def do_query(args):
"""
Perform query to the Materials Project
Args:
args (dict): Args from argparse.
"""
m = MPRester()
try:
criteria = json.loads(args.criteria)
except json.decoder.JSONDecodeError:
criteria = args.criteria
if args.structure:
count = 0
for d in m.query(criteria, properties=["structure", "task_id"]):
s = d["structure"]
formula = re.sub(r"\s+", "", s.formula)
if args.structure == "poscar":
fname = "POSCAR.{}_{}".format(d["task_id"], formula)
else:
fname = "{}-{}.{}".format(d["task_id"], formula, args.structure)
s.to(filename=fname)
count += 1
print("%d structures written!" % count)
elif args.entries:
entries = m.get_entries(criteria)
dumpfn(entries, args.entries)
print("%d entries written to %s!" % (len(entries), args.entries))
else:
props = ["e_above_hull", "spacegroup"]
props += args.data
entries = m.get_entries(criteria, property_data=props)
t = []
headers = [
"mp-id",
"Formula",
"Spacegroup",
"E/atom (eV)",
"E above hull (eV)",
] + args.data
for e in entries:
row = [
e.entry_id,
e.composition.reduced_formula,
e.data["spacegroup"]["symbol"],
e.energy_per_atom,
e.data["e_above_hull"],
]
row += [e.data[s] for s in args.data]
t.append(row)
t = sorted(t, key=lambda x: x[headers.index("E above hull (eV)")])
print(tabulate(t, headers=headers, tablefmt="pipe", floatfmt=".3f"))
def get_electrochemical_stability(mpid, pH, potential):
'''
A wrapper for pymatgen to construct Pourbaix amd calculate electrochemical
stability under reaction condition (i.e. at a given pH and applied potential).
Arg:
mpid Materials project ID of a bulk composition. e.g. Pt: 'mp-126'.
pH: pH at reaction condition. Commonly ones are: acidic: pH=0,
neutral: pH=7, and basic pH=14.
potential: Applied potential at reaction condition.
Returns:
stability Electrochemical stability of a composition under reaction condition,
unit is eV/atom.
'''
mpr = MPRester(read_rc('matproj_api_key'))
try:
entry = mpr.get_entries(mpid)[0]
composition = entry.composition
comp_dict = {str(key): value for key, value in composition.items()
if key not in ELEMENTS_HO}
entries = mpr.get_pourbaix_entries(list(comp_dict.keys()))
entry = [entry for entry in entries if entry.entry_id == mpid][0]
pbx = PourbaixDiagram(entries, comp_dict=comp_dict, filter_solids=False)
stability = pbx.get_decomposition_energy(entry, pH=pH, V=potential)
stability = round(stability, 3)
# Some mpid's stability are not available
except IndexError:
stability = np.nan
return stability
def do_query(args):
m = MPRester()
try:
criteria = json.loads(args.criteria)
except json.decoder.JSONDecodeError:
criteria = args.criteria
if args.structure:
count = 0
for d in m.query(criteria, properties=["structure", "task_id"]):
s = d["structure"]
formula = re.sub(r"\s+", "", s.formula)
if args.structure == "poscar":
fname = "POSCAR.%s_%s" % (d["task_id"], formula)
else:
fname = "%s-%s.%s" % (d["task_id"], formula, args.structure)
s.to(filename=fname)
count += 1
print("%d structures written!" % count)
elif args.entries:
entries = m.get_entries(criteria)
dumpfn(entries, args.entries)
print("%d entries written to %s!" % (len(entries), args.entries))
else:
props = ["e_above_hull", "spacegroup"]
props += args.data
entries = m.get_entries(criteria, property_data=props)
t = []
headers = ["mp-id", "Formula", "Spacegroup", "E/atom (eV)",
"E above hull (eV)"] + args.data
for e in entries:
row = [e.entry_id, e.composition.reduced_formula,
e.data["spacegroup"]["symbol"],
e.energy_per_atom, e.data["e_above_hull"]]
row += [e.data[s] for s in args.data]
t.append(row)
t = sorted(t, key=lambda x: x[headers.index("E above hull (eV)")])
print(tabulate(t, headers=headers, tablefmt="pipe", floatfmt=".3f"))
def get_structure_from_mp(formula) -> str:
"""
Obtain a crystal from the MP database via the API.
Args: formula (str): A formula
Returns: (Structure) the lowest energy structure on the Convex hull form MP
database and its material_id
"""
m = MPRester("N7AIm1s2v43BQ6FT")
entries = m.get_entries(formula, inc_structure="final")
#-- returned the computed final structure (with vasp relaxation)
if len(entries) == 0:
raise ValueError("This crystal structure with formula {} has been "
"removed from the current version of MP DB".format(formula))
elif len(entries) > 1:
logging.warning("{} structures with formula {} found in MP, however only "
"the lowest energy one is returned".format(len(entries), formula))
min_e_mp = min(entries, key = lambda e: e.energy_per_atom)
return min_e_mp.structure, min_e_mp.entry_id
class MPResterTest(PymatgenTest):
_multiprocess_shared_ = True
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
self.rester.session.close()
def test_get_all_materials_ids_doc(self):
mids = self.rester.get_materials_ids("Al2O3")
random.shuffle(mids)
doc = self.rester.get_doc(mids.pop(0))
self.assertEqual(doc["pretty_formula"], "Al2O3")
def test_get_xas_data(self):
# Test getting XAS data
data = self.rester.get_xas_data("mp-19017", "Li")
self.assertEqual("mp-19017,Li", data['mid_and_el'])
self.assertAlmostEqual(data['spectrum']['x'][0], 55.178, places=2)
self.assertAlmostEqual(data['spectrum']['y'][0], 0.0164634, places=2)
def test_get_data(self):
props = ["energy", "energy_per_atom", "formation_energy_per_atom",
"nsites", "unit_cell_formula", "pretty_formula", "is_hubbard",
"elements", "nelements", "e_above_hull", "hubbards",
"is_compatible", "task_ids",
"density", "icsd_ids", "total_magnetization"]
# unicode literals have been reintroduced in py>3.2
expected_vals = [-191.3359011, -6.833425039285714, -2.5515769497278913,
28, {'P': 4, 'Fe': 4, 'O': 16, 'Li': 4},
"LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0,
{'Fe': 5.3, 'Li': 0.0, 'O': 0.0, 'P': 0.0}, True,
{'mp-19017', 'mp-540081', 'mp-601412'},
3.464840709092822,
[159107, 154117, 160776, 99860, 181272, 166815,
260571, 92198, 165000, 155580, 38209, 161479, 153699,
260569, 260570, 200155, 260572, 181341, 181342,
72545, 56291, 97764, 162282, 155635],
15.9996841]
for (i, prop) in enumerate(props):
if prop not in ['hubbards', 'unit_cell_formula', 'elements',
'icsd_ids', 'task_ids']:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val, places=2)
elif prop in ["elements", "icsd_ids", "task_ids"]:
upstream_vals = set(
self.rester.get_data("mp-19017", prop=prop)[0][prop])
self.assertLessEqual(set(expected_vals[i]), upstream_vals)
else:
self.assertEqual(expected_vals[i],
self.rester.get_data("mp-19017",
prop=prop)[0][prop])
props = ['structure', 'initial_structure', 'final_structure', 'entry']
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
# Test chemsys search
data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula')
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(d['unit_cell_formula']).elements).issubset(
elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_data(self):
# Test getting supported properties
self.assertNotEqual(self.rester.get_task_data("mp-30"), [])
# Test aliasing
data = self.rester.get_task_data("mp-30", "energy")
self.assertAlmostEqual(data[0]["energy"], -4.09929227, places=2)
def test_get_materials_id_from_task_id(self):
self.assertEqual(self.rester.get_materials_id_from_task_id(
"mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references('mp-123')
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = self.TEST_FILES_DIR / 'Fe3O4.cif'
data = m.find_structure(str(ciffile))
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
entries = self.rester.get_entries_in_chemsys(syms)
elements = set([Element(sym) for sym in syms])
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}}
props = ['pretty_formula', 'energy']
data = self.rester.query(
criteria=criteria, properties=props, chunk_size=0)
self.assertTrue(len(data) > 6)
data = self.rester.query(
criteria="*2O", properties=props, chunk_size=0)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_query_chunk_size(self):
criteria = {"nelements": 2, "elements": "O"}
props = ['pretty_formula']
data1 = self.rester.query(
criteria=criteria, properties=props, chunk_size=0)
data2 = self.rester.query(
criteria=criteria, properties=props, chunk_size=500)
self.assertEqual({d['pretty_formula'] for d in data1},
{d['pretty_formula'] for d in data2})
self.assertIn("Al2O3", {d['pretty_formula'] for d in data1})
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
bs_unif = self.rester.get_bandstructure_by_material_id(
"mp-2254", line_mode=False)
self.assertIsInstance(bs_unif, BandStructure)
self.assertNotIsInstance(bs_unif, BandStructureSymmLine)
def test_get_phonon_data_by_material_id(self):
bs = self.rester.get_phonon_bandstructure_by_material_id("mp-661")
self.assertIsInstance(bs, PhononBandStructureSymmLine)
dos = self.rester.get_phonon_dos_by_material_id("mp-661")
self.assertIsInstance(dos, CompletePhononDos)
ddb_str = self.rester.get_phonon_ddb_by_material_id("mp-661")
self.assertIsInstance(ddb_str, str)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure=True)
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe", compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
# test if it will retrieve the conventional unit cell of Ni
entry = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=True)
Ni = entry.structure
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Ensure energy per atom is same
primNi = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=False)
self.assertEqual(primNi.energy_per_atom, entry.energy_per_atom)
Ni = self.rester.get_structure_by_material_id(
"mp-23", conventional_unit_cell=True)
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Test case where convs are different from initial and final
th = self.rester.get_structure_by_material_id(
"mp-37", conventional_unit_cell=True)
th_entry = self.rester.get_entry_by_material_id(
"mp-37", inc_structure=True, conventional_unit_cell=True)
th_entry_initial = self.rester.get_entry_by_material_id(
"mp-37", inc_structure="initial", conventional_unit_cell=True)
self.assertEqual(th, th_entry.structure)
self.assertEqual(len(th_entry.structure), 4)
self.assertEqual(len(th_entry_initial.structure), 2)
# Test if the polymorphs of Fe are properly sorted
# by e_above_hull when sort_by_e_above_hull=True
Fe_entries = self.rester.get_entries("Fe", sort_by_e_above_hull=True)
self.assertEqual(Fe_entries[0].data["e_above_hull"], 0)
def test_get_pourbaix_entries(self):
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# Ensure entries are pourbaix compatible
pbx = PourbaixDiagram(pbx_entries)
# Try binary system
#pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
#pbx = PourbaixDiagram(pbx_entries)
# TODO: Shyue Ping: I do not understand this test. You seem to
# be grabbing Zn-S system, but I don't see proper test for anything,
# including Na ref. This test also takes a long time.
# Test Zn-S, which has Na in reference solids
# pbx_entries = self.rester.get_pourbaix_entries(["Zn", "S"])
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
def test_submit_query_delete_snl(self):
s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
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_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates('mp-123', 5, [1, 0, 0])
substrates = [sub_dict['sub_id'] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_get_surface_data(self):
data = self.rester.get_surface_data("mp-126") # Pt
one_surf = self.rester.get_surface_data('mp-129', miller_index=[-2, -3, 1])
self.assertAlmostEqual(one_surf['surface_energy'], 2.99156963, places=2)
self.assertArrayAlmostEqual(one_surf['miller_index'], [3, 2, 1])
self.assertIn("surfaces", data)
surfaces = data["surfaces"]
self.assertTrue(len(surfaces) > 0)
surface = surfaces.pop()
self.assertIn("miller_index", surface)
self.assertIn("surface_energy", surface)
self.assertIn("is_reconstructed", surface)
data_inc = self.rester.get_surface_data("mp-126", inc_structures=True)
self.assertIn("structure", data_inc["surfaces"][0])
def test_get_wulff_shape(self):
ws = self.rester.get_wulff_shape("mp-126")
self.assertTrue(isinstance(ws, WulffShape))
def test_get_cohesive_energy(self):
ecoh = self.rester.get_cohesive_energy("mp-13")
self.assertTrue(ecoh, 5.04543279)
def test_get_gb_data(self):
mo_gbs = self.rester.get_gb_data(chemsys='Mo')
self.assertEqual(len(mo_gbs), 10)
mo_gbs_s5 = self.rester.get_gb_data(pretty_formula='Mo', sigma=5)
self.assertEqual(len(mo_gbs_s5), 3)
mo_s3_112 = self.rester.get_gb_data(material_id='mp-129', sigma=3,
gb_plane=[1, -1, -2],
include_work_of_separation=True)
self.assertEqual(len(mo_s3_112), 1)
gb_f = mo_s3_112[0]['final_structure']
self.assertArrayAlmostEqual(gb_f.rotation_axis, [1, 1, 0])
self.assertAlmostEqual(gb_f.rotation_angle, 109.47122, places=4)
self.assertAlmostEqual(mo_s3_112[0]['gb_energy'], 0.47965, places=2)
self.assertAlmostEqual(mo_s3_112[0]['work_of_separation'], 6.318144, places=2)
self.assertIn("Mo24", gb_f.formula)
hcp_s7 = self.rester.get_gb_data(material_id='mp-87', gb_plane=[0, 0, 0, 1],
include_work_of_separation=True)
self.assertAlmostEqual(hcp_s7[0]['gb_energy'], 1.12, places=2)
self.assertAlmostEqual(hcp_s7[0]['work_of_separation'], 2.46, places=2)
def test_get_interface_reactions(self):
kinks = self.rester.get_interface_reactions("LiCoO2", "Li3PS4")
self.assertTrue(len(kinks) > 0)
kink = kinks[0]
self.assertIn("energy", kink)
self.assertIn("ratio_atomic", kink)
self.assertIn("rxn", kink)
self.assertTrue(isinstance(kink['rxn'], Reaction))
kinks_open_O = self.rester.get_interface_reactions(
"LiCoO2", "Li3PS4", open_el="O", relative_mu=-1)
self.assertTrue(len(kinks_open_O) > 0)
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings("always", message="The reactant.+")
self.rester.get_interface_reactions("LiCoO2", "MnO9")
self.assertTrue("The reactant" in str(w[-1].message))
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
#Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
def test_include_user_agent(self):
headers = self.rester.session.headers
self.assertIn("user-agent", headers, msg="Include user-agent header by default")
m = re.match(
r"pymatgen/(\d+)\.(\d+)\.(\d+) \(Python/(\d+)\.(\d)+\.(\d+) ([^\/]*)/([^\)]*)\)",
headers['user-agent'])
self.assertIsNotNone(m, msg="Unexpected user-agent value {}".format(headers['user-agent']))
self.assertEqual(m.groups()[:3], tuple(pmg_version.split(".")))
