示例#1
0
class TestMITAqueousCompatibility(unittest.TestCase):

    def setUp(self):
        self.compat = MITCompatibility()
        self.aqcompat = MITAqueousCompatibility()
        module_dir = os.path.dirname(os.path.abspath(__file__))
        fp = os.path.join(module_dir, os.path.pardir, "MITCompatibility.yaml")
        self.aqcorr =  AqueousCorrection(fp)
        
    def test_aqueous_compat(self):

        el_li = Element("Li")
        el_o = Element("O")
        el_h = Element("H")
        latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
        elts = [el_h, el_h, el_li, el_li, el_o, el_o]
        coords = [[0.000000, 0.500000, 0.413969],
                  [0.500000, 0.000000, 0.586031], 
                  [0.000000, 0.000000, 0.000000],
                  [0.500000, 0.500000, 0.000000],
                  [0.000000, 0.500000, 0.192672],
                  [0.500000, 0.000000, 0.807328]]
        struct = Structure(latt, elts, coords)
        lioh_entry = ComputedStructureEntry(struct, -3,
                                            parameters={'is_hubbard': False,
                                          'hubbards': None,
                                          'run_type': 'GGA',
                                          'potcar_symbols':
        ['PAW_PBE Fe 17Jan2003', 'PAW_PBE O 08Apr2002', 'PAW_PBE H 15Jun2001']})
        lioh_entry_compat = self.compat.process_entry(lioh_entry)
        lioh_entry_compat_aqcorr = self.aqcorr.correct_entry(lioh_entry_compat)
        lioh_entry_aqcompat = self.aqcompat.process_entry(lioh_entry)
        self.assertAlmostEqual(lioh_entry_compat_aqcorr.energy, lioh_entry_aqcompat.energy, 4)
 def setUp(self):
     self.compat = MITCompatibility()
     self.aqcompat = MITAqueousCompatibility()
     module_dir = os.path.dirname(os.path.abspath(__file__))
     fp = os.path.join(module_dir, os.path.pardir, "MITCompatibility.yaml")
     self.aqcorr =  AqueousCorrection(fp)
class TestMITAqueousCompatibility(unittest.TestCase):

    def setUp(self):
        self.compat = MITCompatibility(check_potcar_hash=True)
        self.aqcompat = MITAqueousCompatibility(check_potcar_hash=True)
        module_dir = os.path.dirname(os.path.abspath(__file__))
        fp = os.path.join(module_dir, os.path.pardir, "MITCompatibility.yaml")
        self.aqcorr =  AqueousCorrection(fp)

    def test_aqueous_compat(self):

        el_li = Element("Li")
        el_o = Element("O")
        el_h = Element("H")
        latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
        elts = [el_h, el_h, el_li, el_li, el_o, el_o]
        coords = [[0.000000, 0.500000, 0.413969],
                  [0.500000, 0.000000, 0.586031],
                  [0.000000, 0.000000, 0.000000],
                  [0.500000, 0.500000, 0.000000],
                  [0.000000, 0.500000, 0.192672],
                  [0.500000, 0.000000, 0.807328]]
        struct = Structure(latt, elts, coords)
        lioh_entry = ComputedStructureEntry(struct, -3,
                                            parameters={'is_hubbard': False,
                                          'hubbards': None,
                                          'run_type': 'GGA',
                                          'potcar_spec': [{'titel':'PAW_PBE Li 17Jan2003',
                                                           'hash': '65e83282d1707ec078c1012afbd05be8'},
                                                          {'titel': 'PAW_PBE O 08Apr2002',
                                                           'hash': '7a25bc5b9a5393f46600a4939d357982'},
                                                          {"titel": 'PAW_PBE H 15Jun2001',
                                                           'hash': "bb43c666e3d36577264afe07669e9582"}]})
        lioh_entry_compat = self.compat.process_entry(lioh_entry)
        lioh_entry_compat_aqcorr = self.aqcorr.correct_entry(lioh_entry_compat)
        lioh_entry_aqcompat = self.aqcompat.process_entry(lioh_entry)
        self.assertAlmostEqual(lioh_entry_compat_aqcorr.energy, lioh_entry_aqcompat.energy, 4)

