient should be dimensionless
-        result = self.s1.get_activity_coefficient("Na+").dimensionality
-        self.assertEqual(result, "")
-
-    def test_activity_pitzer_units(self):
-        # the activity should be dimensionless
-        result = self.s1.get_activity("Na+").dimensionality
-        self.assertEqual(result, "")
-
-    def test_activity_pitzer_equality(self):
-        # the activity coefficient of both the Na+ and Cl- should be the same
-        a1 = self.s1.get_activity_coefficient("Na+")
-        a2 = self.s1.get_activity_coefficient("Cl-")
-        self.assertEqual(a1, a2)
-
-    def test_activity_crc_HCl(self):
-        """
-        calculate the activity coefficient of HCl at each concentration and compare
-        to experimental data
-
-        Experimental activity coefficient values at 25 degC are found in
-        *CRC Handbook of Chemistry and Physics*, Mean Activity Coefficients of Electrolytes as a Function of
-        Concentration, in: W.M. Haynes (Ed.), 92nd ed., 2011.
-
-        """
-        cation = "H+"
-        nu_cation = 1
-        anion = "Cl-"
-        nu_anion = 1
-
-        # list of concentrations to test, mol/kg
-        conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5]
-
-        # list of published experimental activity coefficients
-        pub_activity_coeff = [
-            0.965,
-            0.952,
-            0.929,
-            0.905,
-            0.876,
-            0.832,
-            0.797,
-            0.768,
-            0.759,
-            0.811,
-            1.009,
-            2.380,
-        ]
-
-        for i in range(len(conc_list)):
-            with self.subTest(conc=conc_list[i]):
-                conc_c = str(conc_list[i] * nu_cation) + "mol/kg"
-                conc_a = str(conc_list[i] * nu_anion) + "mol/kg"
-                sol = pyEQL.Solution()
-                sol.add_solute(cation, conc_c)
-                sol.add_solute(anion, conc_a)
-                act_cat = sol.get_activity_coefficient(cation)
-                act_an = sol.get_activity_coefficient(anion)
-                result = (act_cat ** nu_cation * act_an ** nu_anion) ** (
-                    1 / (nu_cation + nu_anion)
-                )
-                expected = pub_activity_coeff[i]
-
-                self.assertWithinExperimentalError(result, expected, self.tol)
-
-    def test_activity_crc_CsI(self):
-        """
-        calculate the activity coefficient of CsI at each concentration and compare
-        to experimental data
-
-        Experimental activity coefficient values at 25 degC are found in
-        *CRC Handbook of Chemistry and Physics*, Mean Activity Coefficients of Electrolytes as a Function of
-        Concentration, in: W.M. Haynes (Ed.), 92nd ed., 2011.
-
-        """
-        cation = "Cs+"
-        nu_cation = 1
-        anion = "I-"
-        nu_anion = 1
-
-        # list of concentrations to test, mol/kg
-        conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2]
-
-        # list of published experimental activity coefficients
-        pub_activity_coeff = [
-            0.965,
-            0.951,
-            0.925,
-            0.898,
-            0.863,
-            0.804,
-            0.749,
-            0.688,
-            0.601,
-            0.534,
-            0.470,
-        ]
-
-        for i in range(len(conc_list)):
-            with self.subTest(conc=conc_list[i]):
-                conc_c = str(conc_list[i] * nu_cation) + "mol/kg"
-                conc_a = str(conc_list[i] * nu_anion) + "mol/kg"
-                sol = pyEQL.Solution()
-                sol.add_solute(cation, conc_c)
-                sol.add_solute(anion, conc_a)
-                act_cat = sol.get_activity_coefficient(cation)
-                act_an = sol.get_activity_coefficient(anion)
-                result = (act_cat ** nu_cation * act_an ** nu_anion) ** (
-                    1 / (nu_cation + nu_anion)
-                )
-                expected = pub_activity_coeff[i]
-
-                self.assertWithinExperimentalError(result, expected, self.tol)
-
-    def test_activity_crc_bacl2(self):
-        """
-        calculate the activity coefficient of BaCl2 at each concentration and compare
-        to experimental data
-
-        Experimental activity coefficient values at 25 degC are found in
-        *CRC Handbook of Chemistry and Physics*, Mean Activity Coefficients of Electrolytes as a Function of
-        Concentration, in: W.M. Haynes (Ed.), 92nd ed., 2011.
