Python compatibility.MaterialsProjectCompatibility类代码示例

 def test_get_stability(self):
     entries = self.rester.get_entries_in_chemsys(["Fe", "O"])
     modified_entries = []
     for entry in entries:
         # Create modified entries with energies that are 0.01eV higher
         # than the corresponding entries.
         if entry.composition.reduced_formula == "Fe2O3":
             modified_entries.append(
                 ComputedEntry(entry.composition,
                               entry.uncorrected_energy + 0.01,
                               parameters=entry.parameters,
                               entry_id="mod_{}".format(entry.entry_id)))
     rest_ehulls = self.rester.get_stability(modified_entries)
     all_entries = entries + modified_entries
     compat = MaterialsProjectCompatibility()
     all_entries = compat.process_entries(all_entries)
     pd = PhaseDiagram(all_entries)
     for e in all_entries:
         if str(e.entry_id).startswith("mod"):
             for d in rest_ehulls:
                 if d["entry_id"] == e.entry_id:
                     data = d
                     break
             self.assertAlmostEqual(pd.get_e_above_hull(e),
                                    data["e_above_hull"])

 def test_requires_hubbard(self):
     compat = MaterialsProjectCompatibility()
     self.assertTrue(compat.requires_hubbard("Fe2O3"))
     self.assertTrue(compat.requires_hubbard("FeSO4"))
     self.assertFalse(compat.requires_hubbard("FeS2"))
     self.assertFalse(compat.requires_hubbard("Li2O"))
     self.assertTrue(compat.requires_hubbard("FeOF"))

    def setUp(self):
        self.entry1 = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
                        'run_type': 'GGA+U',
                        'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
                                         'hash': '994537de5c4122b7f1b77fb604476db4'},
                                        {'titel': 'PAW_PBE O 08Apr2002',
                                         'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
        self.entry2 = ComputedEntry(
            'Fe3O4', -2, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
                        'run_type': 'GGA+U',
                        'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
                                         'hash': '994537de5c4122b7f1b77fb604476db4'},
                                        {'titel': 'PAW_PBE O 08Apr2002',
                                         'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
        self.entry3 = ComputedEntry(
            'FeO', -2, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 4.3, 'O': 0},
                        'run_type': 'GGA+U',
                        'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
                                         'hash': '994537de5c4122b7f1b77fb604476db4'},
                                        {'titel': 'PAW_PBE O 08Apr2002',
                                         'hash': '7a25bc5b9a5393f46600a4939d357982'}]})

        self.compat = MaterialsProjectCompatibility(check_potcar_hash=False)
        self.ggacompat = MaterialsProjectCompatibility("GGA", check_potcar_hash=False)

 def test_get_explanation_dict(self):
     compat = MaterialsProjectCompatibility(check_potcar_hash=False)
     entry = ComputedEntry(
         'Fe2O3', -1, 0.0,
         parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
                     'run_type': 'GGA+U',
                     'potcar_spec': [{'titel': 'PAW_PBE Fe_pv 06Sep2000',
                                      'hash': '994537de5c4122b7f1b77fb604476db4'},
                                     {'titel': 'PAW_PBE O 08Apr2002',
                                      'hash': "7a25bc5b9a5393f46600a4939d357982"}]})
     d = compat.get_explanation_dict(entry)
     self.assertEqual('MPRelaxSet Potcar Correction', d["corrections"][0][
         "name"])

    def test_get_corrections_dict(self):
        compat = MaterialsProjectCompatibility()
        ggacompat = MaterialsProjectCompatibility("GGA")

        #Correct parameters
        entry = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
                        'run_type': 'GGA+U',
                        'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
                                           'PAW_PBE O 08Apr2002']})
        c = compat.get_corrections_dict(entry)

        self.assertAlmostEqual(c["MP Gas Correction"], -2.10687)
        self.assertAlmostEqual(c["MP Advanced Correction"], -5.466)

        entry.parameters["is_hubbard"] = False
        del entry.parameters["hubbards"]
        c = ggacompat.get_corrections_dict(entry)
        self.assertNotIn("MP Advanced Correction", c)

    def test_get_corrections_dict(self):
        compat = MaterialsProjectCompatibility(check_potcar_hash=False)
        ggacompat = MaterialsProjectCompatibility("GGA", check_potcar_hash=False)

