def run_task(self, fw_spec):
user_incar_settings = self["user_incar_settings"]
interpolation_type = self.get("interpolation_type", "IDPP")
idpp_species = fw_spec.get("idpp_species")
user_kpoints_settings = self.get("user_kpoints_settings")
try:
ep0 = Structure.from_dict(fw_spec["ep0"])
ep1 = Structure.from_dict(fw_spec["ep1"])
except:
ep0 = fw_spec["ep0"]
ep1 = fw_spec["ep1"]
# Get number of images.
nimages = user_incar_settings.get("IMAGES", self._get_nimages(ep0, ep1))
if interpolation_type == "IDPP":
from pymatgen_diffusion.neb.pathfinder import IDPPSolver
obj = IDPPSolver.from_endpoints([ep0, ep1], nimages=nimages)
images = obj.run(species=idpp_species)
images_dic_list = [image.as_dict() for image in images]
elif interpolation_type == "linear":
images = self._get_images_by_linear_interp(nimages, ep0, ep1)
images_dic_list = [i.as_dict() for i in images]
else:
raise ValueError("The interpolation method must either be 'linear' or 'IDPP'!")
write = WriteNEBFromImages(neb_label='1', user_incar_settings=user_incar_settings,
user_kpoints_settings=user_kpoints_settings)
fw_spec["neb"] = [images_dic_list]
write.run_task(fw_spec=fw_spec)
def test_disordered_primitive_to_ordered_supercell(self):
sm_atoms = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=True,
attempt_supercell=True,
allow_subset=True,
supercell_size = 'num_atoms',
comparator=OrderDisorderElementComparator())
sm_sites = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=True,
attempt_supercell=True,
allow_subset=True,
supercell_size = 'num_sites',
comparator=OrderDisorderElementComparator())
lp = Lattice.orthorhombic(10, 20, 30)
pcoords = [[0, 0, 0],
[0.5, 0.5, 0.5]]
ls = Lattice.orthorhombic(20,20,30)
scoords = [[0, 0, 0],
[0.75, 0.5, 0.5]]
prim = Structure(lp, [{'Na':0.5}, {'Cl':0.5}], pcoords)
supercell = Structure(ls, ['Na', 'Cl'], scoords)
supercell.make_supercell([[-1,1,0],[0,1,1],[1,0,0]])
self.assertFalse(sm_sites.fit(prim, supercell))
self.assertTrue(sm_atoms.fit(prim, supercell))
self.assertRaises(ValueError, sm_atoms.get_s2_like_s1, prim, supercell)
self.assertEqual(len(sm_atoms.get_s2_like_s1(supercell, prim)), 4)
def setUp(self):
c1 = [[0.5] * 3, [0.9] * 3]
c2 = [[0.5] * 3, [0.9, 0.1, 0.1]]
s1 = Structure(Lattice.cubic(5), ['Si', 'Si'], c1)
s2 = Structure(Lattice.cubic(5), ['Si', 'Si'], c2)
structs = []
for s in s1.interpolate(s2, 3, pbc=True):
structs.append(Structure.from_sites(s.sites, to_unit_cell=True))
self.structures = structs
self.vis = MITNEBSet(self.structures)
def test_supercell_fit(self):
sm = StructureMatcher(attempt_supercell=False)
s1 = Structure.from_file(os.path.join(test_dir, "Al3F9.json"))
s2 = Structure.from_file(os.path.join(test_dir, "Al3F9_distorted.json"))
self.assertFalse(sm.fit(s1, s2))
sm = StructureMatcher(attempt_supercell=True)
self.assertTrue(sm.fit(s1, s2))
self.assertTrue(sm.fit(s2, s1))
def test_get_supercell_matrix(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=True,
attempt_supercell=True)
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Si', 'Si', 'Ag'],
[[0,0,0.1],[0,0,0.2],[.7,.4,.5]])
s1.make_supercell([2,1,1])
s2 = Structure(l, ['Si', 'Si', 'Ag'],
[[0,0.1,0],[0,0.1,-0.95],[-.7,.5,.375]])
result = sm.get_supercell_matrix(s1, s2)
self.assertTrue((result == [[-2,0,0],[0,1,0],[0,0,1]]).all())
def test_electronegativity(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5)
s1 = Structure.from_file(os.path.join(test_dir, "Na2Fe2PAsO4S4.json"))
s2 = Structure.from_file(os.path.join(test_dir, "Na2Fe2PNO4Se4.json"))
self.assertEqual(sm.get_best_electronegativity_anonymous_mapping(s1, s2),
{Element('S'): Element('Se'),
Element('As'): Element('N'),
Element('Fe'): Element('Fe'),
Element('Na'): Element('Na'),
Element('P'): Element('P'),
Element('O'): Element('O'),})
self.assertEqual(len(sm.get_all_anonymous_mappings(s1, s2)), 2)
def test_predict(self):
s = PymatgenTest.get_structure("CsCl")
nacl = PymatgenTest.get_structure("CsCl")
nacl.replace_species({"Cs": "Na"})
nacl.scale_lattice(184.384551033)
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(s, nacl), 342.84905395082535)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(s, nacl), 391.884366481)
lif = PymatgenTest.get_structure("CsCl")
lif.replace_species({"Cs": "Li", "Cl": "F"})
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(lif, nacl), 74.268402413690467)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(lif, nacl), 62.2808125839)
lfpo = PymatgenTest.get_structure("LiFePO4")
lmpo = PymatgenTest.get_structure("LiFePO4")
lmpo.replace_species({"Fe": "Mn"})
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(lmpo, lfpo), 310.08253254420134)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(lmpo, lfpo), 299.607967711)
sto = PymatgenTest.get_structure("SrTiO3")
scoo = PymatgenTest.get_structure("SrTiO3")
scoo.replace_species({"Ti4+": "Co4+"})
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(scoo, sto), 56.162534974936463)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(scoo, sto), 57.4777835108)
