def test7_dump_and_load(self):
sol5a = self.pp.get_solution(5)
self.pp.dump_solutions()
pp2 = PhreeqPython(from_file='dump.gz')
sol5b = pp2.get_solution(5)
assert_almost_equal(sol5a.sc, sol5b.sc, 2)
assert_equal(self.pp.ip.get_solution_list(),
pp2.ip.get_solution_list())
def test10_use_non_default_database_directory(self):
pp_test10 = PhreeqPython(database_directory=Path(__file__).parent)
sol = pp_test10.add_solution_simple({'CaCl2': 1, 'Na2CO3': 1})
# test solution number
assert_equal(sol.number, 0)
# test solution ph, sc, pe and temperature
assert_equal(round(sol.pH, 2), 10.41)
assert_equal(round(sol.sc, 2), 435.35)
assert_equal(round(sol.pe, 2), 7.4)
assert_equal(round(sol.temperature, 2), 25)
def setUp(self):
# self.net = Network(inputfile="tests/Case1.inp")
self.net = Network(inputfile="Case1.inp")
self.pp = PhreeqPython()
self.vic = Victoria(self.net, self.pp)
self.solutions = {}
sol0 = self.pp.add_solution({'Ca': 0, 'units': 'mmol/l'})
sol1 = self.pp.add_solution({'Ca': 1, 'units': 'mmol/l'})
self.solutions[0] = sol0
self.solutions[self.net.reservoirs['1'].uid] = sol1
def fixture_phreeqpython_solutions_excel():
''' Add the solutions of the excel file manually to test
whether they are added correctly and to easily check
whether all derived quantities like EC, and SI of calicite
are correct by hgc methods '''
# {'temp': 10, 'Alkalinity': 0, 'O(0)': '11 ', 'C(-4)': '0 as CH4', 'pH': 4.5, 'Na': '9 charge', 'K': 0.4, 'Ca': 1, 'Mg': 1.1, 'Fe': 0.1, 'Mn': 0.02, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'},
# {'temp': 10, 'Alkalinity': 0, 'O(0)': '2 ', 'C(-4)': '0 as CH4', 'pH': 4.3, 'Na': '15 charge', 'K': 1.1, 'Ca': 2, 'Mg': 1.6, 'Fe': 0.29, 'Mn': 0.05, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10, 'Alkalinity': 0, 'O(0)': '1 ', 'C(-4)': '0 as CH4', 'pH': 4.4, 'Na': '19 charge', 'K': 1.8, 'Ca': 2, 'Mg': 3.0, 'Fe': 0.12, 'Mn': 0.06, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10, 'Alkalinity': 7, 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 5.5, 'Na': '20 charge', 'K': 2.1, 'Ca': 3, 'Mg': 3.9, 'Fe': 2.33, 'Mn': 0.13, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10, 'Alkalinity': 13, 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 5.7, 'Na': '21 charge', 'K': 2.8, 'Ca': 5, 'Mg': 5.4, 'Fe': 3.43, 'Mn': 0.03, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10, 'Alkalinity': 23, 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 6.2, 'Na': '24 charge', 'K': 1.8, 'Ca': 13, 'Mg': 2.7, 'Fe': 0.7, 'Mn': 0.09, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10, 'Alkalinity': 92, 'O(0)': '0 ', 'C(-4)': '0.14 as CH4', 'pH': 7.4, 'Na': '29 charge', 'K': 1.9, 'Ca': 38, 'Mg': 2.8, 'Fe': 0.3, 'Mn': 0.13, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10.1, 'Alkalinity': 146, 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 7.7, 'Na': '29 charge', 'K': 2.0, 'Ca': 51, 'Mg': 3.4, 'Fe': 0.51, 'Mn': 0.13, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10.2, 'Alkalinity': 151, 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 7.7, 'Na': '15 