def test_queryresult(self):
qe = QueryEngine(
connection=self.conn,
database=self.db_name,
collection=self.coll_name,
)
result = qe.query(
criteria={'task_id': 'mp-1002133'},
properties=[
'calcs_reversed.output.ionic_steps.e_0_energy',
'calcs_reversed.output.ionic_steps.electronic_steps.e_0_energy',
],
)
self.assertTrue(isinstance(result, QueryResults))
print(list(qe.query(criteria={'task_id': 'mp-1002133'})))
self.assertEqual(len(result), 1)
doc = list(result)[0]
self.assertIn('calcs_reversed.output.ionic_steps.e_0_energy', doc)
v = doc['calcs_reversed.output.ionic_steps.e_0_energy']
self.assertIsInstance(v, list)
for elt in v:
self.assertIsInstance(elt, list)
for n in elt:
self.assertIsInstance(n, float)
self.assertIn(
'calcs_reversed.output.ionic_steps.electronic_steps.e_0_energy',
doc)
v = doc[
'calcs_reversed.output.ionic_steps.electronic_steps.e_0_energy']
for elt in v:
self.assertIsInstance(elt, list)
for _elt in elt:
self.assertIsInstance(_elt, list)
for n in _elt:
self.assertIsInstance(n, float)
def test_queryresult(self):
qe = QueryEngine(
connection=self.conn,
database=self.db_name,
collection=self.coll_name,
)
result = qe.query(
criteria={'task_id': 'mp-1002133'},
properties=[
'calcs_reversed.output.ionic_steps.e_0_energy',
'calcs_reversed.output.ionic_steps.electronic_steps.e_0_energy',
],
)
self.assertTrue(isinstance(result, QueryResults))
print(list(qe.query(criteria={'task_id': 'mp-1002133'})))
self.assertEqual(len(result), 1)
doc = list(result)[0]
self.assertIn('calcs_reversed.output.ionic_steps.e_0_energy', doc)
v = doc['calcs_reversed.output.ionic_steps.e_0_energy']
self.assertIsInstance(v, list)
for elt in v:
self.assertIsInstance(elt, list)
for n in elt:
self.assertIsInstance(n, float)
self.assertIn('calcs_reversed.output.ionic_steps.electronic_steps.e_0_energy', doc)
v = doc['calcs_reversed.output.ionic_steps.electronic_steps.e_0_energy']
for elt in v:
self.assertIsInstance(elt, list)
for _elt in elt:
self.assertIsInstance(_elt, list)
for n in _elt:
self.assertIsInstance(n, float)
def test_queryresult(self):
qe = QueryEngine(connection=self.conn,
database=self.db_name,
collection=self.coll_name,
aliases={},
query_post=[self.qtx], result_post=[self.rtx])
result = qe.query(criteria={'e_above_hull': {'$lte': 0.0}}).sort('sbxd.e_above_hull', pymongo.ASCENDING)
self.assertTrue(isinstance(result, QueryResults))
self.assertEqual(len(result), self.N)
self.assertTrue(result[0]['e_above_hull'] < 0)
def test_queryresult(self):
qe = QueryEngine(connection=self.conn,
database=self.db_name,
collection=self.coll_name,
aliases={},
query_post=[self.qtx],
result_post=[self.rtx])
result = qe.query(criteria={
'e_above_hull': {
'$lte': 0.0
}
}).sort('sbxd.e_above_hull', pymongo.ASCENDING)
self.assertTrue(isinstance(result, QueryResults))
self.assertEqual(len(result), self.N)
self.assertTrue(result[0]['e_above_hull'] < 0)
def test_no_post_funcs(self):
qe = QueryEngine(connection=self.conn,
database=self.db_name,
collection=self.coll_name,
aliases={},
query_post=[], result_post=[])
cursor = qe.query()
self.assertTrue(isinstance(cursor, QueryResults))
n = 0
for rec in cursor:
pprint.pprint("RESULT: {}".format(rec))
# No Post proccessing should be done
self.assertTrue('e_above_hull' not in rec)
self.assertTrue('add_fake_field' not in rec)
self.assertTrue('sbxd' in rec)
n += 1
# should find all tasks
self.assertEqual(n, self.N)
def test_no_post_funcs(self):
qe = QueryEngine(connection=self.conn,
database=self.db_name,
collection=self.coll_name,
aliases={},
query_post=[],
result_post=[])
cursor = qe.query()
self.assertTrue(isinstance(cursor, QueryResults))
n = 0
for rec in cursor:
pprint.pprint("RESULT: {}".format(rec))
# No Post proccessing should be done
self.assertTrue('e_above_hull' not in rec)
self.assertTrue('add_fake_field' not in rec)
self.assertTrue('sbxd' in rec)
n += 1
# should find all tasks
self.assertEqual(n, self.N)
def test_assimilate(self):
"""Borg assimilation code.