# Use Ag7P3S11 as a test case:
# (i) no oxidation states are assigned and CVP-atomic scheme is selected.
aps = Structure.from_file(os.path.join(dir_path,
"Ag7P3S11_mp-683910_primitive.cif"))
apo = Structure.from_file(os.path.join(dir_path,
"Ag7P3S11_mp-683910_primitive.cif"))
apo.replace_species({"S": "O"})
p = RLSVolumePredictor(radii_type="atomic", check_isostructural=False)
self.assertAlmostEqual(p.predict(apo, aps), 1196.31384276)
# (ii) Oxidation states are assigned.
apo.add_oxidation_state_by_element({"Ag": 1, "P": 5, "O": -2})
aps.add_oxidation_state_by_element({"Ag": 1, "P": 5, "S": -2})
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(apo, aps), 1165.23259079)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(apo, aps), 1196.31384276)
def test_find_match2(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5, primitive_cell=True, scale=True, attempt_supercell=False)
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ["Si", "Si"], [[0, 0, 0.1], [0, 0, 0.2]])
s2 = Structure(l, ["Si", "Si"], [[0, 0.1, 0], [0, 0.1, -0.95]])
s1, s2, fu, s1_supercell = sm._preprocess(s1, s2, False)
match = sm._strict_match(s1, s2, fu, s1_supercell=False, use_rms=True, break_on_match=False)
scale_matrix = match[2]
s2.make_supercell(scale_matrix)
s2.translate_sites(range(len(s2)), match[3])
self.assertAlmostEqual(np.sum(s2.frac_coords), 0.3)
self.assertAlmostEqual(np.sum(s2.frac_coords[:, :2]), 0)
def test_writebandstr(self):
filepath = os.path.join(test_dir, 'CsI3Pb.cif')
structure = Structure.from_file(filepath)
excin = ExcitingInput(structure)
string = excin.write_string('primitive', bandstr=True)
bandstr = string.split('<properties>')[1].split('</properties>')[0]
coord = []
label = []
coord_ref = [[0.0, 0.0, 0.0], [0.5, 0.0, 0.0], [0.5, 0.5, 0.0],
[0.0, 0.5, 0.0],
[0.0, 0.0, 0.0], [0.0, 0.0, 0.5], [0.5, 0.0, 0.5],
[0.5, 0.5, 0.5],
[0.0, 0.5, 0.5], [0.0, 0.0, 0.5], [0.0, 0.5, 0.0],
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5], [0.5, 0.0, 0.0], [0.5, 0.5, 0.0],
[0.5, 0.5, 0.5]]
label_ref = ['GAMMA', 'X', 'S', 'Y', 'GAMMA', 'Z', 'U', 'R', 'T', 'Z',
'Y', 'T',
'U', 'X', 'S', 'R']
root = ET.fromstring(bandstr)
for plot1d in root.iter('plot1d'):
for point in plot1d.iter('point'):
coord.append([float(i) for i in point.get('coord').split()])
label.append(point.get('label'))
self.assertEqual(label, label_ref)
self.assertEqual(coord, coord_ref)
def test_find_match1(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5, primitive_cell=True, scale=True, attempt_supercell=False)
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ["Si", "Si", "Ag"], [[0, 0, 0.1], [0, 0, 0.2], [0.7, 0.4, 0.5]])
s2 = Structure(l, ["Si", "Si", "Ag"], [[0, 0.1, 0], [0, 0.1, -0.95], [0.7, 0.5, 0.375]])
s1, s2, fu, s1_supercell = sm._preprocess(s1, s2, False)
match = sm._strict_match(s1, s2, fu, s1_supercell=True, use_rms=True, break_on_match=False)
scale_matrix = match[2]
s2.make_supercell(scale_matrix)
fc = s2.frac_coords + match[3]
fc -= np.round(fc)
self.assertAlmostEqual(np.sum(fc), 0.9)
self.assertAlmostEqual(np.sum(fc[:, :2]), 0.1)
cart_dist = np.sum(match[1] * (l.volume / 3) ** (1 / 3))
self.assertAlmostEqual(cart_dist, 0.15)
def setUp(self):
with open(os.path.join(test_dir, "TiO2_entries.json"), 'r') as fp:
entries = json.load(fp, cls=MontyDecoder)
self.struct_list = [e.structure for e in entries]
self.oxi_structs = [self.get_structure("Li2O"),
Structure.from_file(os.path.join(
test_dir, "POSCAR.Li2O"))]
def from_dict(cls, d):
structure = Structure.from_dict(d["structure"])
return cls(structure, np.array(d["displacements"]), specie=d["specie"],
temperature=d["temperature"], time_step=d["time_step"],
step_skip=d["step_skip"], min_obs=d["min_obs"],
smoothed=d.get("smoothed", "max"),
avg_nsteps=d.get("avg_nsteps", 1000))
def test_electronegativity(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5)
s1 = Structure.from_file(os.path.join(test_dir, "Na2Fe2PAsO4S4.json"))
s2 = Structure.from_file(os.path.join(test_dir, "Na2Fe2PNO4Se4.json"))
self.assertEqual(
sm.get_best_electronegativity_anonymous_mapping(s1, s2),
{
Element("S"): Element("Se"),
Element("As"): Element("N"),
Element("Fe"): Element("Fe"),
Element("Na"): Element("Na"),
Element("P"): Element("P"),
Element("O"): Element("O"),
},
)
self.assertEqual(len(sm.get_all_anonymous_mappings(s1, s2)), 2)
def from_dict(cls, d):
"""
As in :Class: `pymatgen.core.Structure` except
restoring graphs using `from_dict_of_dicts`
from NetworkX to restore graph information.
