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_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 benchmark_input_scf(request):
pseudos = abidata.pseudos("14si.pspnc", "6c.pspnc", "3li.pspnc", "9f.pspnc",
"12mg.pspnc", "8o.pspnc", "31ga.pspnc", "7n.pspnc")
rest = MPRester()
structure = rest.get_structure_by_material_id(request.param)
try:
return ebands_input(structure, pseudos, kppa=100, ecut=6).split_datasets()[0]
except:
#to deal with missing pseudos
pytest.skip('Cannot create input for material {}.'.format(request.param))
def calculate_stability(self, d):
m = MPRester(self.mapi_key)
functional = d["pseudo_potential"]["functional"]
syms = ["{} {}".format(functional, l)
for l in d["pseudo_potential"]["labels"]]
entry = ComputedEntry(Composition(d["unit_cell_formula"]),
d["output"]["final_energy"],
parameters={"hubbards": d["hubbards"],
"potcar_symbols": syms})
data = m.get_stability([entry])[0]
for k in ("e_above_hull", "decomposes_to"):
d["analysis"][k] = data[k]
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 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 setUp(self):
self.rester = MPRester()
from pymatgen.ext.matproj import MPRester
from pymatgen.analysis.interface_reactions import InterfacialReactivity
from pymatgen.analysis.phase_diagram import PhaseDiagram, GrandPotentialPhaseDiagram
from pymatgen import Composition, Element
# %matplotlib inline
# Initialize the REST API interface. You may need to put your own API key in as an arg.
mpr = MPRester("NKnnBgWXU5o1S5ogiJGE")
# Chemical formulae for two solid reactants.
reactant1 = 'LiCoO2'
reactant2 = 'Li3PS4'
# Is the system open to an elemental reservoir?
grand = True
if grand:
# Element in the elemental reservoir.
open_el = 'Co'
# Relative chemical potential vs. pure substance. Must be non-positive.
relative_mu = -1
# Get the compositions of the reactants
comp1 = Composition(reactant1)
comp2 = Composition(reactant2)
# Gather all elements involved in the chemical system.
elements = [e.symbol for e in comp1.elements + comp2.elements]
if grand:
elements.append(open_el)
elements = list(set(elements)) # Remove duplicates
to generate a new material
POST https://www.materialsproject.org/rest/v2/query by
{"criteria": "{'elements':{'$in':['Li', 'Na', 'K'],
'$all': ['O']}, 'nelements':2}",
"properties": "['formula',
'formation_energy_per_atom']"}
GET or POST api_check https://www.materialsproject.org/rest/v1/api_check
API 得到数据不但可以单独处理，还可以和我们自己计算出来的数据一起处理。
比如我们要计算 Li，Fe，O 三种元素的组成的相图，
我们可以用 mp_entries = m.get_entries_in_chemsys(["Li", "Fe", "O"])得到数据库里有的数据，
还可以通过pymatgen.apps.borg.hive 里的 VaspToComputedEntryDrone 功能把自己计算的结果和数据库种的数据一起分析：
'''
import pymatgen as mg
from pymatgen.ext.matproj import MPRester
import configparser
def getMyKey():
conf = configparser.ConfigParser()
conf.read('config.ini')
return conf.get('MP_INFO', 'MY_MP_KEY')
MY_MP_KEY = getMyKey()
with MPRester(MY_MP_KEY) as m:
# structure = m.get_structure_by_material_id('C')
# dos = m.get_dos_by_material_id('C')
# bandStructure = m.get_bandstructure_by_material_id('C')
# #把mp数据库里第1234号结构的，结构数据，dos和band数据得到了，分别保存在structure, dos, bandstructure这三个变量里
data = m.get_data('Fe2O3')
# enengies = m.get_data('Fe2O3', 'energy')
print(data[0])
class mp_query(object):
def __init__(self, api_key):
self.mpr = MPRester(api_key)
def find_access_strings(self, search):
data = self.mpr.get_data(search)
material_ids = [datum['material_id'] for datum in data]
return material_ids
def mp_structure(self, material_id, standardize=True):
struct = self.mpr.get_structure_by_material_id(material_id)
if standardize:
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
return struct
def make_structures(self, search):
material_ids = self.find_access_strings(search)
structures = []
for ID in material_ids:
struct = self.mp_structure(ID)
structures.append(struct)
return structures
def search_summary(self, search, print_energies=True, barplot=False, write_files=False, format='cif'):
data = self.mpr.get_data(search)
energies = []
for datum in data:
f = datum['pretty_formula']
sn = str(datum['spacegroup']['number'])
ss = datum['spacegroup']['symbol']
i = datum['material_id']
te = float(datum['energy'])
ae = float(datum['energy_per_atom'])
struct = self.mp_structure(i, standardize=False)
ase_atoms = AseAtomsAdaptor.get_atoms(struct)
composition = ase_atoms.get_chemical_formula()
if write_files:
write(f + '_' + sn + '.' + format, ase_atoms, format=format)
energies.append((f, sn, ss, te, ae, composition))
energies.sort(key = lambda x: x[4])
if print_energies:
print('formula spacegroup_number spacegroup_symbol total_energy energy_per_atom composition')
for l in energies:
print('{:7} {:<17} {:<17} {:<12.5f} {:<15f} {:<11}'.format(*l))
if barplot:
energies = np.asarray(energies)
epa = np.array(map(float, energies[:,4]))
epa -= min(epa)
xticks = [i + '_' + j for i,j in energies[:,0:2]]
ind = np.arange(len(energies))
fig = plt.figure()
plt.ylabel('Relative energy per atom / eV')
plt.xlabel('Material')
plt.xticks(ind, xticks, rotation=90)
fig.set_size_inches(6.5,3)
plt.savefig(search + '.tiff', dpi=300, bbox_inches='tight')
from pymatgen.core.periodic_table import Element
from pymatgen.ext.matproj import MPRester
from pymatgen.analysis.phase_diagram import PhaseDiagram,PDPlotter
a = MPRester("Your API Key") #generate on Dashboard of MaterialProject
entries = a.get_entries_in_chemsys(['Ca', 'C','O'])
#generate a PhaseDiagram object
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd)
plotter.show()
#show data using the pd, a PhaseDiagram object
#all_entries(type: list):
#people who use it can query all information of the phase construction,
#which means they will get information about elements,
#components made by those elements. Taking an example of Li-Fe-O system
pd.all_entries
#elements(type:list): generate a list of elements which using in phase diagram calculation.