-
-        """
-        # list of concentrations to test, mol/kg
-        conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1]
-
-        # list of published experimental activity coefficients
-        pub_activity_coeff = [
-            0.887,
-            0.849,
-            0.782,
-            0.721,
-            0.653,
-            0.559,
-            0.492,
-            0.436,
-            0.391,
-            0.393,
-        ]
-
-        for i in range(len(conc_list)):
-            with self.subTest(conc=conc_list[i]):
-                conc_c = str(conc_list[i]) + "mol/kg"
-                conc_a = str(conc_list[i] * 2) + "mol/kg"
-                sol = pyEQL.Solution()
-                sol.add_solute("Ba+2", conc_c)
-                sol.add_solute("Cl-", conc_a)
-                act_cat = sol.get_activity_coefficient("Ba+2")
-                act_an = sol.get_activity_coefficient("Cl-")
-                result = (act_cat ** 1 * act_an ** 2) ** (1 / 3)
-                expected = pub_activity_coeff[i]
-
-                self.assertWithinExperimentalError(result, expected, self.tol)
-
-    def test_activity_crc_licl(self):
-        """
-        calculate the activity coefficient of LiCl at each concentration and compare
-        to experimental data
-
-        Experimental activity coefficient values at 25 degC are found in
-        *CRC Handbook of Chemistry and Physics*, Mean Activity Coefficients of Electrolytes as a Function of
-        Concentration, in: W.M. Haynes (Ed.), 92nd ed., 2011.
-
-        """
-        # list of concentrations to test, mol/kg
-        conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5]
-
-        # list of published experimental activity coefficients
-        pub_activity_coeff = [
-            0.965,
-            0.952,
-            0.928,
-            0.904,
-            0.874,
-            0.827,
-            0.789,
-            0.756,
-            0.739,
-            0.775,
-            0.924,
-            2.0,
-        ]
-
-        for i in range(len(conc_list)):
-            with self.subTest(conc=conc_list[i]):
-                conc_c = str(conc_list[i]) + "mol/kg"
-                conc_a = str(conc_list[i]) + "mol/kg"
-                sol = pyEQL.Solution()
-                sol.add_solute("Li+", conc_c)
-                sol.add_solute("Cl-", conc_a)
-                act_cat = sol.get_activity_coefficient("Li+")
-                act_an = sol.get_activity_coefficient("Cl-")
-                result = (act_cat ** 1 * act_an ** 1) ** (1 / 2)
-                expected = pub_activity_coeff[i]
-
-                self.assertWithinExperimentalError(result, expected, self.tol)
-
-    def test_activity_crc_rbcl(self):
-        """
-        calculate the activity coefficient of RbCl at each concentration and compare
-        to experimental data
-
-        Experimental activity coefficient values at 25 degC are found in
-        *CRC Handbook of Chemistry and Physics*, Mean Activity Coefficients of Electrolytes as a Function of
-        Concentration, in: W.M. Haynes (Ed.), 92nd ed., 2011.
-
-        """
-        # list of concentrations to test, mol/kg
-        conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5]
-
-        # list of published experimental activity coefficients
-        pub_activity_coeff = [
-            0.965,
-            0.951,
-            0.926,
-            0.900,
-            0.867,
-            0.811,
-            0.761,
-            0.707,
-            0.633,
-            0.583,
-            0.546,
-            0.544,
-        ]
-
-        for i in range(len(conc_list)):
-            with self.subTest(conc=conc_list[i]):
-                conc_c = str(conc_list[i]) + "mol/kg"
-                conc_a = str(conc_list[i]) + "mol/kg"
-                sol = pyEQL.Solution()
-                sol.add_solute("Rb+", conc_c)
-                sol.add_solute("Cl-", conc_a)
-                result = sol.get_activity_coefficient("Rb+")
-                expected = pub_activity_coeff[i]
-
-                self.assertWithinExperimentalError(result, expected, self.tol)
-
-    def test_activity_crc_MgCl2(self):
-        """
-        calculate the activity coefficient of MgCl2 at each concentration and compare
-        to experimental data
-
-        Experimental activity coefficient values at 25 degC are found in
-        *CRC Handbook of Chemistry and Physics*, Mean Activity Coefficients of Electrolytes as a Function of
-        Concentration, in: W.M. Haynes (Ed.), 92nd ed., 2011.