"""
s = Structure.from_dict(d['structure'])
return cls(s, d['graphs'])
def test_ignore_species(self):
s1 = Structure.from_file(os.path.join(test_dir, "LiFePO4.cif"))
s2 = Structure.from_file(os.path.join(test_dir, "POSCAR"))
m = StructureMatcher(ignored_species=["Li"], primitive_cell=False, attempt_supercell=True)
self.assertTrue(m.fit(s1, s2))
self.assertTrue(m.fit_anonymous(s1, s2))
groups = m.group_structures([s1, s2])
self.assertEqual(len(groups), 1)
s2.make_supercell((2, 1, 1))
ss1 = m.get_s2_like_s1(s2, s1, include_ignored_species=True)
self.assertAlmostEqual(ss1.lattice.a, 20.820740000000001)
self.assertEqual(ss1.composition.reduced_formula, "LiFePO4")
self.assertEqual(
{k.symbol: v.symbol for k, v in m.get_best_electronegativity_anonymous_mapping(s1, s2).items()},
{"Fe": "Fe", "P": "P", "O": "O"},
)
def test_find_match2(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=True, scale=True,
attempt_supercell=False)
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Si', 'Si'], [[0,0,0.1],[0,0,0.2]])
s2 = Structure(l, ['Si', 'Si'], [[0,0.1,0],[0,0.1,-0.95]])
match = sm._find_match(s1, s2, break_on_match = False,
use_rms = True, niggli = False)
scale_matrix = np.round(np.dot(match[2].matrix,
s2.lattice.inv_matrix)).astype('int')
s2.make_supercell(scale_matrix)
fc = s2.frac_coords + match[3]
fc -= np.round(fc)
self.assertAlmostEqual(np.sum(fc), 0.3)
self.assertAlmostEqual(np.sum(fc[:,:2]), 0)
def setUp(self):
"""
1) Basic check for pymatgen configurations.
2) Setup all test workflow.
"""
super(TestNudgedElasticBandWorkflow, self).setUp()
# Structures used for test:
parent = PymatgenTest.get_structure("Li2O")
parent.remove_oxidation_states()
parent.make_supercell(2)
ep0, ep1 = get_endpoints_from_index(parent, [0, 1])
neb_dir = [os.path.join(module_dir, "..", "..", "test_files", "neb_wf", "4", "inputs", "{:02}",
"POSCAR").format(i) for i in range(5)]
self.structures = [Structure.from_file(n) for n in neb_dir]
# Run fake vasp
test_yaml = os.path.join(module_dir, "../../test_files/neb_wf/config/neb_unittest.yaml")
with open(test_yaml, 'r') as stream:
self.config = yaml.safe_load(stream)
# Use scratch directory as destination directory for testing
self.config["common_params"]["_fw_env"] = {"run_dest_root": self.scratch_dir}
# Config 1: The parent structure & two endpoint indexes provided; need relaxation first.
self.config_1 = copy.deepcopy(self.config)
self.config_1["common_params"]["is_optimized"] = False
self.config_1["common_params"]["wf_name"] = "NEB_test_1"
# Config 2: The parent structure & two endpoint indexes provided; no need to relax.
self.config_2 = copy.deepcopy(self.config)
del self.config_2["fireworks"][0]
self.config_2["common_params"]["is_optimized"] = True
self.config_2["common_params"]["wf_name"] = "NEB_test_2"