    def test_potcar_doenst_match_structure(self):
        compat = MITCompatibility()
        el_li = Element("Li")
        el_o = Element("O")
        el_h = Element("H")
        latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
        elts = [el_h, el_h, el_li, el_li, el_o, el_o]
        coords = [[0.000000, 0.500000, 0.413969],
                  [0.500000, 0.000000, 0.586031],
                  [0.000000, 0.000000, 0.000000],
                  [0.500000, 0.500000, 0.000000],
                  [0.000000, 0.500000, 0.192672],
                  [0.500000, 0.000000, 0.807328]]
        struct = Structure(latt, elts, coords)

        lioh_entry = ComputedStructureEntry(struct, -3,
                                            parameters={'is_hubbard': False,
                                          'hubbards': None,
                                          'run_type': 'GGA',
                                          'potcar_symbols':
        ['PAW_PBE Fe 17Jan2003', 'PAW_PBE O 08Apr2002', 'PAW_PBE H 15Jun2001']})

        self.assertIsNone(compat.process_entry(lioh_entry))
示例#4
0
class TestMITAqueousCompatibility(unittest.TestCase):

    def setUp(self):
        self.compat = MITCompatibility(check_potcar_hash=True)
        self.aqcompat = MITAqueousCompatibility(check_potcar_hash=True)
        module_dir = os.path.dirname(os.path.abspath(__file__))
        fp = os.path.join(module_dir, os.path.pardir, "MITCompatibility.yaml")
        self.aqcorr =  AqueousCorrection(fp)

    def test_aqueous_compat(self):

        el_li = Element("Li")
        el_o = Element("O")
        el_h = Element("H")
        latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
        elts = [el_h, el_h, el_li, el_li, el_o, el_o]
        coords = [[0.000000, 0.500000, 0.413969],
                  [0.500000, 0.000000, 0.586031],
                  [0.000000, 0.000000, 0.000000],
                  [0.500000, 0.500000, 0.000000],
                  [0.000000, 0.500000, 0.192672],
                  [0.500000, 0.000000, 0.807328]]
        struct = Structure(latt, elts, coords)
        lioh_entry = ComputedStructureEntry(struct, -3,
                                            parameters={'is_hubbard': False,
                                          'hubbards': None,
                                          'run_type': 'GGA',
                                          'potcar_spec': [{'titel':'PAW_PBE Li 17Jan2003',
                                                           'hash': '9658a0ffb28da97ee7b36709966a0d1c'},
                                                          {'titel': 'PAW_PBE O 08Apr2002',
                                                           'hash': '7af704ddff29da5354831c4609f1cbc5'},
                                                          {"titel": 'PAW_PBE H 15Jun2001',
                                                           'hash': "57732e53d8a424e5b3721d0277f14ef0"}]})
        lioh_entry_compat = self.compat.process_entry(lioh_entry)
        lioh_entry_compat_aqcorr = self.aqcorr.correct_entry(lioh_entry_compat)
        lioh_entry_aqcompat = self.aqcompat.process_entry(lioh_entry)
        self.assertAlmostEqual(lioh_entry_compat_aqcorr.energy, lioh_entry_aqcompat.energy, 4)

    def test_potcar_doenst_match_structure(self):
        compat = MITCompatibility()
        el_li = Element("Li")
        el_o = Element("O")
        el_h = Element("H")
        latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
        elts = [el_h, el_h, el_li, el_li, el_o, el_o]
        coords = [[0.000000, 0.500000, 0.413969],
                  [0.500000, 0.000000, 0.586031],
                  [0.000000, 0.000000, 0.000000],
                  [0.500000, 0.500000, 0.000000],
                  [0.000000, 0.500000, 0.192672],
                  [0.500000, 0.000000, 0.807328]]
        struct = Structure(latt, elts, coords)

        lioh_entry = ComputedStructureEntry(struct, -3,
                                            parameters={'is_hubbard': False,
                                          'hubbards': None,
                                          'run_type': 'GGA',
                                          'potcar_symbols':
        ['PAW_PBE Fe 17Jan2003', 'PAW_PBE O 08Apr2002', 'PAW_PBE H 15Jun2001']})