#Notes that elements has Element type requiring Element type from pymatgen.core.periodic_table class
pd.elements
#qhull_data(type: numpy.array): matrix contains composition data and energy data
pd.qhull_data
#Simplexes: The list of stable compositional coordinates in the phase diagram,
#which we can use to draw a phase diagram.
def compute_environments(chemenv_configuration):
string_sources = {
'cif': {
'string': 'a Cif file',
'regexp': r'.*\.cif$'
},
'mp': {
'string': 'the Materials Project database',
'regexp': r'mp-[0-9]+$'
}
}
questions = {'c': 'cif'}
questions['m'] = 'mp'
lgf = LocalGeometryFinder()
lgf.setup_parameters()
allcg = AllCoordinationGeometries()
strategy_class = strategies_class_lookup[
chemenv_configuration.package_options['default_strategy']['strategy']]
# TODO: Add the possibility to change the parameters and save them in the chemenv_configuration
default_strategy = strategy_class()
default_strategy.setup_options(
chemenv_configuration.package_options['default_strategy']
['strategy_options'])
max_dist_factor = chemenv_configuration.package_options[
'default_max_distance_factor']
firsttime = True
while True:
if len(questions) > 1:
found = False
print(
'Enter the source from which the structure is coming or <q> to quit :'
)
for key_character, qq in questions.items():
print(' - <{}> for a structure from {}'.format(
key_character, string_sources[qq]['string']))
test = input(' ... ')
if test == 'q':
break
if test not in list(questions.keys()):
for key_character, qq in questions.items():
if re.match(string_sources[qq]['regexp'],
str(test)) is not None:
found = True
source_type = qq
if not found:
print('Wrong key, try again ...')
continue
else:
source_type = questions[test]
else:
found = False
source_type = list(questions.values())[0]
if found and len(questions) > 1:
input_source = test
if source_type == 'cif':
if not found:
input_source = input('Enter path to cif file : ')
cp = CifParser(input_source)
structure = cp.get_structures()[0]
elif source_type == 'mp':
if not found:
input_source = input(
'Enter materials project id (e.g. "mp-1902") : ')
a = MPRester()
structure = a.get_structure_by_material_id(input_source)
lgf.setup_structure(structure)
print('Computing environments for {} ... '.format(
structure.composition.reduced_formula))
se = lgf.compute_structure_environments(
maximum_distance_factor=max_dist_factor)
print('Computing environments finished')
while True:
test = input(
'See list of environments determined for each (unequivalent) site ? '
'("y" or "n", "d" with details, "g" to see the grid) : ')
strategy = default_strategy
if test in ['y', 'd', 'g']:
strategy.set_structure_environments(se)
for eqslist in se.equivalent_sites:
site = eqslist[0]
isite = se.structure.index(site)
try:
if strategy.uniquely_determines_coordination_environments:
ces = strategy.get_site_coordination_environments(
site)
else:
ces = strategy.get_site_coordination_environments_fractions(
site)
except NeighborsNotComputedChemenvError:
continue
if ces is None:
continue
if len(ces) == 0:
continue
comp = site.species
# ce = strategy.get_site_coordination_environment(site)
if strategy.uniquely_determines_coordination_environments:
ce = ces[0]
if ce is None:
continue
thecg = allcg.get_geometry_from_mp_symbol(ce[0])
mystring = 'Environment for site #{} {} ({}) : {} ({})\n'.format(
str(isite),
comp.get_reduced_formula_and_factor()[0],
str(comp), thecg.name, ce[0])
else:
mystring = 'Environments for site #{} {} ({}) : \n'.format(
str(isite),
comp.get_reduced_formula_and_factor()[0],
str(comp))
for ce in ces:
cg = allcg.get_geometry_from_mp_symbol(ce[0])
csm = ce[1]['other_symmetry_measures'][
'csm_wcs_ctwcc']
mystring += ' - {} ({}): {:.2f} % (csm : {:2f})\n'.format(
cg.name, cg.mp_symbol, 100.0 * ce[2], csm)
if test in [
'd', 'g'
] and strategy.uniquely_determines_coordination_environments:
if thecg.mp_symbol != UNCLEAR_ENVIRONMENT_SYMBOL:
mystring += ' <Continuous symmetry measures> '
mingeoms = se.ce_list[isite][
thecg.