# Config 3: Two endpoints provided; need to relax two endpoints.
self.config_3 = copy.deepcopy(self.config)
del self.config_3["fireworks"][0]
self.config_3["common_params"]["is_optimized"] = False
self.config_3["common_params"]["wf_name"] = "NEB_test_3"
# Config 4: Two relaxed endpoints provided; no need to relax two endpoints.
self.config_4 = copy.deepcopy(self.config_3)
del self.config_4["fireworks"][0]
self.config_4["common_params"]["is_optimized"] = True
self.config_4["common_params"]["wf_name"] = "NEB_test_4"
# Config 5: All images including two endpoints are provided.
self.config_5 = copy.deepcopy(self.config)
del self.config_5["fireworks"][0: 2]
self.config_5["common_params"]["wf_name"] = "NEB_test_5"
self.wf_1 = wf_nudged_elastic_band([parent], parent, self.config_1)
self.wf_2 = wf_nudged_elastic_band([parent], parent, self.config_2)
self.wf_3 = wf_nudged_elastic_band([ep0, ep1], parent, self.config_3)
self.wf_4 = wf_nudged_elastic_band([ep0, ep1], parent, self.config_4)
self.wf_5 = wf_nudged_elastic_band(self.structures, parent, self.config_5)
# Workflow without the config file
self.wf_6 = wf_nudged_elastic_band(self.structures, parent)
def test_get_mapping(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=True,
attempt_supercell=False,
allow_subset = True)
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Ag', 'Si', 'Si'],
[[.7,.4,.5],[0,0,0.1],[0,0,0.2]])
s1.make_supercell([2,1,1])
s2 = Structure(l, ['Si', 'Si', 'Ag'],
[[0,0.1,-0.95],[0,0.1,0],[-.7,.5,.375]])
shuffle = [2,0,1,3,5,4]
s1 = Structure.from_sites([s1[i] for i in shuffle])
#test the mapping
s2.make_supercell([2,1,1])
#equal sizes
for i, x in enumerate(sm.get_mapping(s1, s2)):
self.assertEqual(s1[x].species_and_occu,
s2[i].species_and_occu)
del s1[0]
#s1 is subset of s2
for i, x in enumerate(sm.get_mapping(s2, s1)):
self.assertEqual(s1[i].species_and_occu,
s2[x].species_and_occu)
#s2 is smaller than s1
del s2[0]
del s2[1]
self.assertRaises(ValueError, sm.get_mapping, s2, s1)
def test_get_s2_like_s1(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=True,
attempt_supercell=True)
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Si', 'Si', 'Ag'],
[[0,0,0.1],[0,0,0.2],[.7,.4,.5]])
s1.make_supercell([2,1,1])
s2 = Structure(l, ['Si', 'Si', 'Ag'],
[[0,0.1,0],[0,0.1,-0.95],[-.7,.5,.375]])
result = sm.get_s2_like_s1(s1, s2)
self.assertEqual(len(find_in_coord_list_pbc(result.frac_coords,
[0.35,0.4,0.5])), 1)
self.assertEqual(len(find_in_coord_list_pbc(result.frac_coords,
[0,0,0.125])), 1)
self.assertEqual(len(find_in_coord_list_pbc(result.frac_coords,
[0,0,0.175])), 1)
def test_electronegativity(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5)
s1 = Structure.from_file(os.path.join(test_dir, "Na2Fe2PAsO4S4.json"))
s2 = Structure.from_file(os.path.join(test_dir, "Na2Fe2PNO4Se4.json"))
self.assertEqual(sm.get_best_electronegativity_anonymous_mapping(s1, s2),
{Element('S'): Element('Se'),
Element('As'): Element('N'),
Element('Fe'): Element('Fe'),
Element('Na'): Element('Na'),
Element('P'): Element('P'),
Element('O'): Element('O'),})
self.assertEqual(len(sm.get_all_anonymous_mappings(s1, s2)), 2)
# test include_dist
dists = {Element('N'): 0, Element('P'): 0.0010725064}
for mapping, d in sm.get_all_anonymous_mappings(s1, s2, include_dist=True):
self.assertAlmostEqual(dists[mapping[Element('As')]], d)
def setUp(self):
filepath = os.path.join(test_dir, 'Li.cif')
self.s = Structure.from_file(filepath)
self.bulk = MVLGBSet(self.s)
self.slab = MVLGBSet(self.s, slab_mode=True)
self.d_bulk = self.bulk.all_input
self.d_slab = self.slab.all_input
def setUp(self):
filepath = self.TEST_FILES_DIR / 'Li.cif'
self.s = Structure.from_file(filepath)
self.bulk = MVLGBSet(self.s)
self.slab = MVLGBSet(self.s, slab_mode=True)
self.d_bulk = self.bulk.get_vasp_input()
self.d_slab = self.slab.get_vasp_input()
warnings.simplefilter("ignore")
def test_get_s2_large_s2(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=False,
attempt_supercell=True, allow_subset=False,
supercell_size='volume')
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Ag', 'Si', 'Si'],
[[.7,.4,.5],[0,0,0.1],[0,0,0.2]])
l2 = Lattice.orthorhombic(1.01, 2.01, 3.01)
s2 = Structure(l2, ['Si', 'Si', 'Ag'],
[[0,0.1,-0.95],[0,0.1,0],[-.7,.5,.375]])
s2.make_supercell([[0,-1,0],[1,0,0],[0,0,1]])
result = sm.get_s2_like_s1(s1, s2)
for x,y in zip(s1, result):
self.assertLess(x.distance(y), 0.08)
def handle_subcommand_test_relax(args):
default_commands = {
'lammps': 'lammps'
}
command = args.command if args.command else default_commands.get(args.software)
predict = Predict(calculator=args.software, command=command, num_workers=1)
potential = Potential.from_file(args.potential)
structure = get_structure(args.structure)
import warnings
warnings.filterwarnings("ignore") # yes I have sinned
sga = SpacegroupAnalyzer(structure)
conventional_structure = sga.get_conventional_standard_structure()
old_lattice, new_lattice = predict.lattice_constant(conventional_structure, potential)
equilibrium_structure = Structure(
new_lattice,
[s.specie.element for s in conventional_structure.sites],
[s.frac_coords for s in conventional_structure.sites])
equilibrium_structure.to(filename=args.output_filename)
def handle_input_event(self, abiinput, outdir, event):
try:
old_abiinput = abiinput.deepcopy()