        self.assertIsNone(compat.process_entry(lioh_entry))
示例#5
0
class TestMITAqueousCompatibility(unittest.TestCase):

    def setUp(self):
        self.compat = MITCompatibility(check_potcar_hash=True)
        self.aqcompat = MITAqueousCompatibility(check_potcar_hash=True)
        module_dir = os.path.dirname(os.path.abspath(__file__))
        fp = os.path.join(module_dir, os.path.pardir, "MITCompatibility.yaml")
        self.aqcorr =  AqueousCorrection(fp)

    def test_aqueous_compat(self):

        el_li = Element("Li")
        el_o = Element("O")
        el_h = Element("H")
        latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
        elts = [el_h, el_h, el_li, el_li, el_o, el_o]
        coords = [[0.000000, 0.500000, 0.413969],
                  [0.500000, 0.000000, 0.586031],
                  [0.000000, 0.000000, 0.000000],
                  [0.500000, 0.500000, 0.000000],
                  [0.000000, 0.500000, 0.192672],
                  [0.500000, 0.000000, 0.807328]]
        struct = Structure(latt, elts, coords)
        lioh_entry = ComputedStructureEntry(struct, -3,
                                            parameters={'is_hubbard': False,
                                          'hubbards': None,
                                          'run_type': 'GGA',
                                          'potcar_spec': [{'titel':'PAW_PBE Li 17Jan2003',
                                                           'hash': '65e83282d1707ec078c1012afbd05be8'},
                                                          {'titel': 'PAW_PBE O 08Apr2002',
                                                           'hash': '7a25bc5b9a5393f46600a4939d357982'},
                                                          {"titel": 'PAW_PBE H 15Jun2001',
                                                           'hash': "bb43c666e3d36577264afe07669e9582"}]})
        lioh_entry_compat = self.compat.process_entry(lioh_entry)
        lioh_entry_compat_aqcorr = self.aqcorr.correct_entry(lioh_entry_compat)
        lioh_entry_aqcompat = self.aqcompat.process_entry(lioh_entry)
        self.assertAlmostEqual(lioh_entry_compat_aqcorr.energy, lioh_entry_aqcompat.energy, 4)

    def test_potcar_doenst_match_structure(self):
        compat = MITCompatibility()
        el_li = Element("Li")
        el_o = Element("O")
        el_h = Element("H")
        latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
        elts = [el_h, el_h, el_li, el_li, el_o, el_o]
        coords = [[0.000000, 0.500000, 0.413969],
                  [0.500000, 0.000000, 0.586031],
                  [0.000000, 0.000000, 0.000000],
                  [0.500000, 0.500000, 0.000000],
                  [0.000000, 0.500000, 0.192672],
                  [0.500000, 0.000000, 0.807328]]
        struct = Structure(latt, elts, coords)

        lioh_entry = ComputedStructureEntry(struct, -3,
                                            parameters={'is_hubbard': False,
                                          'hubbards': None,
                                          'run_type': 'GGA',
                                          'potcar_symbols':
        ['PAW_PBE Fe 17Jan2003', 'PAW_PBE O 08Apr2002', 'PAW_PBE H 15Jun2001']})

        self.assertIsNone(compat.process_entry(lioh_entry))

    def test_msonable(self):

        compat_dict = self.aqcompat.as_dict()
        decoder = MontyDecoder()
        temp_compat = decoder.process_decoded(compat_dict)
        self.assertIsInstance(temp_compat,MITAqueousCompatibility)

    def test_dont_error_on_weird_elements(self):
        entry = ComputedEntry('AmSi',-1, 0.0,
            parameters={
                "potcar_spec": [{
                    "titel": "PAW_PBE Am 08May2007",
                    "hash": "ed5eebd8a143e35a0c19e9f8a2c42a93"
                }, {
                    "titel": "PAW_PBE Si 05Jan2001",
                    "hash": "b2b0ea6feb62e7cde209616683b8f7f5"
                }]
            })
        self.assertIsNone(self.compat.process_entry(entry))