def _test_from_pm(self):
"""
MPのデータをプロット
"""
ent_list = []
mpr = MPRester("WTxsDhRV7g2Mcbqw")
composition = ['Fe', 'Ni', 'Si']
entries = mpr.get_entries_in_chemsys(composition)
for entry in entries:
formula = entry.as_dict()['data']['unit_cell_formula']
formation_e = entry.as_dict()['data']['formation_energy_per_atom']
if formation_e <= 0:
single_data = []
sum_atoms = 0
for elements, index in formula.items():
sum_atoms += index
for element in composition:
try:
single_data.append(formula[element] / sum_atoms)
except KeyError:
single_data.append(0)
single_data.append(formation_e * 96.485344520851)
ent_list.append(single_data)
initial_base = [[x[0], x[1], x[3]] for x in ent_list[0:3]]
not_base = [[x[0], x[1], x[3]] for x in ent_list[3:]]
fig = pylab.figure()
ax = Axes3D(fig)
convex_hull.draw_convex_hull(ax, initial_base, not_base,
['Fe', 'Ni', 'Si'], [-60, 5],
color='magenta')
#pint(not_base)
pylab.show()
def main(comp="La0.5Sr0.5MnO3", energy=-43.3610, ostart="", oend="", ostep=""):
"""Get energy above hull for a composition
Args:
comp <str>: Composition in string form
energy <float>: Energy PER FORMULA UNIT of composition given
(Leave the following arguments blank for a non-grand potential
phase diagram.)
ostart <float>: Starting oxygen chemical potential.
oend <float>: Ending oxygen chemical potential.
ostep <float>: Step for oxygen chemical potential
Returns:
Prints to screen
"""
#a = MPRester("<YOUR_MPREST_API_KEY_HERE>")
a = MPRester("wfmUu5VSsDCvIrhz")
mycomp=Composition(comp)
print "Composition: ", mycomp
myenergy=energy
print "Energy: ", myenergy
myPDEntry = PDEntry(mycomp, myenergy)
elements = mycomp.elements
ellist = map(str, elements)
chemsys_entries = a.get_entries_in_chemsys(ellist)
#For reference: other ways of getting entries
#entries = a.mpquery(criteria={'elements':{'$in':['La','Mn'],'$all':['O']},'nelements':3})
#entries = a.mpquery(criteria={'elements':{'$in':['La','Mn','O'],'$all':['O']}},properties=['pretty_formula'])
#entries = a.get_entries_in_chemsys(['La', 'Mn', 'O', 'Sr'])
if ostart=="": #Regular phase diagram
entries = list(chemsys_entries)
entries.append(myPDEntry)
pd = PhaseDiagram(entries)
#plotter = PDPlotter(gppd)
#plotter.show()
ppda = PDAnalyzer(pd)
eabove=ppda.get_decomp_and_e_above_hull(myPDEntry)
print "Energy above hull: ", eabove[1]
print "Decomposition: ", eabove[0]
return eabove
else: #Grand potential phase diagram
orange = np.arange(ostart, oend+ostep, ostep) #add ostep because otherwise the range ends before oend
for o_chem_pot in orange:
entries = list(chemsys_entries)
myGrandPDEntry = GrandPotPDEntry(myPDEntry,{Element('O'): float(o_chem_pot)}) #need grand pot pd entry for GPPD
entries.append(myGrandPDEntry)
gppd = GrandPotentialPhaseDiagram(entries,{Element('O'): float(o_chem_pot)})
gppda = PDAnalyzer(gppd)
geabove=gppda.get_decomp_and_e_above_hull(myGrandPDEntry, True)
print "******** Decomposition for mu_O = %s eV ********" % o_chem_pot
print "%30s%1.4f" % ("mu_O: ",o_chem_pot)
print "%30s%1.4f" % ("Energy above hull (eV): ",geabove[1])
decomp=geabove[0]
#print "Decomp: ", decomp
print "%30s" % "Decomposition: "
for dkey in decomp.keys():
print "%30s:%1.4f" % (dkey.composition,decomp[dkey])
return
def create_fle_entry_ion(el_0,el_1):
"""
Creates a directory and creates 3 files:
ion_data_1: contains ion_data for el_0 relevent to Pourbaix Diagrams
ion_data_2: contains ion_data for el_1 relevent to Pourbaix Diagrams