        #Correct parameters
        entry = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
                        'run_type': 'GGA+U',
                        'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
                                            'hash': '994537de5c4122b7f1b77fb604476db4'},
                                           {'titel': 'PAW_PBE O 08Apr2002',
                                            'hash': "7a25bc5b9a5393f46600a4939d357982"}]})
        c = compat.get_corrections_dict(entry)
        self.assertAlmostEqual(c["MP Anion Correction"], -2.10687)
        self.assertAlmostEqual(c["MP Advanced Correction"], -5.466)

        entry.parameters["is_hubbard"] = False
        del entry.parameters["hubbards"]
        c = ggacompat.get_corrections_dict(entry)
        self.assertNotIn("MP Advanced Correction", c)

def calculate_phase_stability(args):
    #This initializes the REST adaptor.
    a = MPRester(args.api_key)

    drone = VaspToComputedEntryDrone()
    entry = drone.assimilate(args.directory)

    compat = MaterialsProjectCompatibility()
    entry = compat.process_entry(entry)

    if not entry:
        print "Calculation parameters are not consistent with Materials " + \
            "Project parameters."
        sys.exit()

    syms = [el.symbol for el in entry.composition.elements]
    #This gets all entries belonging to the relevant system.
    entries = a.get_entries_in_chemsys(syms)
    entries.append(entry)

    #Process entries with Materials Project compatibility.
    entries = compat.process_entries(entries)

    print [e.composition.reduced_formula for e in entries]

#.........这里部分代码省略.........
            data['dir_name'] = get_block_part(dir)
            data['task_id'] = m_task['task_id']
            del data['hall']  # remove because it is too large and not useful
            fs = gridfs.GridFS(tdb, "boltztrap_full_fs")
            btid = fs.put(json.dumps(jsanitize(data)))
            """

            # now for the "sanitized" data
            ted = bta.as_dict()
            del ted['seebeck']
            del ted['hall']
            del ted['kappa']
            del ted['cond']

            # ted['boltztrap_full_fs_id'] = btid
            ted['snlgroup_id'] = fw_spec['snlgroup_id']
            ted['run_tags'] = fw_spec['run_tags']
            ted['snl'] = fw_spec['mpsnl'].as_dict()
            ted['dir_name_full'] = dir
            ted['dir_name'] = get_block_part(dir)
            ted['task_id'] = m_task['task_id']

            ted['pf_doping'] = bta.get_power_factor(output='tensor', relaxation_time=self.TAU)
            ted['zt_doping'] = bta.get_zt(output='tensor', relaxation_time=self.TAU, kl=self.KAPPAL)

            ted['pf_eigs'] = self.get_eigs(ted, 'pf_doping')
            ted['pf_best'] = self.get_extreme(ted, 'pf_eigs')
            ted['pf_best_dope18'] = self.get_extreme(ted, 'pf_eigs', max_didx=3)
            ted['pf_best_dope19'] = self.get_extreme(ted, 'pf_eigs', max_didx=4)
            ted['zt_eigs'] = self.get_eigs(ted, 'zt_doping')
            ted['zt_best'] = self.get_extreme(ted, 'zt_eigs')
            ted['zt_best_dope18'] = self.get_extreme(ted, 'zt_eigs', max_didx=3)
            ted['zt_best_dope19'] = self.get_extreme(ted, 'zt_eigs', max_didx=4)
            ted['seebeck_eigs'] = self.get_eigs(ted, 'seebeck_doping')
            ted['seebeck_best'] = self.get_extreme(ted, 'seebeck_eigs')
            ted['seebeck_best_dope18'] = self.get_extreme(ted, 'seebeck_eigs', max_didx=3)
            ted['seebeck_best_dope19'] = self.get_extreme(ted, 'seebeck_eigs', max_didx=4)
            ted['cond_eigs'] = self.get_eigs(ted, 'cond_doping')
            ted['cond_best'] = self.get_extreme(ted, 'cond_eigs')
            ted['cond_best_dope18'] = self.get_extreme(ted, 'cond_eigs', max_didx=3)
            ted['cond_best_dope19'] = self.get_extreme(ted, 'cond_eigs', max_didx=4)
            ted['kappa_eigs'] = self.get_eigs(ted, 'kappa_doping')
            ted['kappa_best'] = self.get_extreme(ted, 'kappa_eigs', maximize=False)
            ted['kappa_best_dope18'] = self.get_extreme(ted, 'kappa_eigs', maximize=False, max_didx=3)
            ted['kappa_best_dope19'] = self.get_extreme(ted, 'kappa_eigs', maximize=False, max_didx=4)