coordination_number][0].minimum_geometries()
for mingeom in mingeoms:
csm = mingeom[1]['other_symmetry_measures'][
'csm_wcs_ctwcc']
mystring += '{} : {:.2f} '.format(
mingeom[0], csm)
print(mystring)
if test == 'g':
while True:
test = input(
'Enter index of site(s) (e.g. 0 1 2, separated by spaces) for which you want to see the grid '
'of parameters : ')
try:
indices = [int(x) for x in test.split()]
print(str(indices))
for isite in indices:
if isite < 0:
raise IndexError
se.plot_environments(
isite, additional_condition=se.AC.ONLY_ACB)
break
except ValueError:
print('This is not a valid site')
except IndexError:
print('This site is out of the site range')
if no_vis:
test = input('Go to next structure ? ("y" to do so)')
if test == 'y':
break
continue
test = input(
'View structure with environments ? ("y" for the unit cell or "m" for a supercell or "n") : '
)
if test in ['y', 'm']:
if test == 'm':
mydeltas = []
while True:
try:
test = input('Enter multiplicity (e.g. 3 2 2) : ')
nns = test.split()
for i0 in range(int(nns[0])):
for i1 in range(int(nns[1])):
for i2 in range(int(nns[2])):
mydeltas.append(
np.array(
[1.0 * i0, 1.0 * i1, 1.0 * i2],
np.float))
break
except (ValueError, IndexError):
print('Not a valid multiplicity')
else:
mydeltas = [np.zeros(3, np.float)]
if firsttime:
vis = StructureVis(show_polyhedron=False,
show_unit_cell=True)
vis.show_help = False
firsttime = False
vis.set_structure(se.structure)
strategy.set_structure_environments(se)
for isite, site in enumerate(se.structure):
try:
ces = strategy.get_site_coordination_environments(site)
except NeighborsNotComputedChemenvError:
continue
if len(ces) == 0:
continue
ce = strategy.get_site_coordination_environment(site)
if ce is not None and ce[0] != UNCLEAR_ENVIRONMENT_SYMBOL:
for mydelta in mydeltas:
psite = PeriodicSite(site.species,
site.frac_coords + mydelta,
site.lattice,
properties=site.properties)
vis.add_site(psite)
neighbors = strategy.get_site_neighbors(psite)
draw_cg(vis,
psite,
neighbors,
cg=lgf.allcg.get_geometry_from_mp_symbol(
ce[0]),
perm=ce[1]['permutation'])
vis.show()
test = input('Go to next structure ? ("y" to do so) : ')
if test == 'y':
break
print('')
# import for this example
from pymatgen.core.structure import Structure
from pymatgen.core.lattice import Lattice
# create Dash app as normal
app = dash.Dash()
# create the Structure object
structure = Structure(Lattice.cubic(4.2), ["Na", "K"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
from pymatgen.ext.matproj import MPRester
# create an input structure as an example
structure_component = ctc.StructureMoleculeComponent(
MPRester().get_structure_by_material_id("mp-804"), id="structure_in")
# and a way to view the transformed structure
structure_component_transformed = ctc.StructureMoleculeComponent(
MPRester().get_structure_by_material_id("mp-804"), id="structure_out")
# and the transformation component itself
transformation_component = ctc.AllTransformationsComponent(
input_structure_component=structure_component, )
# example layout to demonstrate capabilities of component
my_layout = html.Div([
html.H1("TransformationComponent Example"),
html.H2("Standard Layout"),
transformation_component.layout(),
html.H3("Example Input Structure"),
structure_component.layout(size="500px"),
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
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://www.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, "Failed with property %s" % 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 = 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, -1.12369, 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="mod_{}".format(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 = ["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)
def test_pourbaix_heavy(self):
entries = self.rester.get_pourbaix_entries(["Li", "Mg", "Sn", "Pd"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = self.rester.get_pourbaix_entries(["Ba", "Ca", "V", "Cu", "F"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = self.rester.get_pourbaix_entries(["Ba", "Ca", "V", "Cu", "F", "Fe"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = self.rester.get_pourbaix_entries(["Na", "Ca", "Nd", "Y", "Ho", "F"])
pbx = 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]))
for label in labels:
cnts[label] += 1
print("labels:", cnts)
print("Loading Data ......")
dataset = np.load('data/crystal_structures.npz')
features = np.array(dataset['xrd'], np.float32)
property = sys.argv[1]
if property == "crystal_system":
labels = np.array(dataset['crystal_system'], int)
elif property == "space_group":
labels = np.array(dataset['space_group'], int) - 1 # 0-index
else:
mps = np.array(dataset['mp'])
m = MPRester("wdRVIWP0Sdc4Xp4pxQt")
labels = []
for mp in mps:
val = m.query(criteria={"task_id": mp}, properties=[property])
labels.append(val)
labels = np.array(labels)
print(features.shape)
print(labels.shape, min(labels), max(labels), len(set(labels)))
K = max(labels) + 1
features = features / np.amax(features, axis=1)[:, None]
analyze(K)
features, labels = shuffle(features, labels, random_state=0)
class MaterialsProjectImporter(DbImporter):
"""
Database importer for the Materials Project.
"""
_properties = 'structure'
_supported_keywords = None
def __init__(self, **kwargs):
"""
Instantiate the MaterialsProjectImporter by setting up the Materials API (MAPI)
connection details.
"""
self.setup_db(**kwargs)
def setup_db(self, **kwargs):
"""
Setup the required parameters to the REST API
"""
try:
api_key = kwargs['api_key']
except KeyError:
try:
api_key = os.environ['PMG_MAPI_KEY']
except KeyError as exception:
raise KeyError(
'API key not supplied and PMG_MAPI_KEY environment variable not set. Either pass it when '
'initializing the class, or set the environment variable PMG_MAPI_KEY to your API key.'
) from exception
api_key = None
self._api_key = api_key
self._verify_api_key()
self._mpr = MPRester(self._api_key)
def _verify_api_key(self):
"""
Verify the supplied API key by issuing a request to Materials Project.
"""
response = requests.get(
'https://www.materialsproject.org/rest/v1/api_check', headers={'X-API-KEY': self._api_key}
)
response_content = response.json() # a dict
if 'error' in response_content:
raise RuntimeError(response_content['error'])
if not response_content['valid_response']:
raise RuntimeError('Materials Project did not give a valid response for the API key check.')
if not response_content['api_key_valid']:
raise RuntimeError('Your API key for Materials Project is not valid.')
@property
def api_key(self):
"""
Return the API key configured for the importer
"""
return self._api_key
@property
def properties(self):
"""
Return the properties that will be queried
"""
return self._properties
def get_supported_keywords(self):
"""
Returns the list of all supported query keywords
:return: list of strings
"""
return self._supported_keywords
def query(self, **kwargs):
"""
Query the database with a given dictionary of query parameters for a given properties
:param query: a dictionary with the query parameters
:param properties: the properties to query
"""
try:
query = kwargs['query']
except AttributeError:
raise AttributeError(
'Make sure the supplied dictionary has `query` as a key. This '
'should contain a dictionary with the right query needed.'
)
try:
properties = kwargs['properties']
except AttributeError:
raise AttributeError('Make sure the supplied dictionary has `properties` as a key.')
if not isinstance(query, dict):
raise TypeError('The query argument should be a dictionary')
if properties is None:
properties = self._properties
if properties != 'structure':
raise ValueError(f'Unsupported properties: {properties}')
results = []
properties_list = ['material_id', 'cif']
for entry in self._find(query, properties_list):
results.append(entry)
search_results = MaterialsProjectSearchResults(results, return_class=MaterialsProjectCifEntry)
return search_results
def _find(self, query, properties):
"""
Query the database with a given dictionary of query parameters
:param query: a dictionary with the query parameters
"""
for entry in self._mpr.query(criteria=query, properties=properties):
yield entry
MessageBody(
dcc.Markdown(
"The app is running in debug mode so will be slower than usual and error "
"messages may appear."