mp_entries.txt: entry data from Materials Project
Args:
el_0: Elemental symbol (type: string) of first element
el_1: Elemental symbol (type: string) of second element
"""
fle_nme = el_0+'_'+el_1
os.makedirs(fle_nme)
os.chdir(fle_nme)
mpr = MPRester('TA7RCwHn3PGaN2m1')
if el_0==el_1:
entries = mpr.get_entries_in_chemsys([el_0, 'O', 'H'])
else:
entries = mpr.get_entries_in_chemsys([el_0, el_1, 'O', 'H'])
ion_dict_1 = mpr._make_request('/pourbaix_diagram/reference_data/'+el_0)
ion_dict_2 = mpr._make_request('/pourbaix_diagram/reference_data/'+el_1)
## Writing the Material Project entries to file ##
tmp = json.dumps(entries, cls=MontyEncoder)
f = open('mp_entries.txt','w')
f.write(tmp)
f.close()
## Writing ion data to file ##
f = open('ion_data_1.txt','w')
json.dump(ion_dict_1, f)
f.close()
f = open('ion_data_2.txt','w')
json.dump(ion_dict_2, f)
f.close()
os.chdir('..')
def _test_from_pm_volume(self):
"""
MPのデータ volume をプリント
MD 計算の初期値用
"""
ent_list = []
mpr = MPRester("WTxsDhRV7g2Mcbqw")
composition = ['Fe', 'P']
entries = mpr.get_entries_in_chemsys(composition)
for entry in entries:
if entry.as_dict()['data']['e_above_hull'] == 0:
print(entry.as_dict()['data']['pretty_formula'])
print(entry.as_dict()['data']['volume']/entry.as_dict()['data']['nsites'])
def _test_from_pm_volume(self):
"""
MPのデータ volume をプリント
MD 計算の初期値用
"""
ent_list = []
mpr = MPRester("WTxsDhRV7g2Mcbqw")
composition = ["Fe", "P"]
entries = mpr.get_entries_in_chemsys(composition)
for entry in entries:
if entry.as_dict()["data"]["e_above_hull"] == 0:
print(entry.as_dict()["data"]["pretty_formula"])
print(entry.as_dict()["data"]["volume"] / entry.as_dict()["data"]["nsites"])
def get_decomp(o_chem_pot, mycomp, verbose=1):
"""Get decomposition from open phase diagram
Args:
o_chem_pot <float>: Oxygen chemical potential
mycomp <pymatgen Composition>: Composition
verbose <int>: 1 - verbose (default)
0 - silent
Returns:
decomposition string
"""
a = MPRester("<YOUR_MPREST_API_KEY_HERE>")
elements = mycomp.elements
ellist = map(str, elements)
entries = a.get_entries_in_chemsys(ellist)
#entries = a.get_entries_in_chemsys(['La', 'Mn', 'O', 'Fe'])
pd = PhaseDiagram(entries)
gppd = GrandPotentialPhaseDiagram(entries,
{Element('O'): float(o_chem_pot)})
print gppd
#plotter = PDPlotter(gppd)
#plotter.show()
gppda = PDAnalyzer(gppd)
#mychempots = gppda.get_composition_chempots(mycomp)
#print "My chem pots:"
#print mychempots
mydecompgppd = gppda.get_decomposition(mycomp)
#pdentry = PDEntry(mycomp, 0)
#print "Decomp and energy:"
#decompandenergy = gppda.get_decomp_and_e_above_hull(pdentry)
#print decompandenergy
#mydecomppd = pda.get_decomposition(mycomp)
#print "Mn profile:"
#mnprof= gppda.get_element_profile(Element('Mn'),mycomp)
#print mnprof
if verbose:
for (entry, amount) in mydecompgppd.iteritems():
print "%s: %3.3f" % (entry.name, amount)
#mymurangegppd = gppda.getmu_range_stability_phase(Composition(entry.name),Element('O'))
#print mymurangegppd
#for (entry,amount) in mydecomppd.iteritems():
# print "%s: %3.3f" % (entry.name, amount)
print ""
return mydecompgppd
def get_decomp(o_chem_pot, mycomp, verbose=1):
"""Get decomposition from open phase diagram
Args:
o_chem_pot <float>: Oxygen chemical potential
mycomp <pymatgen Composition>: Composition
verbose <int>: 1 - verbose (default)
0 - silent
Returns:
decomposition string
"""
a = MPRester("<YOUR_MPREST_API_KEY_HERE>")
