def test_requires_hubbard(self):
compat = MaterialsProjectCompatibility()
self.assertTrue(compat.requires_hubbard("Fe2O3"))
self.assertTrue(compat.requires_hubbard("FeSO4"))
self.assertFalse(compat.requires_hubbard("FeS2"))
self.assertFalse(compat.requires_hubbard("Li2O"))
self.assertTrue(compat.requires_hubbard("FeOF"))
def test_requires_hubbard(self):
compat = MaterialsProjectCompatibility()
self.assertTrue(compat.requires_hubbard("Fe2O3"))
self.assertTrue(compat.requires_hubbard("FeSO4"))
self.assertFalse(compat.requires_hubbard("FeS2"))
self.assertFalse(compat.requires_hubbard("Li2O"))
self.assertTrue(compat.requires_hubbard("FeOF"))
def setUp(self):
self.entry1 = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.entry2 = ComputedEntry(
'Fe3O4', -2, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.entry3 = ComputedEntry(
'FeO', -2, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 4.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.compat = MaterialsProjectCompatibility(check_potcar_hash=False)
self.ggacompat = MaterialsProjectCompatibility("GGA", check_potcar_hash=False)
def prepare_entry(structure_type, tot_e, species):
"""
Prepare entries from total energy and species.
Args:
structure_type(str): "garnet" or "perovskite"
tot_e (float): total energy in eV/f.u.
species (dict): species in dictionary.
Returns:
ce (ComputedEntry)
"""
formula = spe2form(structure_type, species)
composition = Composition(formula)
elements = [el.name for el in composition]
potcars = ["pbe %s" % CONFIG['POTCAR'][el] for el in elements]
parameters = {"potcar_symbols": list(potcars), "oxide_type": 'oxide'}
for el in elements:
if el in LDAUU:
parameters.update({"hubbards": {el: LDAUU[el]}})
ce = ComputedEntry(composition=composition,
energy=0,
parameters=parameters)
ce.uncorrected_energy = tot_e
compat = MaterialsProjectCompatibility()
ce = compat.process_entry(ce) # Correction added
return ce
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 get_mp_phase_graph():
mpr = check_apikey()
compat = MaterialsProjectCompatibility()
print("input the elements list")
wait_sep()
in_str = wait()
elements = in_str.split()
web = "materials.org"
proc_str = "Reading Data From " + web + " ..."
step_count = 1
procs(proc_str, step_count, sp='-->>')
unprocessed_entries = mpr.get_entries_in_chemsys(elements)
processed_entries = compat.process_entries(unprocessed_entries)
pd = PhaseDiagram(processed_entries)
pdp = PDPlotter(pd, show_unstable=True)
try:
pdp.show()
except:
pass
finally:
step_count += 1
filename = 'phase' + '-'.join(elements) + '.png'
proc_str = "Writing Data to " + filename + " File..."
procs(proc_str, step_count, sp='-->>')
pdp.write_image(filename)
return True
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 get_decomposed_entries(structure_type, species, oxides_table_path):
"""
Get decomposed entries for mix types
Args:one
species (dict): species in dictionary.
structure_type(str): garnet or perovskite
Returns:
decompose entries(list):
list of entries prepared from unmix
garnets/perovskite decomposed from input mix
garnet/perovskite
"""
def decomposed(specie_complex):
"""Decompose those have sub-dict to individual dict objects."""
for site, specie in specie_complex.items():
spe_copy = specie_complex.copy()
if len(specie) > 1:
for spe, amt in specie.items():
spe_copy[site] = {spe: 1}
yield spe_copy
decompose_entries = []
model, scaler, graph = load_model_and_scaler(structure_type, "unmix")
std_formula = STD_FORMULA[structure_type]
for unmix_species in decomposed(species):
charge = sum([
spe.oxi_state * amt * SITE_INFO[structure_type][site]["num_atoms"]
for site in SITE_INFO[structure_type].keys()
for spe, amt in unmix_species[site].items()
])
if not abs(charge - 2 * std_formula['O']) < 0.1:
continue
formula = spe2form(structure_type, unmix_species)
calc_entries = [entry for entry in CALC_ENTRIES[structure_type] if \
entry.name == Composition(formula).reduced_formula]
if calc_entries:
for entry in calc_entries:
decompose_entries.append(entry)
else:
descriptors = get_descriptor(structure_type, unmix_species)
with graph.as_default():
form_e = get_form_e(descriptors, model, scaler)
# tot_e = get_tote(form_e * std_formula.num_atoms, unmix_species)
tot_e = get_tote(structure_type, form_e * std_formula.num_atoms,
unmix_species, oxides_table_path)
entry = prepare_entry(structure_type, tot_e, unmix_species)
compat = MaterialsProjectCompatibility()
entry = compat.process_entry(entry)
decompose_entries.append(entry)
return decompose_entries
def get_entries(self,
chemsys_formula_id,
compatible_only=True,
inc_structure=None):
"""
Get a list of ComputedEntries or ComputedStructureEntries corresponding
to a chemical system, formula, or materials_id.
Args:
chemsys_formula_id (str): A chemical system (e.g., Li-Fe-O),
or formula (e.g., Fe2O3) or materials_id (e.g., mp-1234).
compatible_only (bool): Whether to return only "compatible"
entries. Compatible entries are entries that have been
processed using the MaterialsProjectCompatibility class,
which performs adjustments to allow mixing of GGA and GGA+U
calculations for more accurate phase diagrams and reaction
energies.
inc_structure (str): If None, entries returned are
ComputedEntries. If inc_structure="final",
ComputedStructureEntries with final structures are returned.
Otherwise, ComputedStructureEntries with initial structures
are returned.
Returns:
List of ComputedEntry or ComputedStructureEntry objects.
"""
# TODO: This is a very hackish way of doing this. It should be fixed
# on the REST end.
if compatible_only:
data = self.get_data(chemsys_formula_id, prop="entry")
entries = [d["entry"] for d in data]
if inc_structure:
for i, e in enumerate(entries):
s = self.get_structure_by_material_id(
e.entry_id, inc_structure == "final")
entries[i] = ComputedStructureEntry(
s, e.energy, e.correction, e.parameters, e.data,
e.entry_id)
entries = MaterialsProjectCompatibility().process_entries(entries)
else:
entries = []
for d in self.get_data(chemsys_formula_id, prop="task_ids"):
for i in d["task_ids"]:
e = self.get_task_data(i, prop="entry")
e = e[0]["entry"]
if inc_structure:
s = self.get_task_data(
i, prop="structure")[0]["structure"]
e = ComputedStructureEntry(s, e.energy, e.correction,
e.parameters, e.data,
e.entry_id)
entries.append(e)
return entries
def get_entries(self, chemsys_formula_id, compatible_only=True,
inc_structure=None):
"""
Get a list of ComputedEntries or ComputedStructureEntries corresponding
to a chemical system, formula, or materials_id.
Args:
chemsys_formula_id (str): A chemical system (e.g., Li-Fe-O),
or formula (e.g., Fe2O3) or materials_id (e.g., mp-1234).
compatible_only (bool): Whether to return only "compatible"
entries. Compatible entries are entries that have been
processed using the MaterialsProjectCompatibility class,
which performs adjustments to allow mixing of GGA and GGA+U
calculations for more accurate phase diagrams and reaction
energies.
inc_structure (str): If None, entries returned are
ComputedEntries. If inc_structure="final",
ComputedStructureEntries with final structures are returned.
Otherwise, ComputedStructureEntries with initial structures
are returned.
Returns:
List of ComputedEntry or ComputedStructureEntry objects.
"""
# TODO: This is a very hackish way of doing this. It should be fixed
# on the REST end.
if compatible_only:
data = self.get_data(chemsys_formula_id, prop="entry")
entries = [d["entry"] for d in data]
if inc_structure:
for i, e in enumerate(entries):
s = self.get_structure_by_material_id(
e.entry_id, inc_structure == "final")
entries[i] = ComputedStructureEntry(
s, e.energy, e.correction, e.parameters, e.data,
e.entry_id)
entries = MaterialsProjectCompatibility().process_entries(entries)
else:
entries = []
for d in self.get_data(chemsys_formula_id, prop="task_ids"):
for i in d["task_ids"]:
e = self.get_task_data(i, prop="entry")
e = e[0]["entry"]
if inc_structure:
s = self.get_task_data(i,
prop="structure")[0]["structure"]
e = ComputedStructureEntry(
s, e.energy, e.correction, e.parameters, e.data,
e.entry_id)
entries.append(e)
return entries
def test_get_explanation_dict(self):
compat = MaterialsProjectCompatibility(check_potcar_hash=False)
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel': 'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': "7a25bc5b9a5393f46600a4939d357982"}]})
d = compat.get_explanation_dict(entry)
self.assertEqual('MPRelaxSet Potcar Correction', d["corrections"][0][
"name"])
def test_get_explanation_dict(self):
compat = MaterialsProjectCompatibility(check_potcar_hash=False)
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel': 'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': "7a25bc5b9a5393f46600a4939d357982"}]})
d = compat.get_explanation_dict(entry)
self.assertEqual('MPRelaxSet Potcar Correction', d["corrections"][0][
"name"])
def getEhull(new=''):
drone = VaspToComputedEntryDrone()
queen = BorgQueen(drone, './', 4)
entriesorig = queen.get_data()
queen.load_data(
os.path.join(os.path.dirname(__file__), '../ML/data/missingels.json'))
entriesextra = queen.get_data()
if new != '':
compat = MaterialsProjectCompatibility(check_potcar=False)
entriesorig = compat.process_entries(entriesorig)
for entry in entriesorig:
name = entry.name
line = re.findall('[A-Z][^A-Z]*',
name.replace('(', '').replace(')', ''))
searchset = set(re.sub('\d', ' ', ' '.join(line)).split())
entries = filter(
lambda e: set(
re.sub('\d', ' ',
str(e.composition).replace(' ', '')).split()) == searchset,
entriesorig)
entriesextra = filter(
lambda e: set(
re.sub('\d', ' ',
str(e.composition).replace(' ', '')).split()) & searchset,
entriesextra)
a = MPRester("s2vUo6mzETOHLdbu")
all_entries = a.get_entries_in_chemsys(
set(searchset)) + list(entries) + list(entriesextra)
pd = PhaseDiagram(all_entries) #,None
for e in pd.stable_entries:
if e.entry_id == None:
reaction = pd.get_equilibrium_reaction_energy(e)
return str(reaction) + ' None'
for e in pd.unstable_entries:
decomp, e_above_hull = pd.get_decomp_and_e_above_hull(e)
pretty_decomp = [("{}:{}".format(k.composition.reduced_formula,
k.entry_id), round(v, 2))
for k, v in decomp.items()]
if e.entry_id == None:
return str(e_above_hull) + ' ' + str(pretty_decomp)
def get_ehull(structure_type,
tot_e,
species,
unmix_entries=None,
all_entries=None,
debug=False):
"""
Get Ehull predicted under given total energy and species. The composition
can be either given by the species dict(for garnet only) or a formula.