self.assertEqual(
m.groups()[3:6],
tuple(str(n) for n in (sys.version_info.major, sys.version_info.minor, sys.version_info.micro))
)
self.rester = MPRester(include_user_agent=False)
self.assertNotIn("user-agent", self.rester.session.headers, msg="user-agent header unwanted")
class MPResterTest(unittest.TestCase):
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
def tearDown(self):
warnings.resetwarnings()
def test_get_all_materials_ids_doc(self):
mids = self.rester.get_materials_ids("Al2O3")
random.shuffle(mids)
doc = self.rester.get_doc(mids.pop(0))
self.assertEqual(doc["pretty_formula"], "Al2O3")
def test_get_data(self):
props = ["energy", "energy_per_atom", "formation_energy_per_atom",
"nsites", "unit_cell_formula", "pretty_formula", "is_hubbard",
"elements", "nelements", "e_above_hull", "hubbards",
"is_compatible", "task_ids",
"density", "icsd_ids", "total_magnetization"]
# unicode literals have been reintroduced in py>3.2
expected_vals = [-191.3359011, -6.833425039285714, -2.5515769497278913,
28, {'P': 4, 'Fe': 4, 'O': 16, 'Li': 4},
"LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0,
{'Fe': 5.3, 'Li': 0.0, 'O': 0.0, 'P': 0.0}, True,
{'mp-19017', 'mp-540081', 'mp-601412'},
3.464840709092822,
[159107, 154117, 160776, 99860, 181272, 166815,
260571, 92198, 165000, 155580, 38209, 161479, 153699,
260569, 260570, 200155, 260572, 181341, 181342,
72545, 56291, 97764, 162282, 155635],
15.9996841]
for (i, prop) in enumerate(props):
if prop not in ['hubbards', 'unit_cell_formula', 'elements',
'icsd_ids', 'task_ids']:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val, places=2)
elif prop in ["elements", "icsd_ids", "task_ids"]:
upstream_vals = set(
self.rester.get_data("mp-19017", prop=prop)[0][prop])
self.assertLessEqual(set(expected_vals[i]), upstream_vals)
else:
self.assertEqual(expected_vals[i],
self.rester.get_data("mp-19017",
prop=prop)[0][prop])
props = ['structure', 'initial_structure', 'final_structure', 'entry']
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
#Test chemsys search
data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula')
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(d['unit_cell_formula']).elements).issubset(
elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_data(self):
# Test getting supported properties
self.assertNotEqual(self.rester.get_task_data("mp-30"), [])
# Test aliasing
data = self.rester.get_task_data("mp-30", "energy")
self.assertAlmostEqual(data[0]["energy"], -4.09929227, places=2)
def test_get_materials_id_from_task_id(self):
self.assertEqual(self.rester.get_materials_id_from_task_id(
"mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references('mp-123')
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = os.path.join(test_dir, 'Fe3O4.cif')
data = m.find_structure(ciffile)
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
entries = self.rester.get_entries_in_chemsys(syms)
elements = set([Element(sym) for sym in syms])
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}}
props = ['pretty_formula', 'energy']
data = self.rester.query(criteria=criteria, properties=props)
self.assertTrue(len(data) > 6)
data = self.rester.query(criteria="*2O", properties=props)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
bs_unif = self.rester.get_bandstructure_by_material_id(
"mp-2254", line_mode=False)
self.assertIsInstance(bs_unif, BandStructure)
self.assertNotIsInstance(bs_unif, BandStructureSymmLine)
def test_get_phonon_data_by_material_id(self):
bs = self.rester.get_phonon_bandstructure_by_material_id("mp-661")
self.assertIsInstance(bs, PhononBandStructureSymmLine)
dos = self.rester.get_phonon_dos_by_material_id("mp-661")
self.assertIsInstance(dos, CompletePhononDos)
ddb_str = self.rester.get_phonon_ddb_by_material_id("mp-661")
self.assertIsInstance(ddb_str, str)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure=True)
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe", compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
# test if it will retrieve the conventional unit cell of Ni
entry = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=True)
Ni = entry.structure
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Ensure energy per atom is same
primNi = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=False)
self.assertEqual(primNi.energy_per_atom, entry.energy_per_atom)
Ni = self.rester.get_structure_by_material_id(
"mp-23", conventional_unit_cell=True)
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Test case where convs are different from initial and final
th = self.rester.get_structure_by_material_id(
"mp-37", conventional_unit_cell=True)
th_entry = self.rester.get_entry_by_material_id(
"mp-37", inc_structure=True, conventional_unit_cell=True)
th_entry_initial = self.rester.get_entry_by_material_id(
"mp-37", inc_structure="initial", conventional_unit_cell=True)
self.assertEqual(th, th_entry.structure)
self.assertEqual(len(th_entry.structure), 4)
self.assertEqual(len(th_entry_initial.structure), 2)
# Test if the polymorphs of Fe are properly sorted
# by e_above_hull when sort_by_e_above_hull=True
Fe_entries = self.rester.get_entries("Fe", sort_by_e_above_hull=True)
self.assertEqual(Fe_entries[0].data["e_above_hull"], 0)
def test_get_pourbaix_entries(self):
pbx_entries = self.rester.get_pourbaix_entries(["Fe"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# Ensure entries are pourbaix compatible
pbx = PourbaixDiagram(pbx_entries)
# Try binary system
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
pbx = PourbaixDiagram(pbx_entries)
# TODO: Shyue Ping: I do not understand this test. You seem to
# be grabbing Zn-S system, but I don't see proper test for anything,
# including Na ref. This test also takes a long time.
# Test Zn-S, which has Na in reference solids
# pbx_entries = self.rester.get_pourbaix_entries(["Zn", "S"])
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
def test_submit_query_delete_snl(self):
s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
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_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates('mp-123', 5, [1, 0, 0])
substrates = [sub_dict['sub_id'] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_get_surface_data(self):
data = self.rester.get_surface_data("mp-126") # Pt
self.assertIn("surfaces", data)
surfaces = data["surfaces"]
self.assertTrue(len(surfaces) > 0)
surface = surfaces.pop()
self.assertIn("miller_index", surface)
self.assertIn("surface_energy", surface)
self.assertIn("is_reconstructed", surface)
data_inc = self.rester.get_surface_data("mp-126", inc_structures=True)
self.assertIn("structure", data_inc["surfaces"][0])
def test_get_wulff_shape(self):
ws = self.rester.get_wulff_shape("mp-126")
self.assertTrue(isinstance(ws, WulffShape))
def test_get_cohesive_energy(self):
ecoh = self.rester.get_cohesive_energy("mp-13")
self.assertTrue(ecoh, 5.04543279)
def test_get_interface_reactions(self):
kinks = self.rester.get_interface_reactions("LiCoO2", "Li3PS4")
self.assertTrue(len(kinks) > 0)
kink = kinks[0]
self.assertIn("energy", kink)
self.assertIn("ratio", kink)
self.assertIn("rxn", kink)
self.assertTrue(isinstance(kink['rxn'], Reaction))
kinks_open_O = self.rester.get_interface_reactions(
"LiCoO2", "Li3PS4", open_el="O", relative_mu=-1)
self.assertTrue(len(kinks_open_O) > 0)
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings("always", message="The reactant.+")
self.rester.get_interface_reactions("LiCoO2", "MnO9")
self.assertTrue("The reactant" in str(w[-1].message))
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
#Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
class MPResterTest(PymatgenTest):
_multiprocess_shared_ = True
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
self.rester.session.close()