-
-        """
-        cation = "Mg+2"
-        nu_cation = 1
-        anion = "Cl-"
-        nu_anion = 2
-
-        # list of concentrations to test, mol/kg
-        conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5]
-
-        # list of published experimental activity coefficients
-        pub_activity_coeff = [
-            0.889,
-            0.852,
-            0.790,
-            0.734,
-            0.672,
-            0.590,
-            0.535,
-            0.493,
-            0.485,
-            0.577,
-            1.065,
-            14.40,
-        ]
-
-        for i in range(len(conc_list)):
-            with self.subTest(conc=conc_list[i]):
-                conc_c = str(conc_list[i] * nu_cation) + "mol/kg"
-                conc_a = str(conc_list[i] * nu_anion) + "mol/kg"
-                sol = pyEQL.Solution()
-                sol.add_solute(cation, conc_c)
-                sol.add_solute(anion, conc_a)
-                act_cat = sol.get_activity_coefficient(cation)
-                act_an = sol.get_activity_coefficient(anion)
-                result = (act_cat ** nu_cation * act_an ** nu_anion) ** (
-                    1 / (nu_cation + nu_anion)
-                )
-                expected = pub_activity_coeff[i]
-
-                self.assertWithinExperimentalError(result, expected, self.tol)
-
-    def test_activity_crc_KBr(self):
-        """
-        calculate the activity coefficient of KBr at each concentration and compare
-        to experimental data
-
-        Experimental activity coefficient values at 25 degC are found in
-        *CRC Handbook of Chemistry and Physics*, Mean Activity Coefficients of Electrolytes as a Function of
-        Concentration, in: W.M. Haynes (Ed.), 92nd ed., 2011.
-
-        """
-        cation = "K+"
-        nu_cation = 1
-        anion = "Br-"
-        nu_anion = 1
-
-        # list of concentrations to test, mol/kg
-        conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5]
-
-        # list of published experimental activity coefficients
-        pub_activity_coeff = [
-            0.965,
-            0.952,
-            0.927,
-            0.902,
-            0.870,
-            0.817,
-            0.771,
-            0.722,
-            0.658,
-            0.617,
-            0.593,
-            0.626,
-        ]
-
-        for i in range(len(conc_list)):
-            with self.subTest(conc=conc_list[i]):
-                conc_c = str(conc_list[i] * nu_cation) + "mol/kg"
-                conc_a = str(conc_list[i] * nu_anion) + "mol/kg"
-                sol = pyEQL.Solution()
-                sol.add_solute(cation, conc_c)
-                sol.add_solute(anion, conc_a)
-                act_cat = sol.get_activity_coefficient(cation)
-                act_an = sol.get_activity_coefficient(anion)
-                result = (act_cat ** nu_cation * act_an ** nu_anion) ** (
-                    1 / (nu_cation + nu_anion)
-                )
-                expected = pub_activity_coeff[i]
-
-                self.assertWithinExperimentalError(result, expected, self.tol)
-
-    def test_activity_crc_k2so4(self):
-        """
-        calculate the activity coefficient of K2SO4 at each concentration and compare
-        to experimental data
-
-        Experimental activity coefficient values at 25 degC are found in
-        *CRC Handbook of Chemistry and Physics*, Mean Activity Coefficients of Electrolytes as a Function of
-        Concentration, in: W.M. Haynes (Ed.), 92nd ed., 2011.
-
-        """
-        # list of concentrations to test, mol/kg
-        conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5]
-
-        # list of published experimental activity coefficients
-        pub_activity_coeff = [
-            0.885,
-            0.844,
-            0.772,
-            0.704,
-            0.625,
-            0.511,
-            0.424,
-            0.343,
-            0.251,
-        ]
-
-        for i in range(len(conc_list)):
-            with self.subTest(conc=conc_list[i]):
-                conc_c = str(conc_list[i] * 2) + "mol/kg"
-                conc_a = str(conc_list[i]) + "mol/kg"
-                sol = pyEQL.Solution()
-                sol.add_solute("K+", conc_c)
-                sol.add_solute("SO4-2", conc_a)
-                act_cat = sol.get_activity_coefficient("K+")
-                act_an = sol.get_activity_coefficient("SO4-2")
-                result = (act_cat ** 2 * act_an ** 1) ** (1 / 3)
-                expected = pub_activity_coeff[i]
-
-                self.assertWithinExperimentalError(result, expected, self.tol)
-
-    def test_activity_pitzer_nacl_1(self):
-        """
-        calculate the activity coefficient at each concentration and compare
-        to experimental data
-
-        Experimental activity coefficient values at 25 degC are found in
-        *J. Phys. Chem. Reference Data* Vol 13 (1), 1984, p.53.