            try:
	        from mpcollab.thermoelectrics.boltztrap_TE import BoltzSPB
                bzspb = BoltzSPB(ted)
                maxpf_p = bzspb.get_maximum_power_factor('p', temperature=0, tau=1E-14, ZT=False, kappal=0.5,\
                    otherprops=('get_seebeck_mu_eig', 'get_conductivity_mu_eig', \
                                                    'get_thermal_conductivity_mu_eig', 'get_average_eff_mass_tensor_mu'))

                maxpf_n = bzspb.get_maximum_power_factor('n', temperature=0, tau=1E-14, ZT=False, kappal=0.5,\
                    otherprops=('get_seebeck_mu_eig', 'get_conductivity_mu_eig', \
                                                    'get_thermal_conductivity_mu_eig', 'get_average_eff_mass_tensor_mu'))

                maxzt_p = bzspb.get_maximum_power_factor('p', temperature=0, tau=1E-14, ZT=True, kappal=0.5, otherprops=('get_seebeck_mu_eig', 'get_conductivity_mu_eig', \
                                                    'get_thermal_conductivity_mu_eig', 'get_average_eff_mass_tensor_mu'))

                maxzt_n = bzspb.get_maximum_power_factor('n', temperature=0, tau=1E-14, ZT=True, kappal=0.5, otherprops=('get_seebeck_mu_eig', 'get_conductivity_mu_eig', \
                                                    'get_thermal_conductivity_mu_eig', 'get_average_eff_mass_tensor_mu'))

                ted['zt_best_finemesh'] = {'p': maxzt_p, 'n': maxzt_n}
                ted['pf_best_finemesh'] = {'p': maxpf_p, 'n': maxpf_n}
            except:
                import traceback
                traceback.print_exc()
                print 'COULD NOT GET FINE MESH DATA'

            # add is_compatible
            mpc = MaterialsProjectCompatibility("Advanced")
            try:
                func = m_task["pseudo_potential"]["functional"]
                labels = m_task["pseudo_potential"]["labels"]
                symbols = ["{} {}".format(func, label) for label in labels]
                parameters = {"run_type": m_task["run_type"],
                          "is_hubbard": m_task["is_hubbard"],
                          "hubbards": m_task["hubbards"],
                          "potcar_symbols": symbols}
                entry = ComputedEntry(Composition(m_task["unit_cell_formula"]),
                                      0.0, 0.0, parameters=parameters,
                                      entry_id=m_task["task_id"])

                ted["is_compatible"] = bool(mpc.process_entry(entry))
            except:
                traceback.print_exc()
                print 'ERROR in getting compatibility, task_id: {}'.format(m_task["task_id"])
                ted["is_compatible"] = None

            tdb.boltztrap.insert(jsanitize(ted))

            update_spec = {'prev_vasp_dir': fw_spec['prev_vasp_dir'],
                       'boltztrap_dir': os.getcwd(),
                       'prev_task_type': fw_spec['task_type'],
                       'mpsnl': fw_spec['mpsnl'].as_dict(),
                       'snlgroup_id': fw_spec['snlgroup_id'],
                       'run_tags': fw_spec['run_tags'], 'parameters': fw_spec.get('parameters')}

        return FWAction(update_spec=update_spec)

    def test_process_entry(self):
        compat = MaterialsProjectCompatibility()
        ggacompat = MaterialsProjectCompatibility("GGA")