def test_get_all_materials_ids_doc(self):
mids = self.rester.get_materials_ids("Al2O3")
random.shuffle(mids)
doc = self.rester.get_doc(mids.pop(0))
self.assertEqual(doc["pretty_formula"], "Al2O3")
def test_get_xas_data(self):
# Test getting XAS data
data = self.rester.get_xas_data("mp-19017", "Li")
self.assertEqual("mp-19017,Li", data["mid_and_el"])
self.assertAlmostEqual(data["spectrum"]["x"][0], 55.178, places=2)
self.assertAlmostEqual(data["spectrum"]["y"][0], 0.0164634, places=2)
def test_get_data(self):
props = {
"energy",
"energy_per_atom",
"formation_energy_per_atom",
"nsites",
"unit_cell_formula",
"pretty_formula",
"is_hubbard",
"elements",
"nelements",
"e_above_hull",
"hubbards",
"is_compatible",
"task_ids",
"density",
"icsd_ids",
"total_magnetization",
}
mpid = "mp-1143"
vals = requests.get(
f"http://legacy.materialsproject.org/materials/{mpid}/json/")
expected_vals = vals.json()
for prop in props:
if prop not in [
"hubbards",
"unit_cell_formula",
"elements",
"icsd_ids",
"task_ids",
]:
val = self.rester.get_data(mpid, prop=prop)[0][prop]
if prop in ["energy", "energy_per_atom"]:
prop = "final_" + prop
self.assertAlmostEqual(expected_vals[prop], val, 2,
f"Failed with property {prop}")
elif prop in ["elements", "icsd_ids", "task_ids"]:
upstream_vals = set(
self.rester.get_data(mpid, prop=prop)[0][prop])
self.assertLessEqual(set(expected_vals[prop]), upstream_vals)
else:
self.assertEqual(
expected_vals[prop],
self.rester.get_data(mpid, prop=prop)[0][prop],
)
props = ["structure", "initial_structure", "final_structure", "entry"]
for prop in props:
obj = self.rester.get_data(mpid, prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data(mpid, prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
# Test chemsys search
data = self.rester.get_data("Fe-Li-O", prop="unit_cell_formula")
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(
d["unit_cell_formula"]).elements).issubset(elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_materials_id_from_task_id(self):
self.assertEqual(
self.rester.get_materials_id_from_task_id("mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references("mp-123")
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = self.TEST_FILES_DIR / "Fe3O4.cif"
data = m.find_structure(str(ciffile))
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
syms2 = "Li-Fe-O"
entries = self.rester.get_entries_in_chemsys(syms)
entries2 = self.rester.get_entries_in_chemsys(syms2)
elements = {Element(sym) for sym in syms}
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
e1 = {i.entry_id for i in entries}
e2 = {i.entry_id for i in entries2}
self.assertTrue(e1 == e2)
stable_entries = self.rester.get_entries_in_chemsys(
syms, additional_criteria={"e_above_hull": {
"$lte": 0.001
}})
self.assertTrue(len(stable_entries) < len(entries))
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
# requesting via task-id instead of mp-id
self.assertWarns(Warning, self.rester.get_structure_by_material_id,
"mp-698856")
# requesting unknown mp-id
self.assertRaises(MPRestError,
self.rester.get_structure_by_material_id,
"mp-does-not-exist")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {"elements": {"$in": ["Li", "Na", "K"], "$all": ["O"]}}
props = ["pretty_formula", "energy"]
data = self.rester.query(criteria=criteria,
properties=props,
chunk_size=0)
self.assertTrue(len(data) > 6)
data = self.rester.query(criteria="*2O",
properties=props,
chunk_size=0)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_query_chunk_size(self):
criteria = {"nelements": 2, "elements": "O"}
props = ["pretty_formula"]
data1 = self.rester.query(criteria=criteria,
properties=props,
chunk_size=0)
data2 = self.rester.query(criteria=criteria,
properties=props,
chunk_size=500)
self.assertEqual({d["pretty_formula"]
for d in data1},
{d["pretty_formula"]
for d in data2})
self.assertIn("Al2O3", {d["pretty_formula"] for d in data1})
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
bs_unif = self.rester.get_bandstructure_by_material_id("mp-2254",
line_mode=False)
self.assertIsInstance(bs_unif, BandStructure)
self.assertNotIsInstance(bs_unif, BandStructureSymmLine)
def test_get_phonon_data_by_material_id(self):
bs = self.rester.get_phonon_bandstructure_by_material_id("mp-661")
self.assertIsInstance(bs, PhononBandStructureSymmLine)
dos = self.rester.get_phonon_dos_by_material_id("mp-661")
self.assertIsInstance(dos, CompletePhononDos)
ddb_str = self.rester.get_phonon_ddb_by_material_id("mp-661")
self.assertIsInstance(ddb_str, str)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure=True)
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe",
compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
# test if it will retrieve the conventional unit cell of Ni
entry = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=True)
Ni = entry.structure
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Ensure energy per atom is same
primNi = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=False)
self.assertEqual(primNi.energy_per_atom, entry.energy_per_atom)
Ni = self.rester.get_structure_by_material_id(
"mp-23", conventional_unit_cell=True)
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Test case where convs are different from initial and final
# th = self.rester.get_structure_by_material_id(
# "mp-37", conventional_unit_cell=True)
# th_entry = self.rester.get_entry_by_material_id(
# "mp-37", inc_structure=True, conventional_unit_cell=True)
# th_entry_initial = self.rester.get_entry_by_material_id(
# "mp-37", inc_structure="initial", conventional_unit_cell=True)
# self.assertEqual(th, th_entry.structure)
# self.assertEqual(len(th_entry.structure), 4)
# self.assertEqual(len(th_entry_initial.structure), 2)
# Test if the polymorphs of Fe are properly sorted
# by e_above_hull when sort_by_e_above_hull=True
Fe_entries = self.rester.get_entries("Fe", sort_by_e_above_hull=True)
self.assertEqual(Fe_entries[0].data["e_above_hull"], 0)
def test_get_pourbaix_entries(self):
# test input chemsys as a list of elements
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# test input chemsys as a string
pbx_entries = self.rester.get_pourbaix_entries("Fe-Cr")
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# fe_two_plus = [e for e in pbx_entries if e.entry_id == "ion-0"][0]
# self.assertAlmostEqual(fe_two_plus.energy, -1.12369, places=3)
#
# feo2 = [e for e in pbx_entries if e.entry_id == "mp-25332"][0]
# self.assertAlmostEqual(feo2.energy, 3.56356, places=3)
#
# # Test S, which has Na in reference solids
# pbx_entries = self.rester.get_pourbaix_entries(["S"])
# so4_two_minus = pbx_entries[9]
# self.assertAlmostEqual(so4_two_minus.energy, 0.301511, places=3)
# Ensure entries are Pourbaix compatible
PourbaixDiagram(pbx_entries)
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
# def test_submit_query_delete_snl(self):
# s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
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=f"mod_{entry.entry_id}",
))
rest_ehulls = self.rester.get_stability(modified_entries)
all_entries = entries + modified_entries
compat = MaterialsProject2020Compatibility()
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_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates("mp-123", 5, [1, 0, 0])
substrates = [sub_dict["sub_id"] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_get_surface_data(self):
data = self.rester.get_surface_data("mp-126") # Pt
one_surf = self.rester.get_surface_data("mp-129",
miller_index=[-2, -3, 1])
self.assertAlmostEqual(one_surf["surface_energy"],
2.99156963,
places=2)
self.assertArrayAlmostEqual(one_surf["miller_index"], [3, 2, 1])
self.assertIn("surfaces", data)
surfaces = data["surfaces"]
self.assertTrue(len(surfaces) > 0)
surface = surfaces.pop()