charge', 'K': 1.4, 'Ca': 48, 'Mg': 3.1, 'Fe': 3.4, 'Mn': 0.18, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10.5, 'Alkalinity': 156, 'O(0)': '0 ', 'C(-4)': '5 as CH4', 'pH': 7.6, 'Na': '15 charge', 'K': 1.2, 'Ca': 48, 'Mg': 2.5, 'Fe': 1.22, 'Mn': 0.13, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10.7, 'Alkalinity': 169, 'O(0)': '0 ', 'C(-4)': '9.1 as CH4', 'pH': 8.1, 'Na': '24 charge', 'K': 9.5, 'Ca': 13, 'Mg': 21, 'Fe': 0.69, 'Mn': 0.04, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10.8, 'Alkalinity': 398, 'O(0)': '0 ', 'C(-4)': '18.2 as CH4', 'pH': 8.5, 'Na': '155 charge', 'K': 11.5, 'Ca': 3, 'Mg': 3.1, 'Fe': 0.62, 'Mn': 0.04, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10.7, 'Alkalinity': 525, 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 8.2, 'Na': '190 charge', 'K': 16.8, 'Ca': 9, 'Mg': 9.5, 'Fe': 0.17, 'Mn': 0.12, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10.8, 'Alkalinity': 801, 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 7.7, 'Na': '445 charge', 'K': 58, 'Ca': 27, 'Mg': 19.9, 'Fe': 1.6, 'Mn': 0.12, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 10.8, 'Alkalinity': 903, 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 8.5, 'Na': '910 charge', 'K': 134, 'Ca': 66, 'Mg': 71, 'Fe': 5.4, 'Mn': 0.3, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# {'temp': 11.0, 'Alkalinity': 2635, 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 7.8, 'Na': '3380 charge', 'K': 95, 'Ca': 160, 'Mg': 390, 'Fe': 2.3, 'Mn': 0.03, 'Amm': '1.29', 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.027, 'Mn(7)': '5.2 as KMnO4'}
# ]
pp = PhreeqPython()
solution_dictionaries = [
{'temp': 10, 'Alkalinity': '0 as HCO3', 'O(0)': '11 ', 'C(-4)': '0 as CH4', 'pH': 4.5, 'Na': '9', 'K': 0.4, 'Ca': 1, 'Mg': 1.1, 'Fe': 0.10, 'Mn': 0.02, 'Amm': 1.29, 'Si': '0.2 as SiO2', 'Cl': 16, 'S(6)': '7 as SO4', 'N(5)': '3.4 as NO3', 'F': 0.02700, 'Mn(7)': '5.2 as KMnO4'},
{'temp': 10, 'Alkalinity': '0 as HCO3', 'O(0)': '2 ', 'C(-4)': '0 as CH4', 'pH': 4.3, 'Na': '15', 'K': 1.1, 'Ca': 2, 'Mg': 1.6, 'Fe': 0.29, 'Mn': 0.05, 'Amm': 0.05, 'Si': '11.2 as SiO2', 'Cl': 19, 'S(6)': '16 as SO4', 'N(5)': '22.6 as NO3', 'F': 0.08000, 'Mn(7)': '17.4 as KMnO4'},
{'temp': 10, 'Alkalinity': '0 as HCO3', 'O(0)': '1 ', 'C(-4)': '0 as CH4', 'pH': 4.4, 'Na': '19', 'K': 1.8, 'Ca': 2, 'Mg': 3.0, 'Fe': 0.12, 'Mn': 0.03, 'Amm': 0.05, 'Si': '10.6 as SiO2', 'Cl': 31, 'S(6)': '18 as SO4', 'N(5)': '12.0 as NO3', 'F': 0.07000, 'Mn(7)': '3.0 as KMnO4'},
{'temp': 10, 'Alkalinity': '7 as HCO3', 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 5.5, 'Na': '20', 'K': 2.1, 'Ca': 3, 'Mg': 3.9, 'Fe': 2.33, 'Mn': 0.06, 'Amm': 0.08, 'Si': '15.4 as SiO2', 'Cl': 34, 'S(6)': '19 as SO4', 'N(5)': '0.1 as NO3', 'F': 0.12000, 'Mn(7)': '5.3 as KMnO4'},
{'temp': 10, 'Alkalinity': '13 as HCO3', 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 5.7, 'Na': '21', 'K': 2.8, 'Ca': 5, 'Mg': 5.4, 'Fe': 3.43, 'Mn': 0.13, 'Amm': 0.19, 'Si': '18.6 as SiO2', 'Cl': 41, 'S(6)': '20 as SO4', 'N(5)': '0.0 as NO3', 'F': 0.00501, 'Mn(7)': '7.3 as KMnO4'},
