def test_stitch_xafs(self):
self.assertRaises(ValueError, XAS.stitch, self.k_xanes, self.k_exafs,
mode="invalid")
xafs = XAS.stitch(self.k_xanes, self.k_exafs, mode="XAFS")
self.assertIsInstance(xafs, XAS)
self.assertEqual("XAFS", xafs.spectrum_type)
self.assertEqual(len(xafs.x), 500)
self.assertAlmostEqual(min(xafs.x), min(self.k_xanes.x), 2)
self.assertAlmostEqual(max(xafs.y), max(self.k_xanes.y), 2)
self.assertAlmostEqual(xafs.x[np.argmax(np.gradient(xafs.y) /
np.gradient(xafs.x))],
self.k_xanes.e0, 2)
self.assertRaises(ValueError, XAS.stitch,
self.k_xanes, self.l2_xanes, mode="XAFS")
self.k_xanes.x = np.zeros(100)
self.assertRaises(ValueError, XAS.stitch,
self.k_xanes, self.k_exafs)
self.k_xanes.absorbing_element = Element("Pt")
self.assertRaises(ValueError, XAS.stitch,
self.k_xanes, self.k_exafs, mode="XAFS")
def test(self):
surfs = glob.glob("POSCAR.01x01x01/01.scale_pert/surf*")
surfs = [ii.split('/')[-1] for ii in surfs]
surfs.sort()
self.assertEqual(surfs, self.surfs)
poscars = glob.glob("POSCAR.01x01x01/00.place_ele/surf*/sys*/POSCAR")
for poscar in poscars:
surf = poscar.split('/')[-3]
st1 = Structure.from_file(surf + '.POSCAR')
st2 = Structure.from_file(poscar)
vacuum_size = float(
Element(self.jdata['elements'][0]).atomic_radius * 2)
self.assertTrue(st1.lattice.c + vacuum_size - st2.lattice.c < 0.01)
for surf in self.surfs:
elongs = glob.glob("POSCAR.01x01x01/01.scale_pert/" + surf +
"/sys-*/scale-1.000/el*")
elongs = [ii.split('/')[-1] for ii in elongs]
elongs.sort()
self.assertEqual(elongs, self.elongs)
def test_structure_to_oxidstructure(self):
cscl = Structure(Lattice([[4.209, 0, 0], [0, 4.209, 0], [0, 0, 4.209]]),
["Cl", "Cs"], [[0.45, 0.5, 0.5], [0, 0, 0]])
d = {'structure': [cscl]}
df = DataFrame(data=d)
df["struct_oxid"] = structure_to_oxidstructure(df["structure"])
self.assertEqual(df["struct_oxid"].tolist()[0][0].specie.oxi_state, -1)
self.assertEqual(df["struct_oxid"].tolist()[0][1].specie.oxi_state, +1)
df["struct_oxid2"] = structure_to_oxidstructure(df["structure"], oxi_states_override={"Cl": [-2], "Cs": [+2]})
self.assertEqual(df["struct_oxid2"].tolist()[0][0].specie.oxi_state, -2)
self.assertEqual(df["struct_oxid2"].tolist()[0][1].specie.oxi_state, +2)
# original is preserved
self.assertEqual(df["structure"].tolist()[0][0].specie, Element("Cl"))
# test in-place
structure_to_oxidstructure(df["structure"], inplace=True)
self.assertEqual(df["structure"].tolist()[0][0].specie.oxi_state, -1)
def _compute_form_en(self):
"""
compute the formation energies for all defects in the analyzer
"""
self._formation_energies = []
for d in self._defects:
#compensate each element in defect with the chemical potential
mu_needed_coeffs = {}
for elt in d.entry.composition.elements:
el_def_comp = d.entry.composition[elt]
el_blk_comp = self._entry_bulk.composition[elt]
mu_needed_coeffs[Element(elt)] = el_blk_comp - el_def_comp
sum_mus = 0.0
for elt in mu_needed_coeffs:
sum_mus += mu_needed_coeffs[elt] * self._mu_elts[elt]
self._formation_energies.append(
d.entry.energy - self._entry_bulk.energy + \
sum_mus + d.charge*self._e_vbm + \
d.charge_correction + d.other_correction)
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_specie, [Element('Ni')])
self.assertEqual(msa.get_exchange_group_info(), ('Fm-3m', 225))
def gen_iupac_ordering():
periodic_table = loadfn("periodic_table.json")
order = [
([18], range(6, 0, -1)), # noble gasses
([1], range(7, 1, -1)), # alkali metals
([2], range(7, 1, -1)), # alkali earth metals
(range(17, 2, -1), [9]), # actinides
(range(17, 2, -1), [8]), # lanthanides
([3], (5, 4)), # Y, Sc
([4], (6, 5, 4)), # Hf -> Ti
([5], (6, 5, 4)), # Ta -> V
([6], (6, 5, 4)), # W -> Cr
([7], (6, 5, 4)), # Re -> Mn
([8], (6, 5, 4)), # Os -> Fe
([9], (6, 5, 4)), # Ir -> Co
([10], (6, 5, 4)), # Pt -> Ni
([11], (6, 5, 4)), # Au -> Cu
([12], (6, 5, 4)), # Hg -> Zn
([13], range(6, 1, -1)), # Tl -> B
([14], range(6, 1, -1)), # Pb -> C
([15], range(6, 1, -1)), # Bi -> N
([1], [1]), # Hydrogen
([16], range(6, 1, -1)), # Po -> O
([17], range(6, 1, -1)),
] # At -> F
order = sum((list(product(x, y)) for x, y in order), [])
iupac_ordering_dict = dict(zip([Element.from_row_and_group(row, group) for group, row in order], range(len(order))))
# first clean periodic table of any IUPAC ordering
for el in periodic_table:
periodic_table[el].pop("IUPAC ordering", None)
# now add iupac ordering
for el in periodic_table:
if "IUPAC ordering" in periodic_table[el]:
# sanity check that we don't cover the same element twice
raise KeyError(f"IUPAC ordering already exists for {el}")
periodic_table[el]["IUPAC ordering"] = iupac_ordering_dict[get_el_sp(el)]
def __init__(self,
cutoff: float,
twojmax: int,
element_profile: Dict,
quadratic: bool = False,
pot_fit: bool = False,
include_stress: bool = False,
feature_batch: str = "pandas_concat",
**kwargs):
"""
Args:
cutoff (float): The cutoff distance.
twojmax (int): Band limit for bispectrum components.
element_profile (dict): Parameters (cutoff factor 'r' and weight 'w')
related to each element, e.g.,
{'Na': {'r': 0.3, 'w': 0.9},
'Cl': {'r': 0.7, 'w': 3.0}}
quadratic (bool): Whether including quadratic terms.
Default to False.
pot_fit (bool): Whether combine the dataframe for potential fitting.
include_stress (bool): Whether to include stress components.
way to batch together a list of features
**kwargs: keyword args to specify memory, verbose, and n_jobs
"""
from maml.apps.pes import SpectralNeighborAnalysis
self.calculator = SpectralNeighborAnalysis(
rcut=cutoff,
twojmax=twojmax,
element_profile=element_profile,
quadratic=quadratic)
self.rcutfac = cutoff
self.twojmax = twojmax
self.elements = sorted(element_profile.keys(),
key=lambda x: Element(x))
self.element_profile = element_profile
self.quadratic = quadratic
self.pot_fit = pot_fit
self.include_stress = include_stress
super().__init__(feature_batch=feature_batch, **kwargs)
def _make_local_species_info(self):
self._species, self._initial_coords, self._final_coords = [], [], []
self._site_info, self._vectors, self._vector_colors = [], {}, []
specie_idx = 1
for specie, disp in zip(self.defect_structure, self.displacements):
if disp and disp.distance_from_defect < self.cutoff:
self._species.append(Element(disp.specie))
self._initial_coords.append(disp.original_pos)
self._final_coords.append(specie.frac_coords)
info = f"{round(disp.distance_from_defect, 1)}"
if disp and disp.displace_distance > self.min_displace_w_arrows:
self._vectors[specie_idx] = \
(v * self.arrow_factor for v in disp.disp_vector)
# max=200 instead of 255 since (255, 255, 255) is white.
rgb = int(200 * disp.angle / 180)
self._vector_colors.append((rgb, rgb, 100))
info += f"_{round(disp.displace_distance, 2)}"
self._site_info.append(info)
specie_idx += 1
def _setup(self):
def add_args(l):
return l + compute_args if l.startswith('compute') else l
compute_args = '1 0.99363 {} '.format(self.twojmax)
el_in_seq = sorted(self.element_profile.keys(), key=lambda x: Element(x))
cutoffs = [self.element_profile[e]['r'] * self.rcutfac for e in el_in_seq]
weights = [self.element_profile[e]['w'] for e in el_in_seq]
compute_args += ' '.join([str(p) for p in cutoffs + weights])
compute_args += ' rmin0 0 quadraticflag {}'.format(int(self.quadratic))
CMDS = list(map(add_args, self._CMDS))
CMDS[2] += ' bzeroflag 0'
CMDS[3] += ' bzeroflag 0'
CMDS[4] += ' bzeroflag 0'
dump_modify = 'dump_modify 1 element '
dump_modify += ' '.join(str(e) for e in el_in_seq)
CMDS.append(dump_modify)
ALL_CMDS = self._COMMON_CMDS[:]
ALL_CMDS[-1:-1] = CMDS
input_file = 'in.sna'
with open(input_file, 'w') as f:
f.write(_pretty_input(ALL_CMDS))
return input_file
def _create_dict_for_feature_table(
picklefile: Union[str, Path]) -> List[dict]:
"""Reads in a pickle with features and returns a list of dictionaries with one dictionary per metal site.