# Read the last structure dumped by ABINIT before aborting.
filepath = outdir.has_abiext("DILATMX_STRUCT.nc")
last_structure = Structure.from_file(filepath)
abiinput.set_structure(last_structure)
return Correction(self, self.compare_inputs(abiinput, old_abiinput), event, False)
except Exception as exc:
logger.warning('Error while trying to apply the handler {}.'.format(str(self)), exc)
return None
def test_metal_check(self):
structure = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3),
["Cu"], [[0, 0, 0]])
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger a warning.
vis = MITRelaxSet(structure)
incar = vis.incar
# Verify some things
self.assertIn("ISMEAR", str(w[-1].message))
def test_mix(self):
structures = [self.get_structure("Li2O"), self.get_structure("Li2O2"), self.get_structure("LiFePO4")]
for fname in ["POSCAR.Li2O", "POSCAR.LiFePO4"]:
structures.append(Structure.from_file(os.path.join(test_dir, fname)))
sm = StructureMatcher(comparator=ElementComparator())
groups = sm.group_structures(structures)
for g in groups:
formula = g[0].composition.reduced_formula
if formula in ["Li2O", "LiFePO4"]:
self.assertEqual(len(g), 2)
else:
self.assertEqual(len(g), 1)
def test_get_supercell_matrix(self):
sm = StructureMatcher(ltol=0.1, stol=0.3, angle_tol=2, primitive_cell=False, scale=True, attempt_supercell=True)
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ["Si", "Si", "Ag"], [[0, 0, 0.1], [0, 0, 0.2], [0.7, 0.4, 0.5]])
s1.make_supercell([2, 1, 1])
s2 = Structure(l, ["Si", "Si", "Ag"], [[0, 0.1, 0], [0, 0.1, -0.95], [-0.7, 0.5, 0.375]])
result = sm.get_supercell_matrix(s1, s2)
self.assertTrue((result == [[-2, 0, 0], [0, 1, 0], [0, 0, 1]]).all())
s1 = Structure(l, ["Si", "Si", "Ag"], [[0, 0, 0.1], [0, 0, 0.2], [0.7, 0.4, 0.5]])
s1.make_supercell([[1, -1, 0], [0, 0, -1], [0, 1, 0]])
s2 = Structure(l, ["Si", "Si", "Ag"], [[0, 0.1, 0], [0, 0.1, -0.95], [-0.7, 0.5, 0.375]])
result = sm.get_supercell_matrix(s1, s2)
self.assertTrue((result == [[-1, -1, 0], [0, 0, -1], [0, 1, 0]]).all())
# test when the supercell is a subset
sm = StructureMatcher(
ltol=0.1, stol=0.3, angle_tol=2, primitive_cell=False, scale=True, attempt_supercell=True, allow_subset=True
)
del s1[0]
result = sm.get_supercell_matrix(s1, s2)
self.assertTrue((result == [[-1, -1, 0], [0, 0, -1], [0, 1, 0]]).all())
def test_ordering_enumeration(self):
# simple afm
structure = Structure.from_file(
os.path.join(test_dir, "magnetic_orderings/LaMnO3.json"))
enumerator = MagneticStructureEnumerator(structure)
self.assertEqual(enumerator.input_origin, "afm")
# ferrimagnetic (Cr produces net spin)
structure = Structure.from_file(
os.path.join(test_dir, "magnetic_orderings/Cr2NiO4.json"))
enumerator = MagneticStructureEnumerator(structure)
self.assertEqual(enumerator.input_origin, "ferri_by_Cr")
# antiferromagnetic on single magnetic site
structure = Structure.from_file(
os.path.join(test_dir, "magnetic_orderings/Cr2WO6.json"))
enumerator = MagneticStructureEnumerator(structure)
self.assertEqual(enumerator.input_origin, "afm_by_Cr")
# afm requiring large cell size
# (enable for further development of workflow, too slow for CI)
# structure = Structure.from_file(os.path.join(ref_dir, "CuO.json"))
# enumerator = MagneticOrderingsenumerator(structure, default_magmoms={'Cu': 1.73},
# transformation_kwargs={'max_cell_size': 4})
# self.assertEqual(enumerator.input_origin, "afm")
# antiferromagnetic by structural motif
structure = Structure.from_file(
os.path.join(test_dir, "magnetic_orderings/Ca3Co2O6.json"))
enumerator = MagneticStructureEnumerator(
structure,
strategies=("antiferromagnetic_by_motif",),
# this example just misses default cut-off, so do not truncate
truncate_by_symmetry=False,
transformation_kwargs={"max_cell_size": 2},
)
self.assertEqual(enumerator.input_origin, "afm_by_motif_2a")
def run_task(self, fw_spec):
user_incar_settings = self.get("user_incar_settings", {})
user_kpoints_settings = self.get("user_kpoints_settings", {})
neb_label = self.get("neb_label")
assert neb_label.isdigit() and int(neb_label) >= 1
images = fw_spec["neb"][int(neb_label) - 1]
try:
images = [Structure.from_dict(i) for i in images]
except:
images = images
vis = MVLCINEBSet(images, user_incar_settings=user_incar_settings,
user_kpoints_settings=user_kpoints_settings)
vis.write_input(".")