{'temp': 10, 'Alkalinity': '23 as HCO3', 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 6.2, 'Na': '24', 'K': 1.8, 'Ca': 13, 'Mg': 2.7, 'Fe': 0.70, 'Mn': 0.03, 'Amm': 0.23, 'Si': '15.1 as SiO2', 'Cl': 41, 'S(6)': '24 as SO4', 'N(5)': '0.0 as NO3', 'F': 0.00501, 'Mn(7)': '13.9 as KMnO4'},
{'temp': 10, 'Alkalinity': '92 as HCO3', 'O(0)': '0 ', 'C(-4)': '0.14 as CH4', 'pH': 7.4, 'Na': '29', 'K': 1.9, 'Ca': 38, 'Mg': 2.8, 'Fe': 0.30, 'Mn': 0.09, 'Amm': 0.24, 'Si': '15.6 as SiO2', 'Cl': 44, 'S(6)': '36 as SO4', 'N(5)': '0.0 as NO3', 'F': 0.00501, 'Mn(7)': '16.8 as KMnO4'},
{'temp': 10, 'Alkalinity': '121 as HCO3', 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 7.6, 'Na': '31', 'K': 2.0, 'Ca': 47, 'Mg': 3.3, 'Fe': 0.40, 'Mn': 0.13, 'Amm': 0.34, 'Si': '13.3 as SiO2', 'Cl': 50, 'S(6)': '35 as SO4', 'N(5)': '0.0 as NO3', 'F': 0.00501, 'Mn(7)': '11.9 as KMnO4'},
{'temp': 10.1, 'Alkalinity': '146 as HCO3', 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 7.7, 'Na': '29', 'K': 2.0, 'Ca': 51, 'Mg': 3.4, 'Fe': 0.51, 'Mn': 0.13, 'Amm': 0.44, 'Si': '20.0 as SiO2', 'Cl': 45, 'S(6)': '22 as SO4', 'N(5)': '0.0 as NO3', 'F': 0.01000, 'Mn(7)': '0.0 as KMnO4'},
{'temp': 10.2, 'Alkalinity': '151 as HCO3', 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 7.7, 'Na': '15', 'K': 1.4, 'Ca': 48, 'Mg': 3.1, 'Fe': 3.40, 'Mn': 0.18, 'Amm': 0.68, 'Si': '16.0 as SiO2', 'Cl': 33, 'S(6)': '0 as SO4', 'N(5)': '0.0 as NO3', 'F': 0.01000, 'Mn(7)': '0.0 as KMnO4'},
{'temp': 10.5, 'Alkalinity': '156 as HCO3', 'O(0)': '0 ', 'C(-4)': '5 as CH4', 'pH': 7.6, 'Na': '15', 'K': 1.2, 'Ca': 48, 'Mg': 2.5, 'Fe': 1.22, 'Mn': 0.13, 'Amm': 0.45, 'Si': '17.6 as SiO2', 'Cl': 29, 'S(6)': '0 as SO4', 'N(5)': '0.0 as NO3', 'F': 0.03000, 'Mn(7)': '16.6 as KMnO4'},
{'temp': 10.7, 'Alkalinity': '169 as HCO3', 'O(0)': '0 ', 'C(-4)': '9.1 as CH4', 'pH': 8.1, 'Na': '24', 'K': 9.5, 'Ca': 13, 'Mg': 21.0, 'Fe': 0.69, 'Mn': 0.04, 'Amm': 0.83, 'Si': '22.9 as SiO2', 'Cl': 33, 'S(6)': '0 as SO4', 'N(5)': '0.0 as NO3', 'F': 0.10000, 'Mn(7)': '11.5 as KMnO4'},
{'temp': 10.8, 'Alkalinity': '398 as HCO3', 'O(0)': '0 ', 'C(-4)': '18.2 as CH4', 'pH': 8.5, 'Na': '155', 'K': 11.5, 'Ca': 3, 'Mg': 3.1, 'Fe': 0.62, 'Mn': 0.04, 'Amm': 6.19, 'Si': '17.4 as SiO2', 'Cl': 35, 'S(6)': '0 as SO4', 'N(5)': '0.0 as NO3', 'F': 1.50000, 'Mn(7)': '84.9 as KMnO4'},
{'temp': 10.7, 'Alkalinity': '525 as HCO3', 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 8.2, 'Na': '190', 'K': 16.8, 'Ca': 9, 'Mg': 9.5, 'Fe': 0.17, 'Mn': 0.12, 'Amm': 8.26, 'Si': '45.0 as SiO2', 'Cl': 60, 'S(6)': '0 as SO4', 'N(5)': '0.0 as NO3', 'F': 1.10000, 'Mn(7)': '132.0 as KMnO4'},
{'temp': 10.8, 'Alkalinity': '801 as HCO3', 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 7.7, 'Na': '445', 'K': 58.0, 'Ca': 27, 'Mg': 19.9, 'Fe': 1.60, 'Mn': 0.12, 'Amm': 20.00, 'Si': '83.2 as SiO2', 'Cl': 390, 'S(6)': '9 as SO4', 'N(5)': '0.0 as NO3', 'F': 0.00000, 'Mn(7)': '470.0 as KMnO4'},