Arguments:
picklefile (Union[str, Path]) -- path to pickle file
Returns:
List[dict] -- list of dicionary
"""
warnings.warn(
"This method will be removed in the next major release",
DeprecationWarning,
)
result = read_pickle(picklefile)
result_list = []
for key, value in result.items():
e = Element(key)
metal_encoding = [
e.number, e.row, e.group,
np.random.randint(1, 18)
]
features = list(value["feature"])
features.extend(metal_encoding)
result_dict = {
"metal": key,
"coords": value["coords"],
"feature": features,
"name": Path(picklefile).stem,
}
if not np.isnan(np.array(features)).any():
result_list.append(result_dict)
return result_list
def test_stitch_l23(self):
self.l2_xanes.y[0] = 0.1
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
XAS.stitch(self.l2_xanes, self.l3_xanes, 100, mode="L23")
self.assertEqual(len(w), 1)
self.assertIs(w[-1].category, UserWarning)
self.assertIn("jump", str(w[-1].message))
self.l2_xanes = XAS.from_dict(l2_xanes_dict)
l23 = XAS.stitch(self.l2_xanes, self.l3_xanes, 100, mode="L23")
self.assertIsInstance(l23, XAS)
self.assertEqual("L23", l23.edge)
self.assertAlmostEqual(min(l23.x), min(self.l3_xanes.x), 3)
self.assertAlmostEqual(max(l23.x), max(self.l3_xanes.x), 3)
self.assertTrue(np.greater_equal(l23.y, self.l2_xanes.y).all())
self.assertEqual(len(l23.x), 100)
self.l2_xanes.spectrum_type = "EXAFS"
self.assertRaises(ValueError, XAS.stitch,
self.l2_xanes, self.l3_xanes, mode="L23")
self.l2_xanes.absorbing_element = Element("Pt")
self.assertRaises(ValueError, XAS.stitch,
self.l2_xanes, self.l3_xanes, mode="L23")
self.assertRaises(ValueError, XAS.stitch,
self.k_xanes, self.l3_xanes, mode="L23")
def _process_multielement_entries(self):
"""
Create entries for multi-element Pourbaix construction
"""
N = len(self._elt_comp) # No. of elements
entries = self._unprocessed_entries
el_list = self._elt_comp.keys()
comp_list = [self._elt_comp[el] for el in el_list]
list_of_entries = list()
for j in range(1, N + 1):
list_of_entries += list(itertools.combinations(
list(range(len(entries))), j))
processed_entries = list()
for entry_list in list_of_entries:
# Check if all elements in composition list are present in
# entry_list
if not (set([Element(el) for el in el_list]).issubset(
set(list(chain.from_iterable([entries[i].composition.keys()
for i in entry_list]))))):
continue
if len(entry_list) == 1:
# If only one entry in entry_list, then check if the composition matches with the set composition.
entry = entries[entry_list[0]]
dict_of_non_oh = dict(zip([key for key in entry.composition.keys() if key.symbol not in ["O", "H"]],
[entry.composition[key] for key in [key for key in entry.composition.keys() if key.symbol not in ["O", "H"]]]))
if Composition(dict(zip(self._elt_comp.keys(), [self._elt_comp[key] / min([self._elt_comp[key] for key in self._elt_comp.keys()])
for key in self._elt_comp.keys()]))).reduced_formula ==\
Composition(dict(zip(dict_of_non_oh.keys(), [dict_of_non_oh[el] / min([dict_of_non_oh[key] for key in dict_of_non_oh.keys()])
for el in dict_of_non_oh.keys()]))).reduced_formula:
processed_entries.append(MultiEntry([entry], [1.0]))
continue
A = [[0.0] * (len(entry_list) - 1) for _ in range(len(entry_list) - 1)]
multi_entries = [entries[j] for j in entry_list]
entry0 = entries[entry_list[0]]
comp0 = entry0.composition
if entry0.phase_type == "Solid":
red_fac = comp0.get_reduced_composition_and_factor()[1]
else:
red_fac = 1.0
sum_nel = sum([comp0[el] / red_fac for el in el_list])
b = [comp0[Element(el_list[i])] / red_fac - comp_list[i] * sum_nel
for i in range(1, len(entry_list))]
for j in range(1, len(entry_list)):
entry = entries[entry_list[j]]
comp = entry.composition
if entry.phase_type == "Solid":
red_fac = comp.get_reduced_composition_and_factor()[1]
else:
red_fac = 1.0
sum_nel = sum([comp[el] / red_fac for el in el_list])
for i in range(1, len(entry_list)):
el = el_list[i]
A[i-1][j-1] = comp_list[i] * sum_nel -\
comp[Element(el)] / red_fac
try:
weights = np.linalg.solve(np.array(A), np.array(b))
except np.linalg.linalg.LinAlgError as err:
if 'Singular matrix' in err.message:
continue
else:
raise Exception("Unknown Error message!")
if not(np.all(weights > 0.0)):
continue
weights = list(weights)
weights.insert(0, 1.0)
super_entry = MultiEntry(multi_entries, weights)
processed_entries.append(super_entry)
return processed_entries
def get_element_representation(name):
"""
generate one-hot representation for a element, e.g, si = [0.0, 1.0, 0.0, 0.0, ...]
Parameters
----------
name: string
element symbol
"""
element = Element(name)
general_element_electronic = {
's1': 0.0,
's2': 0.0,
'p1': 0.0,
'p2': 0.0,
'p3': 0.0,
'p4': 0.0,
'p5': 0.0,
'p6': 0.0,
'd1': 0.0,
'd2': 0.0,
'd3': 0.0,
'd4': 0.0,
'd5': 0.0,
'd6': 0.0,
'd7': 0.0,
'd8': 0.0,
'd9': 0.0,
'd10': 0.0,
'f1': 0.0,
'f2': 0.0,
'f3': 0.0,
'f4': 0.0,
'f5': 0.0,
'f6': 0.0,
'f7': 0.0,
'f8': 0.0,
'f9': 0.0,
'f10': 0.0,
'f11': 0.0,
'f12': 0.0,
'f13': 0.0,
'f14': 0.0
}
general_electron_subshells = [
's1', 's2', 'p1', 'p2', 'p3', 'p4', 'p5', 'p6', 'd1', 'd2', 'd3',
'd4', 'd5', 'd6', 'd7', 'd8', 'd9', 'd10', 'f1', 'f2', 'f3', 'f4',
'f5', 'f6', 'f7', 'f8', 'f9', 'f10', 'f11', 'f12', 'f13', 'f14'
]
if name == 'H':
element_electronic_structure = ['s1']
elif name == 'He':
element_electronic_structure = ['s2']
else:
element_electronic_structure = [
''.join(pair) for pair in re.findall(
r"\.\d(\w+)<sup>(\d+)</sup>", element.electronic_structure)
]
for eletron_subshell in element_electronic_structure:
general_element_electronic[eletron_subshell] = 1.0
return np.array([
general_element_electronic[key]
for key in general_electron_subshells
])
def from_file(cls, filename, atom_style=None):
description, headers, sections = cls._parse_data_file(filename)
errors = cls._validate_data_file(headers, sections)
if errors:
raise ValueError('data file is invalid: {}'.format(errors))
xlo, xhi = headers['xlo xhi']
ylo, yhi = headers['ylo yhi']
zlo, zhi = headers['zlo zhi']
xy, xz, yz = headers.get('xy xz yz', [0, 0, 0])
lammps_box = LammpsBox(xhi, yhi, zhi, xlo, ylo, zlo, xy, xz, yz)
# Guess symbol from closest atomic mass (yes not great for isotopes)
elements = np.array([
tuple([Element(element).atomic_mass,
Element(element)]) for element in periodic_table
],
dtype={
'names': ['mass', 'symbol'],
'formats': [np.float64, np.chararray]
})
symbol_indicies = {}
index_symbols = {} # Makes element lookup quicker
masses = {}
for index, atomic_mass, in sections['Masses']['data']:
symbol = elements['symbol'][np.abs(elements['mass'] -
atomic_mass).argmin()]
symbol_indicies[Element(symbol)] = index
index_symbols[index] = Element(symbol)
masses[Element(symbol)] = atomic_mass
# Default full format or use check format
atoms = []
sections['Atoms']['data'].sort(
order='f0') # f0 is default name of first field
for atom in sections['Atoms']['data']:
if sections['Atoms'].get('check') == 'full':
atom_type, charge, *position = atom['f2'], atom['f3'], atom[
'f4'], atom['f5'], atom['f6']
else:
index, mol, atom_type, charge, *position = atom
element = index_symbols[atom_type]
atoms.append([element, charge, position])
velocities = None
if 'Velocities' in sections:
sections['Velocities']['data'].sort(
order='f0') # f0 is default name of first field
velocities = [[vx, vy, vz] for vx, vy, vz in sections['Velocities']
['data'][['f1', 'f2', 'f3']]]
# Get Potentials
# TODO only gets pair potentials for now and no reason to keep str
pair_potentials = {}
if 'PairIJ Coeffs' in sections:
for s1, s2, *parameters in sections['PairIJ Coeffs']['data']:
pair_potentials[(index_symbols[s1],
index_symbols[s2])] = ' '.join(
list(map(str, parameters)))
potentials = LammpsPotentials(pair_potentials, symbol_indicies)
return cls(description,
symbol_indicies,
masses,
atoms,
lammps_box,
potentials=potentials,
velocities=velocities)
def _parse(self, filename):
start_patt = re.compile(" \(Enter \S+l101\.exe\)")
route_patt = re.compile(" #[pPnNtT]*.*")