)
),
],
kind="warning",
),
],
id="banner",
)
api_offline, api_error = True, "Unknown error connecting to Materials Project API."
try:
with MPRester() as mpr:
api_check = mpr._make_request("/api_check")
if not api_check.get("api_key_valid", False):
api_error = (
"Materials Project API key not supplied or not valid, "
"please set PMG_MAPI_KEY in your environment."
)
else:
api_offline = False
except Exception as exception:
api_error = str(exception)
if api_offline:
banner = html.Div(
[
html.Br(),
MessageContainer(
def download_mp_crystals(self, elements, api_key=None, localpath=None, format='json', indent=4):
"""
Accesses Materials Project and downloads crystal structures containing the given
elements. The structures are saved to the iprPy library as
reference_crystal records.
Parameters
----------
elements : list
A list of element symbols.
api_key : str, optional
The user's Materials Project API key. If not given, will use "MAPI_KEY"
environment variable
"""
assert format in ['json', 'xml']
# Function-specific imports
import pymatgen as pmg
from pymatgen.ext.matproj import MPRester
# Define subset generator
def subsets(fullset):
"""Yields element combination subsets"""
for i, item in enumerate(fullset):
yield [item]
if len(fullset) > 1:
for subset in subsets(fullset[i+1:]):
yield [item] + subset
# Load record style and set universal values
style = 'reference_crystal'
record = load_record(style)
input_dict = {}
input_dict['sourcename'] = "Materials Project"
input_dict['sourcelink'] = "https://materialsproject.org/"
input_dict['length_unit'] = "angstrom"
# Set library subdirectory
if localpath is None:
localpath = self.localpath
style_directory = Path(localpath, style)
if not style_directory.is_dir():
style_directory.mkdir(parents=True)
# Sort elements
elements = aslist(elements)
elements.sort()
# Build list of downloaded entries
have = []
for fname in style_directory.glob('mp-*.*'):
have.append(fname.stem)
# Open connection to Materials Project
with MPRester(api_key) as m:
# Loop over subsets of elements
for subelements in subsets(elements):
# Query MP for all entries corresponding to the elements
entries = m.query({"elements": subelements}, ["material_id"])
# Add entries to the list if not there
missing = []
for entry in entries:
if entry['material_id'] not in have and entry['material_id'] not in missing:
missing.append(entry['material_id'])
# Download missing entries
try:
entries = m.query({"material_id": {"$in": missing}}, ['material_id', 'cif'])
except:
pass
else:
# Convert cif to model and save
for entry in entries:
entry_id = entry['material_id']
struct = pmg.Structure.from_str(entry['cif'], fmt='cif')
struct = pmg.symmetry.analyzer.SpacegroupAnalyzer(struct).get_conventional_standard_structure()
# Build record content
input_dict['id'] = entry_id
input_dict['ucell'] = am.load('pymatgen_Structure', struct).normalize()
record.buildcontent(input_dict)
# Save
with open(Path(style_directory, f'{entry_id}.{format}'), 'w') as f:
if format == 'json':
record.content.json(fp=f, indent=indent)
else:
record.content.xml(fp=f, indent=indent)
print('Added', entry_id)
print(MP_all)
print(len(MP_all))
#test using small testing data
#Data=pd.read_csv('test.csv',index_col=False, sep=',')
f=open('CoulombResults_static.csv','w')
f.write('Material ID,')
for i in range(MaxAtoms):
f.write('cm%s,' %str(i))
f.write('\n')
EValFiles=np.atleast_1d(['CoulombResults_static.csv'])
CMlists=[]
with MPRester(API_Key) as mp:# Materials Project API imported
for i in range(0,len(MP_all)):
#MPName=Data['Materials ID'][i]
MPName=MP_all[i]
StructDat = mp.query(criteria={"task_id": MPName}, properties=['structure','nsites'])
#print(StructDat)
nAtoms=int(StructDat[0]['nsites'])
#print(nAtoms)
print(MPName)
#redefine the size of CMat
MaxAtoms=nAtoms+1
NuclearCharges=[]
for qq in range(0,nAtoms):
current=str(StructDat[0]['structure'].sites[qq]._species)
def get_bulk_gap_data(self):
if not self.bulk_vr:
path_to_bulk = self.defect_entry.parameters["bulk_path"]
self.bulk_vr = Vasprun( os.path.join(path_to_bulk, "vasprun.xml"))
bulk_sc_structure = self.bulk_vr.initial_structure
mpid = self.defect_entry.parameters["mpid"]
if not mpid:
try:
with MPRester() as mp:
tmp_mplist = mp.get_entries_in_chemsys(list(bulk_sc_structure.symbol_set))
mplist = [ment.entry_id for ment in tmp_mplist if ment.composition.reduced_composition == \
bulk_sc_structure.composition.reduced_composition]
except:
raise ValueError("Error with querying MPRester for {}"
"".format( bulk_sc_structure.composition.reduced_formula))
mpid_fit_list = []
for trial_mpid in mplist:
with MPRester() as mp:
mpstruct = mp.get_structure_by_material_id(trial_mpid)
if StructureMatcher(primitive_cell=True, scale=False, attempt_supercell=True,
allow_subset=False).fit(bulk_sc_structure, mpstruct):
mpid_fit_list.append( trial_mpid)
if len(mpid_fit_list) == 1:
mpid = mpid_fit_list[0]
print("Single mp-id found for bulk structure: {}.".format( mpid))
elif len(mpid_fit_list) > 1:
num_mpid_list = [int(mp.split(""-"")[1]) for mp in mpid_fit_list]
num_mpid_list.sort()
mpid = "mp-"+str(num_mpid_list[0])
print("Multiple mp-ids found for bulk structure:{}\nWill use lowest number mpid "
"for bulk band structure = {}.".format(str(mpid_fit_list), mpid))
else:
print("Could not find bulk structure in MP database after tying the "
"following list:\n{}".format( mplist))
mpid = None
else:
print("Manually fed mpid = {}".format( mpid))
vbm, cbm, bandgap = None, None, None
gap_parameters = {}
if mpid is not None:
#TODO: NEED to be smarter about use of +U or HSE etc in MP gga band structure calculations...