self.assertIn("miller_index", surface)
self.assertIn("surface_energy", surface)
self.assertIn("is_reconstructed", surface)
data_inc = self.rester.get_surface_data("mp-126", inc_structures=True)
self.assertIn("structure", data_inc["surfaces"][0])
def test_get_wulff_shape(self):
ws = self.rester.get_wulff_shape("mp-126")
self.assertTrue(isinstance(ws, WulffShape))
def test_get_cohesive_energy(self):
ecoh = self.rester.get_cohesive_energy("mp-13")
self.assertTrue(ecoh, 5.04543279)
def test_get_gb_data(self):
mo_gbs = self.rester.get_gb_data(chemsys="Mo")
self.assertEqual(len(mo_gbs), 10)
mo_gbs_s5 = self.rester.get_gb_data(pretty_formula="Mo", sigma=5)
self.assertEqual(len(mo_gbs_s5), 3)
mo_s3_112 = self.rester.get_gb_data(
material_id="mp-129",
sigma=3,
gb_plane=[1, -1, -2],
include_work_of_separation=True,
)
self.assertEqual(len(mo_s3_112), 1)
gb_f = mo_s3_112[0]["final_structure"]
self.assertArrayAlmostEqual(gb_f.rotation_axis, [1, 1, 0])
self.assertAlmostEqual(gb_f.rotation_angle, 109.47122, places=4)
self.assertAlmostEqual(mo_s3_112[0]["gb_energy"], 0.47965, places=2)
self.assertAlmostEqual(mo_s3_112[0]["work_of_separation"],
6.318144,
places=2)
self.assertIn("Mo24", gb_f.formula)
hcp_s7 = self.rester.get_gb_data(material_id="mp-87",
gb_plane=[0, 0, 0, 1],
include_work_of_separation=True)
self.assertAlmostEqual(hcp_s7[0]["gb_energy"], 1.12, places=2)
self.assertAlmostEqual(hcp_s7[0]["work_of_separation"], 2.47, places=2)
def test_get_interface_reactions(self):
kinks = self.rester.get_interface_reactions("LiCoO2", "Li3PS4")
self.assertTrue(len(kinks) > 0)
kink = kinks[0]
self.assertIn("energy", kink)
self.assertIn("ratio_atomic", kink)
self.assertIn("rxn", kink)
self.assertTrue(isinstance(kink["rxn"], Reaction))
kinks_open_O = self.rester.get_interface_reactions("LiCoO2",
"Li3PS4",
open_el="O",
relative_mu=-1)
self.assertTrue(len(kinks_open_O) > 0)
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings("always", message="The reactant.+")
self.rester.get_interface_reactions("LiCoO2", "MnO9")
self.assertTrue("The reactant" in str(w[-1].message))
def test_download_info(self):
material_ids = ["mvc-2970"]
task_types = [TaskType.GGA_OPT, TaskType.GGAU_UNIFORM]
file_patterns = ["vasprun*", "OUTCAR*"]
meta, urls = self.rester.get_download_info(material_ids,
task_types=task_types,
file_patterns=file_patterns)
self.assertDictEqual(
dict(meta),
{
"mvc-2970": [{
"task_id": "mp-1738602",
"task_type": "GGA+U NSCF Uniform"
}],
},
)
self.assertEqual(
urls[0],
"https://nomad-lab.eu/prod/rae/api/raw/query?file_pattern=vasprun*&file_pattern=OUTCAR*&external_id=mp"
"-1738602",
)
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, f"Failed in {c}")
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
# Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
def test_include_user_agent(self):
headers = self.rester.session.headers
self.assertIn("user-agent",
headers,
msg="Include user-agent header by default")
m = re.match(
r"pymatgen/(\d+)\.(\d+)\.(\d+)\.?(\d+)? \(Python/(\d+)\.(\d)+\.(\d+) ([^\/]*)/([^\)]*)\)",
headers["user-agent"],
)
self.assertIsNotNone(
m, msg=f"Unexpected user-agent value {headers['user-agent']}")
self.rester = MPRester(include_user_agent=False)
self.assertNotIn("user-agent",
self.rester.session.headers,
msg="user-agent header unwanted")
def test_database_version(self):
with MPRester(notify_db_version=True) as mpr:
db_version = mpr.get_database_version()
self.assertIsInstance(db_version, str)
yaml = YAML()
with open(MP_LOG_FILE) as f:
d = yaml.load(f)
self.assertEqual(d["MAPI_DB_VERSION"]["LAST_ACCESSED"], db_version)
self.assertIsInstance(d["MAPI_DB_VERSION"]["LOG"][db_version], int)
def test_pourbaix_heavy(self):
entries = self.rester.get_pourbaix_entries(["Li", "Mg", "Sn", "Pd"])
_ = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = self.rester.get_pourbaix_entries(
["Ba", "Ca", "V", "Cu", "F"])
_ = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = self.rester.get_pourbaix_entries(
["Ba", "Ca", "V", "Cu", "F", "Fe"])
_ = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = self.rester.get_pourbaix_entries(
["Na", "Ca", "Nd", "Y", "Ho", "F"])
_ = PourbaixDiagram(entries, nproc=4, filter_solids=False)
def test_pourbaix_mpr_pipeline(self):
data = self.rester.get_pourbaix_entries(["Zn"])
pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Zn": 1e-8})
pbx.find_stable_entry(10, 0)
data = self.rester.get_pourbaix_entries(["Ag", "Te"])
pbx = PourbaixDiagram(data,
filter_solids=True,
conc_dict={
"Ag": 1e-8,
"Te": 1e-8
})
self.assertEqual(len(pbx.stable_entries), 29)
test_entry = pbx.find_stable_entry(8, 2)
self.assertEqual(sorted(test_entry.entry_id), ["ion-10", "mp-499"])
# Test against ion sets with multiple equivalent ions (Bi-V regression)
entries = self.rester.get_pourbaix_entries(["Bi", "V"])
pbx = PourbaixDiagram(entries,
filter_solids=True,
conc_dict={
"Bi": 1e-8,
"V": 1e-8
})
self.assertTrue(
all([
"Bi" in entry.composition and "V" in entry.composition
for entry in pbx.all_entries
]))
class MPResterTest(PymatgenTest):
_multiprocess_shared_ = True
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
self.rester.session.close()
def test_get_all_materials_ids_doc(self):
mids = self.rester.get_materials_ids("Al2O3")
random.shuffle(mids)
doc = self.rester.get_doc(mids.pop(0))
self.assertEqual(doc["pretty_formula"], "Al2O3")
def test_get_xas_data(self):
# Test getting XAS data
data = self.rester.get_xas_data("mp-19017", "Li")
self.assertEqual("mp-19017,Li", data["mid_and_el"])
self.assertAlmostEqual(data["spectrum"]["x"][0], 55.178, places=2)
self.assertAlmostEqual(data["spectrum"]["y"][0], 0.0164634, places=2)
def test_get_data(self):
props = [
"energy",
"energy_per_atom",
"formation_energy_per_atom",
"nsites",
"unit_cell_formula",
"pretty_formula",
"is_hubbard",
"elements",
"nelements",
"e_above_hull",
"hubbards",
"is_compatible",
"task_ids",
"density",
"icsd_ids",
"total_magnetization",
]
expected_vals = [
-191.7661349,
-6.848790532142857,
-2.5571951564625857,
28,
{
"P": 4,
"Fe": 4,
"O": 16,
"Li": 4
},
"LiFePO4",
True,
["Li", "O", "P", "Fe"],
4,
0.0,
{
"Fe": 5.3,
"Li": 0.0,
"O": 0.0,
"P": 0.0
},
True,
{"mp-19017", "mp-540081", "mp-601412"},
3.4708958823634912,
[
159107,
154117,
160776,
99860,
181272,
166815,
260571,
92198,
165000,
155580,
38209,
161479,
153699,
260569,
260570,
200155,
260572,
181341,
181342,
72545,
56291,
97764,
162282,
155635,
],
0,
]
for (i, prop) in enumerate(props):
if prop not in [
"hubbards",
"unit_cell_formula",
"elements",
"icsd_ids",
"task_ids",
]:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val, 2,
"Failed with property %s" % prop)
elif prop in ["elements", "icsd_ids", "task_ids"]:
upstream_vals = set(
self.rester.get_data("mp-19017", prop=prop)[0][prop])
self.assertLessEqual(set(expected_vals[i]), upstream_vals)
else:
self.assertEqual(
expected_vals[i],
self.rester.get_data("mp-19017", prop=prop)[0][prop],
)
props = ["structure", "initial_structure", "final_structure", "entry"]
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
# Test chemsys search
data = self.rester.get_data("Fe-Li-O", prop="unit_cell_formula")
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(
d["unit_cell_formula"]).elements).issubset(elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
# Test getting supported properties
self.assertNotEqual(self.rester.get_task_data("mp-30"), [])
# Test aliasing
data = self.rester.get_task_data("mp-30", "energy")
self.assertAlmostEqual(data[0]["energy"], -4.09929227, places=2)
def test_get_materials_id_from_task_id(self):
self.assertEqual(
self.rester.get_materials_id_from_task_id("mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references("mp-123")
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = self.TEST_FILES_DIR / "Fe3O4.cif"
data = m.find_structure(str(ciffile))