link0_patt = re.compile("^\s(%.+)\s*=\s*(.+)")
charge_mul_patt = re.compile("Charge\s+=\s*([-\\d]+)\s+"
"Multiplicity\s+=\s*(\d+)")
num_basis_func_patt = re.compile("([0-9]+)\s+basis functions")
pcm_patt = re.compile("Polarizable Continuum Model")
stat_type_patt = re.compile("imaginary frequencies")
scf_patt = re.compile("E\(.*\)\s*=\s*([-\.\d]+)\s+")
mp2_patt = re.compile("EUMP2\s*=\s*(.*)")
oniom_patt = re.compile("ONIOM:\s+extrapolated energy\s*=\s*(.*)")
termination_patt = re.compile("(Normal|Error) termination")
error_patt = re.compile(
"(! Non-Optimized Parameters !|Convergence failure)")
mulliken_patt = re.compile(
"^\s*(Mulliken charges|Mulliken atomic charges)")
mulliken_charge_patt = re.compile(
'^\s+(\d+)\s+([A-Z][a-z]?)\s*(\S*)')
end_mulliken_patt = re.compile(
'(Sum of Mulliken )(.*)(charges)\s*=\s*(\D)')
std_orientation_patt = re.compile("Standard orientation")
end_patt = re.compile("--+")
orbital_patt = re.compile("Alpha\s*\S+\s*eigenvalues --(.*)")
thermo_patt = re.compile("(Zero-point|Thermal) correction(.*)="
"\s+([\d\.-]+)")
forces_on_patt = re.compile(
"Center\s+Atomic\s+Forces\s+\(Hartrees/Bohr\)")
forces_off_patt = re.compile("Cartesian\s+Forces:\s+Max.*RMS.*")
forces_patt = re.compile(
"\s+(\d+)\s+(\d+)\s+([0-9\.-]+)\s+([0-9\.-]+)\s+([0-9\.-]+)")
freq_on_patt = re.compile(
"Harmonic\sfrequencies\s+\(cm\*\*-1\),\sIR\sintensities.*Raman.*")
freq_patt = re.compile("Frequencies\s--\s+(.*)")
normal_mode_patt = re.compile(
"\s+(\d+)\s+(\d+)\s+([0-9\.-]{4,5})\s+([0-9\.-]{4,5}).*")
self.properly_terminated = False
self.is_pcm = False
self.stationary_type = "Minimum"
self.structures = []
self.corrections = {}
self.energies = []
self.pcm = None
self.errors = []
self.Mulliken_charges = {}
self.link0 = {}
self.cart_forces = []
self.frequencies = []
coord_txt = []
read_coord = 0
read_mulliken = False
orbitals_txt = []
parse_stage = 0
num_basis_found = False
terminated = False
parse_forces = False
forces = []
parse_freq = False
frequencies = []
with zopen(filename) as f:
for line in f:
if parse_stage == 0:
if start_patt.search(line):
parse_stage = 1
elif link0_patt.match(line):
m = link0_patt.match(line)
self.link0[m.group(1)] = m.group(2)
elif route_patt.search(line):
params = read_route_line(line)
self.functional = params[0]
self.basis_set = params[1]
self.route = params[2]
self.dieze_tag = params[3]
parse_stage = 1
elif parse_stage == 1:
if charge_mul_patt.search(line):
m = charge_mul_patt.search(line)
self.charge = int(m.group(1))
self.spin_mult = int(m.group(2))
parse_stage = 2
elif parse_stage == 2:
if self.is_pcm:
self._check_pcm(line)
if "FREQ" in self.route and thermo_patt.search(line):
m = thermo_patt.search(line)
if m.group(1) == "Zero-point":
self.corrections["Zero-point"] = float(m.group(3))
else:
key = m.group(2).strip(" to ")
self.corrections[key] = float(m.group(3))
if read_coord:
if not end_patt.search(line):
coord_txt.append(line)
else:
read_coord = (read_coord + 1) % 4
if not read_coord:
sp = []
coords = []
for l in coord_txt[2:]:
toks = l.split()
sp.append(Element.from_Z(int(toks[1])))
coords.append([float(i) for i in toks[3:6]])
self.structures.append(Molecule(sp, coords))
if parse_forces:
m = forces_patt.search(line)
if m:
forces.extend([float(_v) for _v in m.groups()[2:5]])
elif forces_off_patt.search(line):
self.cart_forces.append(forces)
forces = []
parse_forces = False
elif parse_freq:
m = freq_patt.search(line)
if m:
values = [float(_v) for _v in m.groups()[0].split()]
for value in values:
frequencies.append([value, []])
elif normal_mode_patt.search(line):
values = [float(_v) for _v in line.split()[2:]]
n = int(len(values) / 3)
for i in range(0, len(values), 3):
j = -n + int(i / 3)
frequencies[j][1].extend(values[i:i+3])
elif line.find("-------------------") != -1:
parse_freq = False
self.frequencies.append(frequencies)
frequencies = []
elif termination_patt.search(line):
m = termination_patt.search(line)
if m.group(1) == "Normal":
self.properly_terminated = True
terminated = True
elif error_patt.search(line):
error_defs = {
"! Non-Optimized Parameters !": "Optimization "
"error",
"Convergence failure": "SCF convergence error"
}
m = error_patt.search(line)
self.errors.append(error_defs[m.group(1)])
elif (not num_basis_found) and \
num_basis_func_patt.search(line):
m = num_basis_func_patt.search(line)
self.num_basis_func = int(m.group(1))
num_basis_found = True
elif (not self.is_pcm) and pcm_patt.search(line):
self.is_pcm = True
self.pcm = {}
elif "FREQ" in self.route and "OPT" in self.route and \
stat_type_patt.search(line):
self.stationary_type = "Saddle"
elif mp2_patt.search(line):
m = mp2_patt.search(line)
self.energies.append(float(m.group(1).replace("D",
"E")))
elif oniom_patt.search(line):
m = oniom_patt.matcher(line)
self.energies.append(float(m.group(1)))
elif scf_patt.search(line):
m = scf_patt.search(line)
self.energies.append(float(m.group(1)))
elif std_orientation_patt.search(line):
coord_txt = []
read_coord = 1
elif orbital_patt.search(line):
orbitals_txt.append(line)
elif mulliken_patt.search(line):
mulliken_txt = []
read_mulliken = True
elif not parse_forces and forces_on_patt.search(line):
parse_forces = True
elif freq_on_patt.search(line):
parse_freq = True
if read_mulliken:
if not end_mulliken_patt.search(line):
mulliken_txt.append(line)
else:
m = end_mulliken_patt.search(line)
mulliken_charges = {}
for line in mulliken_txt:
if mulliken_charge_patt.search(line):
m = mulliken_charge_patt.search(line)
dict = {int(m.group(1)): [m.group(2), float(m.group(3))]}
mulliken_charges.update(dict)
read_mulliken = False
self.Mulliken_charges = mulliken_charges
if not terminated:
#raise IOError("Bad Gaussian output file.")
warnings.warn("\n" + self.filename + \
": Termination error or bad Gaussian output file !")
return (e_above_hull)
key_element = 'Li'
tieline_dataframe = pd.read_csv(
'Tables/{element}/tieline_distinct.csv'.format(element=key_element))
# remove noble gas
boolean_gas = tieline_dataframe.pretty_formula.apply(
lambda x: True not in [e.is_noble_gas for e in Composition(x).elements])
no_nobel_gas_dataframe = tieline_dataframe[boolean_gas]
# screen phases without the key element
boolean_element = no_nobel_gas_dataframe.pretty_formula.apply(
lambda x: Element(key_element) not in Composition(x).elements)
vanishing_solubility_phases_dataframe = no_nobel_gas_dataframe[boolean_element]
vanishing_solubility_phases_dataframe.reset_index(drop=True, inplace=True)
vanishing_solubility_phases_dataframe.to_csv(
'Tables/{element}/tieline_without_solubility_and_gas.csv'.format(
element=key_element),
index=False)
# pick up those phases with band gap >= 3eV
material_id_list = vanishing_solubility_phases_dataframe[
'material_id'].to_list()
with MPRester(api_key='') as mpr:
# entry id is an alias of task id
candidates = mpr.query(criteria={
'task_id': {
'$in': material_id_list
def test_get_plot_form_energy(self):
mu_elts = {Element('As'): 0, Element('Ga'): 0}
self.dp.get_plot_form_energy(mu_elts).savefig('test.pdf')
self.assertTrue(os.path.exists('test.pdf'))
os.system('rm test.pdf')
def test_get_oxidation(self):
self.assertEqual((3, ),
self.data_source.get_oxidation_states(Element("Nd")))
self.data_source.use_common_oxi_states = False
self.assertEqual((2, 3),
self.data_source.get_oxidation_states(Element("Nd")))
def _parse(self, filename):
start_patt = re.compile(" \(Enter \S+l101\.exe\)")
route_patt = re.compile(" #[pPnNtT]*.*")
link0_patt = re.compile("^\s(%.+)\s*=\s*(.+)")
charge_mul_patt = re.compile("Charge\s+=\s*([-\\d]+)\s+" "Multiplicity\s+=\s*(\d+)")
num_basis_func_patt = re.compile("([0-9]+)\s+basis functions")
num_elec_patt = re.compile("(\d+)\s+alpha electrons\s+(\d+)\s+beta electrons")
pcm_patt = re.compile("Polarizable Continuum Model")
stat_type_patt = re.compile("imaginary frequencies")
scf_patt = re.compile("E\(.*\)\s*=\s*([-\.\d]+)\s+")
mp2_patt = re.compile("EUMP2\s*=\s*(.*)")
oniom_patt = re.compile("ONIOM:\s+extrapolated energy\s*=\s*(.*)")