with MPRester() as mp:
bs = mp.get_bandstructure_by_material_id( mpid)
if bs:
cbm = bs.get_cbm()["energy"]
vbm = bs.get_vbm()["energy"]
bandgap = bs.get_band_gap()["energy"]
gap_parameters.update({"MP_gga_BScalc_data": bs.get_band_gap().copy()}) # contains gap kpt transition
if vbm is None or bandgap is None or cbm is None:
if mpid:
print("WARNING: Mpid {} was provided, but no bandstructure entry currently exists for it. "
"Reverting to use of bulk supercell calculation for band edge extrema.".format( mpid))
else:
print( "WARNING: No mp-id provided, will fetch CBM/VBM details from the "
"bulk calculation.")
print("Note that it would be better to "
"perform real band structure calculation...")
gap_parameters.update( {"MP_gga_BScalc_data": None}) #to signal no MP BS is used
bandgap, cbm, vbm, _ = self.bulk_vr.eigenvalue_band_properties
gap_parameters.update( {"mpid": mpid, "cbm": cbm, "vbm": vbm, "gap": bandgap} )
self.defect_entry.parameters.update( gap_parameters)
return
def get_mp_entries(self, full_sub_approach=False):
"""
This queries MP database for computed entries according to
input bulk and sub elements of interest
Args:
mpid (str): Structure id of the system in the MP databse.
mapi_key (str): Materials API key to access database
(if not in ~/.pmgrc.yaml already)
"""
logger = logging.getLogger(__name__)
if self.bulk_ce:
self.bulk_species_symbol = [s.symbol for s in self.bulk_ce.composition.elements]
self.redcomp = self.bulk_ce.composition.reduced_composition
bce_override = True
elif self.mpid:
with MPRester(api_key=self.mapi_key) as mp:
self.bulk_ce = mp.get_entry_by_material_id(self.mpid)
self.bulk_species_symbol = [s.symbol for s in self.bulk_ce.composition.elements]
self.redcomp = self.bulk_ce.composition.reduced_composition
bce_override = False
else:
msg = "No bulk entry OR mpid supplied. " \
"Cannot compute atomic chempots without know the bulk entry of interest."
logger.warning(msg)
raise ValueError(msg)
if full_sub_approach: #this can be time consuming if several sub species exist
species_symbols = self.bulk_species_symbol[:]
for sub_el in self.sub_species:
species_symbols.append(sub_el)
with MPRester(api_key=self.mapi_key) as mp:
self.entries['bulk_derived'] = mp.get_entries_in_chemsys(species_symbols)
self.entries['subs_set'] = {sub_el:[] for sub_el in self.sub_species}
for entry in self.entries['bulk_derived']:
for sub_el in self.sub_species:
if sub_el in entry.composition:
self.entries['subs_set'][sub_el].append(entry)
else: #this is recommended approach for running sub species seperately (assumes subs are in dilute concentrations)
with MPRester(api_key=self.mapi_key) as mp:
self.entries['bulk_derived'] = mp.get_entries_in_chemsys(self.bulk_species_symbol)
if self.mpid and bce_override: #overriding bulk_ce if mp-id is given.
self.bulk_ce = mp.get_entry_by_material_id(self.mpid)
if not self.entries:
msg = "Could not fetch bulk entries for atomic chempots!" \
"MPRester query error."
logger.warning(msg)
raise ValueError(msg)
# now compile substitution entries
self.entries['subs_set'] = dict()
bulk_entry_set = [entry.entry_id for entry in self.entries['bulk_derived']]
for sub_el in self.sub_species:
els = self.bulk_species_symbol + [sub_el]
with MPRester(api_key=self.mapi_key) as mp:
sub_entry_set = mp.get_entries_in_chemsys(els)
if not sub_entry_set:
msg = "Could not fetch sub entries for {} atomic chempots! " \
"Encountered MPRester query error".format(sub_el)
logger.warning(msg)
raise ValueError(msg)
fin_sub_entry_set = []
for entry in sub_entry_set:
if entry.entry_id not in bulk_entry_set:
fin_sub_entry_set.append(entry)
# All entries apart from the bulk entry set
self.entries['subs_set'][sub_el] = fin_sub_entry_set
return
def setUp(self):
self.rester = MPRester()
#f=open(ff,'r')
os.chdir(str(folder1))
#list_el=[]
#lines=f.readlines()
#content=(lines[3]).split(" ")
#content=(lines[3]).split("' '|\n|\r\n")
#for val in content:
# if val != '' and val !='\n' and val !='\r\n':
# list_el.append(val)
# for i in range(0,len(list_el)):
# if i!=0:
# element_ff.append(list_el[i])
# print ff,' ',element_ff
element_ff = ['C', 'H']
with MPRester(MAPI_KEY) as m:
data = m.get_entries_in_chemsys(
element_ff,
inc_structure='final',
property_data=[
"unit_cell_formula", "material_id", "icsd_id",
"spacegroup", "energy_per_atom",
"formation_energy_per_atom", "pretty_formula", "band_gap",
"total_magnetization", "e_above_hull"
])
if (len(element_ff) > 1):
try:
entries = m.get_entries_in_chemsys(element_ff)
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd, show_unstable=True)
image = str(ff) + str("_DFT") + str(".jpg")
if not os.path.exists(directory):
os.makedirs(directory)
except OSError:
print('Error: Creating directory. ' + directory)
##############################################################################
def check_convergence(directory):
v = Vasprun(directory + '/vasprun.xml')
if not v.converged:
print('Error: not converging !!')
##############################################################################
MATERIAL_API_KEY = 'your_API_key'
mpr = MPRester(MATERIAL_API_KEY)
TM_list = [
'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Y', 'Zr', 'Nb',
'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'Hf', 'Ta', 'W', 'Re', 'Os',
'Ir', 'Pt', 'Au', 'Hg'
]
alkali_elements = [
'Sr', 'Ba', 'K', 'Na', 'Li', 'Rb', 'Cs', 'Be', 'Mg', 'Ca', 'Ba', 'Si'
]
##############################################################################
# Hubbard U choice
U_dict = {
'Co': 3.32,
def get_mp_structures(elements, api_key=None, lib_directory=None):
"""
Accesses the Materials Project and downloads all structures for a list of
elements as poscar files.