This takes too long for a unit test!
"""
simulate = True if VaspToDbTaskDroneTest.conn is None else False
drone = VaspToDbTaskDrone(database="creator_unittest",
simulate_mode=simulate,
parse_dos=True,
compress_dos=1)
queen = BorgQueen(drone)
queen.serial_assimilate(os.path.join(test_dir, 'db_test'))
data = queen.get_data()
self.assertEqual(len(data), 6)
if VaspToDbTaskDroneTest.conn:
db = VaspToDbTaskDroneTest.conn["creator_unittest"]
data = db.tasks.find()
self.assertEqual(data.count(), 6)
warnings.warn("Actual db insertion mode.")
for d in data:
dir_name = d['dir_name']
if dir_name.endswith("killed_mp_aflow"):
self.assertEqual(d['state'], "killed")
self.assertFalse(d['is_hubbard'])
self.assertEqual(d['pretty_formula'], "SiO2")
elif dir_name.endswith("stopped_mp_aflow"):
self.assertEqual(d['state'], "stopped")
self.assertEqual(d['pretty_formula'], "ThFe5P3")
elif dir_name.endswith("success_mp_aflow"):
self.assertEqual(d['state'], "successful")
self.assertEqual(d['pretty_formula'], "TbZn(BO2)5")
self.assertAlmostEqual(d['output']['final_energy'],
-526.66747274, 4)
elif dir_name.endswith("Li2O_aflow"):
self.assertEqual(d['state'], "successful")
self.assertEqual(d['pretty_formula'], "Li2O")
self.assertAlmostEqual(d['output']['final_energy'],
-14.31446494, 6)
self.assertEqual(len(d["calculations"]), 2)
self.assertEqual(d['input']['is_lasph'], False)
self.assertEqual(d['input']['xc_override'], None)
elif dir_name.endswith("Li2O"):
self.assertEqual(d['state'], "successful")
self.assertEqual(d['pretty_formula'], "Li2O")
self.assertAlmostEqual(d['output']['final_energy'],
-14.31337758, 6)
self.assertEqual(len(d["calculations"]), 1)
self.assertEqual(len(d["custodian"]), 1)
self.assertEqual(len(d["custodian"][0]["corrections"]), 1)
elif dir_name.endswith("Li2O_aflow_lasph"):
self.assertEqual(d['state'], "successful")
self.assertEqual(d['pretty_formula'], "Li2O")
self.assertAlmostEqual(d['output']['final_energy'], -13.998171,
6)
self.assertEqual(len(d["calculations"]), 2)
self.assertEqual(d['input']['is_lasph'], True)
self.assertEqual(d['input']['xc_override'], "PS")
if VaspToDbTaskDroneTest.conn:
warnings.warn("Testing query engine mode.")
qe = QueryEngine(database="creator_unittest")
self.assertEqual(qe.query().count(), 6)
#Test mappings by query engine.
for r in qe.query(
criteria={"pretty_formula": "Li2O"},
properties=["dir_name", "energy", "calculations",
"input"]):
if r["dir_name"].endswith("Li2O_aflow"):
self.assertAlmostEqual(r['energy'], -14.31446494, 4)
self.assertEqual(len(r["calculations"]), 2)
self.assertEqual(r["input"]["is_lasph"], False)
self.assertEqual(r['input']['xc_override'], None)
elif r["dir_name"].endswith("Li2O"):
self.assertAlmostEqual(r['energy'], -14.31337758, 4)
self.assertEqual(len(r["calculations"]), 1)
self.assertEqual(r["input"]["is_lasph"], False)
self.assertEqual(r['input']['xc_override'], None)
#Test lasph
e = qe.get_entries({"dir_name": {"$regex": "lasph"}})
self.assertEqual(len(e), 1)
self.assertEqual(e[0].parameters["is_lasph"], True)
self.assertEqual(e[0].parameters["xc_override"], "PS")