def substrate(self) -> Structure:
"""
A pymatgen Structure for just the substrate
"""
return Structure.from_sites(self.substrate_sites)
# load data
cif_path = path.normpath(path.join(getcwd(), args.cif_data))
cif_data = h5py.File(cif_path, "r")
battery_table = pd.read_csv(args.battery_data, index_col=False)
element_data = ElementDataSingleton.get_instance(
element_data_path=args.element_data)
# create features
features = np.zeros((len(battery_table), NUM_OF_FEATURE))
for i, (id_charge, id_discharge, ion) in tqdm(
enumerate(
zip(battery_table['id_charge'], battery_table['id_discharge'],
battery_table['working_ion']))):
# load crystal object from cif
charge_crystal = Structure.from_str(cif_data[id_charge].value, 'cif')
discharge_crystal = Structure.from_str(cif_data[id_discharge].value,
'cif')
# specific features
finder = SpacegroupAnalyzer(charge_crystal)
space_group_feat = np.array([finder.get_space_group_number()])
crystal_system_feat = create_feature_from_crystal_system(
finder.get_crystal_system())
ion_feat = create_feature_from_wokring_ion(ion)
dischr_comp = Composition(discharge_crystal.formula)
ion_concentrate = np.array(
[dischr_comp.get_atomic_fraction(Element(ion))])
# calculate features from element property
charge_formula = charge_crystal.formula
class CollinearMagneticStructureAnalyzerTest(unittest.TestCase):
def setUp(self):
parser = CifParser(os.path.join(test_dir, 'Fe.cif'))
self.Fe = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'LiFePO4.cif'))
self.LiFePO4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'Fe3O4.cif'))
self.Fe3O4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'magnetic.ncl.example.GdB4.mcif'))
self.GdB4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'magnetic.example.NiO.mcif'))
self.NiO_expt = parser.get_structures()[0]
latt = Lattice.cubic(4.17)
species = ["Ni", "O"]
coords = [[0, 0, 0],
[0.5, 0.5, 0.5]]
self.NiO = Structure.from_spacegroup(225, latt, species, coords)
latt = Lattice([[2.085, 2.085, 0.0],
[0.0, -2.085, -2.085],
[-2.085, 2.085, -4.17]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0, 0.5],
[0, 0, 0],
[0.25, 0.5, 0.25],
[0.75, 0.5, 0.75]]
self.NiO_AFM_111 = Structure(latt, species, coords,
site_properties={'magmom': [-5, 5, 0, 0]})
latt = Lattice([[2.085, 2.085, 0],
[0, 0, -4.17],
[-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5],
[0, 0, 0],
[0, 0.5, 0],
[0.5, 0, 0.5]]
self.NiO_AFM_001 = Structure(latt, species, coords,
site_properties={'magmom': [-5, 5, 0, 0]})
latt = Lattice([[2.085, 2.085, 0],
[0, 0, -4.17],
[-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5],
[0, 0, 0],
[0, 0.5, 0],
[0.5, 0, 0.5]]
self.NiO_AFM_001_opposite = Structure(latt, species, coords,
site_properties={'magmom': [5, -5, 0, 0]})
latt = Lattice([[2.085, 2.085, 0],
[0, 0, -4.17],
[-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5],
[0, 0, 0],
[0, 0.5, 0],
[0.5, 0, 0.5]]
self.NiO_unphysical = Structure(latt, species, coords,
site_properties={'magmom': [-3, 0, 0, 0]})
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
def test_get_representations(self):
# tests to convert between storing magnetic moment information
# on site_properties or on Species 'spin' property
# test we store magnetic moments on site properties
self.Fe.add_site_property('magmom', [5])
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertEqual(msa.structure.site_properties['magmom'][0], 5)
# and that we can retrieve a spin representaiton
Fe_spin = msa.get_structure_with_spin()
self.assertFalse('magmom' in Fe_spin.site_properties)
self.assertEqual(Fe_spin[0].specie.spin, 5)
# test we can remove magnetic moment information
Fe_none = msa.get_nonmagnetic_structure()
self.assertFalse('magmom' in Fe_spin.site_properties)
# test with disorder on magnetic site
self.Fe[0] = {Species('Fe', oxidation_state=0, properties={'spin': 5}): 0.5, 'Ni': 0.5}
self.assertRaises(NotImplementedError, CollinearMagneticStructureAnalyzer, self.Fe)
def test_matches(self):
self.assertTrue(self.NiO.matches(self.NiO_AFM_111))
self.assertTrue(self.NiO.matches(self.NiO_AFM_001))