elements = mycomp.elements
ellist = map(str, elements)
entries = a.get_entries_in_chemsys(ellist)
#entries = a.get_entries_in_chemsys(['La', 'Mn', 'O', 'Fe'])
pd = PhaseDiagram(entries)
gppd = GrandPotentialPhaseDiagram(entries,{Element('O'): float(o_chem_pot)})
print gppd
#plotter = PDPlotter(gppd)
#plotter.show()
gppda = PDAnalyzer(gppd)
#mychempots = gppda.get_composition_chempots(mycomp)
#print "My chem pots:"
#print mychempots
mydecompgppd = gppda.get_decomposition(mycomp)
#pdentry = PDEntry(mycomp, 0)
#print "Decomp and energy:"
#decompandenergy = gppda.get_decomp_and_e_above_hull(pdentry)
#print decompandenergy
#mydecomppd = pda.get_decomposition(mycomp)
#print "Mn profile:"
#mnprof= gppda.get_element_profile(Element('Mn'),mycomp)
#print mnprof
if verbose:
for (entry,amount) in mydecompgppd.iteritems():
print "%s: %3.3f" % (entry.name, amount)
#mymurangegppd = gppda.getmu_range_stability_phase(Composition(entry.name),Element('O'))
#print mymurangegppd
#for (entry,amount) in mydecomppd.iteritems():
# print "%s: %3.3f" % (entry.name, amount)
print ""
return mydecompgppd
def test():
"""for test"""
#This initializes the REST adaptor. Put your own API key in.
mpr = MPRester("WTxsDhRV7g2Mcbqw")
#Entries are the basic unit for thermodynamic
#and other analyses in pymatgen.
#This gets all entries belonging to the Ca-C-O system.
composition = ['Fe', 'Ni', 'Si']
entries = mpr.get_entries_in_chemsys(composition)
# entryの内容を確認
entry = entries[0]
print(entry.as_dict())
print(entry.as_dict()['data']['volume']/6)
#With entries, you can do many sophisticated analyses,
#like creating phase diagrams.
pd = PhaseDiagram(entries) #pylint: disable=C0103
#print(dir(pd))
#print(pd.get_form_energy_per_atom(list(pd.stable_entries)[0]))
plotter = PDPlotter(pd)
def calculate_phase_stability(args):
#This initializes the REST adaptor.
a = MPRester(args.api_key)
drone = VaspToComputedEntryDrone()
entry = drone.assimilate(args.directory)
compat = MaterialsProjectCompatibility()
entry = compat.process_entry(entry)
if not entry:
print "Calculation parameters are not consistent with Materials " + \
"Project parameters."
sys.exit()
syms = [el.symbol for el in entry.composition.elements]
#This gets all entries belonging to the relevant system.
entries = a.get_entries_in_chemsys(syms)
entries.append(entry)
#Process entries with Materials Project compatibility.
entries = compat.process_entries(entries)
print [e.composition.reduced_formula for e in entries]
criteria = {prefix: {'$exists': 1}}
projection = {'{}.plotly_urls'.format(prefix): 1}
doc[cid] = mpr.query_contributions(
criteria=criteria, projection=projection,
collection='compositions', contributor_only=False
)[0]
# append spectra to output PDF
plotly_urls = doc[cid]['LBNL'][str(cid)]['plotly_urls']
for plotly_url in plotly_urls:
image_bytes = requests.get('{}.pdf'.format(plotly_url)).content
merger.append(StringIO(image_bytes))
# get phase diagram from MP and append to PDF
chemsys = ["Co", "Fe", "V"]#["Ni", "Fe", "Pt"] # alphabetic
cmap = ['Reds', 'Blues', 'Greens']
entries = mpr.get_entries_in_chemsys(chemsys)
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd)
# grid
gx, gy = [], []
n = 20
fn = float(n)
for i in range(0, n, 1):
for k in range(n-i+1, 0, -1):
j = n+1-i-k
x0, x1, x2 = i/fn, k/fn, j/fn
gx.append(x0+x2/2.) # NOTE x0 might need to be replace with x1
gy.append(x2*math.sqrt(3.)/2.)