Parameters
----------
elements : list
A list of element symbols.
api_key : str, optional
The user's Materials Project API key. If not given, will use "MAPI_KEY"
environment variable
lib_directory : str
Path to the lib_directory to save the poscar files to. Default uses
the iprPy library/dft_structures directory.
"""
# Function-specific imports
import pymatgen as pmg
from pymatgen.ext.matproj import MPRester
# Handle lib_directory
if lib_directory is None:
lib_directory = os.path.join(os.path.dirname(rootdir), 'library',
'ref')
lib_directory = os.path.abspath(lib_directory)
elements.sort()
# Open connection to Materials Project
with MPRester(api_key) as m:
# Loop over subsets of elements
for subelements in subsets(elements):
# Set comp_directory
elements_string = '-'.join(subelements)
comp_directory = os.path.join(lib_directory, elements_string)
if not os.path.isdir(comp_directory):
os.makedirs(comp_directory)
# Build list of downloaded entries
have = []
for fname in glob.iglob(os.path.join(comp_directory,
'mp-*.poscar')):
have.append(os.path.splitext(os.path.basename(fname))[0])
#print('Have', len(have), elements_string, 'records')
# Query MP for all entries corresponding to the elements
entries = m.query({"elements": subelements}, ["material_id"])
# Add entries to the list if not there
missing = []
for entry in entries:
if entry['material_id'] not in have and entry[
'material_id'] not in missing:
missing.append(entry['material_id'])
#print('Missing', len(missing), elements_string, 'records')
# Download missing entries
entries = m.query({"material_id": {
"$in": missing
}}, ['material_id', 'cif'])
# Convert cif to poscar and save
for entry in entries:
struct = pmg.Structure.from_str(entry['cif'], fmt='cif')
struct = pmg.symmetry.analyzer.SpacegroupAnalyzer(
struct).get_conventional_standard_structure()
system = am.load('pymatgen_Structure', struct)
system = system.normalize()
structure_file = os.path.join(comp_directory,
entry['material_id'] + '.poscar')
system.dump('poscar', f=structure_file)
print('Added', entry['material_id'])
from pymatgen.ext.matproj import MPRester
from pymatgen.apps.borg.hive import VaspToComputedEntryDrone
from pymatgen.apps.borg.queen import BorgQueen
from pymatgen.entries.compatibility import MaterialsProjectCompatibility
from pymatgen.analysis.phase_diagram import PhaseDiagram, PDPlotte
# Assimilate VASP calculations into ComputedEntry object. Let's assume that
# the calculations are for a series of new LixSnySz phases that we want to
# know the phase stability.
drone = VaspToComputedEntryDrone()
queen = BorgQueen(drone, rootpath=".")
entries = queen.get_data()
# Obtain all existing Li-Sn-S phases using the Materials Project REST API
with MPRester("Key") as m:
mp_entries = m.get_entries_in_chemsys(["Li", "Sn", "S"])
# Combined entry from calculated run with Materials Project entries
entries.extend(mp_entries)
# Process entries using the MaterialsProjectCompatibility
compat = MaterialsProjectCompatibility()
entries = compat.process_entries(entries)
# Generate and plot Li-Sn-S phase diagram
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd,
color='black',
markerfacecolor='c',
markersize=15,
MPINT_CONFIG = {}
warnings.warn('mpint_config.yaml file not configured')
#try:
# MPINT_CONFIG = loadfn('~/.mpint_config.yaml')
#except:
# MPINT_CONFIG = {}
# warnings.warn('mpint_config.yaml file not configured')
# set environ variables for MAPI_KEY and VASP_PSP_DIR
if MPINT_CONFIG.get('potentials', ''):
os.environ['PMG_VASP_PSP_DIR'] = MPINT_CONFIG.get('potentials', '')
MP_API = MPINT_CONFIG.get('mp_api', '')
if MP_API:
os.environ['MAPI_KEY'] = MP_API
MPR = MPRester(MP_API)
USERNAME = MPINT_CONFIG.get('username', None)
VASP_STD_BIN = MPINT_CONFIG.get('normal_binary', None)
VASP_TWOD_BIN = MPINT_CONFIG.get('twod_binary', None)
VASP_NCL_BIN = MPINT_CONFIG.get('ncl_binary',None)
VASP_SOL_BIN = MPINT_CONFIG.get('sol_binary',None)
VASP_CUSTOM_BIN = MPINT_CONFIG.get('custom_binary',None)
VDW_KERNEL = MPINT_CONFIG.get('vdw_kernel', None)
VASP_PSP = MPINT_CONFIG.get('potentials', None)
QUEUE_SYSTEM = MPINT_CONFIG.get('queue_system', None)
QUEUE_TEMPLATE = MPINT_CONFIG.get('queue_template', None)
if not QUEUE_SYSTEM:
QUEUE_SYSTEM = 'slurm'
def __init__(self, api_key):
self.mpr = MPRester(api_key)
s1 = pyxtal()
try:
s1.from_seed(pmg, tol=1e-3)
except:
print("wrong", pmg)
if s1.group.number == 229 and len(
s1.atom_sites) == 1 and s1.atom_sites[0].wp.multiplicity == 2:
strs = '{:20s} {:3d} {:12s} {:6.2f}'.format(
id, spg, composition.to_pretty_string(), comp)
if comp > 0.45:
strs += '+++++++'
print(strs)
print(s1.atom_sites)
mpr = MPRester('fn8WQGgT9rvZAh6H') # insert your keys here
#define your search criteria
criteria ={#"band_gap": {"$gt":0.1},
"spacegroup.number": {"$gt": 75},
"nelements": {"$in": [2, 3]},
"nsites": {"$lt": 60},
}
#choose the properties which you are interested:
properties = [
"material_id",
"band_gap",
"e_above_hull",
"structure",
"spacegroup.number",
def fetch_materials_data(root_dir):
# properties of interest
properties = [
# ID
"material_id",
"icsd_id",
"icsd_ids",
# structure
"cif",
"spacegroup",
"crystal_system",
"volume",
"nsites",
# composition
"unit_cell_formula",
"pretty_formula",
"elements",
"nelements",
# energy
"energy",
"energy_per_atom",
"formation_energy_per_atom",
"e_above_hull",
# electronic property
"band_gap",
"is_hubbard",
"hubbards",
"is_compatible",
# mechanical property
"elasticity",
"piezo",
'diel',
# other property
"density",
"total_magnetization",
# additional info
"oxide_type",
"warnings",
"task_ids",
"tags"
]
# MaterialsProject API settings
my_API_key = None # put your API key here
if not my_API_key:
print("please specify your Materials Project API key here")
sys.exit()
m = MPRester(api_key=my_API_key)
# query all materials data
query_all = m.query(criteria={}, properties=properties)
MPdata_all = pd.DataFrame(entry.values() for entry in query_all)
MPdata_all.columns = properties
# write cif to file
cif_dir = os.path.join(root_dir, "MP_cifs")
if os.path.exists(cif_dir):
_ = input("MPdata_all/MP_cifs dir already exists, press Enter to continue, Ctrl+C to terminate..")