Args:
tot_e (float): total energy, the unit is in accordance with given
composition.
species (dict): species in dictionary.
unmix_entries (list): additional list of unmix entries.
Returns:
ehull (float): energy above hull.
"""
formula = spe2form(structure_type, species)
composition = Composition(formula)
unmix_entries = [] if unmix_entries is None else unmix_entries
if not all_entries:
all_entries = m.get_entries_in_chemsys([el.name for el in composition],
inc_structure=True)
all_entries = filter_entries(structure_type, all_entries, species)
all_calc_entries = [e for e in CALC_ENTRIES[structure_type]
if set(e.composition).issubset(set(composition)) \
and e.name != composition.reduced_formula]
if all_calc_entries:
all_entries = all_entries + all_calc_entries
compat = MaterialsProjectCompatibility()
all_entries = compat.process_entries(all_entries)
if not all_entries:
raise ValueError("Incomplete")
entry = prepare_entry(structure_type, tot_e, species)
if debug:
return entry, all_entries
phase_diagram = PhaseDiagram(all_entries + [entry] + unmix_entries)
return phase_diagram.get_decomp_and_e_above_hull(entry)
def __init__(self,
materials,
thermo,
query=None,
compatibility=None,
**kwargs):
"""
Calculates thermodynamic quantities for materials from phase
diagram constructions
Args:
materials (Store): Store of materials documents
thermo (Store): Store of thermodynamic data such as formation
energy and decomposition pathway
query (dict): dictionary to limit materials to be analyzed
compatibility (PymatgenCompatability): Compatability module
to ensure energies are compatible
"""
self.materials = materials
self.thermo = thermo
self.query = query if query else {}
self.compatibility = (compatibility if compatibility else
MaterialsProjectCompatibility("Advanced"))
self.completed_tasks = set()
self.entries_cache = defaultdict(list)
super().__init__(sources=[materials], targets=[thermo], **kwargs)
def __init__(self,
materials,
thermo,
query={},
compatibility=MaterialsProjectCompatibility('Advanced'),
**kwargs):
"""
Calculates thermodynamic quantities for materials from phase diagram constructions
Args:
materials (Store): Store of materials documents
thermo (Store): Store of thermodynamic data such as formation energy and decomposition pathway
query (dict): dictionary to limit materials to be analyzed
compatibility (PymatgenCompatability): Compatability module to ensure energies are compatible
"""
self.materials = materials
self.thermo = thermo
self.query = query
self.__compat = compatibility
self.__logger = logging.getLogger(__name__)
self.__logger.addHandler(logging.NullHandler())
super().__init__(sources=[materials], targets=[thermo], **kwargs)
def get_entry(doc):
"""
Helper function to get a processed computed entry from the document
Args:
doc ({}): doc from which to get the entry
Returns:
(ComputedEntry) computed entry derived from doc
"""
params = [
"run_type", "is_hubbard", "pseudo_potential", "hubbards",
"potcar_symbols", "oxide_type"
]
doc["potcar_symbols"] = [
"%s %s" % (doc["pseudo_potential"]["functional"], l)
for l in doc["pseudo_potential"]["labels"]
]
entry = ComputedEntry(doc["unit_cell_formula"],
doc["final_energy"],
parameters={k: doc[k]
for k in params},
data={"oxide_type": doc['oxide_type']},
entry_id=doc["task_id"])
entry = MaterialsProjectCompatibility().process_entries([entry])[0]
return entry
def __init__(self,
materials,
electro,
working_ion,
query=None,
compatibility=MaterialsProjectCompatibility("Advanced"),
**kwargs):
"""
Calculates physical parameters of battery materials the battery entries using
groups of ComputedStructureEntry and the entry for the most stable version of the working_ion in the system
Args:
materials (Store): Store of materials documents that contains the structures
electro (Store): Store of insertion electrodes data such as voltage and capacity
query (dict): dictionary to limit materials to be analyzed --- only applied to the materials when we need to group structures
the phase diagram is still constructed with the entire set
compatibility (PymatgenCompatability): Compatability module
to ensure energies are compatible
"""
self.sm = StructureMatcher(comparator=ElementComparator(),
primitive_cell=False)
self.materials = materials
self.electro = electro
self.working_ion = working_ion
self.query = query if query else {}
self.compatibility = compatibility
self.completed_tasks = set()
self.working_ion_entry = None
super().__init__(sources=[materials], targets=[electro], **kwargs)
def build_corrected_pd(entries):
"""build_corrected_pd
Builds a PD with entries using Mat.Proj. compatibility.
:param entries: List of ComputedEntry objects
:return: A Phase diagram object
"""
corrected = MaterialsProjectCompatibility().process_entries(entries)
return PhaseDiagram(corrected)
def get_pd(self):
"""
get the phase diagram object for this compound
Returns:
phase diagram, entry
"""
#make MP compatible entry from vasprun
entry = self.vasprun.get_computed_entry()
compat = MaterialsProjectCompatibility()
entry = compat.process_entry(entry)
el = [specie.symbol for specie in entry.composition.keys()]
with MPRester(api_key=API_KEY) as mpr:
entries = mpr.get_entries_in_chemsys(el)
entries.append(entry)
pd = PhaseDiagram(entries)
return pd, entry
def get_pd(self):
"""
get the phase diagram object
Returns:
pd: the phase diagram object
entry: entry contained in vasprun
entries: all entries used to construct the phase diagram
"""
entry = self.vasprun.get_computed_entry()
compat = MaterialsProjectCompatibility()
entry = compat.process_entry(entry)
el = [specie.symbol for specie in entry.composition.keys()]
with MPRester(api_key="64JmsIV32c8lUaxu") as mpr:
entries = mpr.get_entries_in_chemsys(el)
entries.append(entry)
pd = PhaseDiagram(entries)
return pd, entry, entries
def main():
"""
Main function.
"""
# Read the calculation results into a ComputedEntry.
entl = VaspToComputedEntryDrone().assimilate(sys.argv[1])
# Check if our local calculation is compatible with MP.
if MaterialsProjectCompatibility().process_entry(entl) is None:
print("Calculation not compatible with MP.")
sys.exit(0)
# Get other entries sharing a chemical system with the results.
chemsys = [ele for ele in entl.composition.as_dict()]
with MPRester() as mpr:
chemsys_entries = mpr.get_entries_in_chemsys(chemsys)
# Append our local calculation to the list of entries.
chemsys_entries.append(entl)
# Process the entries.
p_e = MaterialsProjectCompatibility().process_entries(chemsys_entries)
# Build a phase diagram and an analyzer for it.
p_d = PhaseDiagram(p_e)
pda = PDAnalyzer(p_d)
# Scan stable entries for our calculation.
for ent in p_d.stable_entries:
if ent.entry_id is None:
print(str(ent.composition.reduced_formula) + " 0.0")
sys.exit(0)
# Scan unstable entries for our calculation and print decomposition.
for ent in p_d.unstable_entries:
if ent.entry_id is None:
dco, ehull = pda.get_decomp_and_e_above_hull(ent)
pretty_dc = [("{}:{}".format(k.composition.reduced_formula,
k.entry_id), round(v, 2))
for k, v in dco.items()]
print(
str(ent.composition.reduced_formula) + " %.3f" % ehull + " " +
str(pretty_dc))
def test_get_corrections_dict(self):
compat = MaterialsProjectCompatibility()
ggacompat = MaterialsProjectCompatibility("GGA")
#Correct parameters
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
'PAW_PBE O 08Apr2002']})
c = compat.get_corrections_dict(entry)
self.assertAlmostEqual(c["MP Gas Correction"], -2.10687)
self.assertAlmostEqual(c["MP Advanced Correction"], -5.466)
entry.parameters["is_hubbard"] = False
del entry.parameters["hubbards"]
c = ggacompat.get_corrections_dict(entry)
self.assertNotIn("MP Advanced Correction", c)
def test_get_corrections_dict(self):
compat = MaterialsProjectCompatibility(check_potcar_hash=False)
ggacompat = MaterialsProjectCompatibility("GGA", check_potcar_hash=False)
#Correct parameters
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': "7a25bc5b9a5393f46600a4939d357982"}]})
c = compat.get_corrections_dict(entry)
self.assertAlmostEqual(c["MP Anion Correction"], -2.10687)
self.assertAlmostEqual(c["MP Advanced Correction"], -5.466)
entry.parameters["is_hubbard"] = False
del entry.parameters["hubbards"]
c = ggacompat.get_corrections_dict(entry)
self.assertNotIn("MP Advanced Correction", c)
def test_get_corrections_dict(self):
compat = MaterialsProjectCompatibility()
ggacompat = MaterialsProjectCompatibility("GGA")
#Correct parameters
entry = ComputedEntry(
'Fe2O3',
-1,
0.0,
parameters={
'is_hubbard':
True,
'hubbards': {
'Fe': 5.3,
'O': 0
},
'run_type':
'GGA+U',
'potcar_symbols':
['PAW_PBE Fe_pv 06Sep2000', 'PAW_PBE O 08Apr2002']
})
c = compat.get_corrections_dict(entry)
self.assertAlmostEqual(c["MP Gas Correction"], -2.10687)
self.assertAlmostEqual(c["MP Advanced Correction"], -5.466)
entry.parameters["is_hubbard"] = False
del entry.parameters["hubbards"]
c = ggacompat.get_corrections_dict(entry)
self.assertNotIn("MP Advanced Correction", c)
def setUp(self):
self.entry1 = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.entry_sulfide = ComputedEntry(
'FeS', -1, 0.0,
parameters={'is_hubbard': False,
'run_type': 'GGA',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE S 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.entry2 = ComputedEntry(
'Fe3O4', -2, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.entry3 = ComputedEntry(
'FeO', -2, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 4.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.compat = MaterialsProjectCompatibility(check_potcar_hash=False)
self.ggacompat = MaterialsProjectCompatibility("GGA", check_potcar_hash=False)
warnings.simplefilter("ignore")
def get_pourbaix_entries(
self, chemsys, solid_compat=MaterialsProjectCompatibility()
):
"""
A helper function to get all entries necessary to generate
a pourbaix diagram from the rest interface.