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
syms2 = "Li-Fe-O"
entries = self.rester.get_entries_in_chemsys(syms)
entries2 = self.rester.get_entries_in_chemsys(syms2)
elements = set([Element(sym) for sym in syms])
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
e1 = set([i.entry_id for i in entries])
e2 = set([i.entry_id for i in entries2])
self.assertTrue(e1 == e2)
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
# requesting via task-id instead of mp-id
self.assertWarns(Warning, self.rester.get_structure_by_material_id,
"mp-698856")
# requesting unknown mp-id
self.assertRaises(MPRestError,
self.rester.get_structure_by_material_id,
"mp-does-not-exist")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {"elements": {"$in": ["Li", "Na", "K"], "$all": ["O"]}}
props = ["pretty_formula", "energy"]
data = self.rester.query(criteria=criteria,
properties=props,
chunk_size=0)
self.assertTrue(len(data) > 6)
data = self.rester.query(criteria="*2O",
properties=props,
chunk_size=0)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_query_chunk_size(self):
criteria = {"nelements": 2, "elements": "O"}
props = ["pretty_formula"]
data1 = self.rester.query(criteria=criteria,
properties=props,
chunk_size=0)
data2 = self.rester.query(criteria=criteria,
properties=props,
chunk_size=500)
self.assertEqual({d["pretty_formula"]
for d in data1},
{d["pretty_formula"]
for d in data2})
self.assertIn("Al2O3", {d["pretty_formula"] for d in data1})
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
bs_unif = self.rester.get_bandstructure_by_material_id("mp-2254",
line_mode=False)
self.assertIsInstance(bs_unif, BandStructure)
self.assertNotIsInstance(bs_unif, BandStructureSymmLine)
def test_get_phonon_data_by_material_id(self):
bs = self.rester.get_phonon_bandstructure_by_material_id("mp-661")
self.assertIsInstance(bs, PhononBandStructureSymmLine)
dos = self.rester.get_phonon_dos_by_material_id("mp-661")
self.assertIsInstance(dos, CompletePhononDos)
ddb_str = self.rester.get_phonon_ddb_by_material_id("mp-661")
self.assertIsInstance(ddb_str, str)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure=True)
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe",
compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
# test if it will retrieve the conventional unit cell of Ni
entry = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=True)
Ni = entry.structure
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Ensure energy per atom is same
primNi = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=False)
self.assertEqual(primNi.energy_per_atom, entry.energy_per_atom)
Ni = self.rester.get_structure_by_material_id(
"mp-23", conventional_unit_cell=True)
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Test case where convs are different from initial and final
# th = self.rester.get_structure_by_material_id(
# "mp-37", conventional_unit_cell=True)
# th_entry = self.rester.get_entry_by_material_id(
# "mp-37", inc_structure=True, conventional_unit_cell=True)
# th_entry_initial = self.rester.get_entry_by_material_id(
# "mp-37", inc_structure="initial", conventional_unit_cell=True)
# self.assertEqual(th, th_entry.structure)
# self.assertEqual(len(th_entry.structure), 4)
# self.assertEqual(len(th_entry_initial.structure), 2)
# Test if the polymorphs of Fe are properly sorted
# by e_above_hull when sort_by_e_above_hull=True
Fe_entries = self.rester.get_entries("Fe", sort_by_e_above_hull=True)
self.assertEqual(Fe_entries[0].data["e_above_hull"], 0)
def test_get_pourbaix_entries(self):
# test input chemsys as a list of elements
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# test input chemsys as a string
pbx_entries = self.rester.get_pourbaix_entries("Fe-Cr")
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
fe_two_plus = [e for e in pbx_entries if e.entry_id == "ion-0"][0]
self.assertAlmostEqual(fe_two_plus.energy,
-1.6228450214319294,
places=2)
feo2 = [e for e in pbx_entries if e.entry_id == "mp-25332"][0]
self.assertAlmostEqual(feo2.energy, 2.5523680849999995, places=2)
# Test S, which has Na in reference solids
pbx_entries = self.rester.get_pourbaix_entries(["S"])
so4_two_minus = pbx_entries[9]
self.assertAlmostEqual(so4_two_minus.energy,
0.0644980568750011,
places=2)
# Ensure entries are pourbaix compatible
PourbaixDiagram(pbx_entries)
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
# def test_submit_query_delete_snl(self):
# s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
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_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates("mp-123", 5, [1, 0, 0])
substrates = [sub_dict["sub_id"] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_get_surface_data(self):
data = self.rester.get_surface_data("mp-126") # Pt
one_surf = self.rester.get_surface_data("mp-129",
miller_index=[-2, -3, 1])
self.assertAlmostEqual(one_surf["surface_energy"],
2.99156963,
places=2)
self.assertArrayAlmostEqual(one_surf["miller_index"], [3, 2, 1])
self.assertIn("surfaces", data)
surfaces = data["surfaces"]
self.assertTrue(len(surfaces) > 0)
surface = surfaces.pop()
self.assertIn("miller_index", surface)
self.assertIn("surface_energy", surface)
self.assertIn("is_reconstructed", surface)
data_inc = self.rester.get_surface_data("mp-126", inc_structures=True)
self.assertIn("structure", data_inc["surfaces"][0])
def test_get_wulff_shape(self):
ws = self.rester.get_wulff_shape("mp-126")
self.assertTrue(isinstance(ws, WulffShape))
def test_get_cohesive_energy(self):
ecoh = self.rester.get_cohesive_energy("mp-13")
self.assertTrue(ecoh, 5.04543279)
def test_get_gb_data(self):
mo_gbs = self.rester.get_gb_data(chemsys="Mo")
self.assertEqual(len(mo_gbs), 10)
mo_gbs_s5 = self.rester.get_gb_data(pretty_formula="Mo", sigma=5)
self.assertEqual(len(mo_gbs_s5), 3)
mo_s3_112 = self.rester.get_gb_data(
material_id="mp-129",
sigma=3,
gb_plane=[1, -1, -2],
include_work_of_separation=True,
)
self.assertEqual(len(mo_s3_112), 1)
gb_f = mo_s3_112[0]["final_structure"]
self.assertArrayAlmostEqual(gb_f.rotation_axis, [1, 1, 0])
self.assertAlmostEqual(gb_f.rotation_angle, 109.47122, places=4)
self.assertAlmostEqual(mo_s3_112[0]["gb_energy"], 0.47965, places=2)
self.assertAlmostEqual(mo_s3_112[0]["work_of_separation"],
6.318144,
places=2)
self.assertIn("Mo24", gb_f.formula)
hcp_s7 = self.rester.get_gb_data(material_id="mp-87",
gb_plane=[0, 0, 0, 1],
include_work_of_separation=True)
self.assertAlmostEqual(hcp_s7[0]["gb_energy"], 1.12, places=2)
self.assertAlmostEqual(hcp_s7[0]["work_of_separation"], 2.47, places=2)
def test_get_interface_reactions(self):
kinks = self.rester.get_interface_reactions("LiCoO2", "Li3PS4")
self.assertTrue(len(kinks) > 0)
kink = kinks[0]
self.assertIn("energy", kink)
self.assertIn("ratio_atomic", kink)
self.assertIn("rxn", kink)
self.assertTrue(isinstance(kink["rxn"], Reaction))
kinks_open_O = self.rester.get_interface_reactions("LiCoO2",
"Li3PS4",
open_el="O",
relative_mu=-1)
self.assertTrue(len(kinks_open_O) > 0)
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings("always", message="The reactant.+")
self.rester.get_interface_reactions("LiCoO2", "MnO9")
self.assertTrue("The reactant" in str(w[-1].message))
def test_download_info(self):
material_ids = ["mp-32800", "mp-23494"]
task_types = [TaskType.GGA_OPT, TaskType.GGA_UNIFORM]
file_patterns = ["vasprun*", "OUTCAR*"]
meta, urls = self.rester.get_download_info(material_ids,
task_types=task_types,
file_patterns=file_patterns)
self.assertDictEqual(
dict(meta),
{
"mp-23494": [{
"task_id": "mp-1752825",
"task_type": "GGA NSCF Uniform"
}],
"mp-32800": [{
"task_id": "mp-739635",
"task_type": "GGA NSCF Uniform"
}],
},
)
prefix = "http://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/mp/api/raw/query?"