grid_triang = tri.Triangulation(gx, gy)
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:
print(prop)
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_rest.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_rest.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)
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
def test_submit_query_delete_snl(self):
s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
def test_get_stability(self):
entries = self.rester.get_entries_in_chemsys(["Fe", "O"])
modified_entries = []
for entry in entries:
# Create modified entries with energies that are 0.01eV higher
# than the corresponding entries.
if entry.composition.reduced_formula == "Fe2O3":
modified_entries.append(
ComputedEntry(entry.composition,
entry.uncorrected_energy + 0.01,
parameters=entry.parameters,
entry_id="mod_{}".format(entry.entry_id)))
rest_ehulls = self.rester.get_stability(modified_entries)
all_entries = entries + modified_entries
compat = MaterialsProjectCompatibility()
all_entries = compat.process_entries(all_entries)
pd = PhaseDiagram(all_entries)
a = PDAnalyzer(pd)
for e in all_entries:
if str(e.entry_id).startswith("mod"):
for d in rest_ehulls:
if d["entry_id"] == e.entry_id:
data = d
break
self.assertAlmostEqual(a.get_e_above_hull(e),
data["e_above_hull"])
def test_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates('mp-123', 5, [1, 0, 0])
substrates = [sub_dict['sub_id'] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
#Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
class MPResterTest(unittest.TestCase):
def setUp(self):
self.rester = MPRester()
def test_get_data(self):
props = [
"energy", "energy_per_atom", "formation_energy_per_atom", "nsites",
"unit_cell_formula", "pretty_formula", "is_hubbard", "elements",
"nelements", "e_above_hull", "hubbards", "is_compatible",
"task_ids", "density", "icsd_ids", "total_magnetization"
]
# unicode literals have been reintroduced in py>3.2
expected_vals = [
-191.33812137, -6.833504334642858, -2.551358929370749, 28,
{k: v
for k, v in {
'P': 4,
'Fe': 4,
'O': 16,
'Li': 4
}.items()}, "LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0,
{
k: v
for k, v in {
'Fe': 5.3,
'Li': 0.0,
'O': 0.0,
'P': 0.0
}.items()
}, True,
[
u'mp-601412', u'mp-19017', u'mp-796535', u'mp-797820',
u'mp-540081', u'mp-797269'
], 3.4662026991351147,
[
159107, 154117, 160776, 99860, 181272, 166815, 260571, 92198,
165000, 155580, 38209, 161479, 153699, 260569, 260570, 200155,
260572, 181341, 181342, 72545, 56291, 97764, 162282, 155635
], 16.0002716
]
for (i, prop) in enumerate(props):
if prop not in [
'hubbards', 'unit_cell_formula', 'elements', 'icsd_ids',
'task_ids'
]:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val)
elif prop in ["elements", "icsd_ids", "task_ids"]:
self.assertEqual(
set(expected_vals[i]),
set(self.rester.get_data("mp-19017", prop=prop)[0][prop]))
else:
self.assertEqual(
expected_vals[i],
self.rester.get_data("mp-19017", prop=prop)[0][prop])
props = ['structure', 'initial_structure', 'final_structure', 'entry']
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
#Test chemsys search
data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula')
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(
d['unit_cell_formula']).elements).issubset(elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_materials_id_from_task_id(self):
self.assertEqual(
self.rester.get_materials_id_from_task_id("mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_rest.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_rest.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)
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_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
#Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
class MPResterTest(unittest.TestCase):
def setUp(self):
self.rester = MPRester()
def test_get_data(self):
props = ["energy", "energy_per_atom", "formation_energy_per_atom",
"nsites", "unit_cell_formula", "pretty_formula", "is_hubbard",
"elements", "nelements", "e_above_hull", "hubbards",
"is_compatible", "task_ids",
"density", "icsd_ids", "total_magnetization"]
expected_vals = [-191.33812137, -6.833504334642858, -2.551358929370749,
28, {u'P': 4, u'Fe': 4, u'O': 16, u'Li': 4},
"LiFePO4", True, [u'Li', u'O', u'P', u'Fe'], 4, 0.0,
{u'Fe': 5.3, u'Li': 0.0, u'O': 0.0, u'P': 0.0}, True,
['mp-540081', 'mp-601412', 'mp-19017'],
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_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
all_entries = self.rester.get_entries_in_chemsys(syms, False)
entries = self.rester.get_entries_in_chemsys(syms)
self.assertTrue(len(entries) <= len(all_entries))
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 = ['formula', 'energy']
data = self.rester.query(criteria=criteria, properties=props)
self.assertTrue(len(data) > 6)
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")
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("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 main(comp="La0.5Sr0.5MnO3", energy=-43.3610, ostart="", oend="", ostep=""):
"""Get energy above hull for a composition
Args:
comp <str>: Composition in string form
energy <float>: Energy PER FORMULA UNIT of composition given
(Leave the following arguments blank for a non-grand potential
phase diagram.)