        #Correct parameters
        self.assertIsNotNone(compat.process_entry(self.entry1))
        self.assertIsNone(ggacompat.process_entry(self.entry1))

        #Correct parameters
        entry = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': False, "hubbards": {}, 'run_type': 'GGA',
                        'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
                                           'PAW_PBE O 08Apr2002']})
        self.assertIsNone(compat.process_entry(entry))
        self.assertIsNotNone(ggacompat.process_entry(entry))

        entry = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
                        'run_type': 'GGA+U',
                        'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
                                           'PAW_PBE O 08Apr2002']})
        self.assertIsNotNone(compat.process_entry(entry))

        #Check actual correction
        self.assertAlmostEqual(compat.process_entry(entry).correction,
                               - 2.733 * 2 - 0.70229 * 3)

        entry = ComputedEntry(
            'FeF3', -2, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'F': 0},
                        'run_type': 'GGA+U',
                        'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
                                           'PAW_PBE F 08Apr2002']})
        self.assertIsNotNone(compat.process_entry(entry))

        #Check actual correction
        self.assertAlmostEqual(compat.process_entry(entry).correction, -2.733)

        #Wrong U value
        entry = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': True,
                        'hubbards': {'Fe': 5.2, 'O': 0}, 'run_type': 'GGA+U',
                        'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
                                           'PAW_PBE O 08Apr2002']})
        self.assertIsNone(compat.process_entry(entry))

        #GGA run of U
        entry = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': False, 'hubbards': None,
                        'run_type': 'GGA',
                        'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
                                           'PAW_PBE O 08Apr2002']})
        self.assertIsNone(compat.process_entry(entry))

        #GGA+U run of non-U
        entry = ComputedEntry(
            'Al2O3', -1, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Al': 5.3, 'O': 0},
                        'run_type': 'GGA+U',
                        'potcar_symbols': ['PAW_PBE Al 06Sep2000',
                                           'PAW_PBE O 08Apr2002']})
        self.assertIsNone(compat.process_entry(entry))

        #Materials project should not have a U for sulfides
        entry = ComputedEntry(
            'FeS2', -2, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'S': 0},
                        'run_type': 'GGA+U',
                        'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
                                           'PAW_PBE S 08Apr2002']})
        self.assertIsNone(compat.process_entry(entry))

        #Wrong psp
        entry = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
                        'run_type': 'GGA+U',
                        'potcar_symbols': ['PAW_PBE Fe 06Sep2000',
                                           'PAW_PBE O 08Apr2002']})
        self.assertIsNone(compat.process_entry(entry))

        #Testing processing of elements.
        entry = ComputedEntry(
            'O', -1, 0.0,
            parameters={'is_hubbard': False, 'hubbards': {},
                        'potcar_symbols': ['PAW_PBE O 08Apr2002'],
                        'run_type': 'GGA'})
        entry = compat.process_entry(entry)
#        self.assertEqual(entry.entry_id, -8)
        self.assertAlmostEqual(entry.energy, -1)
        self.assertAlmostEqual(ggacompat.process_entry(entry).energy,
                               -1)

 def test_process_entries(self):
     compat = MaterialsProjectCompatibility()
     entries = compat.process_entries([self.entry1, self.entry2,
                                       self.entry3])
     self.assertEqual(len(entries), 2)

    def get_entries(self, chemsys_formula_id_criteria, compatible_only=True,
                    inc_structure=None, property_data=None):
        """
        Get a list of ComputedEntries or ComputedStructureEntries corresponding
        to a chemical system, formula, or materials_id or full criteria.