Args:
chemsys ([str]): A list of elements comprising the chemical
system, e.g. ['Li', 'Fe']
solid_compat: Compatiblity scheme used to pre-process solid DFT energies prior to applying aqueous
energy adjustments. Default: MaterialsProjectCompatibility().
"""
raise NotImplementedError
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]
def build_complete_pd(f, calc_list):
"""build_complete_pd
Builds a PD including appropriate local calcs.
:param f: Formula for which we seek to construct a PD.
:param calc_list: A list of folders containing local calculations.
:return: A Phasediagram object.
"""
entries = pd_tools.get_pruned_chemsys(f)
csys = [el for el in Composition(f).as_dict()]
for d in calc_list:
data_dir = root_dir + "/" + d + "/relax_final"
if set(eles_in_calc(data_dir)).issubset(set(csys)):
entries.append(create_entry(data_dir))
entries_proc = MaterialsProjectCompatibility().process_entries(entries)
return PhaseDiagram(entries_proc)
def get_entries(self,
chemsys_formula_id,
compatible_only=True,
inc_structure=None):
"""
Get a list of ComputedEntries or ComputedStructureEntries corresponding
to a chemical system, formula, or materials_id.
Args:
chemsys_formula_id:
A chemical system (e.g., Li-Fe-O), or formula (e.g., Fe2O3) or
materials_id (e.g., mp-1234).
compatible_only:
Whether to return only "compatible" entries. Compatible entries
are entries that have been processed using the
MaterialsProjectCompatibility class, which performs adjustments
to allow mixing of GGA and GGA+U calculations for more accurate
phase diagrams and reaction energies.
inc_structure:
If None, entries returned are ComputedEntries. If
inc_structure="final", ComputedStructureEntries with final
structures are returned. Otherwise, ComputedStructureEntries
with initial structures are returned.
Returns:
List of ComputedEntry or ComputedStructureEntry objects.
"""
data = self.get_data(chemsys_formula_id, prop="entry")
entries = [d["entry"] for d in data]
def make_struct_entry(entry):
s = self.get_structure_by_material_id(entry.entry_id,
inc_structure == "final")
return ComputedStructureEntry(s, entry.energy, entry.correction,
entry.parameters, entry.data,
entry.entry_id)
if inc_structure:
entries = map(make_struct_entry, entries)
if compatible_only:
entries = MaterialsProjectCompatibility().process_entries(entries)
return entries
def test_get_corrections_dict(self):
compat = MaterialsProjectCompatibility(check_potcar_hash=False)
ggacompat = MaterialsProjectCompatibility("GGA", check_potcar_hash=False)
#Correct parameters
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': "7a25bc5b9a5393f46600a4939d357982"}]})
c = compat.get_corrections_dict(entry)
self.assertAlmostEqual(c["MP Anion Correction"], -2.10687)
self.assertAlmostEqual(c["MP Advanced Correction"], -5.466)
entry.parameters["is_hubbard"] = False
del entry.parameters["hubbards"]
c = ggacompat.get_corrections_dict(entry)
self.assertNotIn("MP Advanced Correction", c)
def run_task(self, fw_spec):
# import here to prevent import errors in bigger MPCollab
# get the band structure and nelect from files
"""
prev_dir = get_loc(fw_spec['prev_vasp_dir'])
vasprun_loc = zpath(os.path.join(prev_dir, 'vasprun.xml'))
kpoints_loc = zpath(os.path.join(prev_dir, 'KPOINTS'))
vr = Vasprun(vasprun_loc)
bs = vr.get_band_structure(kpoints_filename=kpoints_loc)
"""
filename = get_slug(
'JOB--' + fw_spec['mpsnl'].structure.composition.reduced_formula + '--'
+ fw_spec['task_type'])
with open(filename, 'w+') as f:
f.write('')
# get the band structure and nelect from DB
block_part = get_block_part(fw_spec['prev_vasp_dir'])
db_dir = os.environ['DB_LOC']
assert isinstance(db_dir, object)
db_path = os.path.join(db_dir, 'tasks_db.json')
with open(db_path) as f:
creds = json.load(f)
connection = MongoClient(creds['host'], creds['port'])
tdb = connection[creds['database']]
tdb.authenticate(creds['admin_user'], creds['admin_password'])
props = {"calculations": 1, "task_id": 1, "state": 1, "pseudo_potential": 1, "run_type": 1, "is_hubbard": 1, "hubbards": 1, "unit_cell_formula": 1}
m_task = tdb.tasks.find_one({"dir_name": block_part}, props)
if not m_task:
time.sleep(60) # only thing to think of is wait for DB insertion(?)
m_task = tdb.tasks.find_one({"dir_name": block_part}, props)
if not m_task:
raise ValueError("Could not find task with dir_name: {}".format(block_part))
if m_task['state'] != 'successful':
raise ValueError("Cannot run Boltztrap; parent job unsuccessful")
nelect = m_task['calculations'][0]['input']['parameters']['NELECT']
bs_id = m_task['calculations'][0]['band_structure_fs_id']
print bs_id, type(bs_id)
fs = gridfs.GridFS(tdb, 'band_structure_fs')
bs_dict = json.loads(fs.get(bs_id).read())
bs_dict['structure'] = m_task['calculations'][0]['output']['crystal']
bs = BandStructure.from_dict(bs_dict)
print 'Band Structure found:', bool(bs)
print nelect
# run Boltztrap
runner = BoltztrapRunner(bs, nelect)
dir = runner.run(path_dir=os.getcwd())
# put the data in the database
bta = BoltztrapAnalyzer.from_files(dir)
# 8/21/15 - Anubhav removed fs_id (also see line further below, ted['boltztrap_full_fs_id'] ...)
# 8/21/15 - this is to save space in MongoDB, as well as non-use of full Boltztrap output (vs rerun)
"""
data = bta.as_dict()
data.update(get_meta_from_structure(bs._structure))
data['snlgroup_id'] = fw_spec['snlgroup_id']
data['run_tags'] = fw_spec['run_tags']
data['snl'] = fw_spec['mpsnl']
data['dir_name_full'] = dir
data['dir_name'] = get_block_part(dir)
data['task_id'] = m_task['task_id']
del data['hall'] # remove because it is too large and not useful
fs = gridfs.GridFS(tdb, "boltztrap_full_fs")
btid = fs.put(json.dumps(jsanitize(data)))
"""
# now for the "sanitized" data
ted = bta.as_dict()
del ted['seebeck']
del ted['hall']
del ted['kappa']
del ted['cond']
# ted['boltztrap_full_fs_id'] = btid
ted['snlgroup_id'] = fw_spec['snlgroup_id']
ted['run_tags'] = fw_spec['run_tags']
ted['snl'] = fw_spec['mpsnl'].as_dict()
ted['dir_name_full'] = dir
ted['dir_name'] = get_block_part(dir)
ted['task_id'] = m_task['task_id']
ted['pf_doping'] = bta.get_power_factor(output='tensor', relaxation_time=self.TAU)
ted['zt_doping'] = bta.get_zt(output='tensor', relaxation_time=self.TAU, kl=self.KAPPAL)
ted['pf_eigs'] = self.get_eigs(ted, 'pf_doping')
ted['pf_best'] = self.get_extreme(ted, 'pf_eigs')
ted['pf_best_dope18'] = self.get_extreme(ted, 'pf_eigs', max_didx=3)
ted['pf_best_dope19'] = self.get_extreme(ted, 'pf_eigs', max_didx=4)
ted['zt_eigs'] = self.get_eigs(ted, 'zt_doping')
ted['zt_best'] = self.get_extreme(ted, 'zt_eigs')
ted['zt_best_dope18'] = self.get_extreme(ted, 'zt_eigs', max_didx=3)
ted['zt_best_dope19'] = self.get_extreme(ted, 'zt_eigs', max_didx=4)
ted['seebeck_eigs'] = self.get_eigs(ted, 'seebeck_doping')
ted['seebeck_best'] = self.get_extreme(ted, 'seebeck_eigs')
ted['seebeck_best_dope18'] = self.get_extreme(ted, 'seebeck_eigs', max_didx=3)
ted['seebeck_best_dope19'] = self.get_extreme(ted, 'seebeck_eigs', max_didx=4)
ted['cond_eigs'] = self.get_eigs(ted, 'cond_doping')
ted['cond_best'] = self.get_extreme(ted, 'cond_eigs')
ted['cond_best_dope18'] = self.get_extreme(ted, 'cond_eigs', max_didx=3)
ted['cond_best_dope19'] = self.get_extreme(ted, 'cond_eigs', max_didx=4)
ted['kappa_eigs'] = self.get_eigs(ted, 'kappa_doping')
ted['kappa_best'] = self.get_extreme(ted, 'kappa_eigs', maximize=False)
ted['kappa_best_dope18'] = self.get_extreme(ted, 'kappa_eigs', maximize=False, max_didx=3)
ted['kappa_best_dope19'] = self.get_extreme(ted, 'kappa_eigs', maximize=False, max_didx=4)
try:
from mpcollab.thermoelectrics.boltztrap_TE import BoltzSPB
bzspb = BoltzSPB(ted)
maxpf_p = bzspb.get_maximum_power_factor('p', temperature=0, tau=1E-14, ZT=False, kappal=0.5,\
otherprops=('get_seebeck_mu_eig', 'get_conductivity_mu_eig', \
'get_thermal_conductivity_mu_eig', 'get_average_eff_mass_tensor_mu'))
maxpf_n = bzspb.get_maximum_power_factor('n', temperature=0, tau=1E-14, ZT=False, kappal=0.5,\
otherprops=('get_seebeck_mu_eig', 'get_conductivity_mu_eig', \