ostart <float>: Starting oxygen chemical potential.
oend <float>: Ending oxygen chemical potential.
ostep <float>: Step for oxygen chemical potential
Returns:
Prints to screen
"""
#a = MPRester("<YOUR_MPREST_API_KEY_HERE>")
a = MPRester("wfmUu5VSsDCvIrhz")
mycomp = Composition(comp)
print "Composition: ", mycomp
myenergy = energy
print "Energy: ", myenergy
myPDEntry = PDEntry(mycomp, myenergy)
elements = mycomp.elements
ellist = map(str, elements)
chemsys_entries = a.get_entries_in_chemsys(ellist)
#For reference: other ways of getting entries
#entries = a.mpquery(criteria={'elements':{'$in':['La','Mn'],'$all':['O']},'nelements':3})
#entries = a.mpquery(criteria={'elements':{'$in':['La','Mn','O'],'$all':['O']}},properties=['pretty_formula'])
#entries = a.get_entries_in_chemsys(['La', 'Mn', 'O', 'Sr'])
if ostart == "": #Regular phase diagram
entries = list(chemsys_entries)
entries.append(myPDEntry)
pd = PhaseDiagram(entries)
#plotter = PDPlotter(gppd)
#plotter.show()
ppda = PDAnalyzer(pd)
eabove = ppda.get_decomp_and_e_above_hull(myPDEntry)
print "Energy above hull: ", eabove[1]
print "Decomposition: ", eabove[0]
return eabove
else: #Grand potential phase diagram
orange = np.arange(
ostart, oend + ostep,
ostep) #add ostep because otherwise the range ends before oend
for o_chem_pot in orange:
entries = list(chemsys_entries)
myGrandPDEntry = GrandPotPDEntry(
myPDEntry, {Element('O'): float(o_chem_pot)
}) #need grand pot pd entry for GPPD
entries.append(myGrandPDEntry)
gppd = GrandPotentialPhaseDiagram(
entries, {Element('O'): float(o_chem_pot)})
gppda = PDAnalyzer(gppd)
geabove = gppda.get_decomp_and_e_above_hull(myGrandPDEntry, True)
print "******** Decomposition for mu_O = %s eV ********" % o_chem_pot
print "%30s%1.4f" % ("mu_O: ", o_chem_pot)
print "%30s%1.4f" % ("Energy above hull (eV): ", geabove[1])
decomp = geabove[0]
#print "Decomp: ", decomp
print "%30s" % "Decomposition: "
for dkey in decomp.keys():
print "%30s:%1.4f" % (dkey.composition, decomp[dkey])
return
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_id", "total_magnetization"]
expected_vals = [-191.33812137, -6.833504334642858, -2.551358929370749,
28, {u'P': 4, u'Fe': 4, u'O': 16, u'Li': 4},
"LiFePO4", True, [u'Li', u'O', u'P', u'Fe'], 4, 0.0,
{u'Fe': 5.3, u'Li': 0.0, u'O': 0.0, u'P': 0.0}, True,
['mp-540081', 'mp-601412', 'mp-19017'],
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_id']:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val)
elif prop in ["elements", "icsd_id"]:
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_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
all_entries = self.rester.get_entries_in_chemsys(syms, False)
entries = self.rester.get_entries_in_chemsys(syms)
self.assertTrue(len(entries) <= len(all_entries))
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_mpquery(self):
criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}}
props = ['formula', 'energy']
data = self.rester.mpquery(criteria=criteria, properties=props)
self.assertTrue(len(data) > 6)
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)
for s in structs:
self.assertEqual(s.composition.reduced_formula, "Mn3O4")
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")
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("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 entry_data(mtnme_1, mtnme_2, direct_0, mprester_key):
"""
Obtaining entry and ion data from local source. If the data cannot be
found, it will do an HTTP request to the Materials Project database.