# MSA adds magmoms to Structure, so not equal
msa = CollinearMagneticStructureAnalyzer(self.NiO,
overwrite_magmom_mode="replace_all")
self.assertFalse(msa.matches_ordering(self.NiO))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_111))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_001))
msa = CollinearMagneticStructureAnalyzer(self.NiO_AFM_001,
overwrite_magmom_mode="respect_sign")
self.assertFalse(msa.matches_ordering(self.NiO))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_111))
self.assertTrue(msa.matches_ordering(self.NiO_AFM_001))
self.assertTrue(msa.matches_ordering(self.NiO_AFM_001_opposite))
msa = CollinearMagneticStructureAnalyzer(self.NiO_AFM_111,
overwrite_magmom_mode="respect_sign")
self.assertFalse(msa.matches_ordering(self.NiO))
self.assertTrue(msa.matches_ordering(self.NiO_AFM_111))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_001))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_001_opposite))
def test_modes(self):
mode = "none"
msa = CollinearMagneticStructureAnalyzer(self.NiO,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [0, 0])
mode = "respect_sign"
msa = CollinearMagneticStructureAnalyzer(self.NiO_unphysical,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [-5, 0, 0, 0])
mode = "respect_zeros"
msa = CollinearMagneticStructureAnalyzer(self.NiO_unphysical,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [5, 0, 0, 0])
mode = "replace_all"
msa = CollinearMagneticStructureAnalyzer(self.NiO_unphysical,
overwrite_magmom_mode=mode,
make_primitive=False)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [5, 5, 0, 0])
mode = "replace_all_if_undefined"
msa = CollinearMagneticStructureAnalyzer(self.NiO,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [5, 0])
mode = "normalize"
msa = CollinearMagneticStructureAnalyzer(msa.structure,
overwrite_magmom_mode='normalize')
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [1, 0])
def test_net_positive(self):
msa = CollinearMagneticStructureAnalyzer(self.NiO_unphysical)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [3, 0, 0, 0])
def test_get_ferromagnetic_structure(self):
msa = CollinearMagneticStructureAnalyzer(self.NiO,
overwrite_magmom_mode="replace_all_if_undefined")
s1 = msa.get_ferromagnetic_structure()
s1_magmoms = [float(m) for m in s1.site_properties['magmom']]
s1_magmoms_ref = [5.0, 0.0]
self.assertListEqual(s1_magmoms, s1_magmoms_ref)
msa2 = CollinearMagneticStructureAnalyzer(self.NiO_AFM_111,
overwrite_magmom_mode="replace_all_if_undefined")
s2 = msa.get_ferromagnetic_structure(make_primitive=False)
s2_magmoms = [float(m) for m in s2.site_properties['magmom']]
s2_magmoms_ref = [5.0, 0.0]
self.assertListEqual(s2_magmoms, s2_magmoms_ref)
s2_prim = msa.get_ferromagnetic_structure(make_primitive=True)
self.assertTrue(CollinearMagneticStructureAnalyzer(s1).matches_ordering(s2_prim))
def test_magnetic_properties(self):
msa = CollinearMagneticStructureAnalyzer(self.GdB4)
self.assertFalse(msa.is_collinear)
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertFalse(msa.is_magnetic)
self.Fe.add_site_property('magmom', [5])
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertTrue(msa.is_magnetic)
self.assertTrue(msa.is_collinear)
self.assertEqual(msa.ordering, Ordering.FM)
msa = CollinearMagneticStructureAnalyzer(self.NiO, make_primitive=False,
overwrite_magmom_mode="replace_all_if_undefined")
self.assertEqual(msa.number_of_magnetic_sites, 4)
self.assertEqual(msa.number_of_unique_magnetic_sites(), 1)
self.assertEqual(msa.types_of_magnetic_species, (Element.Ni,))
self.assertEqual(msa.get_exchange_group_info(), ('Fm-3m', 225))
def test_str(self):
msa = CollinearMagneticStructureAnalyzer(self.NiO_AFM_001)
ref_msa_str = """Structure Summary
Lattice
abc : 2.948635277547903 4.17 2.948635277547903
angles : 90.0 90.0 90.0
volume : 36.2558565
A : 2.085 2.085 0.0
B : 0.0 0.0 -4.17
C : -2.085 2.085 0.0
Magmoms Sites
+5.00 PeriodicSite: Ni (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
PeriodicSite: O (0.0000, 0.0000, -2.0850) [0.0000, 0.5000, 0.0000]
PeriodicSite: O (0.0000, 2.0850, 0.0000) [0.5000, 0.0000, 0.5000]