        Args:
            chemsys_formula_id_criteria (str/dict): A chemical system
                (e.g., Li-Fe-O), or formula (e.g., Fe2O3) or materials_id
                (e.g., mp-1234) or full Mongo-style dict criteria.
            compatible_only (bool): Whether to return only "compatible"
                entries. Compatible entries are entries that have been
                processed using the MaterialsProjectCompatibility class,
                which performs adjustments to allow mixing of GGA and GGA+U
                calculations for more accurate phase diagrams and reaction
                energies.
            inc_structure (str): If None, entries returned are
                ComputedEntries. If inc_structure="final",
                ComputedStructureEntries with final structures are returned.
                Otherwise, ComputedStructureEntries with initial structures
                are returned.
            property_data (list): Specify additional properties to include in
                entry.data. If None, no data. Should be a subset of
                supported_properties.

        Returns:
            List of ComputedEntry or ComputedStructureEntry objects.
        """
        # TODO: This is a very hackish way of doing this. It should be fixed
        # on the REST end.
        params = ["run_type", "is_hubbard", "pseudo_potential", "hubbards",
                  "potcar_symbols"]
        if compatible_only:
            props = ["energy", "unit_cell_formula", "task_id"] + params
            if property_data:
                props += property_data
            if inc_structure:
                if inc_structure == "final":
                    props.append("structure")
                else:
                    props.append("initial_structure")

            if not isinstance(chemsys_formula_id_criteria, dict):
                criteria = MPRester.parse_criteria(chemsys_formula_id_criteria)
            else:
                criteria = chemsys_formula_id_criteria

            data = self.query(criteria, props)

            entries = []
            for d in data:
                d["potcar_symbols"] = [
                    "%s %s" % (d["pseudo_potential"]["functional"], l)
                    for l in d["pseudo_potential"]["labels"]]
                data = {k: d[k] for k in property_data} if property_data else None
                if not inc_structure:
                    e = ComputedEntry(d["unit_cell_formula"], d["energy"],
                                      parameters={k: d[k] for k in params},
                                      data=data,
                                      entry_id=d["task_id"])

                else:
                    s = d["structure"] if inc_structure == "final" else d[
                        "initial_structure"]
                    e = ComputedStructureEntry(
                        s, d["energy"],
                        parameters={k: d[k] for k in params},
                        data=data,
                        entry_id=d["task_id"])
                entries.append(e)
            from pymatgen.entries.compatibility import \
                MaterialsProjectCompatibility
            entries = MaterialsProjectCompatibility().process_entries(entries)
        else:
            entries = []
            for d in self.get_data(chemsys_formula_id_criteria,
                                   prop="task_ids"):
                for i in d["task_ids"]:
                    e = self.get_task_data(i, prop="entry")
                    e = e[0]["entry"]
                    if inc_structure:
                        s = self.get_task_data(i,
                                               prop="structure")[0]["structure"]
                        e = ComputedStructureEntry(
                            s, e.energy, e.correction, e.parameters, e.data,
                            e.entry_id)
                    entries.append(e)

        return entries

#.........这里部分代码省略.........
                    struct=Structure.from_dict(d["output"]["crystal"])
                    d["oxide_type"]=oxide_type(struct)
                except:
                    logger.error("can't get oxide_type for {}".format(d["task_id"]))
                    d["oxide_type"] = None

                #Override incorrect outcar subdocs for two step relaxations
                if "optimize structure" in d['task_type'] and \
                    os.path.exists(os.path.join(path, "relax2")):
                    try:
                        run_stats = {}
                        for i in [1,2]:
                            o_path = os.path.join(path,"relax"+str(i),"OUTCAR")
                            o_path = o_path if os.path.exists(o_path) else o_path+".gz"
                            outcar = Outcar(o_path)
                            d["calculations"][i-1]["output"]["outcar"] = outcar.as_dict()
                            run_stats["relax"+str(i)] = outcar.run_stats
                    except:
                        logger.error("Bad OUTCAR for {}.".format(path))

                    try:
                        overall_run_stats = {}
                        for key in ["Total CPU time used (sec)", "User time (sec)",
                                    "System time (sec)", "Elapsed time (sec)"]:
                            overall_run_stats[key] = sum([v[key]
                                              for v in run_stats.values()])
                        run_stats["overall"] = overall_run_stats
                    except:
                        logger.error("Bad run stats for {}.".format(path))