Args:
mtnme_1: Material 1
mtnme_2: Material 2
direct_0: Directory of entry database for binary systems
"""
#| - entry_data
from pymatgen.matproj.rest import MPRester # Access species in MP
import warnings; import json; from monty.json import MontyDecoder
warnings.filterwarnings('ignore') # Ignore errors related to HTTP request
mpr = MPRester(mprester_key) # REST api adaptor, INPUT
try:
direct_0 = direct_0 #INPUT#
direct = direct_0+mtnme_1+'_'+mtnme_2+'/'
entries = json.loads(open(direct+'mp_entries.txt','r').read(), cls=MontyDecoder)
ion_dict_1 = json.loads(open(direct+'ion_data_1.txt','r').read())
if not mtnme_1==mtnme_2:
ion_dict_2 = json.loads(open(direct+'ion_data_2.txt','r').read())
except:
pass
################################################################################
## Obtains all entries in MP corresponding to input element, O and H
if mtnme_1==mtnme_2:
try:
entries = entries
except:
print 'pd_make.entry_data - made http request line 64'
entries = mpr.get_entries_in_chemsys([mtnme_1, 'O', 'H'])
## Dictionary of reference state:experimental formation energy
try:
ion_dict_1 = ion_dict_1
except:
print 'pd_make.entry_data - made http request line 69'
ion_dict_1 = mpr._make_request('/pourbaix_diagram/reference_data/'+mtnme_1)
out_dict = {"entries" : entries, "ion_dict_1" : ion_dict_1}
return out_dict
if not mtnme_1==mtnme_2:
try:
entries = entries
except:
print 'pd_make.entry_data - made http request - line 146'
## Obtains all entries in MP corresponding to input element, O and H
entries = mpr.get_entries_in_chemsys([mtnme_1, mtnme_2, 'O', 'H'])
## Dictionary of reference state:experimental formation energy
try:
ion_dict_1 == ion_dict_1
ion_dict_2 == ion_dict_2
except:
print 'pd_make.entry_data - made http request - line 154'
ion_dict_1 = mpr._make_request('/pourbaix_diagram/reference_data/'+mtnme_1)
ion_dict_2 = mpr._make_request('/pourbaix_diagram/reference_data/'+mtnme_2)
out_dict = {"entries" : entries, "ion_dict_1" : ion_dict_1, "ion_dict_2" : ion_dict_2}
return out_dict
doc[cid] = mpr.query_contributions(
criteria=criteria,
projection=projection,
collection="compositions",
contributor_only=False,
)[0]
# append spectra to output PDF
plotly_urls = doc[cid]["LBNL"][str(cid)]["plotly_urls"]
for plotly_url in plotly_urls:
image_bytes = requests.get("{}.pdf".format(plotly_url)).content
merger.append(StringIO(image_bytes))
# get phase diagram from MP and append to PDF
chemsys = ["Co", "Fe", "V"] # ["Ni", "Fe", "Pt"] # alphabetic
cmap = ["Reds", "Blues", "Greens"]
entries = mpr.get_entries_in_chemsys(chemsys)
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd)
# grid
gx, gy = [], []
n = 20
fn = float(n)
for i in range(0, n, 1):
for k in range(n - i + 1, 0, -1):
j = n + 1 - i - k
x0, x1, x2 = i / fn, k / fn, j / fn
gx.append(x0 +
x2 / 2.0) # NOTE x0 might need to be replace with x1
gy.append(x2 * math.sqrt(3.0) / 2.0)
grid_triang = tri.Triangulation(gx, gy)
def __init__(self, elements):
mpr = MPRester("WTxsDhRV7g2Mcbqw")
self.elements = elements
self.entries = mpr.get_entries_in_chemsys(elements)