'get_thermal_conductivity_mu_eig', 'get_average_eff_mass_tensor_mu'))
maxzt_p = bzspb.get_maximum_power_factor('p', temperature=0, tau=1E-14, ZT=True, kappal=0.5, otherprops=('get_seebeck_mu_eig', 'get_conductivity_mu_eig', \
'get_thermal_conductivity_mu_eig', 'get_average_eff_mass_tensor_mu'))
maxzt_n = bzspb.get_maximum_power_factor('n', temperature=0, tau=1E-14, ZT=True, kappal=0.5, otherprops=('get_seebeck_mu_eig', 'get_conductivity_mu_eig', \
'get_thermal_conductivity_mu_eig', 'get_average_eff_mass_tensor_mu'))
ted['zt_best_finemesh'] = {'p': maxzt_p, 'n': maxzt_n}
ted['pf_best_finemesh'] = {'p': maxpf_p, 'n': maxpf_n}
except:
import traceback
traceback.print_exc()
print 'COULD NOT GET FINE MESH DATA'
# add is_compatible
mpc = MaterialsProjectCompatibility("Advanced")
try:
func = m_task["pseudo_potential"]["functional"]
labels = m_task["pseudo_potential"]["labels"]
symbols = ["{} {}".format(func, label) for label in labels]
parameters = {"run_type": m_task["run_type"],
"is_hubbard": m_task["is_hubbard"],
"hubbards": m_task["hubbards"],
"potcar_symbols": symbols}
entry = ComputedEntry(Composition(m_task["unit_cell_formula"]),
0.0, 0.0, parameters=parameters,
entry_id=m_task["task_id"])
ted["is_compatible"] = bool(mpc.process_entry(entry))
except:
traceback.print_exc()
print 'ERROR in getting compatibility, task_id: {}'.format(m_task["task_id"])
ted["is_compatible"] = None
tdb.boltztrap.insert(jsanitize(ted))
update_spec = {'prev_vasp_dir': fw_spec['prev_vasp_dir'],
'boltztrap_dir': os.getcwd(),
'prev_task_type': fw_spec['task_type'],
'mpsnl': fw_spec['mpsnl'].as_dict(),
'snlgroup_id': fw_spec['snlgroup_id'],
'run_tags': fw_spec['run_tags'], 'parameters': fw_spec.get('parameters')}
return FWAction(update_spec=update_spec)
def get_decomposed_entries(structure_type, species):
"""
Get decomposed entries for mix types
Args:
structure_type(str): "garnet" or "perovskite"
species (dict): species in dictionary.
structure_type(str): garnet or perovskite
Returns:
decompose entries(list):
list of entries prepared from unmix
garnets/perovskite decomposed from input mix
garnet/perovskite
"""
def decomposed(specie_complex):
"""Decompose those have sub-dict to individual dict objects."""
for site, specie in specie_complex.items():
spe_copy = specie_complex.copy()
if len(specie) > 1:
for spe, amt in specie.items():
spe_copy[site] = {spe: 1}
yield spe_copy
decompose_entries = []
model, scaler = load_model_and_scaler(structure_type, "unmix")
std_formula = STD_FORMULA[structure_type]
for unmix_species in decomposed(species):
charge = sum([
spe.oxi_state * amt * SITE_INFO[structure_type][site]["num_atoms"]
for site in SITE_INFO[structure_type].keys()
for spe, amt in unmix_species[site].items()
])
if not abs(charge - 2 * std_formula['O']) < 0.1:
continue
formula = spe2form(structure_type, unmix_species)
composition = Composition(formula)
elements = [el.name for el in composition]
chemsy = '-'.join(sorted(elements))
calc_entries = []
if CALC_ENTRIES[structure_type].get(chemsy):
calc_entries = [entry for entry in CALC_ENTRIES[structure_type][chemsy] if \
entry.name == Composition(formula).reduced_formula]
else:
pass
if calc_entries:
decompose_entries.extend(calc_entries)
else:
cn_specific = True if structure_type == 'garnet' else False
descriptors = get_descriptor(structure_type,
unmix_species,
cn_specific=cn_specific)
form_e = get_form_e(descriptors, model, scaler)
# tot_e = get_tote(form_e * std_formula.num_atoms, unmix_species)
tot_e = get_tote(structure_type, form_e * std_formula.num_atoms,
unmix_species)
entry = prepare_entry(structure_type, tot_e, unmix_species)
compat = MaterialsProjectCompatibility()
entry = compat.process_entry(entry)
decompose_entries.append(entry)
return decompose_entries
def biased_hull(atomate_db, comp_list, anions=['N', 'O'], bias=[0]):
with MPRester() as mpr:
for pretty in comp_list:
composition = Composition(pretty)
composition = [str(i) for i in composition.elements]
# anion_num = composition[2]
# composition.pop()
# composition.append(anions[0])
# composition.append(anions[1])
#First, build the phase diagram and hull
orig_entries = mpr.get_entries_in_chemsys(composition)
#orig_entries = mpr.get_entries_in_chemsys(chemsys_list[k])
entries = []
for i in range(len(bias)):
entries.append(copy.deepcopy(orig_entries))
for j in range(0, len(entries[i])):
temp = entries[i][j].parameters['potcar_symbols']
if temp in [['PBE ' + anions[0]], ['PBE ' + anions[1]],
['PBE ' + anions[0], 'PBE ' + anions[1]],
['PBE ' + anions[1], 'PBE ' + anions[0]]]:
new_entry = ComputedEntry(
entries[i][j].composition, entries[i][j].energy +
bias[i]) #add arbitrary energy to gas phase
entries[i][j] = copy.deepcopy(new_entry)
#Then, find each entry in atomate_db which has this composition and get its hull energy
print(pretty)
structures = []
cursor = atomate_db.collection.find({
'task_label': 'static',
'formula_pretty': pretty
})
for structure in cursor:
structures.append(structure)
struct_entries = []
for structure in structures:
temp = structure['calcs_reversed'][0]
struct_entry = ComputedEntry(
temp['composition_unit_cell'],
temp['output']['energy'],
parameters={
'run_type':
temp['run_type'],
'is_hubbard':
structure['input']['is_hubbard'],
'pseudo_potential':
structure['input']['pseudo_potential'],
'hubbards':
structure['input']['hubbards'],
'potcar_symbols':
structure['orig_inputs']['potcar']['symbols'],
'oxide_type':
'oxide'
},
data={'oxide_type': 'oxide'})
for i in range(0, 4):
struct_entry.parameters['potcar_symbols'][
i] = 'PBE ' + struct_entry.parameters[
'potcar_symbols'][i]
struct_entry = MaterialsProjectCompatibility().process_entries(
[struct_entry
])[0] #takes list as argument and returns list
struct_entries.append(struct_entry)
bias_strings = []
stable_polymorph = {'id': 0, 'tilt_order': ''}
for i in range(len(bias)):
entries[i].extend(struct_entries)
pd = PhaseDiagram(entries[i])
bias_string = 'ehull_' + str(bias[i]) + 'eV'
bias_strings.append(bias_string)
stable_polymorph[bias_strings[i]] = 1000
print(bias_strings)
for j in range(0, len(struct_entries)):
stability = pd.get_decomp_and_e_above_hull(
struct_entries[j])
print(structures[j]['formula_pretty'],
structures[j]['task_id'],
[phase.composition
for phase in stability[0]], stability[1])
if stability[1] < stable_polymorph[bias_strings[i]]:
stable_polymorph['id'] = structures[j]['task_id']
stable_polymorph[bias_strings[i]] = stability[1]
if 'tags' in structures[j]:
if structures[j]['tags'][1] == 'tetra':
stable_polymorph['tilt_order'] = structures[j][
'tags'][2]
else:
stable_polymorph['tilt_order'] = structures[j][
'tags'][1]
output_dict[structures[j]
['formula_pretty']] = stable_polymorph
return output_dict
def get_entries(self,
chemsys_formula_id_criteria,
compatible_only=True,
inc_structure=None,
property_data=None,
conventional_unit_cell=False):
"""
Get a list of ComputedEntries or ComputedStructureEntries corresponding
to a chemical system, formula, or materials_id or full criteria.
Args:
chemsys_formula_id_criteria (str/dict): A chemical system
(e.g., Li-Fe-O), or formula (e.g., Fe2O3) or materials_id
(e.g., mp-1234) or full Mongo-style dict criteria.
compatible_only (bool): Whether to return only "compatible"
entries. Compatible entries are entries that have been
processed using the MaterialsProjectCompatibility class,
which performs adjustments to allow mixing of GGA and GGA+U
calculations for more accurate phase diagrams and reaction
energies.
inc_structure (str): If None, entries returned are
ComputedEntries. If inc_structure="final",
ComputedStructureEntries with final structures are returned.
Otherwise, ComputedStructureEntries with initial structures
are returned.
property_data (list): Specify additional properties to include in
entry.data. If None, no data. Should be a subset of
supported_properties.
conventional_unit_cell (bool): Whether to get the standard
conventional unit cell
Returns:
List of ComputedEntry or ComputedStructureEntry objects.