-
-        """
-        # list of concentrations to test, mol/kg
-        conc_list = [0.1, 0.25, 0.5, 0.75, 1, 2, 3, 4, 5, 6]
-
-        # list of published experimental activity coefficients
-        pub_activity_coeff = [
-            0.778,
-            0.72,
-            0.681,
-            0.665,
-            0.657,
-            0.669,
-            0.714,
-            0.782,
-            0.873,
-            0.987,
-        ]
-
-        for i in range(len(conc_list)):
-            with self.subTest(conc=conc_list[i]):
-                conc = str(conc_list[i]) + "mol/kg"
-                sol = pyEQL.Solution()
-                sol.add_solute("Na+", conc)
-                sol.add_solute("Cl-", conc)
-                result = sol.get_activity_coefficient("Na+")
-                expected = pub_activity_coeff[i]
-
-                self.assertWithinExperimentalError(result, expected, self.tol)
-
-    # The pitzer model diverges a bit from experimental data at high concentration
-    @unittest.expectedFailure
-    def test_water_activity_pitzer_nacl_1(self):
-        """
-        calculate the water activity at each concentration and compare
-        to experimental data
-
-        Experimental osmotic coefficients for NaCl are found in:
-        Pitzer and Pelper, 1984. "Thermodyamic Properties of Aqueous Sodium Chloride Solutions"
-        *J. Phys. Chem. Ref. Data* 13(1).
-
-        Osmotic coefficients were converted into water activity according to the equation
-        found in
-        Blandamer, Mike J., Engberts, Jan B. F. N., Gleeson, Peter T., Reis,
-        Joao Carlos R., 2005. "Activity of water in aqueous systems: A frequently
-        neglected property." *Chemical Society Review* 34, 440-458.
-
-        .. math:: ln a_w = - \\Phi M_w \\sum_i m_i
-
-        Where :math:`M_w` is the molar mass of water (0.018015 kg/mol) and :math:`m_i` is the molal concentration
-        of each species.
-
-        """
-        # list of concentrations to test, mol/kg
-        conc_list = [0.1, 0.25, 0.5, 0.75, 1, 2, 3, 4, 5, 6]
-
-        # list of published experimental water activity
-        pub_water_activity = [
-            0.9964,
-            0.9910,
-            0.9821,
-            0.9733,
-            0.9646,
-            0.9304,
-            0.8975,
-            0.8657,
-            0.8351,
-            0.8055,
-        ]
-
-        for i in range(len(conc_list)):
-            with self.subTest(conc=conc_list[i]):
-                conc = str(conc_list[i]) + "mol/kg"
-                sol = pyEQL.Solution()
-                sol.add_solute("Na+", conc)
-                sol.add_solute("Cl-", conc)
-                result = sol.get_water_activity()
-                expected = pub_water_activity[i]
-
-                self.assertWithinExperimentalError(result, expected, self.tol)
-
-    def test_activity_pitzer_phreeqc_nacl_2(self):
-        """
-        calculate the activity coefficient at each concentration and compare
-        to the output of the PHREEQC model
-
-        PHREEQC version 3.1.4 was used to calculate density, conductivity, water
-        activity, and NaCl activity coefficient for NaCl solutions up to 6m.
-        The Pitzer model (pitzer.dat) database was used.
-        <http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/>
-
-        """
-        # list of concentrations to test, mol/kg
-        conc_list = [0.1, 0.25, 0.5, 0.75, 1, 2, 3, 4, 5, 6]
-
-        # list of modeled activity coefficients
-        phreeqc_pitzer_activity_coeff = [
-            0.7771,
-            0.7186,
-            0.6799,
-            0.6629,
-            0.6561,
-            0.6675,
-            0.7128,
-            0.7825,
-            0.8729,
-            0.9874,
-        ]
-
-        for i in range(len(conc_list)):
-            with self.subTest(conc=conc_list[i]):
-                conc = str(conc_list[i]) + "mol/kg"
-                sol = pyEQL.Solution()
-                sol.add_solute("Na+", conc)
-                sol.add_solute("Cl-", conc)
-                result = sol.get_activity_coefficient("Na+")
-                expected = phreeqc_pitzer_activity_coeff[i]
-
-                self.assertWithinExperimentalError(result, expected, self.tol)
-
-    def test_water_activity_phreeqc_pitzer_nacl_2(self):
-        """
-        calculate the water activity at each concentration and compare
-        to the output of the PHREEQC model
-
-        PHREEQC version 3.1.4 was used to calculate density, conductivity, water
-        activity, and NaCl activity coefficient for NaCl solutions up to 6m.