{'temp': 10.8, 'Alkalinity': '903 as HCO3', 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 8.5, 'Na': '910', 'K': 134.0, 'Ca': 66, 'Mg': 71.0, 'Fe': 5.40, 'Mn': 0.30, 'Amm': 49.00, 'Si': '71.6 as SiO2', 'Cl': 1320, 'S(6)': '15 as SO4', 'N(5)': '0.0 as NO3', 'F': 0.00000, 'Mn(7)': '130.0 as KMnO4'},
{'temp': 11.0, 'Alkalinity': '2635 as HCO3', 'O(0)': '0 ', 'C(-4)': '0 as CH4', 'pH': 7.8, 'Na': '3380', 'K': 95.0, 'Ca': 160, 'Mg': 390.0, 'Fe': 2.30, 'Mn': 0.03, 'Amm': 49.00, 'Si': '71.6 as SiO2', 'Cl': 5285, 'S(6)': '4 as SO4', 'N(5)': '0.0 as NO3', 'F': 0.00000, 'Mn(7)': '160.0 as KMnO4'},
]
solutions = [None] * len(solution_dictionaries)
for _i, sol_dict in enumerate(solution_dictionaries):
sol_dict['units'] = 'mg/L'
solutions[_i] = pp.add_solution(sol_dict)
return pp, solutions
def __init__(self, pandas_obj):
self._obj = pandas_obj
self._pp = PhreeqPython(
) # bind 1 phreeqpython instance to the dataframe
self._valid_atoms = constants.atoms
self._valid_ions = constants.ions
self._valid_properties = constants.properties
def test_add_oxygen(consolidated_data, phreeqpython_solutions_excel):
''' Test oxygen is added and returned correctly to and from
phreeqpython with or without. Test it in pure phreeqpython (because there
it is not working as expected)
- test that no O(0) added yields no O in solution
- test that adding `O(0)` `as O2` yields wrong result
- test that adding `O(0)` without `as O2` yields correct result
- test that adding in the SamplesFrame O2 concentration yields correct results '''
pp = PhreeqPython()
test_solution_dict = {'units': 'mg/L',
'Cl': 8.0,
'Na': '2.0 charge',
'Alkalinity': '2.0 as HCO3',
'Ca': 1.0,
'pH': 7,
'temp': 11
}
sol = pp.add_solution(test_solution_dict)
assert sol.total_element('O') == 0.0
test_solution_dict['O(0)'] = '3 as O2'
sol1 = pp.add_solution(test_solution_dict)
assert sol1.species['O2'] * 2 * mw('O') * 1000. != pytest.approx(3., 1.e-4)
test_solution_dict['O(0)'] = 3
sol1 = pp.add_solution(test_solution_dict)
assert sol1.species['O2'] * 2 * mw('O') * 1000. == pytest.approx(3., 1.e-4)
test_data = pd.DataFrame({'Cl': 8, 'Na': 2, 'alkalinity': 2,
'Ca': 1, 'O2': 3, 'ph': 7,
'temp': 11}, index=[0])
test_data.hgc.make_valid()
test_data.hgc.consolidate(
use_so4=None, use_ph=None, use_ec=None, use_temp=None)
sols = test_data.hgc.get_phreeqpython_solutions(inplace=False)
assert sols[0].species['O2'] * 2 * \
mw('O') * 1000. == pytest.approx(3., 1.e-4)
def test_phreeqpython_installed():
'''test phreeqpython can be imported and used. test
this by adding 1 simple solution to the PhreeqPython instance'''
pp = PhreeqPython()
pp.add_solution_simple({'CaCl2': 1.0, 'NaHCO3': 2.0})
class TestPhreeqPython(object):
pp = PhreeqPython()
def test1_basiscs(self):
sol = self.pp.add_solution_simple({'CaCl2': 1, 'Na2CO3': 1})
# test solution number
assert_equal(sol.number, 0)
# test solution ph, sc, pe and temperature
assert_equal(round(sol.pH, 2), 10.41)
assert_equal(round(sol.sc, 2), 435.35)
assert_equal(round(sol.pe, 2), 7.4)
assert_equal(round(sol.temperature, 2), 25)
# test solution composition
assert_equal(round(sol.total("Ca", units='mol'), 4), 0.001)