# previous test
# ids = 'mp-23494,mp-688563,mp-32800,mp-746913'
ids = "mp-1752825,mp-739635"
self.assertEqual(
urls[0],
f"{prefix}file_pattern=vasprun*&file_pattern=OUTCAR*&external_id={ids}",
)
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
# Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
def test_include_user_agent(self):
headers = self.rester.session.headers
self.assertIn("user-agent",
headers,
msg="Include user-agent header by default")
m = re.match(
r"pymatgen/(\d+)\.(\d+)\.(\d+)\.?(\d+)? \(Python/(\d+)\.(\d)+\.(\d+) ([^\/]*)/([^\)]*)\)",
headers["user-agent"],
)
self.assertIsNotNone(m,
msg="Unexpected user-agent value {}".format(
headers["user-agent"]))
self.rester = MPRester(include_user_agent=False)
self.assertNotIn("user-agent",
self.rester.session.headers,
msg="user-agent header unwanted")
def test_database_version(self):
with MPRester(notify_db_version=True) as mpr:
db_version = mpr.get_database_version()
self.assertIsInstance(db_version, str)
with open(SETTINGS_FILE, "rt") as f:
d = yaml.safe_load(f)
self.assertEqual(d["MAPI_DB_VERSION"]["LAST_ACCESSED"], db_version)
self.assertIsInstance(d["MAPI_DB_VERSION"]["LOG"][db_version], int)
class MaterialsEhullBuilder(AbstractBuilder):
def __init__(self, materials_write, mapi_key=None, update_all=False):
"""
Starting with an existing materials collection, adds stability information and
The Materials Project ID.
Args:
materials_write: mongodb collection for materials (write access needed)
mapi_key: (str) Materials API key (if MAPI_KEY env. var. not set)
update_all: (bool) - if true, updates all docs. If false, only updates
docs w/o a stability key
"""
self._materials = materials_write
self.mpr = MPRester(api_key=mapi_key)
self.update_all = update_all
def run(self):
logger.info("MaterialsEhullBuilder starting...")
self._build_indexes()
q = {"thermo.energy": {"$exists": True}}
if not self.update_all:
q["stability"] = {"$exists": False}
mats = [
m for m in self._materials.find(
q, {
"calc_settings": 1,
"structure": 1,
"thermo.energy": 1,
"material_id": 1
})
]
pbar = tqdm(mats)
for m in pbar:
pbar.set_description("Processing materials_id: {}".format(
m['material_id']))
try:
params = {}
for x in ["is_hubbard", "hubbards", "potcar_spec"]:
params[x] = m["calc_settings"][x]
structure = Structure.from_dict(m["structure"])
energy = m["thermo"]["energy"]
my_entry = ComputedEntry(structure.composition,
energy,
parameters=params)
# TODO: @computron This only calculates Ehull with respect to Materials Project.
# It should also account for the current database's results. -computron
self._materials.update_one({"material_id": m["material_id"]}, {
"$set": {
"stability": self.mpr.get_stability([my_entry])[0]
}
})
# TODO: @computron: also add additional properties like inverse hull energy?
# TODO: @computron it's better to use PD tool or reaction energy calculator
# Otherwise the compatibility schemes might have issues...one strategy might be
# use MP only to retrieve entries but compute the PD locally -computron
for el, elx in my_entry.composition.items():
entries = self.mpr.get_entries(el.symbol,
compatible_only=True)
min_e = min(
entries,
key=lambda x: x.energy_per_atom).energy_per_atom
energy -= elx * min_e
self._materials.update_one({"material_id": m["material_id"]}, {
"$set": {
"thermo.formation_energy_per_atom":
energy / structure.num_sites
}
})
mpids = self.mpr.find_structure(structure)
self._materials.update_one({"material_id": m["material_id"]},
{"$set": {
"mpids": mpids
}})
except:
import traceback
logger.exception("<---")
logger.exception(
"There was an error processing material_id: {}".format(m))
logger.exception(traceback.format_exc())
logger.exception("--->")
logger.info("MaterialsEhullBuilder finished processing.")
def reset(self):
logger.info("Resetting MaterialsEhullBuilder")
self._materials.update_many({}, {"$unset": {"stability": 1}})
self._build_indexes()
logger.info("Finished resetting MaterialsEhullBuilder")
def _build_indexes(self):
self._materials.create_index("stability.e_above_hull")
@classmethod
def from_file(cls, db_file, m="materials", **kwargs):
"""
Get a MaterialsEhullBuilder using only a db file
Args:
db_file: (str) path to db file
m: (str) name of "materials" collection
**kwargs: other parameters to feed into the builder, e.g. mapi_key
"""
db_write = get_database(db_file, admin=True)
return cls(db_write[m], **kwargs)
class MPResterTest(unittest.TestCase):
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
def tearDown(self):
warnings.resetwarnings()
def test_get_all_materials_ids_doc(self):
mids = self.rester.get_materials_ids("Al2O3")
random.shuffle(mids)
doc = self.rester.get_doc(mids.pop(0))
self.assertEqual(doc["pretty_formula"], "Al2O3")
def test_get_data(self):
props = ["energy", "energy_per_atom", "formation_energy_per_atom",
"nsites", "unit_cell_formula", "pretty_formula", "is_hubbard",
"elements", "nelements", "e_above_hull", "hubbards",
"is_compatible", "task_ids",
"density", "icsd_ids", "total_magnetization"]
# unicode literals have been reintroduced in py>3.2
expected_vals = [-191.33812137, -6.833504334642858, -2.551358929370749,
28, {k: v for k, v in {'P': 4, 'Fe': 4, 'O': 16, 'Li': 4}.items()},
"LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0,
{k: v for k, v in {'Fe': 5.3, 'Li': 0.0, 'O': 0.0, 'P': 0.0}.items()}, True,
[u'mp-601412', u'mp-19017', u'mp-796535', u'mp-797820',
u'mp-540081', u'mp-797269'],
3.4662026991351147,
[159107, 154117, 160776, 99860, 181272, 166815,
260571, 92198, 165000, 155580, 38209, 161479, 153699,
260569, 260570, 200155, 260572, 181341, 181342,
72545, 56291, 97764, 162282, 155635],
16.0002716]
for (i, prop) in enumerate(props):
if prop not in ['hubbards', 'unit_cell_formula', 'elements',
'icsd_ids', 'task_ids']:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val)
elif prop in ["elements", "icsd_ids", "task_ids"]:
self.assertEqual(set(expected_vals[i]),
set(self.rester.get_data("mp-19017",
prop=prop)[0][prop]))
else:
self.assertEqual(expected_vals[i],
self.rester.get_data("mp-19017",
prop=prop)[0][prop])
props = ['structure', 'initial_structure', 'final_structure', 'entry']
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
#Test chemsys search
data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula')
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(d['unit_cell_formula']).elements).issubset(
elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_materials_id_from_task_id(self):
self.assertEqual(self.rester.get_materials_id_from_task_id(
"mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references('mp-123')
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = os.path.join(test_dir, 'Fe3O4.cif')
data = m.find_structure(ciffile)
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
entries = self.rester.get_entries_in_chemsys(syms)
elements = set([Element(sym) for sym in syms])
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}}
props = ['pretty_formula', 'energy']
data = self.rester.query(criteria=criteria, properties=props)
self.assertTrue(len(data) > 6)
data = self.rester.query(criteria="*2O", properties=props)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
bs_unif = self.rester.get_bandstructure_by_material_id(
"mp-2254", line_mode=False)
self.assertIsInstance(bs_unif, BandStructure)
self.assertNotIsInstance(bs_unif, BandStructureSymmLine)
def test_get_phonon_data_by_material_id(self):
bs = self.rester.get_phonon_bandstructure_by_material_id("mp-661")
self.assertIsInstance(bs, PhononBandStructureSymmLine)
dos = self.rester.get_phonon_dos_by_material_id("mp-661")
self.assertIsInstance(dos, CompletePhononDos)
ddb_str = self.rester.get_phonon_ddb_by_material_id("mp-661")
self.assertIsInstance(ddb_str, str)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure=True)
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe", compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
# test if it will retrieve the conventional unit cell of Ni
entry = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=True)
Ni = entry.structure
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Ensure energy per atom is same
primNi = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=False)
self.assertEqual(primNi.energy_per_atom, entry.energy_per_atom)
Ni = self.rester.get_structure_by_material_id(
"mp-23", conventional_unit_cell=True)
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Test case where convs are different from initial and final
th = self.rester.get_structure_by_material_id(
"mp-37", conventional_unit_cell=True)
th_entry = self.rester.get_entry_by_material_id(
