def get_chempot_limits(self):
"""
Returns atomic chempots from bulk_composition based on data in
the materials project database. This is abstractly handled in the
ChemPotAnalyzer
Note to user: If personal phase diagram desired,
option exists in the pycdt.core.chemical_potentials to setup,
run and parse personal phase diagrams for purposes of chemical potentials
"""
logger = logging.getLogger(__name__)
if self._mpid:
cpa = MPChemPotAnalyzer( mpid = self._mpid, sub_species = self._substitution_species,
mapi_key = self._mapi_key)
else:
bulkvr = Vasprun(os.path.join( self._root_fldr, "bulk", "vasprun.xml"), parse_potcar_file=False)
if not bulkvr:
msg = "Could not fetch computed entry for atomic chempots!"
logger.warning(msg)
raise ValueError(msg)
cpa = MPChemPotAnalyzer( bulk_ce=bulkvr.get_computed_entry(),
sub_species = self._substitution_species,
mapi_key = self._mapi_key)
chem_lims = cpa.analyze_GGA_chempots()
return chem_lims
class MPChemPotAnalyzerTest(PymatgenTest):
def setUp(self):
self.MPCPA = MPChemPotAnalyzer()
def test_analyze_GGA_chempots(self):
"""
Test-cases to cover:
(0) (stable + mpid given = tested in the CPA.test_get_chempots_from_pda unit test)
(i) user's computed entry is stable w.r.t MP phase diagram; full_sub_approach = False
(ii) user's computed entry is stable w.r.t MP phase diagram (and not currently in phase diagram);
full_sub_approach = False
(iii) not stable, composition exists in list of stable comps of PD; full_sub_approach = False
(iv) not stable, composition DOESNT exists in list of stable comps of PD; full_sub_approach = False
(v) one example of full_sub_approach = True... (just do for case with user's entry being stable)
"""
with MPRester() as mp:
bulk_ce = mp.get_entry_by_material_id(
'mp-2534') #simulates an entry to play with for this unit test
#test (i) user's computed entry is stable w.r.t MP phase diagram; full_sub_approach = False
bce = copy.copy(bulk_ce)
self.MPCPA = MPChemPotAnalyzer(bulk_ce=bce,
sub_species=set(['Sb', 'In']))
cp_fsaf = self.MPCPA.analyze_GGA_chempots(full_sub_approach=False)
self.assertEqual(set([u'Ga-GaAs-GaSb-In', u'As-GaAs-InAs-SbAs']),
set(cp_fsaf.keys()))
true_answer = [
cp_fsaf['Ga-GaAs-GaSb-In'][Element(elt)]
for elt in ['Sb', 'As', 'Ga', 'In']
]
self.assertEqual([
-4.44626405, -5.352569090000001, -3.03723344, -2.7518583366666665
], true_answer)
# true_answer = [cp_fsaf['InAs-GaSb-In-GaAs'][Element(elt)] for elt in ['Sb', 'As', 'Ga', 'In']]
# self.assertEqual([-4.243837989999999, -5.15014303, -3.239659500000001, -2.72488125],
# true_answer)
# true_answer = [cp_fsaf['InAs-GaSb-Sb-GaAs'][Element(elt)] for elt in ['Sb', 'As', 'Ga', 'In']]
# self.assertEqual([-4.127761275, -5.0340663150000005, -3.3557362150000003, -2.8409579649999994],
# true_answer)
true_answer = [
cp_fsaf['As-GaAs-InAs-SbAs'][Element(elt)]
for elt in ['Sb', 'As', 'Ga', 'In']
]
self.assertEqual([
-4.1687393749999995, -4.658070555, -3.7317319750000006,
-3.2169537249999998
], true_answer)
#test (v) one example of full_sub_approach = True... (just doing for case with user's entry being stable)
cp_fsat = self.MPCPA.analyze_GGA_chempots(full_sub_approach=True)
self.assertEqual(
set([
'Ga-GaAs-GaSb-In', 'GaAs-InAs-InSb-Sb', 'GaAs-In-InAs-InSb',
'As-GaAs-InAs-SbAs', 'GaAs-GaSb-In-InSb', 'GaAs-InAs-Sb-SbAs',
'GaAs-GaSb-InSb-Sb'
]), set(cp_fsat.keys()))
true_answer = [
cp_fsat["Ga-GaAs-GaSb-In"][Element(elt)]
for elt in ['Sb', 'As', 'Ga', 'In']
]
self.assertEqual([
-4.44626405, -5.352569090000001, -3.03723344, -2.7518583366666665
], true_answer)
true_answer = [
cp_fsat["GaAs-InAs-InSb-Sb"][Element(elt)]
for elt in ['Sb', 'As', 'Ga', 'In']
]
self.assertEqual([
-4.127761275, -4.895951335, -3.4938511950000004,
-2.9790729449999995
], true_answer)
true_answer = [
cp_fsat["GaAs-In-InAs-InSb"][Element(elt)]
for elt in ['Sb', 'As', 'Ga', 'In']
]
self.assertEqual([
-4.354975883333333, -5.123165943333333, -3.2666365866666673,
-2.7518583366666665
], true_answer)
true_answer = [
cp_fsat["As-GaAs-InAs-SbAs"][Element(elt)]
