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 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 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 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]
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}")
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_phase_diagram_data(self):
"""
Returns grand potential phase diagram data to external plot
Assumes openelement specific element equals None
:return: Data to external plot
"""
open_elements_specific = None
open_element_all = Element(self.open_element)
mpr = MPRester("key")
# import do dados dos arquivos tipo vasp
drone = VaspToComputedEntryDrone()
queen = BorgQueen(drone, rootpath=".")
entries = queen.get_data()
# Get data to make phase diagram
mp_entries = mpr.get_entries_in_chemsys(self.system,
compatible_only=True)
entries.extend(mp_entries)
compat = MaterialsProjectCompatibility()
entries = compat.process_entries(entries)
#explanation_output = open("explain.txt",'w')
entries_output = open("entries.txt", 'w')
compat.explain(entries[0])
print(entries, file=entries_output)
#print(entries)
if open_elements_specific:
gcpd = GrandPotentialPhaseDiagram(entries, open_elements_specific)
self.plot_phase_diagram(gcpd, False)
self.analyze_phase_diagram(gcpd)
if open_element_all:
pd = PhaseDiagram(entries)
chempots = pd.get_transition_chempots(open_element_all)
#print(chempots)
#all_gcpds = list()
toplot = []
# dic = {}
for idx in range(len(chempots)):
if idx == len(chempots) - 1:
avgchempot = chempots[idx] - 0.1
else:
avgchempot = 0.5 * (chempots[idx] + chempots[idx + 1])
gcpd = GrandPotentialPhaseDiagram(
entries, {open_element_all: avgchempot}, pd.elements)
# toplot.append(self.get_grand_potential_phase_diagram(gcpd))
min_chempot = None if idx == len(chempots) - 1 else chempots[
idx + 1]
max_chempot = chempots[idx]
#gcpd = GrandPotentialPhaseDiagram(entries, {open_element_all: max_chempot}, pd.elements)
toplot.append(self.get_grand_potential_phase_diagram(gcpd))
#toplot.append(max_chempot)
#self.plot_phase_diagram(gcpd, False)
#print({open_element_all: max_chempot})
# Data to plot phase diagram
return toplot
def test_process_entries(self):
compat = MaterialsProjectCompatibility()
entries = compat.process_entries([self.entry1, self.entry2,
self.entry3])
self.assertEqual(len(entries), 2)
def get_phase_diagram_data(self):
"""
Returns grand potential phase diagram data to external plot
Assumes openelement specific element equals None
:return: Data to external plot
"""
open_elements_specific = None
open_element_all = Element(self.open_element)
mpr = MPRester(settings.apiKey)
drone = VaspToComputedEntryDrone()
queen = BorgQueen(drone, rootpath=".")
entries = queen.get_data()
# Get data to make phase diagram
mp_entries = mpr.get_entries_in_chemsys(self.system,
compatible_only=True)
entries.extend(mp_entries)
compat = MaterialsProjectCompatibility()
entries = compat.process_entries(entries)
#explanation_output = open("explain.txt",'w')
#entries_output = open("entries.txt", 'w')
compat.explain(entries[0])
#print(entries, file=entries_output)
if open_elements_specific:
gcpd = GrandPotentialPhaseDiagram(entries, open_elements_specific)
self.plot_phase_diagram(gcpd, False)
self.analyze_phase_diagram(gcpd)
if open_element_all:
pd = PhaseDiagram(entries)
chempots = pd.get_transition_chempots(open_element_all)
# print(chempots)
#all_gcpds = list()
toplot = []
# dic = {}
for idx in range(len(chempots)):
if idx == len(chempots) - 1:
avgchempot = chempots[idx] - 0.1
else:
avgchempot = 0.5 * (chempots[idx] + chempots[idx + 1])
gcpd = GrandPotentialPhaseDiagram(
entries, {open_element_all: avgchempot}, pd.elements)
# min_chempot = None if idx == len(
# chempots) - 1 else chempots[idx + 1]
# max_chempot = chempots[idx]
#gcpd = GrandPotentialPhaseDiagram(entries, {open_element_all: max_chempot}, pd.elements)
toplot.append(self.get_grand_potential_phase_diagram(gcpd))
# toplot.append(max_chempot)
#self.plot_phase_diagram(gcpd, False)
#print({open_element_all: max_chempot})
all_phase_diagrams = toplot
# print(all_phase_diagrams)
number_of_phase_diagrams = len(all_phase_diagrams)
#pd3 = PhaseDiagram(entries)
chempot_list = pd.get_transition_chempots(open_element_all)
pd_index = 0
chempots_range_of_each_phase = {}
for particular_phase_diagram in all_phase_diagrams:
chempot = chempot_list[pd_index]
if pd_index is not number_of_phase_diagrams - 1:
next_chempot = chempot_list[pd_index + 1]
else:
next_chempot = chempot_list[pd_index] - 2.0
chempot_range = [chempot, next_chempot]
phases_list = particular_phase_diagram[0]
for phase in phases_list:
if phase in chempots_range_of_each_phase.keys():
chempots_range_of_each_phase[phase][1] = next_chempot.copy(
)
else:
chempots_range_of_each_phase[phase] = chempot_range.copy()
pd_index = pd_index + 1
return chempots_range_of_each_phase
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
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.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)
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)
self.assertAlmostEqual(self.compat.process_entry(
self.entry_sulfide).correction, -0.66346)
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 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_process_entries(self):
entries = self.compat.process_entries([self.entry1,
self.entry2,
self.entry3])
self.assertEqual(len(entries), 2)
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_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)
#!/home/universe/local_env/anaconda3/envs/abinit/bin/python from pymatgen.entries.compatibility import MaterialsProjectCompatibility compat = MaterialsProjectCompatibility() processed_entries=compat.process_entries(unprocessed_entr)