"""
# TODO: This is a very hackish way of doing this. It should be fixed
# on the REST end.
params = [
"run_type", "is_hubbard", "pseudo_potential", "hubbards",
"potcar_symbols", "oxide_type"
]
props = ["energy", "unit_cell_formula", "task_id"] + params
if property_data:
props += property_data
if inc_structure:
if inc_structure == "final":
props.append("structure")
else:
props.append("initial_structure")
if not isinstance(chemsys_formula_id_criteria, dict):
criteria = MPRester.parse_criteria(chemsys_formula_id_criteria)
else:
criteria = chemsys_formula_id_criteria
try:
data = self.query(criteria, props)
except MPRestError:
return []
entries = []
for d in data:
d["potcar_symbols"] = [
"%s %s" % (d["pseudo_potential"]["functional"], l)
for l in d["pseudo_potential"]["labels"]
]
data = {"oxide_type": d["oxide_type"]}
if property_data:
data.update({k: d[k] for k in property_data})
if not inc_structure:
e = ComputedEntry(d["unit_cell_formula"],
d["energy"],
parameters={k: d[k]
for k in params},
data=data,
entry_id=d["task_id"])
else:
prim = d["structure"] if inc_structure == "final" else d[
"initial_structure"]
if conventional_unit_cell:
s = SpacegroupAnalyzer(
prim).get_conventional_standard_structure()
energy = d["energy"] * (len(s) / len(prim))
else:
s = prim.copy()
energy = d["energy"]
e = ComputedStructureEntry(
s,
energy,
parameters={k: d[k]
for k in params},
data=data,
entry_id=d["task_id"])
entries.append(e)
if compatible_only:
from pymatgen.entries.compatibility import \
MaterialsProjectCompatibility
entries = MaterialsProjectCompatibility().process_entries(entries)
return entries
def test_process_entries(self):
compat = MaterialsProjectCompatibility()
entries = compat.process_entries([self.entry1, self.entry2,
self.entry3])
self.assertEqual(len(entries), 2)
class MaterialsProjectCompatibilityTest(unittest.TestCase):
def setUp(self):
self.entry1 = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.entry2 = ComputedEntry(
'Fe3O4', -2, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.entry3 = ComputedEntry(
'FeO', -2, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 4.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.compat = MaterialsProjectCompatibility(check_potcar_hash=False)
self.ggacompat = MaterialsProjectCompatibility("GGA", check_potcar_hash=False)
def test_process_entry(self):
#Correct parameters
self.assertIsNotNone(self.compat.process_entry(self.entry1))
self.assertIsNone(self.ggacompat.process_entry(self.entry1))
#Correct parameters
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': False, "hubbards": {}, 'run_type': 'GGA',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.assertIsNone(self.compat.process_entry(entry))
self.assertIsNotNone(self.ggacompat.process_entry(entry))
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.assertIsNotNone(self.compat.process_entry(entry))
def test_correction_values(self):
#test_corrections
self.assertAlmostEqual(self.compat.process_entry(self.entry1).correction,
- 2.733 * 2 - 0.70229 * 3)
entry = ComputedEntry(
'FeF3', -2, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'F': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE F 08Apr2002',
'hash': '180141c33d032bfbfff30b3bea9d23dd'}]})
self.assertIsNotNone(self.compat.process_entry(entry))
#Check actual correction
self.assertAlmostEqual(self.compat.process_entry(entry).correction, -2.733)
def test_U_values(self):
#Wrong U value
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 5.2, 'O': 0}, 'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.assertIsNone(self.compat.process_entry(entry))
#GGA run of U
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': False, 'hubbards': None,
'run_type': 'GGA',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.assertIsNone(self.compat.process_entry(entry))
#GGA+U run of non-U
entry = ComputedEntry(
'Al2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Al': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel': 'PAW_PBE Al 06Sep2000',
'hash': '805c888bbd2793e462311f6a20d873d9'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.assertIsNone(self.compat.process_entry(entry))
#Materials project should not have a U for sulfides
entry = ComputedEntry(
'FeS2', -2, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'S': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{"titel": 'PAW_PBE S 08Apr2002',
'hash': "f7f8e4a74a6cbb8d63e41f4373b54df2"}]})
self.assertIsNone(self.compat.process_entry(entry))
def test_wrong_psp(self):
#Wrong psp
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe 06Sep2000',
'hash': '9530da8244e4dac17580869b4adab115'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
self.assertIsNone(self.compat.process_entry(entry))
def test_element_processing(self):
entry = ComputedEntry(
'O', -1, 0.0,
parameters={'is_hubbard': False, 'hubbards': {},
'potcar_spec': [{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}],
'run_type': 'GGA'})
entry = self.compat.process_entry(entry)
# self.assertEqual(entry.entry_id, -8)
self.assertAlmostEqual(entry.energy, -1)
self.assertAlmostEqual(self.ggacompat.process_entry(entry).energy,
-1)
def test_get_corrections_dict(self):
compat = MaterialsProjectCompatibility(check_potcar_hash=False)
ggacompat = MaterialsProjectCompatibility("GGA", check_potcar_hash=False)
#Correct parameters
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe_pv 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': "7a25bc5b9a5393f46600a4939d357982"}]})
c = compat.get_corrections_dict(entry)
self.assertAlmostEqual(c["MP Gas Correction"], -2.10687)
self.assertAlmostEqual(c["MP Advanced Correction"], -5.466)
entry.parameters["is_hubbard"] = False
del entry.parameters["hubbards"]
c = ggacompat.get_corrections_dict(entry)
self.assertNotIn("MP Advanced Correction", c)
def test_process_entries(self):
entries = self.compat.process_entries([self.entry1,
self.entry2,
self.entry3])
self.assertEqual(len(entries), 2)
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
from pymatgen.analysis.phase_diagram import PDPlotter
# Assimilate VASP calculations into ComputedEntry object. Let's assume that
# the calculations are for a series of new LixFeyOz phases that we want to
# know the phase stability.
drone = VaspToComputedEntryDrone()
queen = BorgQueen(drone, rootpath=".")
entries = queen.get_data()
# Obtain all existing Li-Fe-O 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-Fe-O phase diagram
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd)
plotter.show()
def get_entries(self, chemsys_formula_id_criteria, compatible_only=True,
inc_structure=None, property_data=None):
"""
Get a list of ComputedEntries or ComputedStructureEntries corresponding
to a chemical system, formula, or materials_id or full criteria.
Args:
chemsys_formula_id_criteria (str/dict): A chemical system
(e.g., Li-Fe-O), or formula (e.g., Fe2O3) or materials_id
(e.g., mp-1234) or full Mongo-style dict criteria.
compatible_only (bool): Whether to return only "compatible"
entries. Compatible entries are entries that have been
processed using the MaterialsProjectCompatibility class,
which performs adjustments to allow mixing of GGA and GGA+U
calculations for more accurate phase diagrams and reaction
energies.
inc_structure (str): If None, entries returned are
ComputedEntries. If inc_structure="final",
ComputedStructureEntries with final structures are returned.
Otherwise, ComputedStructureEntries with initial structures
are returned.
property_data (list): Specify additional properties to include in
entry.data. If None, no data. Should be a subset of
supported_properties.
Returns:
List of ComputedEntry or ComputedStructureEntry objects.
"""
# TODO: This is a very hackish way of doing this. It should be fixed
# on the REST end.
params = ["run_type", "is_hubbard", "pseudo_potential", "hubbards",
"potcar_symbols"]
if compatible_only:
props = ["energy", "unit_cell_formula", "task_id"] + params
if property_data:
props += property_data
if inc_structure:
if inc_structure == "final":
props.append("structure")
else:
props.append("initial_structure")
if not isinstance(chemsys_formula_id_criteria, dict):
criteria = MPRester.parse_criteria(chemsys_formula_id_criteria)
else:
criteria = chemsys_formula_id_criteria
data = self.query(criteria, props)
entries = []
for d in data:
d["potcar_symbols"] = [
"%s %s" % (d["pseudo_potential"]["functional"], l)
for l in d["pseudo_potential"]["labels"]]
data = {k: d[k] for k in property_data} if property_data else None
if not inc_structure:
e = ComputedEntry(d["unit_cell_formula"], d["energy"],
parameters={k: d[k] for k in params},
data=data,
entry_id=d["task_id"])
else:
s = d["structure"] if inc_structure == "final" else d[
"initial_structure"]
e = ComputedStructureEntry(
s, d["energy"],
parameters={k: d[k] for k in params},
data=data,
entry_id=d["task_id"])
entries.append(e)
from pymatgen.entries.compatibility import \
MaterialsProjectCompatibility
entries = MaterialsProjectCompatibility().process_entries(entries)
else:
entries = []
for d in self.get_data(chemsys_formula_id_criteria,
prop="task_ids"):
for i in d["task_ids"]:
e = self.get_task_data(i, prop="entry")
e = e[0]["entry"]
if inc_structure:
s = self.get_task_data(i,
prop="structure")[0]["structure"]
e = ComputedStructureEntry(
s, e.energy, e.correction, e.parameters, e.data,
e.entry_id)
entries.append(e)
return entries
def assimilate(self, path, launches_coll=None):
"""
Parses vasp runs. Then insert the result into the db. and return the
task_id or doc of the insertion.
Returns:
If in simulate_mode, the entire doc is returned for debugging
purposes. Else, only the task_id of the inserted doc is returned.