-5.00 PeriodicSite: Ni (0.0000, 2.0850, -2.0850) [0.5000, 0.5000, 0.5000]"""
# just compare lines form 'Magmoms Sites',
# since lattice param string can vary based on machine precision
self.assertEqual("\n".join(str(msa).split("\n")[-5:-1]),
"\n".join(ref_msa_str.split("\n")[-5:-1]))
def test_round_magmoms(self):
struct = self.NiO_AFM_001.copy()
struct.add_site_property('magmom', [-5.0143, -5.02, 0.147, 0.146])
msa = CollinearMagneticStructureAnalyzer(struct, round_magmoms=0.001, make_primitive=False)
self.assertTrue(np.allclose(msa.magmoms, [5.0171, 5.0171, -0.1465, -0.1465]))
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['Ni'], 5.0171)
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['O'], 0.1465)
struct.add_site_property('magmom', [-5.0143, 4.5, 0.147, 0.146])
msa = CollinearMagneticStructureAnalyzer(struct, round_magmoms=0.001, make_primitive=False)
self.assertTrue(np.allclose(msa.magmoms, [5.0143, -4.5, -0.1465, -0.1465]))
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['Ni'][0], 4.5)
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['Ni'][1], 5.0143)
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['O'], 0.1465)
def setUp(self):
parser = CifParser(os.path.join(test_dir, 'Fe.cif'))
self.Fe = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'LiFePO4.cif'))
self.LiFePO4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'Fe3O4.cif'))
self.Fe3O4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'magnetic.ncl.example.GdB4.mcif'))
self.GdB4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'magnetic.example.NiO.mcif'))
self.NiO_expt = parser.get_structures()[0]
latt = Lattice.cubic(4.17)
species = ["Ni", "O"]
coords = [[0, 0, 0],
[0.5, 0.5, 0.5]]
self.NiO = Structure.from_spacegroup(225, latt, species, coords)
latt = Lattice([[2.085, 2.085, 0.0],
[0.0, -2.085, -2.085],
[-2.085, 2.085, -4.17]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0, 0.5],
[0, 0, 0],
[0.25, 0.5, 0.25],
[0.75, 0.5, 0.75]]
self.NiO_AFM_111 = Structure(latt, species, coords,
site_properties={'magmom': [-5, 5, 0, 0]})
latt = Lattice([[2.085, 2.085, 0],
[0, 0, -4.17],
[-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5],
[0, 0, 0],
[0, 0.5, 0],
[0.5, 0, 0.5]]
self.NiO_AFM_001 = Structure(latt, species, coords,
site_properties={'magmom': [-5, 5, 0, 0]})
latt = Lattice([[2.085, 2.085, 0],
[0, 0, -4.17],
[-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5],
[0, 0, 0],
[0, 0.5, 0],
[0.5, 0, 0.5]]
self.NiO_AFM_001_opposite = Structure(latt, species, coords,
site_properties={'magmom': [5, -5, 0, 0]})
latt = Lattice([[2.085, 2.085, 0],
[0, 0, -4.17],
[-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5],
[0, 0, 0],
[0, 0.5, 0],
[0.5, 0, 0.5]]
self.NiO_unphysical = Structure(latt, species, coords,
site_properties={'magmom': [-3, 0, 0, 0]})
warnings.simplefilter("ignore")
return {"-".join(sorted(c)) for c in [elements, elements - {self.working_ion}]}
def _mat_doc2comp_entry(self, docs, store_struct=True):
def get_prim_host(struct):
"""
Get the primitive structure with all of the lithiums removed
"""
structure = struct.copy()
structure.remove_species([self.working_ion])
prim = PrimitiveCellTransformation()
return prim.apply_transformation(structure)
entries = []
for d in docs:
<<<<<<< HEAD
struct = Structure.from_dict(d["structure"])
en = ComputedStructureEntry(
structure=struct,
energy=d["thermo"]["energy"],
parameters=d["calc_settings"],
entry_id=d["task_id"],
)
if "_sbxn" in d:
en.data["_sbxn"] = d["_sbxn"]
else:
en.data["_sbxn"] = ["core"]
=======
struct = Structure.from_dict(d['structure'])
en = ComputedStructureEntry(structure=struct,
energy=d['thermo']['energy'],
parameters=d['calc_settings'],
def _structure(self):
# avoid overlapping structure for e.g., phonon forces.
if self.args.prev_dir and self.task.fine_to_inherit_structure_from_prev:
return Structure.from_file(self.args.prev_dir / defaults.contcar)
return Structure.from_file(self.args.poscar)
def film(self) -> Structure:
"""
A pymatgen Structure for just the film
"""
return Structure.from_sites(self.film_sites)