termination_patt = re.compile("(Normal|Error) termination")
error_patt = re.compile("(! Non-Optimized Parameters !|Convergence failure)")
mulliken_patt = re.compile("^\s*(Mulliken charges|Mulliken atomic charges)")
mulliken_charge_patt = re.compile("^\s+(\d+)\s+([A-Z][a-z]?)\s*(\S*)")
end_mulliken_patt = re.compile("(Sum of Mulliken )(.*)(charges)\s*=\s*(\D)")
std_orientation_patt = re.compile("Standard orientation")
end_patt = re.compile("--+")
orbital_patt = re.compile("(Alpha|Beta)\s*\S+\s*eigenvalues --(.*)")
thermo_patt = re.compile("(Zero-point|Thermal) correction(.*)=" "\s+([\d\.-]+)")
forces_on_patt = re.compile("Center\s+Atomic\s+Forces\s+\(Hartrees/Bohr\)")
forces_off_patt = re.compile("Cartesian\s+Forces:\s+Max.*RMS.*")
forces_patt = re.compile("\s+(\d+)\s+(\d+)\s+([0-9\.-]+)\s+([0-9\.-]+)\s+([0-9\.-]+)")
freq_on_patt = re.compile("Harmonic\sfrequencies\s+\(cm\*\*-1\),\sIR\sintensities.*Raman.*")
freq_patt = re.compile("Frequencies\s--\s+(.*)")
normal_mode_patt = re.compile("\s+(\d+)\s+(\d+)\s+([0-9\.-]{4,5})\s+([0-9\.-]{4,5}).*")
mo_coeff_patt = re.compile("Molecular Orbital Coefficients:")
mo_coeff_name_patt = re.compile("\d+\s((\d+|\s+)\s+([a-zA-Z]{1,2}|\s+))\s+(\d+\S+)")
self.properly_terminated = False
self.is_pcm = False
self.stationary_type = "Minimum"
self.structures = []
self.corrections = {}
self.energies = []
self.pcm = None
self.errors = []
self.Mulliken_charges = {}
self.link0 = {}
self.cart_forces = []
self.frequencies = []
self.eigenvalues = []
self.is_spin = False
coord_txt = []
read_coord = 0
read_mulliken = False
read_eigen = False
eigen_txt = []
parse_stage = 0
num_basis_found = False
terminated = False
parse_forces = False
forces = []
parse_freq = False
frequencies = []
read_mo = False
with zopen(filename) as f:
for line in f:
if parse_stage == 0:
if start_patt.search(line):
parse_stage = 1
elif link0_patt.match(line):
m = link0_patt.match(line)
self.link0[m.group(1)] = m.group(2)
elif route_patt.search(line):
params = read_route_line(line)
self.functional = params[0]
self.basis_set = params[1]
self.route = params[2]
self.dieze_tag = params[3]
parse_stage = 1
elif parse_stage == 1:
if charge_mul_patt.search(line):
m = charge_mul_patt.search(line)
self.charge = int(m.group(1))
self.spin_mult = int(m.group(2))
parse_stage = 2
elif parse_stage == 2:
if self.is_pcm:
self._check_pcm(line)
if "FREQ" in self.route and thermo_patt.search(line):
m = thermo_patt.search(line)
if m.group(1) == "Zero-point":
self.corrections["Zero-point"] = float(m.group(3))
else:
key = m.group(2).strip(" to ")
self.corrections[key] = float(m.group(3))
if read_coord:
if not end_patt.search(line):
coord_txt.append(line)
else:
read_coord = (read_coord + 1) % 4
if not read_coord:
sp = []
coords = []
for l in coord_txt[2:]:
toks = l.split()
sp.append(Element.from_Z(int(toks[1])))
coords.append([float(i) for i in toks[3:6]])
self.structures.append(Molecule(sp, coords))
if parse_forces:
m = forces_patt.search(line)
if m:
forces.extend([float(_v) for _v in m.groups()[2:5]])
elif forces_off_patt.search(line):
self.cart_forces.append(forces)
forces = []
parse_forces = False
# read molecular orbital eigenvalues
if read_eigen:
m = orbital_patt.search(line)
if m:
eigen_txt.append(line)
else:
read_eigen = False
self.eigenvalues = {Spin.up: []}
for eigenline in eigen_txt:
if "Alpha" in eigenline:
self.eigenvalues[Spin.up] += [float(e) for e in float_patt.findall(eigenline)]
elif "Beta" in eigenline:
if Spin.down not in self.eigenvalues:
self.eigenvalues[Spin.down] = []
self.eigenvalues[Spin.down] += [float(e) for e in float_patt.findall(eigenline)]
eigen_txt = []
# read molecular orbital coefficients
if read_mo:
# build a matrix with all coefficients
all_spin = [Spin.up]
if self.is_spin:
all_spin.append(Spin.down)
mat_mo = {}
for spin in all_spin:
mat_mo[spin] = np.zeros((self.num_basis_func, self.num_basis_func))
nMO = 0
end_mo = False
while nMO < self.num_basis_func and not end_mo:
f.readline()
f.readline()
self.atom_basis_labels = []
for i in range(self.num_basis_func):
line = f.readline()
# identify atom and OA labels
m = mo_coeff_name_patt.search(line)
if m.group(1).strip() != "":
iat = int(m.group(2)) - 1
# atname = m.group(3)
self.atom_basis_labels.append([m.group(4)])
else:
self.atom_basis_labels[iat].append(m.group(4))
# MO coefficients
coeffs = [float(c) for c in float_patt.findall(line)]
for j in range(len(coeffs)):
mat_mo[spin][i, nMO + j] = coeffs[j]
nMO += len(coeffs)
line = f.readline()
# manage pop=regular case (not all MO)
if nMO < self.num_basis_func and (
"Density Matrix:" in line or mo_coeff_patt.search(line)
):
end_mo = True
warnings.warn("POP=regular case, matrix coefficients not complete")
f.readline()
self.eigenvectors = mat_mo
read_mo = False
# build a more convenient array dict with MO coefficient of
# each atom in each MO.
# mo[Spin][OM j][atom i] = {AO_k: coeff, AO_k: coeff ... }
mo = {}
for spin in all_spin:
mo[spin] = [
[{} for iat in range(len(self.atom_basis_labels))] for j in range(self.num_basis_func)
]
for j in range(self.num_basis_func):
i = 0
for iat in range(len(self.atom_basis_labels)):
for label in self.atom_basis_labels[iat]:
mo[spin][j][iat][label] = self.eigenvectors[spin][i, j]
i += 1
self.molecular_orbital = mo
elif parse_freq:
m = freq_patt.search(line)
if m:
values = [float(_v) for _v in m.groups()[0].split()]
for value in values:
frequencies.append([value, []])
elif normal_mode_patt.search(line):
values = [float(_v) for _v in line.split()[2:]]
n = int(len(values) / 3)
for i in range(0, len(values), 3):
j = -n + int(i / 3)
frequencies[j][1].extend(values[i : i + 3])
elif line.find("-------------------") != -1:
parse_freq = False
self.frequencies.append(frequencies)
frequencies = []
elif termination_patt.search(line):
m = termination_patt.search(line)
if m.group(1) == "Normal":
self.properly_terminated = True
terminated = True
elif error_patt.search(line):
error_defs = {
"! Non-Optimized Parameters !": "Optimization " "error",
"Convergence failure": "SCF convergence error",
}
m = error_patt.search(line)
self.errors.append(error_defs[m.group(1)])
elif (not num_basis_found) and num_basis_func_patt.search(line):
m = num_basis_func_patt.search(line)
self.num_basis_func = int(m.group(1))
num_basis_found = True
elif num_elec_patt.search(line):
m = num_elec_patt.search(line)
self.electrons = (int(m.group(1)), int(m.group(2)))
elif (not self.is_pcm) and pcm_patt.search(line):
self.is_pcm = True
self.pcm = {}
elif "FREQ" in self.route and "OPT" in self.route and stat_type_patt.search(line):
self.stationary_type = "Saddle"
elif mp2_patt.search(line):
m = mp2_patt.search(line)
self.energies.append(float(m.group(1).replace("D", "E")))
elif oniom_patt.search(line):
m = oniom_patt.matcher(line)
self.energies.append(float(m.group(1)))
elif scf_patt.search(line):
m = scf_patt.search(line)
self.energies.append(float(m.group(1)))
elif std_orientation_patt.search(line):
coord_txt = []
read_coord = 1
elif not read_eigen and orbital_patt.search(line):
eigen_txt.append(line)
read_eigen = True
elif mulliken_patt.search(line):
mulliken_txt = []
read_mulliken = True
elif not parse_forces and forces_on_patt.search(line):
parse_forces = True
elif freq_on_patt.search(line):
parse_freq = True
elif mo_coeff_patt.search(line):
if "Alpha" in line:
self.is_spin = True
read_mo = True
if read_mulliken:
if not end_mulliken_patt.search(line):
mulliken_txt.append(line)
else:
m = end_mulliken_patt.search(line)
mulliken_charges = {}
for line in mulliken_txt:
if mulliken_charge_patt.search(line):
m = mulliken_charge_patt.search(line)
dict = {int(m.group(1)): [m.group(2), float(m.group(3))]}
mulliken_charges.update(dict)
read_mulliken = False
self.Mulliken_charges = mulliken_charges
if not terminated:
# raise IOError("Bad Gaussian output file.")
warnings.warn("\n" + self.filename + ": Termination error or bad Gaussian output file !")