"""
d = self.get_task_doc(path)
if self.additional_fields:
d.update(self.additional_fields) # always add additional fields, even for failed jobs
try:
d["dir_name_full"] = d["dir_name"].split(":")[1]
d["dir_name"] = get_block_part(d["dir_name_full"])
d["stored_data"] = {}
except:
print 'COULD NOT GET DIR NAME'
pprint.pprint(d)
print traceback.format_exc()
raise ValueError('IMPROPER PARSING OF {}'.format(path))
if not self.simulate:
# Perform actual insertion into db. Because db connections cannot
# be pickled, every insertion needs to create a new connection
# to the db.
conn = MongoClient(self.host, self.port)
db = conn[self.database]
if self.user:
db.authenticate(self.user, self.password)
coll = db[self.collection]
# Insert dos data into gridfs and then remove it from the dict.
# DOS data tends to be above the 4Mb limit for mongo docs. A ref
# to the dos file is in the dos_fs_id.
result = coll.find_one({"dir_name": d["dir_name"]})
if result is None or self.update_duplicates:
if self.parse_dos and "calculations" in d:
for calc in d["calculations"]:
if "dos" in calc:
dos = json.dumps(calc["dos"], cls=MontyEncoder)
fs = gridfs.GridFS(db, "dos_fs")
dosid = fs.put(dos)
calc["dos_fs_id"] = dosid
del calc["dos"]
d["last_updated"] = datetime.datetime.today()
if result is None:
if ("task_id" not in d) or (not d["task_id"]):
d["task_id"] = "mp-{}".format(
db.counter.find_one_and_update(
{"_id": "taskid"}, {"$inc": {"c": 1}}
)["c"])
logger.info("Inserting {} with taskid = {}"
.format(d["dir_name"], d["task_id"]))
elif self.update_duplicates:
d["task_id"] = result["task_id"]
logger.info("Updating {} with taskid = {}"
.format(d["dir_name"], d["task_id"]))
#Fireworks processing
self.process_fw(path, d)
try:
#Add oxide_type
struct=Structure.from_dict(d["output"]["crystal"])
d["oxide_type"]=oxide_type(struct)
except:
logger.error("can't get oxide_type for {}".format(d["task_id"]))
d["oxide_type"] = None
#Override incorrect outcar subdocs for two step relaxations
if "optimize structure" in d['task_type'] and \
os.path.exists(os.path.join(path, "relax2")):
try:
run_stats = {}
for i in [1,2]:
o_path = os.path.join(path,"relax"+str(i),"OUTCAR")
o_path = o_path if os.path.exists(o_path) else o_path+".gz"
outcar = Outcar(o_path)
d["calculations"][i-1]["output"]["outcar"] = outcar.as_dict()
run_stats["relax"+str(i)] = outcar.run_stats
except:
logger.error("Bad OUTCAR for {}.".format(path))
try:
overall_run_stats = {}
for key in ["Total CPU time used (sec)", "User time (sec)",
"System time (sec)", "Elapsed time (sec)"]:
overall_run_stats[key] = sum([v[key]
for v in run_stats.values()])
run_stats["overall"] = overall_run_stats
except:
logger.error("Bad run stats for {}.".format(path))
d["run_stats"] = run_stats
# add is_compatible
mpc = MaterialsProjectCompatibility("Advanced")
try:
func = d["pseudo_potential"]["functional"]
labels = d["pseudo_potential"]["labels"]
symbols = ["{} {}".format(func, label) for label in labels]
parameters = {"run_type": d["run_type"],
"is_hubbard": d["is_hubbard"],
"hubbards": d["hubbards"],
"potcar_symbols": symbols}
entry = ComputedEntry(Composition(d["unit_cell_formula"]),
0.0, 0.0, parameters=parameters,
entry_id=d["task_id"])
d['is_compatible'] = bool(mpc.process_entry(entry))
except:
traceback.print_exc()
print 'ERROR in getting compatibility'
d['is_compatible'] = None
#task_type dependent processing
if 'static' in d['task_type']:
launch_doc = launches_coll.find_one({"fw_id": d['fw_id'], "launch_dir": {"$regex": d["dir_name"]}}, {"action.stored_data": 1})
for i in ["conventional_standard_structure", "symmetry_operations",
"symmetry_dataset", "refined_structure"]:
try:
d['stored_data'][i] = launch_doc['action']['stored_data'][i]
except:
pass
#parse band structure if necessary
if ('band structure' in d['task_type'] or "Uniform" in d['task_type'])\
and d['state'] == 'successful':
launch_doc = launches_coll.find_one({"fw_id": d['fw_id'], "launch_dir": {"$regex": d["dir_name"]}},
{"action.stored_data": 1})
vasp_run = Vasprun(zpath(os.path.join(path, "vasprun.xml")), parse_projected_eigen=False)
if 'band structure' in d['task_type']:
def string_to_numlist(stringlist):
g=re.search('([0-9\-\.eE]+)\s+([0-9\-\.eE]+)\s+([0-9\-\.eE]+)', stringlist)
return [float(g.group(i)) for i in range(1,4)]
for i in ["kpath_name", "kpath"]:
d['stored_data'][i] = launch_doc['action']['stored_data'][i]
kpoints_doc = d['stored_data']['kpath']['kpoints']
for i in kpoints_doc:
kpoints_doc[i]=string_to_numlist(kpoints_doc[i])
bs=vasp_run.get_band_structure(efermi=d['calculations'][0]['output']['outcar']['efermi'],
line_mode=True)
else:
bs=vasp_run.get_band_structure(efermi=d['calculations'][0]['output']['outcar']['efermi'],
line_mode=False)
bs_json = json.dumps(bs.as_dict(), cls=MontyEncoder)
fs = gridfs.GridFS(db, "band_structure_fs")
bs_id = fs.put(bs_json)
d['calculations'][0]["band_structure_fs_id"] = bs_id
# also override band gap in task doc
gap = bs.get_band_gap()
vbm = bs.get_vbm()
cbm = bs.get_cbm()
update_doc = {'bandgap': gap['energy'], 'vbm': vbm['energy'], 'cbm': cbm['energy'], 'is_gap_direct': gap['direct']}
d['analysis'].update(update_doc)
d['calculations'][0]['output'].update(update_doc)
coll.update_one({"dir_name": d["dir_name"]}, {'$set': d}, upsert=True)
return d["task_id"], d
else:
logger.info("Skipping duplicate {}".format(d["dir_name"]))
return result["task_id"], result
else:
d["task_id"] = 0
logger.info("Simulated insert into database for {} with task_id {}"
.format(d["dir_name"], d["task_id"]))
return 0, d
def test_process_entry(self):
compat = MaterialsProjectCompatibility()
ggacompat = MaterialsProjectCompatibility("GGA")
#Correct parameters
self.assertIsNotNone(compat.process_entry(self.entry1))
self.assertIsNone(ggacompat.process_entry(self.entry1))
#Correct parameters
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': False, "hubbards": {}, 'run_type': 'GGA',
'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
'PAW_PBE O 08Apr2002']})
self.assertIsNone(compat.process_entry(entry))
self.assertIsNotNone(ggacompat.process_entry(entry))
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
'PAW_PBE O 08Apr2002']})
self.assertIsNotNone(compat.process_entry(entry))
#Check actual correction
self.assertAlmostEqual(compat.process_entry(entry).correction,
- 2.733 * 2 - 0.70229 * 3)
entry = ComputedEntry(
'FeF3', -2, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'F': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
'PAW_PBE F 08Apr2002']})
self.assertIsNotNone(compat.process_entry(entry))
#Check actual correction
self.assertAlmostEqual(compat.process_entry(entry).correction, -2.733)
#Wrong U value
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 5.2, 'O': 0}, 'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
'PAW_PBE O 08Apr2002']})
self.assertIsNone(compat.process_entry(entry))
#GGA run of U
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': False, 'hubbards': None,
'run_type': 'GGA',
'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
'PAW_PBE O 08Apr2002']})
self.assertIsNone(compat.process_entry(entry))
#GGA+U run of non-U
entry = ComputedEntry(
'Al2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Al': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Al 06Sep2000',
'PAW_PBE O 08Apr2002']})
self.assertIsNone(compat.process_entry(entry))
#Materials project should not have a U for sulfides
entry = ComputedEntry(
'FeS2', -2, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'S': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
'PAW_PBE S 08Apr2002']})
self.assertIsNone(compat.process_entry(entry))
#Wrong psp
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 5.3, 'O': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe 06Sep2000',
'PAW_PBE O 08Apr2002']})
self.assertIsNone(compat.process_entry(entry))
#Testing processing of elements.
entry = ComputedEntry(
'O', -1, 0.0,
parameters={'is_hubbard': False, 'hubbards': {},
'potcar_symbols': ['PAW_PBE O 08Apr2002'],
'run_type': 'GGA'})
entry = compat.process_entry(entry)
# self.assertEqual(entry.entry_id, -8)
self.assertAlmostEqual(entry.energy, -1)
self.assertAlmostEqual(ggacompat.process_entry(entry).energy,
-1)
class AnalyseMaterialsProjectJsonDataWithComputedEntries():
"""
Class which will wrap around boilerplate analysis of MaterialsProject-like
json files, containing data extracted using borgs and queens.
It will be assumed that we are providing ComputedEntries objects directly.
"""
def __init__(self):
# some MP analysis power tools
self.compat = MaterialsProjectCompatibility()
return
def extract_alkali_energy(self, computed_Alkali_entry ):
processed_Alkali_entry = self.compat.process_entry(computed_Alkali_entry)
self.E_Alkali = processed_Alkali_entry.energy
return
def extract_phase_diagram_info(self,MP_phase_diagram_json_data_filename):
computed_entries = self._extract_MP_data(MP_phase_diagram_json_data_filename)
processed_entries = self.compat.process_entries(computed_entries)
pd = PhaseDiagram(processed_entries)
self.phase_diagram_analyser = PDAnalyzer(pd)
return
def extract_processed_entries(self,computed_entries):
processed_entries = self.compat.process_entries(computed_entries)
return processed_entries
def extract_energies_above_hull(self,computed_entries,alkali):
processed_entries = self.extract_processed_entries(computed_entries)
list_energy_above_hull = []
list_alkali_content = []
for entry in processed_entries:
decomposition_dict, energy_above_hull = \
self.phase_diagram_analyser.get_decomp_and_e_above_hull(entry, allow_negative=True)
list_energy_above_hull.append(energy_above_hull)
list_alkali_content.append(entry.composition[alkali])
list_energy_above_hull = np.array(list_energy_above_hull)
list_alkali_content = np.array(list_alkali_content )
return list_alkali_content, list_energy_above_hull
def extract_energies(self,computed_entries,alkali):
processed_entries = self.extract_processed_entries(computed_entries)
list_energy = []
list_alkali_content = []
for entry in processed_entries:
list_energy.append(entry.energy)
list_alkali_content.append(entry.composition[alkali])
list_energy = np.array(list_energy)
list_alkali_content = np.array(list_alkali_content )
I = np.argsort(list_alkali_content )
return list_alkali_content[I], list_energy[I]
def _extract_MP_data(self,MP_data_filename):
drone = VaspToComputedEntryDrone()
queen = BorgQueen(drone, "dummy", 1)
queen.load_data(MP_data_filename)
computed_entries = queen.get_data()
del drone
del queen
return computed_entries
def test_properties(self):
filepath = os.path.join(test_dir, 'vasprun.xml.nonlm')
vasprun = Vasprun(filepath, parse_potcar_file=False)
orbs = list(vasprun.complete_dos.pdos[vasprun.final_structure[
0]].keys())
self.assertIn(OrbitalType.s, orbs)
filepath = os.path.join(test_dir, 'vasprun.xml')
vasprun = Vasprun(filepath, parse_potcar_file=False)
#Test NELM parsing.