                    d["run_stats"] = run_stats

                # add is_compatible
                mpc = MaterialsProjectCompatibility("Advanced")

                try:
                    func = d["pseudo_potential"]["functional"]
                    labels = d["pseudo_potential"]["labels"]
                    symbols = ["{} {}".format(func, label) for label in labels]
                    parameters = {"run_type": d["run_type"],
                              "is_hubbard": d["is_hubbard"],
                              "hubbards": d["hubbards"],
                              "potcar_symbols": symbols}
                    entry = ComputedEntry(Composition(d["unit_cell_formula"]),
                                          0.0, 0.0, parameters=parameters,
                                          entry_id=d["task_id"])

                    d['is_compatible'] = bool(mpc.process_entry(entry))
                except:
                    traceback.print_exc()
                    print 'ERROR in getting compatibility'
                    d['is_compatible'] = None


                #task_type dependent processing
                if 'static' in d['task_type']:
                    launch_doc = launches_coll.find_one({"fw_id": d['fw_id'], "launch_dir": {"$regex": d["dir_name"]}}, {"action.stored_data": 1})
                    for i in ["conventional_standard_structure", "symmetry_operations",
                              "symmetry_dataset", "refined_structure"]:
                        try:
                            d['stored_data'][i] = launch_doc['action']['stored_data'][i]
                        except:
                            pass

                #parse band structure if necessary
                if ('band structure' in d['task_type'] or "Uniform" in d['task_type'])\

class MaterialsProjectCompatibilityTest(unittest.TestCase):

    def setUp(self):
        self.entry1 = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
                        'run_type': 'GGA+U',
                        'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
                                         'hash': '994537de5c4122b7f1b77fb604476db4'},
                                        {'titel': 'PAW_PBE O 08Apr2002',
                                         'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
        self.entry2 = ComputedEntry(
            'Fe3O4', -2, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
                        'run_type': 'GGA+U',
                        'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
                                         'hash': '994537de5c4122b7f1b77fb604476db4'},
                                        {'titel': 'PAW_PBE O 08Apr2002',
                                         'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
        self.entry3 = ComputedEntry(
            'FeO', -2, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 4.3, 'O': 0},
                        'run_type': 'GGA+U',
                        'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
                                         'hash': '994537de5c4122b7f1b77fb604476db4'},
                                        {'titel': 'PAW_PBE O 08Apr2002',
                                         'hash': '7a25bc5b9a5393f46600a4939d357982'}]})

        self.compat = MaterialsProjectCompatibility(check_potcar_hash=False)
        self.ggacompat = MaterialsProjectCompatibility("GGA", check_potcar_hash=False)

    def test_process_entry(self):
        #Correct parameters
        self.assertIsNotNone(self.compat.process_entry(self.entry1))
        self.assertIsNone(self.ggacompat.process_entry(self.entry1))

        #Correct parameters
        entry = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': False, "hubbards": {}, 'run_type': 'GGA',
                        'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
                                         'hash': '994537de5c4122b7f1b77fb604476db4'},
                                        {'titel': 'PAW_PBE O 08Apr2002',
                                         'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
        self.assertIsNone(self.compat.process_entry(entry))
        self.assertIsNotNone(self.ggacompat.process_entry(entry))

        entry = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
                        'run_type': 'GGA+U',
                        'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
                                         'hash': '994537de5c4122b7f1b77fb604476db4'},
                                        {'titel': 'PAW_PBE O 08Apr2002',
                                         'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
        self.assertIsNotNone(self.compat.process_entry(entry))

    def test_correction_values(self):
        #test_corrections
        self.assertAlmostEqual(self.compat.process_entry(self.entry1).correction,
                               - 2.733 * 2 - 0.70229 * 3)

        entry = ComputedEntry(
            'FeF3', -2, 0.0,
            parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'F': 0},
                        'run_type': 'GGA+U',
                        'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
                                         'hash': '994537de5c4122b7f1b77fb604476db4'},
                                        {'titel': 'PAW_PBE F 08Apr2002',
                                         'hash': '180141c33d032bfbfff30b3bea9d23dd'}]})
        self.assertIsNotNone(self.compat.process_entry(entry))