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 _parse(self, filename):
start_patt = re.compile(" \(Enter \S+l101\.exe\)")
route_patt = re.compile(" #[pPnNtT]*.*")
charge_mul_patt = re.compile("Charge\s+=\s*([-\\d]+)\s+" "Multiplicity\s+=\s*(\d+)")
num_basis_func_patt = re.compile("([0-9]+)\s+basis functions")
pcm_patt = re.compile("Polarizable Continuum Model")
stat_type_patt = re.compile("imaginary frequencies")
scf_patt = re.compile("E\(.*\)\s*=\s*([-\.\d]+)\s+")
mp2_patt = re.compile("EUMP2\s*=\s*(.*)")
oniom_patt = re.compile("ONIOM:\s+extrapolated energy\s*=\s*(.*)")
termination_patt = re.compile("(Normal|Error) termination of Gaussian")
std_orientation_patt = re.compile("Standard orientation")
end_patt = re.compile("--+")
orbital_patt = re.compile("Alpha\s*\S+\s*eigenvalues --(.*)")
thermo_patt = re.compile("(Zero-point|Thermal) correction(.*)=" "\s+([\d\.-]+)")
self.properly_terminated = False
self.is_pcm = False
self.stationary_type = "Minimum"
self.structures = []
self.corrections = {}
self.energies = []
self.pcm = None
coord_txt = []
read_coord = 0
orbitals_txt = []
parse_stage = 0
num_basis_found = False
terminated = False
with zopen(filename) as f:
for line in f:
if parse_stage == 0:
if start_patt.search(line):
parse_stage = 1
elif route_patt.search(line):
self.route = {}
for tok in line.split():
sub_tok = tok.strip().split("=")
key = sub_tok[0].upper()
self.route[key] = sub_tok[1].upper() if len(sub_tok) > 1 else ""
m = re.match("(\w+)/([^/]+)", key)
if m:
self.functional = m.group(1)
self.basis_set = m.group(2)
elif parse_stage == 1:
if charge_mul_patt.search(line):
m = charge_mul_patt.search(line)
self.charge = int(m.group(1))
self.spin_mult = int(m.group(2))
parse_stage = 2
elif parse_stage == 2:
if self.is_pcm:
self._check_pcm(line)
if "FREQ" in self.route and thermo_patt.search(line):
m = thermo_patt.search(line)
if m.group(1) == "Zero-point":
self.corrections["Zero-point"] = float(m.group(3))
else:
key = m.group(2).strip(" to ")
self.corrections[key] = float(m.group(3))
if read_coord:
if not end_patt.search(line):
coord_txt.append(line)
else:
read_coord = (read_coord + 1) % 4
if not read_coord:
sp = []
coords = []
for l in coord_txt[2:]:
toks = l.split()
sp.append(Element.from_Z(int(toks[1])))
coords.append(map(float, toks[3:6]))
self.structures.append(Molecule(sp, coords))
elif termination_patt.search(line):
m = termination_patt.search(line)
if m.group(1) == "Normal":
self.properly_terminated = True
terminated = True
elif (not num_basis_found) and num_basis_func_patt.search(line):
m = num_basis_func_patt.search(line)
self.num_basis_func = int(m.group(1))
num_basis_found = True
elif (not self.is_pcm) and pcm_patt.search(line):
self.is_pcm = True
self.pcm = {}
elif "FREQ" in self.route and "OPT" in self.route and stat_type_patt.search(line):
self.stationary_type = "Saddle"
elif mp2_patt.search(line):
m = mp2_patt.search(line)
self.energies.append(float(m.group(1).replace("D", "E")))
elif oniom_patt.search(line):
m = oniom_patt.matcher(line)
self.energies.append(float(m.group(1)))
elif scf_patt.search(line):
m = scf_patt.search(line)
self.energies.append(float(m.group(1)))
elif std_orientation_patt.search(line):
coord_txt = []
read_coord = 1
elif orbital_patt.search(line):
orbitals_txt.append(line)
if not terminated:
raise IOError("Bad Gaussian output file.")
def train(self,
train_structures,
train_energies,
train_forces,
train_stresses=None,
**kwargs):
"""
Training data with moment tensor method.
Args:
train_structures ([Structure]): The list of Pymatgen Structure object.
energies ([float]): The list of total energies of each structure
in structures list.
train_energies ([float]): List of total energies of each structure in
structures list.
train_forces ([np.array]): List of (m, 3) forces array of each structure
with m atoms in structures list. m can be varied with each
single structure case.
train_stresses (list): List of (6, ) virial stresses of each
structure in structures list.
kwargs: Parameters in write_input method.
"""
if not which('nnp-train'):
raise RuntimeError("NNP Trainer has not been found.")
train_structures, train_forces, train_stresses = \
check_structures_forces_stresses(train_structures, train_forces, train_stresses)
train_pool = pool_from(train_structures, train_energies, train_forces,
train_stresses)
atoms_filename = 'input.data'
with ScratchDir('.'):
_ = self.write_cfgs(filename=atoms_filename, cfg_pool=train_pool)
output = 'training_output'
self.write_input(**kwargs)
p_scaling = subprocess.Popen(['nnp-scaling', '100'],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdout, stderr = p_scaling.communicate()
rc = p_scaling.returncode
if rc != 0:
error_msg = 'n2p2 exited with return code %d' % rc
msg = stderr.decode("utf-8").split('\n')[:-1]
try:
error_line = [
i for i, m in enumerate(msg) if m.startswith('ERROR')
][0]
error_msg += ', '.join(msg[error_line:])
except Exception:
error_msg += ', '
error_msg += msg[-1]
raise RuntimeError(error_msg)
p_train = subprocess.Popen(['nnp-train'],
stdout=open(output, 'w'),
stderr=subprocess.PIPE)
stdout, stderr = p_train.communicate()
rc = p_train.returncode
if rc != 0:
error_msg = 'n2p2 exited with return code %d' % rc
msg = stderr.decode("utf-8").split('\n')[:-1]
try:
error_line = [
i for i, m in enumerate(msg) if m.startswith('ERROR')
][0]
error_msg += ', '.join(msg[error_line:])
except Exception:
error_msg += ', '
error_msg += msg[-1]
raise RuntimeError(error_msg)
with zopen(output) as f:
error_lines = f.read()
energy_rmse_pattern = re.compile(
r'ENERGY\s*\S*\s*(\S*)\s*(\S*).*?\n')
forces_rmse_pattern = re.compile(
r'FORCES\s*\S*\s*(\S*)\s*(\S*).*?\n')
errors = np.array(energy_rmse_pattern.findall(error_lines),
dtype=np.float).T.tolist()
self.train_energy_rmse = errors[0]
self.validation_energy_rmse = errors[1]
errors = np.array(forces_rmse_pattern.findall(error_lines),
dtype=np.float).T.tolist()
self.train_forces_rmse = errors[0]
self.validation_forces_rmse = errors[1]
for specie in self.elements:
weights_filename = 'weights.{}.{}.out'.format(
str(Element(specie).number).zfill(3),
str(self.param['epochs']).zfill(6))
self.weights[specie] = []
self.bs[specie] = []
self.weight_param[specie] = []
self.load_weights(weights_filename, specie)
self.load_scaler('scaling.data')
return rc
def load_input(self, filename='input.nn'):
"""
Load input file from trained Neural Network Potential.
Args:
filename (str): The input filename.
"""
PARAMS = {
'general': [
'cutoff_type', 'scale_features', 'scale_min_short',
'scale_max_short', 'hidden_layers'
],
'additional': [
'epochs', 'updater_type', 'parallel_mode', 'jacobian_mode',
'update_strategy', 'selection_mode', 'task_batch_size_energy',
'task_batch_size_force', 'random_seed', 'test_fraction',
'force_weight', 'short_energy_fraction',
'short_force_fraction', 'short_energy_error_threshold',
'short_force_error_threshold', 'rmse_threshold_trials',
'weights_min', 'weights_max', 'write_trainpoints',
'write_trainforces', 'write_weights_epoch',
'write_neuronstats', 'kalman_type', 'kalman_epsilon',
'kalman_q0', 'kalman_qtau', 'kalman_qmin', 'kalman_eta',
'kalman_etatau', 'kalman_etamax'
]
}
def str_formatify(string):
return float(string) if '.' in string \
or 'e' in string else int(string)
param = {}
with open(filename, 'r') as f:
lines = f.readlines()
df = pd.DataFrame([line.split() for line in lines if "#" not in line])
self.elements = sorted([
element for element in np.ravel(df[df[0] == 'elements'])[1:]
if element is not None
],
key=lambda x: Element(x))
atom_energy = {}
for atom, energy in zip(
np.array(df[df[0] == 'atom_energy'])[:, 1],
np.array(df[df[0] == 'atom_energy'])[:, 2]):
atom_energy[atom] = float(energy)
param.update({'atom_energy': atom_energy})
for tag in PARAMS.get('general'):
if tag == 'scale_features':
scale_features = '1' \
if len(df[df[0] == 'scale_symmetry_functions']) != 0 else 0
param.update({'scale_features': scale_features})
elif tag == 'hidden_layers':
hidden_layers = [
int(neuron) for neuron in np.array(df[
df[0] == 'global_nodes_short'])[0][1:] if neuron
]
param.update({'hidden_layers': hidden_layers})
activations = np.array(
df[df[0] == 'global_activation_short'])[0][1]
param.update({'activations': activations})
else:
value = str_formatify(np.array(df[df[0] == tag])[0][1])
param.update({tag: value})
if len(df[df[0] == 'normalize_nodes']) != 0:
param.update({'normalize_nodes': True})
for tag in PARAMS.get('additional'):
value = str_formatify(np.array(df[df[0] == tag])[0][1])
param.update({tag: value})
r_cut = np.sort(
np.array(df[(df[0] == 'symfunction_short') & (df[2] == '2')][6],
dtype=np.float))[0]
r_cut = float('{:.1f}'.format(r_cut * units.bohr_to_angstrom))
param.update({'r_cut': r_cut})
r_etas = np.sort(
np.array(np.unique(df[(df[0] == 'symfunction_short')
& (df[2] == '2')][4]),
dtype=np.float)).tolist()
param.update({'r_etas': r_etas})
r_shift = np.sort(
np.array(np.unique(df[(df[0] == 'symfunction_short')
& (df[2] == '2')][5]),
dtype=np.float)).tolist()
r_shift = [
float('{:.1f}'.format(r * units.bohr_to_angstrom)) for r in r_shift
]
param.update({'r_shift': r_shift})
a_etas = np.sort(
np.array(np.unique(df[(df[0] == 'symfunction_short')
& (df[2] == '3')][5]),
dtype=np.float)).tolist()
param.update({'a_etas': a_etas})
lambdas = np.sort(
np.array(np.unique(df[(df[0] == 'symfunction_short')
& (df[2] == '3')][6]),
dtype=np.int)).tolist()
param.update({'lambdas': lambdas})
zetas = np.sort(
np.array(np.unique(df[(df[0] == 'symfunction_short')
& (df[2] == '3')][7]),
dtype=np.float)).tolist()
param.update({'zetas': zetas})
self.num_symm_functions = \
sum([len(list(itertools.product(r_etas, r_shift))) for _ in self.elements]) + \
sum([len(list(itertools.product(a_etas, lambdas, zetas)))
for _, _ in itertools.combinations_with_replacement(self.elements, 2)])
self.layer_sizes = [self.num_symm_functions] + hidden_layers
self.param = param
def train(self,
train_structures,
train_energies,
train_forces,
train_stresses=None,
default_sigma=[0.0005, 0.1, 0.05, 0.01],
use_energies=True,
use_forces=True,
use_stress=False,
**kwargs):
"""
Training data with gaussian process regression.