# Test query one.
d = qe.query_one(criteria={"pretty_formula": "TbZn(BO2)5"},
properties=["energy"])
self.assertAlmostEqual(d['energy'], -526.66747274, 4)
d = qe.get_entries_in_system(["Li", "O"])
self.assertEqual(len(d), 3)
self.assertIsInstance(d[0], ComputedEntry)
s = qe.get_structure_from_id(d[0].entry_id)
self.assertIsInstance(s, Structure)
self.assertEqual(s.formula, "Li2 O1")
self.assertIsInstance(qe.get_dos_from_id(d[0].entry_id),
CompleteDos)
def test_assimilate(self):
simulate = True if VaspToDbTaskDroneTest.conn is None else False
drone = VaspToDbTaskDrone(database="creator_unittest",
simulate_mode=simulate)
queen = BorgQueen(drone)
queen.serial_assimilate(os.path.join(test_dir, 'db_test'))
data = queen.get_data()
self.assertEqual(len(data), 5)
if VaspToDbTaskDroneTest.conn:
db = VaspToDbTaskDroneTest.conn["creator_unittest"]
data = db.tasks.find()
self.assertEqual(data.count(), 5)
warnings.warn("Actual db insertion mode.")
for d in data:
dir_name = d['dir_name']
if dir_name.endswith("killed_mp_aflow"):
self.assertEqual(d['state'], "killed")
self.assertFalse(d['is_hubbard'])
self.assertEqual(d['pretty_formula'], "SiO2")
elif dir_name.endswith("stopped_mp_aflow"):
self.assertEqual(d['state'], "stopped")
self.assertEqual(d['pretty_formula'], "ThFe5P3")
elif dir_name.endswith("success_mp_aflow"):
self.assertEqual(d['state'], "successful")
self.assertEqual(d['pretty_formula'], "TbZn(BO2)5")
self.assertAlmostEqual(d['output']['final_energy'],
-526.66747274, 4)
elif dir_name.endswith("Li2O_aflow"):
self.assertEqual(d['state'], "successful")
self.assertEqual(d['pretty_formula'], "Li2O")
self.assertAlmostEqual(d['output']['final_energy'],
-14.31446494, 6)
self.assertEqual(len(d["calculations"]), 2)
elif dir_name.endswith("Li2O"):
self.assertEqual(d['state'], "successful")
self.assertEqual(d['pretty_formula'], "Li2O")
self.assertAlmostEqual(d['output']['final_energy'],
-14.31337758, 6)
self.assertEqual(len(d["calculations"]), 1)
self.assertEqual(len(d["custodian"]), 1)
self.assertEqual(len(d["custodian"][0]["corrections"]), 1)
if VaspToDbTaskDroneTest.conn:
warnings.warn("Testing query engine mode.")
qe = QueryEngine(database="creator_unittest")
self.assertEqual(qe.query().count(), 5)
#Test mappings by query engine.
for r in qe.query(criteria={"pretty_formula": "Li2O"},
properties=["dir_name", "energy",
"calculations"]):
if r["dir_name"].endswith("Li2O_aflow"):
self.assertAlmostEqual(r['energy'], -14.31446494, 4)
self.assertEqual(len(r["calculations"]), 2)
elif r["dir_name"].endswith("Li2O"):
self.assertAlmostEqual(r['energy'],
-14.31337758, 4)
self.assertEqual(len(r["calculations"]), 1)
# Test query one.
d = qe.query_one(criteria={"pretty_formula": "TbZn(BO2)5"},
properties=["energy"])
self.assertAlmostEqual(d['energy'], -526.66747274, 4)
d = qe.get_entries_in_system(["Li", "O"])
self.assertEqual(len(d), 2)
self.assertIsInstance(d[0], ComputedEntry)
s = qe.get_structure_from_id(d[0].entry_id)
self.assertIsInstance(s, Structure)
self.assertEqual(s.formula, "Li2 O1")
def test_assimilate(self):
"""Borg assimilation code.
This takes too long for a unit test!