for elt in ['Sb', 'As', 'Ga', 'In']
]
self.assertEqual([
-4.1687393749999995, -4.658070555, -3.7317319750000006,
-3.2169537249999998
], true_answer)
true_answer = [
cp_fsat["GaAs-GaSb-In-InSb"][Element(elt)]
for elt in ['Sb', 'As', 'Ga', 'In']
]
self.assertEqual([
-4.354975883333333, -5.2612809233333335, -3.1285216066666672,
-2.7518583366666665
], true_answer)
true_answer = [
cp_fsat["GaAs-InAs-Sb-SbAs"][Element(elt)]
for elt in ['Sb', 'As', 'Ga', 'In']
]
self.assertEqual([
-4.127761275, -4.6990486549999995, -3.6907538750000013,
-3.1759756250000004
], true_answer)
true_answer = [
cp_fsat["GaAs-GaSb-InSb-Sb"][Element(elt)]
for elt in ['Sb', 'As', 'Ga', 'In']
]
self.assertEqual([
-4.127761275, -5.0340663150000005, -3.3557362150000003,
-2.9790729449999995
], true_answer)
#test (iii) not stable, composition exists in list of stable comps of PD; full_sub_approach = False
us_bce = ComputedEntry(Composition({'Ga': 1, 'As': 1}), -8)
self.MPCPA = MPChemPotAnalyzer(bulk_ce=us_bce)
cp_fsaf_us_ce = self.MPCPA.analyze_GGA_chempots(
full_sub_approach=False)
self.assertEqual(set(['As-GaAs', 'Ga-GaAs']),
set(cp_fsaf_us_ce.keys()))
self.assertEqual(
[-4.6580705550000001, -3.7317319750000006],
[cp_fsaf_us_ce['As-GaAs'][Element(elt)] for elt in ['As', 'Ga']])
self.assertEqual(
[-5.352569090000001, -3.03723344],
[cp_fsaf_us_ce['Ga-GaAs'][Element(elt)] for elt in ['As', 'Ga']])
#test (ii) user's computed entry is stable w.r.t MP phase diagram
# AND composition DOESNT exists in list of stable comps of PD; full_sub_approach = False
s_cdne_bce = ComputedEntry(Composition({'Ga': 2, 'As': 3}), -21.5)
self.MPCPA = MPChemPotAnalyzer(bulk_ce=s_cdne_bce)
cp_fsaf_s_cdne = self.MPCPA.analyze_GGA_chempots(
full_sub_approach=False)
self.assertEqual(set(['Ga2As3-GaAs', 'As-Ga2As3']),
set(cp_fsaf_s_cdne.keys()))
for tested, answer in zip([
cp_fsaf_s_cdne['Ga2As3-GaAs'][Element(elt)]
for elt in ['As', 'Ga']
], [-4.720394939999998, -3.669407590000002]):
self.assertAlmostEqual(answer, tested)
self.assertEqual([-4.6580705550000001, -3.7628941674999994], [
cp_fsaf_s_cdne['As-Ga2As3'][Element(elt)] for elt in ['As', 'Ga']
])
#test (iv) not stable, composition DOESNT exists in list of stable comps of PD; full_sub_approach = False
# case a) simple 2D phase diagram
us_cdne_bce_a = ComputedEntry(Composition({'Ga': 2, 'As': 3}), -20.)
self.MPCPA = MPChemPotAnalyzer(bulk_ce=us_cdne_bce_a)
cp_fsaf_us_cdne_a = self.MPCPA.analyze_GGA_chempots(
full_sub_approach=False)
self.assertEqual(set(['As-GaAs']), set(cp_fsaf_us_cdne_a.keys()))
self.assertEqual([-4.658070555, -3.7317319750000006], [
cp_fsaf_us_cdne_a['As-GaAs'][Element(elt)] for elt in ['As', 'Ga']
])
# case b) larger phase diagram
us_cdne_bce_b = ComputedEntry(Composition({
'Ga': 2,
'As': 3,
'Sb': 2
}), -20.)
self.MPCPA = MPChemPotAnalyzer(bulk_ce=us_cdne_bce_b)
cp_fsaf_us_cdne_b = self.MPCPA.analyze_GGA_chempots(
full_sub_approach=False)
self.assertEqual(set(['GaAs-Sb-SbAs']), set(cp_fsaf_us_cdne_b.keys()))
self.assertEqual(
[-4.127761275, -4.6990486549999995, -3.6907538750000013], [
cp_fsaf_us_cdne_b['GaAs-Sb-SbAs'][Element(elt)]
for elt in ['Sb', 'As', 'Ga']
])
def test_get_chempots_from_composition(self):
bulk_comp = Composition("Cr2O3")
self.MPCPA = MPChemPotAnalyzer() #reinitalize
cro_cp = self.MPCPA.get_chempots_from_composition(bulk_comp)
self.assertEqual(set(['Cr2O3-CrO2', 'Cr-Cr2O3']), set(cro_cp.keys()))
self.assertAlmostEqual(-14.635303979999982,
cro_cp['Cr2O3-CrO2'][Element('Cr')])
self.assertAlmostEqual(-5.51908629500001,
cro_cp['Cr2O3-CrO2'][Element('O')])
self.assertAlmostEqual(-9.63670386, cro_cp['Cr-Cr2O3'][Element('Cr')])
self.assertAlmostEqual(-8.851486374999999,
cro_cp['Cr-Cr2O3'][Element('O')])
def test_get_mp_entries(self):
#name mp-id of GaAs system and get mp-entries...
self.MPCPA = MPChemPotAnalyzer(mpid='mp-2534')
self.MPCPA.get_mp_entries()
ents = self.MPCPA.entries
self.assertEqual(set(['bulk_derived', 'subs_set']), set(ents.keys()))
self.assertTrue(len(ents['bulk_derived']))