Args:
train_structures ([Structure]): The list of Pymatgen Structure object.
energies ([float]): The list of total energies of each structure
in structures list.
train_energies ([float]): List of total energies of each structure in
structures list.
train_forces ([np.array]): List of (m, 3) forces array of each structure
with m atoms in structures list. m can be varied with each
single structure case.
train_stresses (list): List of (6, ) virial stresses of each
structure in structures list.
default_sigma (list): Error criteria in energies, forces, stress
and hessian. Should have 4 numbers.
use_energies (bool): Whether to use dft total energies for training.
Default to True.
use_forces (bool): Whether to use dft atomic forces for training.
Default to True.
use_stress (bool): Whether to use dft virial stress for training.
Default to False.
kwargs:
l_max (int): Parameter to configure GAP. The band limit of
spherical harmonics basis function. Default to 12.
n_max (int): Parameter to configure GAP. The number of radial basis
function. Default to 10.
atom_sigma (float): Parameter to configure GAP. The width of gaussian
atomic density. Default to 0.5.
zeta (float): Present when covariance function type is do product.
Default to 4.
cutoff (float): Parameter to configure GAP. The cutoff radius.
Default to 4.0.
cutoff_transition_width (float): Parameter to configure GAP.
The transition width of cutoff radial. Default to 0.5.
delta (float): Parameter to configure Sparsification.
The signal variance of noise. Default to 1.
f0 (float): Parameter to configure Sparsification.
The signal mean of noise. Default to 0.0.
n_sparse (int): Parameter to configure Sparsification.
Number of sparse points.
covariance_type (str): Parameter to configure Sparsification.
The type of convariance function. Default to dot_product.
sparse_method (str): Method to perform clustering in sparsification.
Default to 'cur_points'.
sparse_jitter (float): Intrisic error of atomic/bond energy,
used to regularise the sparse covariance matrix.
Default to 1e-8.
e0 (float): Atomic energy value to be subtracted from energies
before fitting. Default to 0.0.
e0_offset (float): Offset of baseline. If zero, the offset is
the average atomic energy of the input data or the e0
specified manually. Default to 0.0.
"""
if not which('gap_fit'):
raise RuntimeError(
"gap_fit has not been found.\n",
"Please refer to https://github.com/libAtoms/QUIP for ",
"further detail.")
train_structures, train_forces, train_stresses = \
check_structures_forces_stresses(train_structures, train_forces, train_stresses)
gap_sorted_elements = []
for struct in train_structures:
for specie in struct.species:
if str(specie) not in gap_sorted_elements:
gap_sorted_elements.append(str(specie))
self.elements = sorted(gap_sorted_elements, key=lambda x: Element(x))
atoms_filename = 'train.xyz'
xml_filename = 'train.xml'
train_pool = pool_from(train_structures, train_energies, train_forces,
train_stresses)
exe_command = ["gap_fit"]
exe_command.append('at_file={}'.format(atoms_filename))
gap_configure_params = [
'l_max', 'n_max', 'atom_sigma', 'zeta', 'cutoff',
'cutoff_transition_width', 'delta', 'f0', 'n_sparse',
'covariance_type', 'sparse_method'
]
preprocess_params = ['sparse_jitter', 'e0', 'e0_offset']
if len(default_sigma) != 4:
raise ValueError(
"The default sigma is supposed to have 4 numbers.")
gap_command = ['soap']
for param_name in gap_configure_params:
param = kwargs.get(param_name) if kwargs.get(param_name) \
else soap_params.get(param_name)
gap_command.append(param_name + '=' + '{}'.format(param))
gap_command.append('add_species=T')
exe_command.append("gap=" + "{" + "{}".format(' '.join(gap_command)) +
"}")
for param_name in preprocess_params:
param = kwargs.get(param_name) if kwargs.get(param_name) \
else soap_params.get(param_name)
exe_command.append(param_name + '=' + '{}'.format(param))
default_sigma = [str(f) for f in default_sigma]
exe_command.append("default_sigma={%s}" % (' '.join(default_sigma)))
if use_energies:
exe_command.append('energy_parameter_name=dft_energy')
if use_forces:
exe_command.append('force_parameter_name=dft_force')
if use_stress:
exe_command.append('virial_parameter_name=dft_virial')
exe_command.append('gp_file={}'.format(xml_filename))
with ScratchDir('.'):
self.write_cfgs(filename=atoms_filename, cfg_pool=train_pool)
p = subprocess.Popen(exe_command, stdout=subprocess.PIPE)
stdout = p.communicate()[0]
rc = p.returncode
if rc != 0:
error_msg = 'gap_fit exited with return code %d' % rc
msg = stdout.decode("utf-8").split('\n')[:-1]
try:
error_line = [
i for i, m in enumerate(msg) if m.startswith('ERROR')
][0]
error_msg += ', '.join(msg[error_line:])
except Exception:
error_msg += msg[-1]
raise RuntimeError(error_msg)
def get_xml(xml_file):
tree = ET.parse(xml_file)
root = tree.getroot()
potential_label = root.tag
element_param = {}
for gpcoordinates in list(root.iter('gpCoordinates')):
gp_descriptor = list(gpcoordinates.iter('descriptor'))[0]
gp_descriptor_text = gp_descriptor.findtext('.')
Z_pattern = re.compile(' Z=(.*?) ', re.S)
element = str(
get_el_sp(int(
Z_pattern.findall(gp_descriptor_text)[0])))
param = np.loadtxt(gpcoordinates.get('sparseX_filename'))
element_param[element] = param.tolist()
return tree, element_param, potential_label
tree, element_param, potential_label = get_xml(xml_filename)
self.param['xml'] = tree
self.param['element_param'] = element_param
self.param['potential_label'] = potential_label
return rc
def get_wf_hubbard_hund_linresp(structure,
user_incar_settings=None,
relax_nonmagnetic=True,
spin_polarized=True,
applied_potential_range=(-0.2, 0.2),
num_evals=9,
site_indices_perturb=None,
species_perturb=None,
find_nearest_sites=True,
parallel_scheme=0,
ediff_tight=None,
c=None):
"""
Compute Hubbard U (and Hund J) on-site interaction values using GGA+U
linear response method proposed by Cococcioni et. al.
(DOI: 10.1103/PhysRevB.71.035105)
and the spin-polarized response formalism developed by Linscott et. al.
(DOI: 10.1103/PhysRevB.98.235157)
This workflow relies on the constrained on-site potential functional implemented in VASP,
with a helpful tutorial found here:
https://www.vasp.at/wiki/index.php/Calculate_U_for_LSDA%2BU
Args:
structure:
user_incar_settings: user INCAR settings
relax_nonmagnetic: Restart magnetic SCF runs from
non-magnetic calculation, using WAVECAR
spin_polarized: Perform spin-dependent perturbations
applied_potential_range: Bounds of applied potential
num_evals: Number of perturbation evalutaions
site_indices_perturb: (must specify if species_perturb=None)
List of site indices within
Structure indicating perturbation sites;
species_perturb: (must specify if site_indices_perturb=None)
List of names of species (string)
of sites to perturb; First site of that species
is selected in the structure
find_nearest_sites: If set to true and species_perturb != None,
the closest sites (by the Structure distance matrix) will be selected
in the response analysis to account for inter-site screening effects
parallel_scheme: 0 - (default) self-consistent (SCF)
runs use WAVECAR from non-self consistent (NSCF) run
at same applied potential; 1 - SCF runs use WAVECAR
from ground-state (V=0) run.
While reusing the WAVECAR from NSCF run in SCF run may be more
efficient (parallel_scheme: 0), the user may also choose to
remove the dependency between NSCF and SCF runs
(parallel_scheme: 1)
ediff_tight: Final energy convergence tolerance,
if restarting from a previous run
(if not specified, will default to pymatgen default EDIFF)
c: Workflow config dict, in the same format
as in presets/core.py and elsewhere in atomate
Returns: Workflow
"""
if not structure.is_ordered:
raise ValueError(
"Please obtain an ordered approximation of the input structure.")
if not site_indices_perturb:
site_indices_perturb = []
if species_perturb:
if find_nearest_sites:
site_indices_perturb = find_closest_sites(structure,
species_perturb)
else:
for specie_u in species_perturb:
found_specie = False
for s in range(len(structure)):
site = structure[s]
if (Element(str(site.specie)) == Element(specie_u)) \
and (s not in site_indices_perturb):
found_specie = True
break
if not found_specie:
raise ValueError("Could not find specie(s) in structure.")