"mp-37", inc_structure=True, conventional_unit_cell=True)
th_entry_initial = self.rester.get_entry_by_material_id(
"mp-37", inc_structure="initial", conventional_unit_cell=True)
self.assertEqual(th, th_entry.structure)
self.assertEqual(len(th_entry.structure), 4)
self.assertEqual(len(th_entry_initial.structure), 2)
def test_get_pourbaix_entries(self):
pbx_entries = self.rester.get_pourbaix_entries(["Fe"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# Ensure entries are pourbaix compatible
pbx = PourbaixDiagram(pbx_entries)
# Try binary system
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
pbx = PourbaixDiagram(pbx_entries)
# Test Zn-S, which has Na in reference solids
pbx_entries = self.rester.get_pourbaix_entries(["Zn", "S"])
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
def test_submit_query_delete_snl(self):
s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
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_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates('mp-123', 5, [1, 0, 0])
substrates = [sub_dict['sub_id'] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_get_surface_data(self):
data = self.rester.get_surface_data("mp-126") # Pt
self.assertIn("surfaces", data)
surfaces = data["surfaces"]
self.assertTrue(len(surfaces) > 0)
surface = surfaces.pop()
self.assertIn("miller_index", surface)
self.assertIn("surface_energy", surface)
self.assertIn("is_reconstructed", surface)
data_inc = self.rester.get_surface_data("mp-126", inc_structures=True)
self.assertIn("structure", data_inc["surfaces"][0])
def test_get_wulff_shape(self):
ws = self.rester.get_wulff_shape("mp-126")
self.assertTrue(isinstance(ws, WulffShape))
def test_get_interface_reactions(self):
kinks = self.rester.get_interface_reactions("LiCoO2", "Li3PS4")
self.assertTrue(len(kinks) > 0)
kink = kinks[0]
self.assertIn("energy", kink)
self.assertIn("ratio", kink)
self.assertIn("rxn", kink)
self.assertTrue(isinstance(kink['rxn'], Reaction))
kinks_open_O = self.rester.get_interface_reactions(
"LiCoO2", "Li3PS4", open_el="O", relative_mu=-1)
self.assertTrue(len(kinks_open_O) > 0)
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings("always", message="The reactant.+")
self.rester.get_interface_reactions("LiCoO2", "MnO3")
self.assertTrue("The reactant" in str(w[-1].message))
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
#Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
class MPResterTest(unittest.TestCase):
def setUp(self):
self.rester = MPRester()
def test_get_data(self):
props = ["energy", "energy_per_atom", "formation_energy_per_atom",
"nsites", "unit_cell_formula", "pretty_formula", "is_hubbard",
"elements", "nelements", "e_above_hull", "hubbards",
"is_compatible", "task_ids",
"density", "icsd_ids", "total_magnetization"]
# unicode literals have been reintroduced in py>3.2
expected_vals = [-191.33812137, -6.833504334642858, -2.551358929370749,
28, {k: v for k, v in {'P': 4, 'Fe': 4, 'O': 16, 'Li': 4}.items()},
"LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0,
{k: v for k, v in {'Fe': 5.3, 'Li': 0.0, 'O': 0.0, 'P': 0.0}.items()}, True,
[u'mp-601412', u'mp-19017', u'mp-796535', u'mp-797820',
u'mp-540081', u'mp-797269'],
3.4662026991351147,
[159107, 154117, 160776, 99860, 181272, 166815,
260571, 92198, 165000, 155580, 38209, 161479, 153699,
260569, 260570, 200155, 260572, 181341, 181342,
72545, 56291, 97764, 162282, 155635],
16.0002716]
for (i, prop) in enumerate(props):
if prop not in ['hubbards', 'unit_cell_formula', 'elements',
'icsd_ids', 'task_ids']:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val)
elif prop in ["elements", "icsd_ids", "task_ids"]:
self.assertEqual(set(expected_vals[i]),
set(self.rester.get_data("mp-19017",
prop=prop)[0][prop]))
else:
self.assertEqual(expected_vals[i],
self.rester.get_data("mp-19017",
prop=prop)[0][prop])
props = ['structure', 'initial_structure', 'final_structure', 'entry']
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
#Test chemsys search
data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula')
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(d['unit_cell_formula']).elements).issubset(
elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_materials_id_from_task_id(self):
self.assertEqual(self.rester.get_materials_id_from_task_id(
"mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references('mp-123')
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = os.path.join(test_dir, 'Fe3O4.cif')
data = m.find_structure(ciffile)
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
entries = self.rester.get_entries_in_chemsys(syms)
elements = set([Element(sym) for sym in syms])
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}}
props = ['pretty_formula', 'energy']
data = self.rester.query(criteria=criteria, properties=props)
self.assertTrue(len(data) > 6)
data = self.rester.query(criteria="*2O", properties=props)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure="final")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe", compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
def test_submit_query_delete_snl(self):
s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
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)
a = PDAnalyzer(pd)
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(a.get_e_above_hull(e),
data["e_above_hull"])
def test_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates('mp-123', 5, [1, 0, 0])
substrates = [sub_dict['sub_id'] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
#Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
class MPResterTest(unittest.TestCase):
def setUp(self):
self.rester = MPRester()
def test_get_data(self):
props = ["energy", "energy_per_atom", "formation_energy_per_atom",
"nsites", "unit_cell_formula", "pretty_formula", "is_hubbard",
"elements", "nelements", "e_above_hull", "hubbards",
"is_compatible", "task_ids",
"density", "icsd_ids", "total_magnetization"]
# unicode literals have been reintroduced in py>3.2
expected_vals = [-191.33812137, -6.833504334642858, -2.551358929370749,
28, {k: v for k, v in {'P': 4, 'Fe': 4, 'O': 16, 'Li': 4}.items()},
"LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0,
{k: v for k, v in {'Fe': 5.3, 'Li': 0.0, 'O': 0.0, 'P': 0.0}.items()}, True,
[u'mp-601412', u'mp-19017', u'mp-796535', u'mp-797820',
u'mp-540081', u'mp-797269'],
3.4662026991351147,
[159107, 154117, 160776, 99860, 181272, 166815,
260571, 92198, 165000, 155580, 38209, 161479, 153699,
260569, 260570, 200155, 260572, 181341, 181342,
72545, 56291, 97764, 162282, 155635],
16.0002716]
for (i, prop) in enumerate(props):
if prop not in ['hubbards', 'unit_cell_formula', 'elements',
'icsd_ids', 'task_ids']:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val)
elif prop in ["elements", "icsd_ids", "task_ids"]:
self.assertEqual(set(expected_vals[i]),
set(self.rester.get_data("mp-19017",
prop=prop)[0][prop]))
else:
self.assertEqual(expected_vals[i],
self.rester.get_data("mp-19017",
prop=prop)[0][prop])
props = ['structure', 'initial_structure', 'final_structure', 'entry']
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
#Test chemsys search
data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula')
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(d['unit_cell_formula']).elements).issubset(
elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_materials_id_from_task_id(self):
self.assertEqual(self.rester.get_materials_id_from_task_id(
"mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references('mp-123')
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = os.path.join(test_dir, 'Fe3O4.cif')
data = m.find_structure(ciffile)
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
entries = self.rester.get_entries_in_chemsys(syms)
elements = set([Element(sym) for sym in syms])
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}}
props = ['pretty_formula', 'energy']
data = self.rester.query(criteria=criteria, properties=props)
self.assertTrue(len(data) > 6)
data = self.rester.query(criteria="*2O", properties=props)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure="final")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe", compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
def test_submit_query_delete_snl(self):
s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
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_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates('mp-123', 5, [1, 0, 0])
substrates = [sub_dict['sub_id'] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
#Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])