self.assertEqual(vasprun.parameters["NELM"], 60)
#test pdos parsing
pdos0 = vasprun.complete_dos.pdos[vasprun.final_structure[0]]
self.assertAlmostEqual(pdos0[Orbital.s][Spin.up][16], 0.0026)
self.assertAlmostEqual(pdos0[Orbital.pz][Spin.down][16], 0.0012)
self.assertEqual(pdos0[Orbital.s][Spin.up].shape, (301, ))
filepath2 = os.path.join(test_dir, 'lifepo4.xml')
vasprun_ggau = Vasprun(filepath2, parse_projected_eigen=True,
parse_potcar_file=False)
totalscsteps = sum([len(i['electronic_steps'])
for i in vasprun.ionic_steps])
self.assertEqual(29, len(vasprun.ionic_steps))
self.assertEqual(len(vasprun.structures), len(vasprun.ionic_steps))
self.assertEqual(vasprun.lattice,
vasprun.lattice_rec.reciprocal_lattice)
for i, step in enumerate(vasprun.ionic_steps):
self.assertEqual(vasprun.structures[i], step["structure"])
self.assertTrue(all([vasprun.structures[i] == vasprun.ionic_steps[i][
"structure"] for i in range(len(vasprun.ionic_steps))]))
self.assertEqual(308, totalscsteps,
"Incorrect number of energies read from vasprun.xml")
self.assertEqual(['Li'] + 4 * ['Fe'] + 4 * ['P'] + 16 * ["O"],
vasprun.atomic_symbols)
self.assertEqual(vasprun.final_structure.composition.reduced_formula,
"LiFe4(PO4)4")
self.assertIsNotNone(vasprun.incar, "Incar cannot be read")
self.assertIsNotNone(vasprun.kpoints, "Kpoints cannot be read")
self.assertIsNotNone(vasprun.eigenvalues, "Eigenvalues cannot be read")
self.assertAlmostEqual(vasprun.final_energy, -269.38319884, 7)
self.assertAlmostEqual(vasprun.tdos.get_gap(), 2.0589, 4)
expectedans = (2.539, 4.0906, 1.5516, False)
(gap, cbm, vbm, direct) = vasprun.eigenvalue_band_properties
self.assertAlmostEqual(gap, expectedans[0])
self.assertAlmostEqual(cbm, expectedans[1])
self.assertAlmostEqual(vbm, expectedans[2])
self.assertEqual(direct, expectedans[3])
self.assertFalse(vasprun.is_hubbard)
self.assertEqual(vasprun.potcar_symbols,
['PAW_PBE Li 17Jan2003', 'PAW_PBE Fe 06Sep2000',
'PAW_PBE Fe 06Sep2000', 'PAW_PBE P 17Jan2003',
'PAW_PBE O 08Apr2002'])
self.assertIsNotNone(vasprun.kpoints, "Kpoints cannot be read")
self.assertIsNotNone(vasprun.actual_kpoints,
"Actual kpoints cannot be read")
self.assertIsNotNone(vasprun.actual_kpoints_weights,
"Actual kpoints weights cannot be read")
for atomdoses in vasprun.pdos:
for orbitaldos in atomdoses:
self.assertIsNotNone(orbitaldos, "Partial Dos cannot be read")
# test skipping ionic steps.
vasprun_skip = Vasprun(filepath, 3, parse_potcar_file=False)
self.assertEqual(vasprun_skip.nionic_steps, 29)
self.assertEqual(len(vasprun_skip.ionic_steps),
int(vasprun.nionic_steps / 3) + 1)
self.assertEqual(len(vasprun_skip.ionic_steps),
len(vasprun_skip.structures))
self.assertEqual(len(vasprun_skip.ionic_steps),
int(vasprun.nionic_steps / 3) + 1)
# Check that nionic_steps is preserved no matter what.
self.assertEqual(vasprun_skip.nionic_steps,
vasprun.nionic_steps)
self.assertNotAlmostEqual(vasprun_skip.final_energy,
vasprun.final_energy)
# Test with ionic_step_offset
vasprun_offset = Vasprun(filepath, 3, 6, parse_potcar_file=False)
self.assertEqual(len(vasprun_offset.ionic_steps),
int(len(vasprun.ionic_steps) / 3) - 1)
self.assertEqual(vasprun_offset.structures[0],
vasprun_skip.structures[2])
self.assertTrue(vasprun_ggau.is_hubbard)
self.assertEqual(vasprun_ggau.hubbards["Fe"], 4.3)
self.assertAlmostEqual(vasprun_ggau.projected_eigenvalues[(Spin.up, 0,
0, 96,
Orbital.s)],
0.0032)
d = vasprun_ggau.as_dict()
self.assertEqual(d["elements"], ["Fe", "Li", "O", "P"])
self.assertEqual(d["nelements"], 4)
filepath = os.path.join(test_dir, 'vasprun.xml.unconverged')
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger a warning.
vasprun_unconverged = Vasprun(filepath, parse_potcar_file=False)
# Verify some things
self.assertEqual(len(w), 1)
self.assertTrue(issubclass(w[-1].category,
UnconvergedVASPWarning))
self.assertTrue(vasprun_unconverged.converged_ionic)
self.assertFalse(vasprun_unconverged.converged_electronic)
self.assertFalse(vasprun_unconverged.converged)
filepath = os.path.join(test_dir, 'vasprun.xml.dfpt')
vasprun_dfpt = Vasprun(filepath, parse_potcar_file=False)
self.assertAlmostEqual(vasprun_dfpt.epsilon_static[0][0], 3.26105533)
self.assertAlmostEqual(vasprun_dfpt.epsilon_static[0][1], -0.00459066)
self.assertAlmostEqual(vasprun_dfpt.epsilon_static[2][2], 3.24330517)
self.assertAlmostEqual(vasprun_dfpt.epsilon_static_wolfe[0][0], 3.33402531)
self.assertAlmostEqual(vasprun_dfpt.epsilon_static_wolfe[0][1], -0.00559998)
self.assertAlmostEqual(vasprun_dfpt.epsilon_static_wolfe[2][2], 3.31237357)
self.assertTrue(vasprun_dfpt.converged)
entry = vasprun_dfpt.get_computed_entry()
entry = MaterialsProjectCompatibility(check_potcar_hash=False).process_entry(entry)
self.assertAlmostEqual(entry.uncorrected_energy + entry.correction,
entry.energy)
filepath = os.path.join(test_dir, 'vasprun.xml.dfpt.ionic')
vasprun_dfpt_ionic = Vasprun(filepath, parse_potcar_file=False)
self.assertAlmostEqual(vasprun_dfpt_ionic.epsilon_ionic[0][0], 515.73485838)
self.assertAlmostEqual(vasprun_dfpt_ionic.epsilon_ionic[0][1], -0.00263523)
self.assertAlmostEqual(vasprun_dfpt_ionic.epsilon_ionic[2][2], 19.02110169)
filepath = os.path.join(test_dir, 'vasprun.xml.dfpt.unconverged')
vasprun_dfpt_unconv = Vasprun(filepath, parse_potcar_file=False)
self.assertFalse(vasprun_dfpt_unconv.converged_electronic)
self.assertTrue(vasprun_dfpt_unconv.converged_ionic)
self.assertFalse(vasprun_dfpt_unconv.converged)
vasprun_uniform = Vasprun(os.path.join(test_dir, "vasprun.xml.uniform"),
parse_potcar_file=False)
self.assertEqual(vasprun_uniform.kpoints.style,
Kpoints.supported_modes.Reciprocal)
vasprun_no_pdos = Vasprun(os.path.join(test_dir, "Li_no_projected.xml"),
parse_potcar_file=False)
self.assertIsNotNone(vasprun_no_pdos.complete_dos)
self.assertFalse(vasprun_no_pdos.dos_has_errors)
vasprun_diel = Vasprun(os.path.join(test_dir, "vasprun.xml.dielectric"),
parse_potcar_file=False)
self.assertAlmostEqual(0.4294,vasprun_diel.dielectric[0][10])
self.assertAlmostEqual(19.941,vasprun_diel.dielectric[1][51][0])
self.assertAlmostEqual(19.941,vasprun_diel.dielectric[1][51][1])
self.assertAlmostEqual(19.941,vasprun_diel.dielectric[1][51][2])
self.assertAlmostEqual(0.0,vasprun_diel.dielectric[1][51][3])
self.assertAlmostEqual(34.186,vasprun_diel.dielectric[2][85][0])
self.assertAlmostEqual(34.186,vasprun_diel.dielectric[2][85][1])
self.assertAlmostEqual(34.186,vasprun_diel.dielectric[2][85][2])
self.assertAlmostEqual(0.0,vasprun_diel.dielectric[2][85][3])
v = Vasprun(os.path.join(test_dir, "vasprun.xml.indirect.gz"))
(gap, cbm, vbm, direct) = v.eigenvalue_band_properties
self.assertFalse(direct)
from pymatgen.entries.compatibility import MaterialsProjectCompatibility
from pymatgen.analysis.phase_diagram import PhaseDiagram, PDPlotter, PDEntry
from pymatgen.core.periodic_table import Element
from pymatgen.core.composition import Composition
from pymatgen.io.vasp.outputs import Vasprun
import sys
print("Usage: get_phase_diagram_from_MP.py 'Element1,Element2,Element3,...'")