"""
simulate = True if VaspToDbTaskDroneTest.conn is None else False
drone = VaspToDbTaskDrone(database="creator_unittest",
simulate_mode=simulate,
parse_dos=True, compress_dos=1)
queen = BorgQueen(drone)
queen.serial_assimilate(os.path.join(test_dir, 'db_test'))
data = queen.get_data()
self.assertEqual(len(data), 6)
if VaspToDbTaskDroneTest.conn:
db = VaspToDbTaskDroneTest.conn["creator_unittest"]
data = db.tasks.find()
self.assertEqual(data.count(), 6)
warnings.warn("Actual db insertion mode.")
for d in data:
dir_name = d['dir_name']
if dir_name.endswith("killed_mp_aflow"):
self.assertEqual(d['state'], "killed")
self.assertFalse(d['is_hubbard'])
self.assertEqual(d['pretty_formula'], "SiO2")
elif dir_name.endswith("stopped_mp_aflow"):
self.assertEqual(d['state'], "stopped")
self.assertEqual(d['pretty_formula'], "ThFe5P3")
elif dir_name.endswith("success_mp_aflow"):
self.assertEqual(d['state'], "successful")
self.assertEqual(d['pretty_formula'], "TbZn(BO2)5")
self.assertAlmostEqual(d['output']['final_energy'],
-526.66747274, 4)
elif dir_name.endswith("Li2O_aflow"):
self.assertEqual(d['state'], "successful")
self.assertEqual(d['pretty_formula'], "Li2O")
self.assertAlmostEqual(d['output']['final_energy'],
-14.31446494, 6)
self.assertEqual(len(d["calculations"]), 2)
self.assertEqual(d['input']['is_lasph'], False)
self.assertEqual(d['input']['xc_override'], None)
self.assertEqual(d["oxide_type"], "oxide")
elif dir_name.endswith("Li2O"):
self.assertEqual(d['state'], "successful")
self.assertEqual(d['pretty_formula'], "Li2O")
self.assertAlmostEqual(d['output']['final_energy'],
-14.31337758, 6)
self.assertEqual(len(d["calculations"]), 1)
self.assertEqual(len(d["custodian"]), 1)
self.assertEqual(len(d["custodian"][0]["corrections"]), 1)
elif dir_name.endswith("Li2O_aflow_lasph"):
self.assertEqual(d['state'], "successful")
self.assertEqual(d['pretty_formula'], "Li2O")
self.assertAlmostEqual(d['output']['final_energy'],
-13.998171, 6)
self.assertEqual(len(d["calculations"]), 2)
self.assertEqual(d['input']['is_lasph'], True)
self.assertEqual(d['input']['xc_override'], "PS")
if VaspToDbTaskDroneTest.conn:
warnings.warn("Testing query engine mode.")
qe = QueryEngine(database="creator_unittest")
self.assertEqual(qe.query().count(), 6)
#Test mappings by query engine.
for r in qe.query(criteria={"pretty_formula": "Li2O"},
properties=["dir_name", "energy",
"calculations", "input"]):
if r["dir_name"].endswith("Li2O_aflow"):
self.assertAlmostEqual(r['energy'], -14.31446494, 4)
self.assertEqual(len(r["calculations"]), 2)
self.assertEqual(r["input"]["is_lasph"], False)
self.assertEqual(r['input']['xc_override'], None)
self.assertEqual(d["oxide_type"], "oxide")
elif r["dir_name"].endswith("Li2O"):
self.assertAlmostEqual(r['energy'],
-14.31337758, 4)
self.assertEqual(len(r["calculations"]), 1)
self.assertEqual(r["input"]["is_lasph"], False)
self.assertEqual(r['input']['xc_override'], None)
# Test lasph
e = qe.get_entries({"dir_name":{"$regex":"lasph"}})
self.assertEqual(len(e), 1)
self.assertEqual(e[0].parameters["is_lasph"], True)
self.assertEqual(e[0].parameters["xc_override"], "PS")
# Test query one.
d = qe.query_one(criteria={"pretty_formula": "TbZn(BO2)5"},
properties=["energy"])
self.assertAlmostEqual(d['energy'], -526.66747274, 4)
d = qe.get_entries_in_system(["Li", "O"])
self.assertEqual(len(d), 3)
self.assertIsInstance(d[0], ComputedEntry)
self.assertEqual(d[0].data["oxide_type"], "oxide")
s = qe.get_structure_from_id(d[0].entry_id)
self.assertIsInstance(s, Structure)
self.assertEqual(s.formula, "Li2 O1")
self.assertIsInstance(qe.get_dos_from_id(d[0].entry_id), CompleteDos)