assert_equal(round(sol.total("Cl"), 4), 2)
assert_equal(round(sol.total_element("C"), 4), 1)
# test si
assert_equal(round(sol.si("Calcite"), 2), 1.71)
# test phases
assert_equal(len(sol.phases), 10)
assert_equal(len(sol.elements), 5)
# test ionic strength
assert_equal(round(sol.I, 4), 0.0045)
# test mass
assert_equal(round(sol.mass, 2), 1.0)
# test activity
assert_equal(round(sol.activity('Ca+2', units='mol'), 5), 0.00054)
# test moles
assert_equal(round(sol.moles('Ca+2', units='mol'), 5), 0.00071)
assert_equal(round(sol.molality('Ca+2', units='mol'), 5), 0.00071)
# test species_moles
assert_equal(round(sol.species_moles['Ca+2'], 5), 0.00071)
assert_equal(round(sol.species_molalities['Ca+2'], 5), 0.00071)
assert_equal(round(sol.species_activities['Ca+2'], 5), 0.00054)
def test2_solution_functions(self):
sol = self.pp.add_solution_simple({'CaCl2': 1})
# add components
sol.add('NaHCO3', 1)
assert_equal(round(sol.total('Na'), 4), 1)
# desaturate
sol.desaturate('Calcite')
assert_equal(sol.si('Calcite'), 0)
# remove mmol
sol.remove('Na', 0.5)
assert_equal(round(sol.total('Na'), 4), 0.5)
# remove fraction
sol.remove_fraction('Na', 0.5)
assert_equal(round(sol.total('Na'), 5), 0.25)
# change ph using base
sol.change_ph(10)
assert_equal(round(sol.pH, 2), 10)
# change ph using acid
sol.change_ph(5)
assert_equal(round(sol.pH, 2), 5)
# raise ph using custom chemical (NaOH)
sol.change_ph(8, 'NaOH')
assert_equal(round(sol.pH, 2), 8)
sol.saturate('Calcite', 1)
assert_equal(sol.si('Calcite'), 1)
sol.change_temperature(10)
assert_equal(sol.temperature, 10)
def test3_mixing(self):
sol1 = self.pp.add_solution_simple({'NaCl': 1})
sol2 = self.pp.add_solution_simple({})
sol3 = self.pp.mix_solutions({sol1: 0.5, sol2: 0.5})
assert_equal(round(sol3.total('Na'), 1), 0.5)
def test4_solution_listing(self):
# test solution list
sol_list = self.pp.ip.get_solution_list()
assert_equal(len(sol_list), 7)
# test forgetting solutions
self.pp.remove_solutions([1, 2, 3])
sol_list = self.pp.ip.get_solution_list()
assert_equal(len(sol_list), 4)
def test5_addition(self):
sol1 = self.pp.add_solution_simple({'NaCl': 1})
sol2 = self.pp.add_solution_simple({'NaCl': 2})
sol3 = sol1 + sol2
assert_equal(round(sol3.mass), 2.0)
sol4 = sol1 / 2 + sol2 / 2
assert_equal(round(sol4.total('Na'), 1), 1.5)
sol5 = sol1 * 0.5 + sol2 * 0.5
assert_equal(round(sol5.total('Na'), 1), 1.5)
# test invalid mixtures
def testadd(sol, other):
return sol + other
def testdiv(sol, other):
return sol / other
def testmul(sol, other):
return sol * other
assert_raises(TypeError, testadd, sol1, 1)
assert_raises(TypeError, testdiv, sol1, sol2)
assert_raises(TypeError, testmul, sol1, sol2)
def test6_misc(self):
sol1 = self.pp.add_solution_simple({'NaCl': 1})
sol2 = sol1.copy()
assert_equal(sol1.sc, sol2.sc)
sol2.forget()
assert_equal(sol2.pH, -999)
def test7_dump_and_load(self):
sol5a = self.pp.get_solution(5)
self.pp.dump_solutions()
pp2 = PhreeqPython(from_file='dump.gz')
sol5b = pp2.get_solution(5)
assert_almost_equal(sol5a.sc, sol5b.sc, 2)
assert_equal(self.pp.ip.get_solution_list(),