site_indices_perturb.append(s)
elif not site_indices_perturb:
logger.warning("Sites for computing U value are not specified. "
"Computing U for first site in structure. ")
site_indices_perturb = list(tuple(site_indices_perturb))
num_perturb = len(site_indices_perturb)
sites_perturb = []
for site_index_perturb in site_indices_perturb:
site = structure[site_index_perturb]
sites_perturb.append(site)
structure.remove_sites(indices=site_indices_perturb)
for site in sites_perturb:
structure.insert(i=0,
species=site.specie,
coords=site.frac_coords,
properties=site.properties)
# using a uuid for book-keeping,
# in a similar way to other workflows
uuid = str(uuid4())
c_defaults = {"vasp_cmd": VASP_CMD, "db_file": DB_FILE}
if c:
c.update(c_defaults)
else:
c = c_defaults
# Calculate groundstate
# set user_incar_settings
if not user_incar_settings:
user_incar_settings = {}
# setup VASP input sets
uis_gs, uis_ldau, val_dict, vis_ldau = init_linresp_input_sets(
user_incar_settings, structure, num_perturb)
fws = []
index_fw_gs = [0]
ediff_default = vis_ldau.incar['EDIFF']
if not ediff_tight:
ediff_tight = 0.1 * ediff_default
append_linresp_ground_state_fws(fws, structure, num_perturb, index_fw_gs,
uis_gs, relax_nonmagnetic, ediff_default,
ediff_tight)
# generate list of applied on-site potentials in linear response
applied_potential_value_list = []
for counter_perturb in range(num_perturb):
applied_potential_values = np.linspace(applied_potential_range[0],
applied_potential_range[1],
num_evals)
applied_potential_values = np.around(applied_potential_values,
decimals=9)
if 0.0 in applied_potential_values:
applied_potential_values = list(applied_potential_values)
applied_potential_values.pop(applied_potential_values.index(0.0))
applied_potential_values = np.array(applied_potential_values)
applied_potential_value_list.append(applied_potential_values.copy())
for counter_perturb in range(num_perturb):
applied_potential_values = applied_potential_value_list[
counter_perturb]
for v in applied_potential_values:
append_linresp_perturb_fws(v, fws, structure, counter_perturb,
num_perturb, index_fw_gs, uis_ldau,
val_dict, spin_polarized,
relax_nonmagnetic, ediff_default,
ediff_tight, parallel_scheme)
wf = Workflow(fws)
fw_analysis = Firework(
HubbardHundLinRespToDb(num_perturb=num_perturb,
spin_polarized=spin_polarized,
relax_nonmagnetic=relax_nonmagnetic,
db_file=DB_FILE,
wf_uuid=uuid),
name="HubbardHundLinRespToDb",
)
wf.append_wf(Workflow.from_Firework(fw_analysis), wf.leaf_fw_ids)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
wf = add_additional_fields_to_taskdocs(
wf,
{
"wf_meta": {
"wf_uuid": uuid,
"wf_name": "hubbard_hund_linresp",
"wf_version": __hubbard_hund_linresp_wf_version__,
}
},
)
return wf
def displacement_energies(self, structure, potential, displacement_energies_schema, supercell=(1, 1, 1), tollerance=0.1, max_displacement_energy=75, resolution=1, num_steps=1000, site_radius=0.5, timestep=0.001):
""" Calculate displacement energy for each atom.
Uses bisection method to determine displacement energy.
"""
def ev2Aps(Z, energy):
# sqrt((2 * energy[eV] [J/eV]) / (amu [g/mole] [kg/g])) * [m/s] [A/ps]
return math.sqrt((2 * energy * 1.6021766208e-19) / (Z / (6.02214085e23 * 1e3))) * 1e-2
if self.calculator_type == 'lammps':
logger.warning('"lammps" calculator is depriciated use "lammps_cython" cannot promise working')
relax_lammps_script = load_lammps_set('nve')
relax_lammps_script['thermo'] = []
relax_lammps_script
relax_lammps_script['timestep'] = timestep # fs
relax_lammps_script['run'] = num_steps
kwargs = {'lammps_set': relax_lammps_script}
elif self.calculator_type == 'lammps_cython':
kwargs = {'lammps_additional_commands': [
'timestep %f' % timestep,
'velocity all zero linear',
'fix 1 all nve',
'run %d' % num_steps
]}
energies = {}
displacement_energies_schema = displacement_energies_schema.copy()
for displacement_energy_name, d in displacement_energies_schema.items():
base_structure = structure.copy()
v = base_structure.lattice.get_cartesian_coords(d['direction'])
cart_coords = base_structure.lattice.get_cartesian_coords(d['position'])
base_structure = base_structure * supercell
site = base_structure.get_sites_in_sphere(cart_coords, tollerance)[0][0]
original_positions = base_structure.cart_coords
original_frac_positions = base_structure.lattice.get_fractional_coords(original_positions)
index = base_structure.index(site)
min_energy, max_energy = 0.0, max_displacement_energy
guess_energy = None
while abs(max_energy - min_energy) > resolution:
guess_energy = (max_energy - min_energy) / 2 + min_energy
velocity = (v / np.linalg.norm(v)) * ev2Aps(Element(d['element']).atomic_mass, guess_energy)
velocities = np.zeros((len(base_structure), 3))
velocities[index] = velocity
base_structure.add_site_property('velocities', velocities)
async def calculate():
future = await self.calculator.submit(
base_structure, potential,
properties={'positions', 'initial_positions'},
**kwargs)
await future
return future.result()
print('starting calculation (displacement energy): %s ion %s velocity: %f [eV] %f [A/ps]' % (displacement_energy_name, d['element'], guess_energy, ev2Aps(Element(d['element']).atomic_mass, guess_energy)))
result = self._run_async_func(calculate())
initial_frac_positions = base_structure.lattice.get_fractional_coords(result['results']['initial_positions'])
final_frac_positions = base_structure.lattice.get_fractional_coords(result['results']['positions'])
displacements = np.linalg.norm(
base_structure.lattice.get_cartesian_coords(
pbc_diff(final_frac_positions, initial_frac_positions)), axis=1)
is_original_state = np.all(displacements < site_radius)
print('finished calculation (displacement energy): %s resulted in ground_state (%s) max displacment %f [A] median %f [A] min %f [A]' % (displacement_energy_name, is_original_state, np.max(displacements), np.median(displacements), np.min(displacements)))
if is_original_state:
min_energy = guess_energy
else:
max_energy = guess_energy
energies[displacement_energy_name] = guess_energy
return energies
from pymatgen.core import Composition, Element
from pymatgen.ext.matproj import MPRester
key_element = 'Li'
target_phase = 'BeO'
chemsys = key_element + '-' + Composition(target_phase).chemical_system
with MPRester(api_key='') as mpr:
entries = mpr.get_entries_in_chemsys(chemsys)
pd = PhaseDiagram(entries)
for facet in pd.facets:
# read-made, chempots = pd._get_facet_chempots(facet)
# implement again
namelist = [pd.qhull_entries[i].name for i in facet]
complist = [pd.qhull_entries[i].composition for i in facet]
energylist = [pd.qhull_entries[i].energy_per_atom for i in facet]
m = [[c.get_atomic_fraction(e) for e in pd.elements] for c in
complist]
# solve a linear matrix equation, sum(μ*n) = E
chempots = np.linalg.solve(m, energylist)
chempots = dict(zip(pd.elements, chempots))
mu = chempots[Element(key_element)]
# print chemical potential of key element in each equilibrium
print('-'.join(namelist)+': '+str(np.round(mu,3)))
# print transition points of phase equilibria in terms of chemical potential
chempotlist = np.round(pd.get_transition_chempots(Element(key_element)), 3)
print(chempotlist)
def get_atom_feature(
self,
mol,
atom # type: ignore
) -> Dict: # type: ignore
"""
Generate all features of a particular atom
Args:
mol (pybel.Molecule): Molecule being evaluated
atom (pybel.Atom): Specific atom being evaluated
Return:
(dict): All features for that atom
"""
# Get the link to the OpenBabel representation of the atom
obatom = atom.OBAtom
atom_idx = atom.idx - 1 # (pybel atoms indices start from 1)
# Get the element
element = Element.from_Z(obatom.GetAtomicNum()).symbol
# Get the fast-to-compute properties
output = {
"element":
element,
"atomic_num":
obatom.GetAtomicNum(),
"formal_charge":
obatom.GetFormalCharge(),
"hybridization":
6 if element == "H" else obatom.GetHyb(),
"acceptor":
obatom.IsHbondAcceptor(),
"donor":
obatom.IsHbondDonorH()
if atom.type == "H" else obatom.IsHbondDonor(),
"aromatic":
obatom.IsAromatic(),
"coordid":
atom.coordidx,
}
# Get the chirality, if desired
if "chirality" in self.atom_features:
# Determine whether the molecule has chiral centers
chiral_cc = self._get_chiral_centers(mol)
if atom_idx not in chiral_cc:
output["chirality"] = 0
else:
# 1 --> 'R', 2 --> 'S'
output["chirality"] = 1 if chiral_cc[atom_idx] == "R" else 2
# Find the rings, if desired
if "ring_sizes" in self.atom_features:
rings = mol.OBMol.GetSSSR(
) # OpenBabel caches ring computation internally, no need to cache ourselves
output["ring_sizes"] = [
r.Size() for r in rings if r.IsInRing(atom.idx)
]
return output
def _parse(self, filename):
start_patt = re.compile(" \(Enter \S+l101\.exe\)")
route_patt = re.compile(" #[pPnNtT]*.*")
link0_patt = re.compile("^\s(%.+)\s*=\s*(.+)")
charge_mul_patt = re.compile("Charge\s+=\s*([-\\d]+)\s+"
"Multiplicity\s+=\s*(\d+)")
num_basis_func_patt = re.compile("([0-9]+)\s+basis functions")
num_elec_patt = re.compile(
"(\d+)\s+alpha electrons\s+(\d+)\s+beta electrons")
pcm_patt = re.compile("Polarizable Continuum Model")
stat_type_patt = re.compile("imaginary frequencies")
scf_patt = re.compile("E\(.*\)\s*=\s*([-\.\d]+)\s+")