-        The Pitzer model (pitzer.dat) database was used.
-        <http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/>
-
-        """
-        # list of concentrations to test, mol/kg
-        conc_list = [0.1, 0.25, 0.5, 0.75, 1, 2, 3, 4, 5, 6]
-
-        # list of modeled water activities
-        phreeqc_pitzer_water_activity = [
-            0.997,
-            0.992,
-            0.984,
-            0.975,
-            0.967,
-            0.932,
-            0.893,
-            0.851,
-            0.807,
-            0.759,
-        ]
-
-        for i in range(len(conc_list)):
-            with self.subTest(conc=conc_list[i]):
-                conc = str(conc_list[i]) + "mol/kg"
-                sol = pyEQL.Solution()
-                sol.add_solute("Na+", conc)
-                sol.add_solute("Cl-", conc)
-                result = sol.get_water_activity()
-                expected = phreeqc_pitzer_water_activity[i]
-
-                self.assertWithinExperimentalError(result, expected, self.tol)
-
-
-if __name__ == "__main__":
-    unittest.main()

pyEQL/tests/test_bulk_properties.py

@@ -1,86 +0,0 @@
-"""
-pyEQL test suite for bulk property calculations
-===============================================
-
-This file contains tests for the bulk properties calculated by
-Solution class methods. Currently included methods are:
-
-- get_hardness()
-
-"""
-
-import pyEQL
-import unittest
-
-
-class test_hardness(unittest.TestCase, pyEQL.CustomAssertions):
-    """
-    test the get_hardness() method
-    ------------------------------
-    """
-
-    # an empty solution should have zero hardness
-    def test_empty_solution(self):
-        s1 = pyEQL.Solution()
-        result = s1.get_hardness().magnitude
-        expected = 0
-
-        self.assertEqual(result, expected)
-
-    # a solution with only monovalent ions should have zero hardness
-    def test_hardness_1(self):
-        s1 = pyEQL.Solution([["Na+", "0.2 mol/L"], ["Cl-", "0.2 mol/L"]])
-        result = s1.get_hardness().magnitude
-        expected = 0
-
-        self.assertEqual(result, expected)
-
-    # a solution with only multivalent anions should have zero hardness
-    def test_hardness_2(self):
-        s1 = pyEQL.Solution([["Na+", "0.4 mol/L"], ["SO4-2", "0.2 mol/L"]])
-        result = s1.get_hardness().magnitude
-        expected = 0
-
-        self.assertEqual(result, expected)
-
-    # the hardness should return the equivalent concentration, not just the
-    # molar concentration (e.g. multiply by the charge)
-    def test_hardness_3(self):
-        s1 = pyEQL.Solution([["Fe+3", "0.1 mol/L"], ["Cl-", "0.3 mol/L"]])
-        result = s1.get_hardness().magnitude
-        expected = 15013.5
-
-        self.assertAlmostEqual(result, expected)
-
-    # the hardness should account for multiple cations but count only those
-    # that are multivalent
-    def test_hardness_4(self):
-        s1 = pyEQL.Solution(
-            [
-                ["Na+", "0.1 mol/L"],
-                ["K+", "0.1 mol/L"],
-                ["Mg+2", "0.1 mol/L"],
-                ["Ca+2", "0.1 mol/L"],
-                ["Fe+3", "0.1 mol/L"],
-                ["Cl-", "0.1 mol/L"],
-                ["F-", "0.1 mol/L"],
-                ["SO4-2", "0.2 mol/L"],
-                ["PO4-3", "0.1 mol/L"],
-            ]
-        )
-        result = s1.get_hardness().magnitude
-        expected = 35031.5
-
-        self.assertAlmostEqual(result, expected)
-
-    # the hardness should return g/L units
-    def test_hardness_5(self):
-        s1 = pyEQL.Solution([["Fe+3", "0.1 mol/L"], ["Cl-", "0.3 mol/L"]])
-        result = str(s1.get_hardness().dimensionality)
-        expected = "[mass] / [length] ** 3"
-
-        self.assertEqual(result, expected)
-
-
-if __name__ == "__main__":
-    unittest.main()