system = [el for el in sys.argv[1].split(',')] # system we want to get PD for
MAPI_KEY = 'DSR45TfHVuyuB1WvP1' # You must change this to your Materials API key! (or set MAPI_KEY env variable)
system_name = '-'.join(system)
mpr = MPRester(MAPI_KEY) # object for connecting to MP Rest interface
compat = MaterialsProjectCompatibility(
) # sets energy corrections and +U/pseudopotential choice
unprocessed_entries = mpr.get_entries_in_chemsys(system, inc_structure=True)
processed_entries = compat.process_entries(
unprocessed_entries) # filter and add energy corrections
pd = PhaseDiagram(processed_entries)
pd_dict = pd.as_dict()
filename = f'PD_{system_name}.json'
with open(filename, 'w') as f:
json.dump(pd_dict, f)
print(f"PhaseDiagram object saved as dict in {filename}")
def run_task(self, fw_spec):
# import here to prevent import errors in bigger MPCollab
# get the band structure and nelect from files
"""
prev_dir = get_loc(fw_spec['prev_vasp_dir'])
vasprun_loc = zpath(os.path.join(prev_dir, 'vasprun.xml'))
kpoints_loc = zpath(os.path.join(prev_dir, 'KPOINTS'))
vr = Vasprun(vasprun_loc)
bs = vr.get_band_structure(kpoints_filename=kpoints_loc)
"""
filename = get_slug(
'JOB--' + fw_spec['mpsnl'].structure.composition.reduced_formula +
'--' + fw_spec['task_type'])
with open(filename, 'w+') as f:
f.write('')
# get the band structure and nelect from DB
block_part = get_block_part(fw_spec['prev_vasp_dir'])
db_dir = os.environ['DB_LOC']
assert isinstance(db_dir, object)
db_path = os.path.join(db_dir, 'tasks_db.json')
with open(db_path) as f:
creds = json.load(f)
connection = MongoClient(creds['host'], creds['port'])
tdb = connection[creds['database']]
tdb.authenticate(creds['admin_user'], creds['admin_password'])
props = {
"calculations": 1,
"task_id": 1,
"state": 1,
"pseudo_potential": 1,
"run_type": 1,
"is_hubbard": 1,
"hubbards": 1,
"unit_cell_formula": 1
}
m_task = tdb.tasks.find_one({"dir_name": block_part}, props)
if not m_task:
time.sleep(
60) # only thing to think of is wait for DB insertion(?)
m_task = tdb.tasks.find_one({"dir_name": block_part}, props)
if not m_task:
raise ValueError(
"Could not find task with dir_name: {}".format(block_part))
if m_task['state'] != 'successful':
raise ValueError(
"Cannot run Boltztrap; parent job unsuccessful")
nelect = m_task['calculations'][0]['input']['parameters']['NELECT']
bs_id = m_task['calculations'][0]['band_structure_fs_id']
print bs_id, type(bs_id)
fs = gridfs.GridFS(tdb, 'band_structure_fs')
bs_dict = json.loads(fs.get(bs_id).read())
bs_dict['structure'] = m_task['calculations'][0]['output'][
'crystal']
bs = BandStructure.from_dict(bs_dict)
print("find previous run with block_part {}".format(block_part))
print 'Band Structure found:', bool(bs)
print(bs.as_dict())
print("nelect: {}".format(nelect))
# run Boltztrap
doping = []
for d in [1e16, 1e17, 1e18, 1e19, 1e20]:
doping.extend([1 * d, 2.5 * d, 5 * d, 7.5 * d])
doping.append(1e21)
runner = BoltztrapRunner(bs, nelect, doping=doping)
dir = runner.run(path_dir=os.getcwd())
# put the data in the database
bta = BoltztrapAnalyzer.from_files(dir)
# 8/21/15 - Anubhav removed fs_id (also see line further below, ted['boltztrap_full_fs_id'] ...)
# 8/21/15 - this is to save space in MongoDB, as well as non-use of full Boltztrap output (vs rerun)
"""
data = bta.as_dict()
data.update(get_meta_from_structure(bs._structure))
data['snlgroup_id'] = fw_spec['snlgroup_id']
data['run_tags'] = fw_spec['run_tags']
data['snl'] = fw_spec['mpsnl']
data['dir_name_full'] = dir
data['dir_name'] = get_block_part(dir)
data['task_id'] = m_task['task_id']
del data['hall'] # remove because it is too large and not useful
fs = gridfs.GridFS(tdb, "boltztrap_full_fs")
btid = fs.put(json.dumps(jsanitize(data)))
"""
# now for the "sanitized" data
ted = bta.as_dict()
del ted['seebeck']
del ted['hall']
del ted['kappa']
del ted['cond']
# ted['boltztrap_full_fs_id'] = btid
ted['snlgroup_id'] = fw_spec['snlgroup_id']
ted['run_tags'] = fw_spec['run_tags']
ted['snl'] = fw_spec['mpsnl'].as_dict()
ted['dir_name_full'] = dir
ted['dir_name'] = get_block_part(dir)
ted['task_id'] = m_task['task_id']
ted['pf_doping'] = bta.get_power_factor(output='tensor',
relaxation_time=self.TAU)
ted['zt_doping'] = bta.get_zt(output='tensor',
relaxation_time=self.TAU,
kl=self.KAPPAL)
ted['pf_eigs'] = self.get_eigs(ted, 'pf_doping')
ted['pf_best'] = self.get_extreme(ted, 'pf_eigs')
ted['pf_best_dope18'] = self.get_extreme(ted,
'pf_eigs',
max_didx=3)
ted['pf_best_dope19'] = self.get_extreme(ted,
'pf_eigs',
max_didx=4)
ted['zt_eigs'] = self.get_eigs(ted, 'zt_doping')
ted['zt_best'] = self.get_extreme(ted, 'zt_eigs')
ted['zt_best_dope18'] = self.get_extreme(ted,
'zt_eigs',
max_didx=3)
ted['zt_best_dope19'] = self.get_extreme(ted,
'zt_eigs',
max_didx=4)
ted['seebeck_eigs'] = self.get_eigs(ted, 'seebeck_doping')
ted['seebeck_best'] = self.get_extreme(ted, 'seebeck_eigs')
ted['seebeck_best_dope18'] = self.get_extreme(ted,
'seebeck_eigs',
max_didx=3)
ted['seebeck_best_dope19'] = self.get_extreme(ted,
'seebeck_eigs',
max_didx=4)
ted['cond_eigs'] = self.get_eigs(ted, 'cond_doping')
ted['cond_best'] = self.get_extreme(ted, 'cond_eigs')
ted['cond_best_dope18'] = self.get_extreme(ted,
'cond_eigs',
max_didx=3)
ted['cond_best_dope19'] = self.get_extreme(ted,
'cond_eigs',
max_didx=4)
ted['kappa_eigs'] = self.get_eigs(ted, 'kappa_doping')
ted['kappa_best'] = self.get_extreme(ted,
'kappa_eigs',
maximize=False)
ted['kappa_best_dope18'] = self.get_extreme(ted,
'kappa_eigs',
maximize=False,
max_didx=3)
ted['kappa_best_dope19'] = self.get_extreme(ted,
'kappa_eigs',
maximize=False,
max_didx=4)
try:
from mpcollab.thermoelectrics.boltztrap_TE import BoltzSPB
bzspb = BoltzSPB(ted)
maxpf_p = bzspb.get_maximum_power_factor(
'p',
temperature=0,
tau=1E-14,
ZT=False,
kappal=0.5,
otherprops=('get_seebeck_mu_eig',
'get_conductivity_mu_eig',
'get_thermal_conductivity_mu_eig',
'get_average_eff_mass_tensor_mu'))
maxpf_n = bzspb.get_maximum_power_factor(
'n',
temperature=0,
tau=1E-14,
ZT=False,
kappal=0.5,
otherprops=('get_seebeck_mu_eig',
'get_conductivity_mu_eig',
'get_thermal_conductivity_mu_eig',
'get_average_eff_mass_tensor_mu'))
maxzt_p = bzspb.get_maximum_power_factor(
'p',
temperature=0,
tau=1E-14,
ZT=True,
kappal=0.5,
otherprops=('get_seebeck_mu_eig',
'get_conductivity_mu_eig',
'get_thermal_conductivity_mu_eig',
'get_average_eff_mass_tensor_mu'))
maxzt_n = bzspb.get_maximum_power_factor(
'n',
temperature=0,
tau=1E-14,
ZT=True,
kappal=0.5,
otherprops=('get_seebeck_mu_eig',
'get_conductivity_mu_eig',
'get_thermal_conductivity_mu_eig',
'get_average_eff_mass_tensor_mu'))
ted['zt_best_finemesh'] = {'p': maxzt_p, 'n': maxzt_n}
ted['pf_best_finemesh'] = {'p': maxpf_p, 'n': maxpf_n}
except:
import traceback
traceback.print_exc()
print 'COULD NOT GET FINE MESH DATA'
# add is_compatible
mpc = MaterialsProjectCompatibility("Advanced")
try:
func = m_task["pseudo_potential"]["functional"]
labels = m_task["pseudo_potential"]["labels"]
symbols = ["{} {}".format(func, label) for label in labels]
parameters = {
"run_type": m_task["run_type"],
"is_hubbard": m_task["is_hubbard"],
"hubbards": m_task["hubbards"],
"potcar_symbols": symbols
}
entry = ComputedEntry(Composition(m_task["unit_cell_formula"]),
0.0,
0.0,
parameters=parameters,
entry_id=m_task["task_id"])
ted["is_compatible"] = bool(mpc.process_entry(entry))
except:
traceback.print_exc()
print 'ERROR in getting compatibility, task_id: {}'.format(
m_task["task_id"])
ted["is_compatible"] = None
tdb.boltztrap.insert(jsanitize(ted))
update_spec = {
'prev_vasp_dir': fw_spec['prev_vasp_dir'],
'boltztrap_dir': os.getcwd(),
'prev_task_type': fw_spec['task_type'],
'mpsnl': fw_spec['mpsnl'].as_dict(),
'snlgroup_id': fw_spec['snlgroup_id'],
'run_tags': fw_spec['run_tags'],
'parameters': fw_spec.get('parameters')
}
return FWAction(update_spec=update_spec)
def __init__(self):
# some MP analysis power tools
self.compat = MaterialsProjectCompatibility()
return