else:
os.mkdir(cif_dir)
for _, irow in MPdata_all[["material_id", "cif"]].iterrows():
cif_file = os.path.join(cif_dir, irow["material_id"] + ".cif")
with open(cif_file, 'w') as f:
f.write(irow["cif"])
MPdata_all = MPdata_all.drop(columns=["cif"])
# materials with calculated band structures
query_band = m.query(criteria={"has": "bandstructure"},
properties=["material_id"])
band_filenames = [list(entry.values())[0] for entry in query_band]
MPdata_all['has_band_structure'] = MPdata_all["material_id"].isin(band_filenames)
# write properties to file
out_file = os.path.join(root_dir, "MPdata_all.csv")
MPdata_all.to_csv(out_file, sep=';', index=False, header=MPdata_all.columns, mode='w')
def _download(self):
"""
Downloads dataset provided it does not exist in self.path
Returns:
works (bool): true if download succeeded or file already exists
"""
if self.apikey is None:
raise AtomsDataError(
"Provide a valid API key in order to download the "
"Materials Project data!")
try:
from pymatgen.ext.matproj import MPRester
from pymatgen.core import Structure
import pymatgen as pmg
except:
raise ImportError(
"In order to download Materials Project data, you have to install "
"pymatgen")
# collect data
atms_list = []
properties_list = []
key_value_pairs_list = []
with MPRester(self.apikey) as m:
for N in range(1, 9):
for nsites in range(0, 300, 30):
ns = {"$lt": nsites + 31, "$gt": nsites}
query = m.query(
criteria={
"nelements": N,
"is_compatible": True,
"nsites": ns,
},
properties=[
"structure",
"energy_per_atom",
"formation_energy_per_atom",
"total_magnetization",
"band_gap",
"material_id",
"warnings",
"created_at",
],
)
for k, q in enumerate(query):
s = q["structure"]
if type(s) is Structure:
atms_list.append(
Atoms(
numbers=s.atomic_numbers,
positions=s.cart_coords,
cell=s.lattice.matrix,
pbc=True,
))
properties_list.append({
MaterialsProject.EPerAtom:
q["energy_per_atom"],
MaterialsProject.EformationPerAtom:
q["formation_energy_per_atom"],
MaterialsProject.TotalMagnetization:
q["total_magnetization"],
MaterialsProject.BandGap:
q["band_gap"],
})
key_value_pairs_list.append({
"material_id":
q["material_id"],
"created_at":
q["created_at"],
})
# write systems to database
self.add_systems(
atms_list,
property_list=properties_list,
key_value_pairs_list=key_value_pairs_list,
)
self.set_metadata({})
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()
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"])
def compute_environments(chemenv_configuration):
string_sources = {'cif': {'string': 'a Cif file', 'regexp': r'.*\.cif$'},
'mp': {'string': 'the Materials Project database',
'regexp': r'mp-[0-9]+$'}}
questions = {'c': 'cif'}
questions['m'] = 'mp'
lgf = LocalGeometryFinder()
lgf.setup_parameters()
allcg = AllCoordinationGeometries()
strategy_class = strategies_class_lookup[chemenv_configuration.package_options['default_strategy']['strategy']]
#TODO: Add the possibility to change the parameters and save them in the chemenv_configuration
default_strategy = strategy_class()
default_strategy.setup_options(chemenv_configuration.package_options['default_strategy']['strategy_options'])
max_dist_factor = chemenv_configuration.package_options['default_max_distance_factor']
firsttime = True
while True:
if len(questions) > 1:
found = False
print('Enter the source from which the structure is coming or <q> to quit :')
for key_character, qq in questions.items():
print(' - <{}> for a structure from {}'.format(key_character, string_sources[qq]['string']))
test = input(' ... ')
if test == 'q':
break
if test not in list(questions.keys()):
for key_character, qq in questions.items():
if re.match(string_sources[qq]['regexp'], str(test)) is not None:
found = True
source_type = qq
if not found:
print('Wrong key, try again ...')