pp2.ip.get_solution_list())
def test8_raw_solutions(self):
sol8 = self.pp.add_solution_raw({
'pH': '8.0',
'temp': '20',
'units': 'mg/l',
'Alkalinity': '200 as HCO3',
'Ca': '40.1',
'Cl': '71.0'
})
assert_equal(sol8.pH, 8.0)
assert_almost_equal(sol8.total_element('Ca'), 1, 2)
assert_almost_equal(sol8.total_element('Cl'), 2, 2)
def test9_gas_phases(self):
gas1 = self.pp.add_gas({
'CH4(g)': 0.5,
'Ntg(g)': 0.5
},
volume=1,
pressure=1,
fixed_pressure=False,
fixed_volume=True)
assert_equal(gas1.pressure, 1)
assert_almost_equal(gas1.volume, 1, 2)
assert_almost_equal(gas1.total_moles, 0.041, 2)
assert_almost_equal(gas1.pressure, 1, 2)
assert_almost_equal(gas1.partial_pressures['CH4(g)'], 0.5, 2)
assert_almost_equal(gas1.partial_pressures['Ntg(g)'], 0.5, 2)
sol9 = self.pp.add_solution({})
sol9.interact(gas1)
assert_almost_equal(gas1.pressure, 0.975, 3)
assert_almost_equal(gas1.volume, 1, 2)
assert_almost_equal(gas1.partial_pressures['CH4(g)'], 0.48, 2)
assert_almost_equal(gas1.partial_pressures['Ntg(g)'], 0.49, 2)
def test10_use_non_default_database_directory(self):
pp_test10 = PhreeqPython(database_directory=Path(__file__).parent)
sol = pp_test10.add_solution_simple({'CaCl2': 1, 'Na2CO3': 1})
# test solution number
assert_equal(sol.number, 0)
# test solution ph, sc, pe and temperature
assert_equal(round(sol.pH, 2), 10.41)
assert_equal(round(sol.sc, 2), 435.35)
assert_equal(round(sol.pe, 2), 7.4)
assert_equal(round(sol.temperature, 2), 25)
class TestPhreeqPython(object):
pp = PhreeqPython()
def test1_basiscs(self):
sol = self.pp.add_solution({'CaCl2': 1, 'Na2CO3': 1})
# test solution number
assert_equal(sol.number, 1)
# test solution ph, sc, pe and temperature
assert_equal(round(sol.pH, 2), 10.41)
assert_equal(round(sol.sc, 2), 435.35)
assert_equal(round(sol.pe, 2), 7.4)
assert_equal(round(sol.temperature, 2), 25)
# test solution composition
assert_equal(round(sol.total("Ca"), 4), 0.001)
assert_equal(round(sol.total("Cl"), 4), 0.002)
assert_equal(round(sol.total_element("C"), 4), 0.001)
# test si
assert_equal(round(sol.si("Calcite"), 2), 1.71)
# test phases
assert_equal(len(sol.phases), 10)
assert_equal(len(sol.elements), 5)
# test ionic strength
assert_equal(round(sol.I, 4), 0.0045)
# test mass
assert_equal(round(sol.mass, 2), 1.0)
# test activity
assert_equal(round(sol.activity('Ca+2'), 5), 0.00054)
# test moles
assert_equal(round(sol.moles('Ca+2'), 5), 0.00071)
assert_equal(round(sol.molality('Ca+2'), 5), 0.00071)
# test species_moles
assert_equal(round(sol.species_moles['Ca+2'], 5), 0.00071)
assert_equal(round(sol.species_molalities['Ca+2'], 5), 0.00071)
assert_equal(round(sol.species_activities['Ca+2'], 5), 0.00054)
def test2_solution_functions(self):
sol = self.pp.add_solution({'CaCl2': 1})
# add components
sol.add('NaHCO3', 1)
assert_equal(round(sol.total('Na'), 4), 0.001)
# desaturate
sol.desaturate('Calcite')
assert_equal(sol.si('Calcite'), 0)
# remove mmol
sol.remove('Na', 0.5)
assert_equal(round(sol.total('Na'), 4), 0.0005)
# remove fraction
sol.remove_fraction('Na', 0.5)