        #Check actual correction
        self.assertAlmostEqual(self.compat.process_entry(entry).correction, -2.733)

    def test_U_values(self):
        #Wrong U value
        entry = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': True,
                        'hubbards': {'Fe': 5.2, 'O': 0}, 'run_type': 'GGA+U',
                        'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
                                         'hash': '994537de5c4122b7f1b77fb604476db4'},
                                        {'titel': 'PAW_PBE O 08Apr2002',
                                         'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
        self.assertIsNone(self.compat.process_entry(entry))

        #GGA run of U
        entry = ComputedEntry(
            'Fe2O3', -1, 0.0,
            parameters={'is_hubbard': False, 'hubbards': None,
                        'run_type': 'GGA',
                        'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
                                         'hash': '994537de5c4122b7f1b77fb604476db4'},
                                        {'titel': 'PAW_PBE O 08Apr2002',
                                         'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
        self.assertIsNone(self.compat.process_entry(entry))

        #GGA+U run of non-U
        entry = ComputedEntry(
#.........这里部分代码省略.........

    def __init__(self):
        # some MP analysis power tools
        self.compat  = MaterialsProjectCompatibility()

        return

class AnalyseMaterialsProjectJsonDataWithComputedEntries():
    """
    Class which will wrap around boilerplate analysis of MaterialsProject-like
    json files, containing data extracted using borgs and queens.

    It will be assumed that we are providing ComputedEntries objects directly.
    """

    def __init__(self):
        # some MP analysis power tools
        self.compat  = MaterialsProjectCompatibility()

        return

    def extract_alkali_energy(self, computed_Alkali_entry ):
        processed_Alkali_entry = self.compat.process_entry(computed_Alkali_entry)
        self.E_Alkali = processed_Alkali_entry.energy
        return

    def extract_phase_diagram_info(self,MP_phase_diagram_json_data_filename):

        computed_entries  = self._extract_MP_data(MP_phase_diagram_json_data_filename)
        processed_entries = self.compat.process_entries(computed_entries)

        pd = PhaseDiagram(processed_entries)
        self.phase_diagram_analyser = PDAnalyzer(pd)

        return

    def extract_processed_entries(self,computed_entries):
        processed_entries = self.compat.process_entries(computed_entries)

        return processed_entries

    def extract_energies_above_hull(self,computed_entries,alkali):

        processed_entries = self.extract_processed_entries(computed_entries)

        list_energy_above_hull  = []
        list_alkali_content = []

        for entry in processed_entries: 
            decomposition_dict, energy_above_hull  = \
                self.phase_diagram_analyser.get_decomp_and_e_above_hull(entry, allow_negative=True)

            list_energy_above_hull.append(energy_above_hull)  
            list_alkali_content.append(entry.composition[alkali])

        list_energy_above_hull  = np.array(list_energy_above_hull)
        list_alkali_content     = np.array(list_alkali_content )

        return list_alkali_content, list_energy_above_hull  

    def extract_energies(self,computed_entries,alkali):

        processed_entries = self.extract_processed_entries(computed_entries)

        list_energy         = []
        list_alkali_content = []
        for entry in processed_entries:
            list_energy.append(entry.energy)
            list_alkali_content.append(entry.composition[alkali])

        list_energy         = np.array(list_energy)
        list_alkali_content = np.array(list_alkali_content )

        I = np.argsort(list_alkali_content )
        
        return list_alkali_content[I], list_energy[I]

    def _extract_MP_data(self,MP_data_filename):

        drone = VaspToComputedEntryDrone()
        queen = BorgQueen(drone, "dummy", 1)

        queen.load_data(MP_data_filename)
        computed_entries = queen.get_data()

        del drone
        del queen

        return computed_entries