def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(self.elements, self.entries) = PDEntryIO.from_csv(
os.path.join(module_dir, "pdentries_test.csv"))
self.pd = GrandPotentialPhaseDiagram(self.entries, {Element("O"): -5},
self.elements)
self.pd6 = GrandPotentialPhaseDiagram(self.entries, {Element("O"): -6})
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(self.elements, self.entries) = PDEntryIO.from_csv(
os.path.join(module_dir, "pdentries_test.csv"))
self.pd = GrandPotentialPhaseDiagram(self.entries, {Element("O"): -5},
self.elements)
self.pd6 = GrandPotentialPhaseDiagram(self.entries, {Element("O"): -6})
class GrandPotentialPhaseDiagramTest(unittest.TestCase):
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(self.elements, self.entries) = PDEntryIO.from_csv(os.path.join(module_dir,
"pdentries_test.csv"))
self.pd = GrandPotentialPhaseDiagram(self.entries, {Element("O"):-5},
self.elements)
self.pd6 = GrandPotentialPhaseDiagram(self.entries, {Element("O"):-6})
def test_stable_entries(self):
stable_formulas = [ent.original_entry.composition.reduced_formula
for ent in self.pd.stable_entries]
expected_stable = ['Li5FeO4', 'Li2FeO3', 'LiFeO2', 'Fe2O3', 'Li2O2']
for formula in expected_stable:
self.assertTrue(formula in stable_formulas, formula +
" not in stable entries!")
self.assertEqual(len(self.pd6.stable_entries), 4)
def test_get_formation_energy(self):
stable_formation_energies = {ent.original_entry.composition.reduced_formula:self.pd.get_form_energy(ent) for ent in self.pd.stable_entries}
expected_formation_energies = {'Fe2O3': 0.0,
'Li5FeO4':-5.305515040000046,
'Li2FeO3':-2.3424741500000152,
'LiFeO2':-0.43026396250000154,
'Li2O2': 0.0}
for formula, energy in expected_formation_energies.items():
self.assertAlmostEqual(energy, stable_formation_energies[formula],
7, "Calculated formation for " +
formula + " is not correct!")
def test_str(self):
self.assertIsNotNone(str(self.pd))
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
class GrandPotentialPhaseDiagramTest(unittest.TestCase):
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(self.elements, self.entries) = PDEntryIO.from_csv(
os.path.join(module_dir, "pdentries_test.csv"))
self.pd = GrandPotentialPhaseDiagram(self.entries, {Element("O"): -5},
self.elements)
self.pd6 = GrandPotentialPhaseDiagram(self.entries, {Element("O"): -6})
def test_stable_entries(self):
stable_formulas = [
ent.original_entry.composition.reduced_formula
for ent in self.pd.stable_entries
]
expected_stable = ['Li5FeO4', 'Li2FeO3', 'LiFeO2', 'Fe2O3', 'Li2O2']
for formula in expected_stable:
self.assertTrue(formula in stable_formulas,
formula + " not in stable entries!")
self.assertEqual(len(self.pd6.stable_entries), 4)
def test_get_formation_energy(self):
stable_formation_energies = {
ent.original_entry.composition.reduced_formula:
self.pd.get_form_energy(ent)
for ent in self.pd.stable_entries
}
expected_formation_energies = {
'Fe2O3': 0.0,
'Li5FeO4': -5.305515040000046,
'Li2FeO3': -2.3424741500000152,
'LiFeO2': -0.43026396250000154,
'Li2O2': 0.0
}
for formula, energy in expected_formation_energies.items():
self.assertAlmostEqual(
energy, stable_formation_energies[formula], 7,
"Calculated formation for " + formula + " is not correct!")
def test_str(self):
self.assertIsNotNone(str(self.pd))
def get_element_profile(self, element, comp, comp_tol=1e-5):
"""
Provides the element evolution data for a composition.
For example, can be used to analyze Li conversion voltages by varying
uLi and looking at the phases formed. Also can be used to analyze O2
evolution by varying uO2.
Args:
element: An element. Must be in the phase diagram.
comp: A Composition
comp_tol: The tolerance to use when calculating decompositions.
Phases with amounts less than this tolerance are excluded.
Defaults to 1e-5.
Returns:
Evolution data as a list of dictionaries of the following format:
[ {'chempot': -10.487582010000001, 'evolution': -2.0,
'reaction': Reaction Object], ...]
"""
if element not in self._pd.elements:
raise ValueError("get_transition_chempots can only be called with"
" elements in the phase diagram.")
chempots = self.get_transition_chempots(element)
stable_entries = self._pd.stable_entries
gccomp = Composition({el: amt for el, amt in comp.items()
if el != element})
elref = self._pd.el_refs[element]
elcomp = Composition(element.symbol)
prev_decomp = []
evolution = []
def are_same_decomp(decomp1, decomp2):
for comp in decomp2:
if comp not in decomp1:
return False
return True
for c in chempots:
gcpd = GrandPotentialPhaseDiagram(
stable_entries, {element: c - 1e-5}, self._pd.elements
)
analyzer = PDAnalyzer(gcpd)
gcdecomp = analyzer.get_decomposition(gccomp)
decomp = [gcentry.original_entry.composition
for gcentry, amt in gcdecomp.items()
if amt > comp_tol]
decomp_entries = [gcentry.original_entry
for gcentry, amt in gcdecomp.items()
if amt > comp_tol]
if not are_same_decomp(prev_decomp, decomp):
if elcomp not in decomp:
decomp.insert(0, elcomp)
rxn = Reaction([comp], decomp)
rxn.normalize_to(comp)
prev_decomp = decomp
amt = -rxn.coeffs[rxn.all_comp.index(elcomp)]
evolution.append({'chempot': c,
'evolution': amt,
'element_reference': elref,
'reaction': rxn, 'entries': decomp_entries})
return evolution
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