assert_equal(round(sol.total('Na'), 5), 0.00025)
# change ph using base
sol.change_ph(10)
assert_equal(round(sol.pH, 2), 10)
# change ph using acid
sol.change_ph(5)
assert_equal(round(sol.pH, 2), 5)
# raise ph using custom chemical (NaOH)
sol.change_ph(8, 'NaOH')
assert_equal(round(sol.pH, 2), 8)
sol.saturate('Calcite', 1)
assert_equal(sol.si('Calcite'), 1)
sol.change_temperature(10)
assert_equal(sol.temperature, 10)
def test3_mixing(self):
sol1 = self.pp.add_solution({'NaCl': 1})
sol2 = self.pp.add_solution({})
sol3 = self.pp.mix_solutions({sol1: 0.5, sol2: 0.5})
assert_equal(round(sol3.total('Na'), 4), 0.0005)
def test4_solution_listing(self):
# test solution list
sol_list = self.pp.ip.get_solution_list()
assert_equal(len(sol_list), 7)
# test forgetting solutions
self.pp.remove_solutions([1, 2, 3])
sol_list = self.pp.ip.get_solution_list()
assert_equal(len(sol_list), 4)
def test5_addition(self):
sol1 = self.pp.add_solution({'NaCl': 1})
sol2 = self.pp.add_solution({'NaCl': 2})
sol3 = sol1 + sol2
assert_equal(round(sol3.mass), 2.0)
sol4 = sol1 / 2 + sol2 / 2
assert_equal(round(sol4.total('Na') * 1000, 1), 1.5)
sol5 = sol1 * 0.5 + sol2 * 0.5
assert_equal(round(sol5.total('Na') * 1000, 1), 1.5)
# test invalid mixtures
def testadd(sol, other):
return sol + other
def testdiv(sol, other):
return sol / other
def testmul(sol, other):
return sol * other
assert_raises(TypeError, testadd, sol1, 1)
assert_raises(TypeError, testdiv, sol1, sol2)
assert_raises(TypeError, testmul, sol1, sol2)
def test6_misc(self):
sol1 = self.pp.add_solution({'NaCl': 1})
sol2 = sol1.copy()
assert_equal(sol1.sc, sol2.sc)
sol2.forget()
assert_equal(sol2.pH, -999)
def test7_dump_and_load(self):
sol5a = self.pp.get_solution(5)
self.pp.dump_solutions()
pp2 = PhreeqPython('dump.gz')
sol5b = pp2.get_solution(5)
assert_almost_equal(sol5a.sc, sol5b.sc, 2)
assert_equal(self.pp.ip.get_solution_list(),
pp2.ip.get_solution_list())
def test8_raw_solutions(self):
sol8 = self.pp.add_solution_raw({
'pH': '8.0',
'temp': '20',
'units': 'mg/l',
'Alkalinity': '200 as HCO3',
'Ca': '40.1',
'Cl': '71.0'
})
assert_equal(sol8.pH, 8.0)
assert_almost_equal(sol8.total_element('Ca'), 1e-3, 5)
assert_almost_equal(sol8.total_element('Cl'), 2e-3, 5)
class Test_line_network(unittest.TestCase):
# Test simple network consisting of 4 nodes in a line
def setUp(self):
# self.net = Network(inputfile="tests/Case1.inp")
self.net = Network(inputfile="Case1.inp")
self.pp = PhreeqPython()
self.vic = Victoria(self.net, self.pp)
self.solutions = {}
sol0 = self.pp.add_solution({'Ca': 0, 'units': 'mmol/l'})
sol1 = self.pp.add_solution({'Ca': 1, 'units': 'mmol/l'})
self.solutions[0] = sol0
self.solutions[self.net.reservoirs['1'].uid] = sol1
def test1(self):
models = self.vic.solver.models
# Test node count
self.assertEqual(len(self.net.nodes), len(models.nodes))
# Test junction count
self.assertEqual(len(self.net.junctions), len(models.junctions))
# Test reservoir count
self.assertEqual(len(self.net.reservoirs), len(models.reservoirs))
# Test tank count
self.assertEqual(len(self.net.tanks), len(models.tanks))