continue
else:
source_type = questions[test]
else:
found = False
source_type = list(questions.values())[0]
if found and len(questions) > 1:
input_source = test
if source_type == 'cif':
if not found:
input_source = input('Enter path to cif file : ')
cp = CifParser(input_source)
structure = cp.get_structures()[0]
elif source_type == 'mp':
if not found:
input_source = input('Enter materials project id (e.g. "mp-1902") : ')
a = MPRester()
structure = a.get_structure_by_material_id(input_source)
lgf.setup_structure(structure)
print('Computing environments for {} ... '.format(structure.composition.reduced_formula))
se = lgf.compute_structure_environments(maximum_distance_factor=max_dist_factor)
print('Computing environments finished')
while True:
test = input('See list of environments determined for each (unequivalent) site ? '
'("y" or "n", "d" with details, "g" to see the grid) : ')
strategy = default_strategy
if test in ['y', 'd', 'g']:
strategy.set_structure_environments(se)
for eqslist in se.equivalent_sites:
site = eqslist[0]
isite = se.structure.index(site)
try:
if strategy.uniquely_determines_coordination_environments:
ces = strategy.get_site_coordination_environments(site)
else:
ces = strategy.get_site_coordination_environments_fractions(site)
except NeighborsNotComputedChemenvError:
continue
if ces is None:
continue
if len(ces) == 0:
continue
comp = site.species_and_occu
#ce = strategy.get_site_coordination_environment(site)
if strategy.uniquely_determines_coordination_environments:
ce = ces[0]
if ce is None:
continue
thecg = allcg.get_geometry_from_mp_symbol(ce[0])
mystring = 'Environment for site #{} {} ({}) : {} ({})\n'.format(str(isite),
comp.get_reduced_formula_and_factor()[0],
str(comp),
thecg.name,
ce[0])
else:
mystring = 'Environments for site #{} {} ({}) : \n'.format(str(isite),
comp.get_reduced_formula_and_factor()[0],
str(comp))
for ce in ces:
cg = allcg.get_geometry_from_mp_symbol(ce[0])
csm = ce[1]['other_symmetry_measures']['csm_wcs_ctwcc']
mystring += ' - {} ({}): {:.2f} % (csm : {:2f})\n'.format(cg.name, cg.mp_symbol,
100.0*ce[2],
csm)
if test in ['d', 'g'] and strategy.uniquely_determines_coordination_environments:
if thecg.mp_symbol != UNCLEAR_ENVIRONMENT_SYMBOL:
mystring += ' <Continuous symmetry measures> '
mingeoms = se.ce_list[isite][thecg.coordination_number][0].minimum_geometries()
for mingeom in mingeoms:
csm = mingeom[1]['other_symmetry_measures']['csm_wcs_ctwcc']
mystring += '{} : {:.2f} '.format(mingeom[0], csm)
print(mystring)
if test == 'g':
while True:
test = input('Enter index of site(s) (e.g. 0 1 2, separated by spaces) for which you want to see the grid of parameters : ')
try:
indices=[int(x) for x in test.split()]
print(str(indices))
for isite in indices:
if isite <0:
raise IndexError
se.plot_environments(isite, additional_condition=se.AC.ONLY_ACB)
break
except ValueError:
print('This is not a valid site')
except IndexError:
print('This site is out of the site range')
if no_vis:
test = input('Go to next structure ? ("y" to do so)')
if test == 'y':
break
continue
test = input('View structure with environments ? ("y" for the unit cell or "m" for a supercell or "n") : ')
if test in ['y', 'm']:
if test == 'm':
mydeltas = []
while True:
try:
test = input('Enter multiplicity (e.g. 3 2 2) : ')
nns = test.split()
for i0 in range(int(nns[0])):
for i1 in range(int(nns[1])):
for i2 in range(int(nns[2])):
mydeltas.append(np.array([1.0*i0, 1.0*i1, 1.0*i2], np.float))
break
except (ValueError,IndexError):
print('Not a valid multiplicity')
else:
mydeltas = [np.zeros(3, np.float)]
if firsttime:
vis = StructureVis(show_polyhedron=False, show_unit_cell=True)
vis.show_help = False
firsttime = False
vis.set_structure(se.structure)
strategy.set_structure_environments(se)
for isite, site in enumerate(se.structure):
try:
ces = strategy.get_site_coordination_environments(site)
except NeighborsNotComputedChemenvError:
continue
if len(ces) == 0:
continue
ce = strategy.get_site_coordination_environment(site)
if ce is not None and ce[0] != UNCLEAR_ENVIRONMENT_SYMBOL:
for mydelta in mydeltas:
psite = PeriodicSite(site._species, site._fcoords + mydelta, site._lattice,
properties=site._properties)
vis.add_site(psite)
neighbors = strategy.get_site_neighbors(psite)
draw_cg(vis, psite, neighbors, cg=lgf.allcg.get_geometry_from_mp_symbol(ce[0]),
perm=ce[1]['permutation'])
vis.show()
test = input('Go to next structure ? ("y" to do so) : ')
if test == 'y':
break
print('')
class MPResterTest(unittest.TestCase):
_multiprocess_shared_ = True
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
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,
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
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"])
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)
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"])
#!/usr/bin/env python
from pymatgen.ext.matproj import MPRester
from pymatgen.io.vasp.inputs import Poscar
import argparse as ap
from pynter.__init__ import load_config
API_KEY = load_config()['API_KEY']
with MPRester(API_KEY) as mpr:
class MPDatabase:
def __init__(self, mp_id=None):
"""
Class to retrieve data from Materials Project database
Parameters
----------
mp_id : (str), optional
Materials-ID. The default is None.
"""
self.mp_id = mp_id if mp_id else None
self.api_key = API_KEY
@property
def mp_rester(self):
return mpr
def args(self):
"""
from pymatgen.ext.matproj import MPRester #REST API的适配器
from pymatgen import Composition #可以非常灵活的处理化学元素
from pymatgen.entries.computed_entries import ComputedEntry #从数据获取的数据生成的ComputedEntries列表，主要用于管理数据的
from pymatgen.core.units import FloatWithUnit #相关化学计算的单位转换功能
from pymatgen.analysis.reaction_calculator import ComputedReaction #通过化学反应物和化学反应生成物生成化学反应的类
#This initializes the REST adaptor. Put your own API key in if necessary.
a = MPRester("S3lw1QomLO8bTiT7") #将API 秘钥输入适配器中，并且初始化适配器
#得到包含Ca.C O三种元素的所有化学式的所有条目
all_entries = a.get_entries_in_chemsys(['Ca', 'C',
'O']) #获取MP数据库中的所有ComputedEntries列表
#找出所有条目中能量最低的化学式信息
def get_most_stable_entry(formula):
relevant_entries = [
entry for entry in all_entries if entry.composition.reduced_formula ==
Composition(formula).reduced_formula
]
relevant_entries = sorted(relevant_entries,
key=lambda e: e.energy_per_atom)
return relevant_entries[0]
CaO = get_most_stable_entry("CaO")
CO2 = get_most_stable_entry("CO2")
CaCO3 = get_most_stable_entry("CaCO3")
reaction = ComputedReaction([CaO, CO2], [CaCO3]) #得到化学反应
energy = FloatWithUnit(reaction.calculated_reaction_energy,
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
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)