def __init__(self, entries, chempots, elements=None):
"""
Standard constructor for grand potential phase diagram.
Args:
entries ([PDEntry]): A list of PDEntry-like objects having an
energy, energy_per_atom and composition.
chempots {Element: float}: Specify the chemical potentials
of the open elements.
elements ([Element]): Optional list of elements in the phase
diagram. If set to None, the elements are determined from
the the entries themselves.
"""
if elements is None:
elements = set()
map(elements.update,
[entry.composition.elements for entry in entries])
self.chempots = {get_el_sp(el): u for el, u in chempots.items()}
elements = set(elements).difference(self.chempots.keys())
all_entries = [
GrandPotPDEntry(e, self.chempots) for e in entries
if (not e.is_element) or e.composition.elements[0] in elements
]
super(GrandPotentialPhaseDiagram, self).__init__(all_entries, elements)
def setUp(self):
comp = Composition("LiFeO2")
self.entry = PDEntry(comp, 53)
self.gpentry = GrandPotPDEntry(self.entry, {Element('O'): 1.5})
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