# Test link count
self.assertEqual(len(self.net.links), len(models.links))
# Test pipe count
self.assertEqual(len(self.net.pipes), len(models.pipes))
# Test pump count
self.assertEqual(len(self.net.pumps), len(models.pumps))
# Test valve count
self.assertEqual(len(self.net.valves), len(models.valves))
def test2(self):
# Fill the network with a standard solution
self.net.solve()
self.vic.fill_network(self.solutions, from_reservoir=False)
# Test the initial concentrations of Ca
self.assertEqual(
self.vic.get_conc_pipe_avg(self.net.links['1'], 'Ca', 'mmol'), 0)
self.assertEqual(
self.vic.get_conc_pipe_avg(self.net.links['2'], 'Ca', 'mmol'), 0)
self.assertEqual(
self.vic.get_conc_pipe_avg(self.net.links['3'], 'Ca', 'mmol'), 0)
self.assertEqual(
self.vic.get_conc_pipe_avg(self.net.links['6'], 'Ca', 'mmol'), 0)
def test3(self):
# Fill the network with the initial reservoir solution
self.net.solve()
self.vic.fill_network(self.solutions, from_reservoir=True)
# Test the initial concentrations of Ca
self.assertAlmostEqual(
self.vic.get_conc_pipe_avg(self.net.links['1'], 'Ca', 'mmol'), 1,
4)
self.assertAlmostEqual(
self.vic.get_conc_pipe_avg(self.net.links['2'], 'Ca', 'mmol'), 1,
4)
self.assertAlmostEqual(
self.vic.get_conc_pipe_avg(self.net.links['3'], 'Ca', 'mmol'), 1,
4)
self.assertAlmostEqual(
self.vic.get_conc_pipe_avg(self.net.links['6'], 'Ca', 'mmol'), 1,
4)
def test4(self):
# Test the residence time in the pipes. Each pipe has a residence time of 1000 seconds
# Time parameters Victoria
time_end = 2 # hours
timestep_network = 60 # minutes
timestep_victoria = 1 # second
# Convert units to seconds
time_end *= 3600
timestep_network *= 60
time_count = 0
# Fill the network
self.net.solve() # Need to run Epynet for a single timestep
self.vic.fill_network(self.solutions, from_reservoir=False)
for t1 in range(0, time_end, timestep_network):
self.net.solve(simtime=t1)
self.vic.check_flow_direction()
for t2 in range(0, timestep_network, timestep_victoria):
self.vic.step(timestep_victoria, self.solutions)
time_count += t2
if time_count == 999:
node = self.vic.get_conc_node(self.net.nodes['2'], 'Ca',
'mmol')
self.assertAlmostEqual(node, 0, 4)
elif time_count == 1000:
node = self.vic.get_conc_node(self.net.nodes['2'], 'Ca',
'mmol')
self.assertAlmostEqual(node, 1, 4)
elif time_count == 1999:
node = self.vic.get_conc_node(self.net.nodes['3'], 'Ca',
'mmol')
self.assertAlmostEqual(node, 0, 4)
elif time_count == 2000:
node = self.vic.get_conc_node(self.net.nodes['3'], 'Ca',
'mmol')
self.assertAlmostEqual(node, 1, 4)
elif time_count == 2999:
node = self.vic.get_conc_node(self.net.nodes['4'], 'Ca',
'mmol')
self.assertAlmostEqual(node, 0, 4)
elif time_count == 3000:
node = self.vic.get_conc_node(self.net.nodes['4'], 'Ca',
'mmol')
self.assertAlmostEqual(node, 1, 4)
elif time_count == 3999:
node = self.vic.get_conc_node(self.net.nodes['6'], 'Ca',
'mmol')
self.assertAlmostEqual(node, 0, 4)
elif time_count == 4000:
node = self.vic.get_conc_node(self.net.nodes['6'], 'Ca',
'mmol')
self.assertAlmostEqual(node, 1, 4)