mp2_patt = re.compile("EUMP2\s*=\s*(.*)")
oniom_patt = re.compile("ONIOM:\s+extrapolated energy\s*=\s*(.*)")
termination_patt = re.compile("(Normal|Error) termination")
error_patt = re.compile(
"(! Non-Optimized Parameters !|Convergence failure)")
mulliken_patt = re.compile(
"^\s*(Mulliken charges|Mulliken atomic charges)")
mulliken_charge_patt = re.compile('^\s+(\d+)\s+([A-Z][a-z]?)\s*(\S*)')
end_mulliken_patt = re.compile(
'(Sum of Mulliken )(.*)(charges)\s*=\s*(\D)')
std_orientation_patt = re.compile("Standard orientation")
end_patt = re.compile("--+")
orbital_patt = re.compile("(Alpha|Beta)\s*\S+\s*eigenvalues --(.*)")
thermo_patt = re.compile("(Zero-point|Thermal) correction(.*)="
"\s+([\d\.-]+)")
forces_on_patt = re.compile(
"Center\s+Atomic\s+Forces\s+\(Hartrees/Bohr\)")
forces_off_patt = re.compile("Cartesian\s+Forces:\s+Max.*RMS.*")
forces_patt = re.compile(
"\s+(\d+)\s+(\d+)\s+([0-9\.-]+)\s+([0-9\.-]+)\s+([0-9\.-]+)")
freq_on_patt = re.compile(
"Harmonic\sfrequencies\s+\(cm\*\*-1\),\sIR\sintensities.*Raman.*")
freq_patt = re.compile("Frequencies\s--\s+(.*)")
normal_mode_patt = re.compile(
"\s+(\d+)\s+(\d+)\s+([0-9\.-]{4,5})\s+([0-9\.-]{4,5}).*")
mo_coeff_patt = re.compile("Molecular Orbital Coefficients:")
mo_coeff_name_patt = re.compile(
"\d+\s((\d+|\s+)\s+([a-zA-Z]{1,2}|\s+))\s+(\d+\S+)")
self.properly_terminated = False
self.is_pcm = False
self.stationary_type = "Minimum"
self.structures = []
self.corrections = {}
self.energies = []
self.pcm = None
self.errors = []
self.Mulliken_charges = {}
self.link0 = {}
self.cart_forces = []
self.frequencies = []
self.eigenvalues = []
self.is_spin = False
coord_txt = []
read_coord = 0
read_mulliken = False
read_eigen = False
eigen_txt = []
parse_stage = 0
num_basis_found = False
terminated = False
parse_forces = False
forces = []
parse_freq = False
frequencies = []
read_mo = False
with zopen(filename) as f:
for line in f:
if parse_stage == 0:
if start_patt.search(line):
parse_stage = 1
elif link0_patt.match(line):
m = link0_patt.match(line)
self.link0[m.group(1)] = m.group(2)
elif route_patt.search(line):
params = read_route_line(line)
self.functional = params[0]
self.basis_set = params[1]
self.route = params[2]
self.dieze_tag = params[3]
parse_stage = 1
elif parse_stage == 1:
if charge_mul_patt.search(line):
m = charge_mul_patt.search(line)
self.charge = int(m.group(1))
self.spin_mult = int(m.group(2))
parse_stage = 2
elif parse_stage == 2:
if self.is_pcm:
self._check_pcm(line)
if "FREQ" in self.route and thermo_patt.search(line):
m = thermo_patt.search(line)
if m.group(1) == "Zero-point":
self.corrections["Zero-point"] = float(m.group(3))
else:
key = m.group(2).strip(" to ")
self.corrections[key] = float(m.group(3))
if read_coord:
if not end_patt.search(line):
coord_txt.append(line)
else:
read_coord = (read_coord + 1) % 4
if not read_coord:
sp = []
coords = []
for l in coord_txt[2:]:
toks = l.split()
sp.append(Element.from_Z(int(toks[1])))
coords.append(
[float(i) for i in toks[3:6]])
self.structures.append(Molecule(sp, coords))
if parse_forces:
m = forces_patt.search(line)
if m:
forces.extend(
[float(_v) for _v in m.groups()[2:5]])
elif forces_off_patt.search(line):
self.cart_forces.append(forces)
forces = []
parse_forces = False
# read molecular orbital eigenvalues
if read_eigen:
m = orbital_patt.search(line)
if m:
eigen_txt.append(line)
else:
read_eigen = False
self.eigenvalues = {Spin.up: []}
for eigenline in eigen_txt:
if "Alpha" in eigenline:
self.eigenvalues[Spin.up] += [
float(e)
for e in float_patt.findall(eigenline)
]
elif "Beta" in eigenline:
if Spin.down not in self.eigenvalues:
self.eigenvalues[Spin.down] = []
self.eigenvalues[Spin.down] += [
float(e)
for e in float_patt.findall(eigenline)
]
eigen_txt = []
# read molecular orbital coefficients
if read_mo:
# build a matrix with all coefficients
all_spin = [Spin.up]
if self.is_spin:
all_spin.append(Spin.down)
mat_mo = {}
for spin in all_spin:
mat_mo[spin] = np.zeros(
(self.num_basis_func, self.num_basis_func))
nMO = 0
end_mo = False
while nMO < self.num_basis_func and not end_mo:
f.readline()
f.readline()
self.atom_basis_labels = []
for i in range(self.num_basis_func):
line = f.readline()
# identify atom and OA labels
m = mo_coeff_name_patt.search(line)
if m.group(1).strip() != "":
iat = int(m.group(2)) - 1
# atname = m.group(3)
self.atom_basis_labels.append(
[m.group(4)])
else:
self.atom_basis_labels[iat].append(
m.group(4))
# MO coefficients
coeffs = [
float(c)
for c in float_patt.findall(line)
]
for j in range(len(coeffs)):
mat_mo[spin][i, nMO + j] = coeffs[j]
nMO += len(coeffs)
line = f.readline()
# manage pop=regular case (not all MO)
if nMO < self.num_basis_func and \
("Density Matrix:" in line or mo_coeff_patt.search(line)):
end_mo = True
warnings.warn(
"POP=regular case, matrix coefficients not complete"
)
f.readline()
self.eigenvectors = mat_mo
read_mo = False
# build a more convenient array dict with MO coefficient of
# each atom in each MO.
# mo[Spin][OM j][atom i] = {AO_k: coeff, AO_k: coeff ... }
mo = {}
for spin in all_spin:
mo[spin] = [[
{}
for iat in range(len(self.atom_basis_labels))
] for j in range(self.num_basis_func)]
for j in range(self.num_basis_func):
i = 0
for iat in range(len(self.atom_basis_labels)):
for label in self.atom_basis_labels[iat]:
mo[spin][j][iat][
label] = self.eigenvectors[spin][i,
j]
i += 1
self.molecular_orbital = mo
elif parse_freq:
m = freq_patt.search(line)
if m:
values = [
float(_v) for _v in m.groups()[0].split()
]
for value in values:
frequencies.append([value, []])
elif normal_mode_patt.search(line):
values = [float(_v) for _v in line.split()[2:]]
n = int(len(values) / 3)
for i in range(0, len(values), 3):
j = -n + int(i / 3)
frequencies[j][1].extend(values[i:i + 3])
elif line.find("-------------------") != -1:
parse_freq = False
self.frequencies.append(frequencies)
frequencies = []
elif termination_patt.search(line):
m = termination_patt.search(line)
if m.group(1) == "Normal":
self.properly_terminated = True
terminated = True
elif error_patt.search(line):
error_defs = {
"! Non-Optimized Parameters !": "Optimization "
"error",
"Convergence failure": "SCF convergence error"
}
m = error_patt.search(line)
self.errors.append(error_defs[m.group(1)])
elif (not num_basis_found) and \
num_basis_func_patt.search(line):
m = num_basis_func_patt.search(line)
self.num_basis_func = int(m.group(1))
num_basis_found = True
elif num_elec_patt.search(line):
m = num_elec_patt.search(line)
self.electrons = (int(m.group(1)), int(m.group(2)))
elif (not self.is_pcm) and pcm_patt.search(line):
self.is_pcm = True
self.pcm = {}
elif "FREQ" in self.route and "OPT" in self.route and \
stat_type_patt.search(line):
self.stationary_type = "Saddle"
elif mp2_patt.search(line):
m = mp2_patt.search(line)
self.energies.append(
float(m.group(1).replace("D", "E")))
elif oniom_patt.search(line):
m = oniom_patt.matcher(line)
self.energies.append(float(m.group(1)))
elif scf_patt.search(line):
m = scf_patt.search(line)
self.energies.append(float(m.group(1)))
elif std_orientation_patt.search(line):
coord_txt = []
read_coord = 1
elif not read_eigen and orbital_patt.search(line):
eigen_txt.append(line)
read_eigen = True
elif mulliken_patt.search(line):
mulliken_txt = []
read_mulliken = True
elif not parse_forces and forces_on_patt.search(line):
parse_forces = True
elif freq_on_patt.search(line):
parse_freq = True
elif mo_coeff_patt.search(line):
if "Alpha" in line:
self.is_spin = True
read_mo = True
if read_mulliken:
if not end_mulliken_patt.search(line):
mulliken_txt.append(line)
else:
m = end_mulliken_patt.search(line)
mulliken_charges = {}
for line in mulliken_txt:
if mulliken_charge_patt.search(line):
m = mulliken_charge_patt.search(line)
dict = {
int(m.group(1)):
[m.group(2),
float(m.group(3))]
}
mulliken_charges.update(dict)
read_mulliken = False
self.Mulliken_charges = mulliken_charges
if not terminated:
#raise IOError("Bad Gaussian output file.")
warnings.warn("\n" + self.filename + \
": Termination error or bad Gaussian output file !")
def test_get_property(self):
self.assertAlmostEqual(
9.012182,
self.data_source.get_elemental_property(Element("Be"),
"AtomicWeight"))
def Bk_symbol():
return [str(Element.from_Z(97))]
def process_item(self, item):
"""
Read the entries from the thermo database and group them based on the reduced composition
of the framework material (without working ion).
Args:
chemsys(string): the chemical system string to be queried
returns:
(chemsys, [group]): entry contains a list of entries the materials together by composition
"""
# sort the entries intro subgroups
# then perform PD analysis
all_entries = item['all_entries']
pd_ents = item['pd_ents']
phdi = PhaseDiagram(pd_ents)
# The working ion entries
ents_wion = list(
filter(
lambda x: x.composition.get_integer_formula_and_factor()[0] ==
self.working_ion, pd_ents))
self.working_ion_entry = min(ents_wion,
key=lambda e: e.energy_per_atom)
assert (self.working_ion_entry != None)
grouped_entries = list(self.get_sorted_subgroups(all_entries))
docs = [] # results
for group in grouped_entries:
self.logger.debug(
f"Grouped entries in all sandboxes {', '.join([en.name for en in group])}"
)
for en in group:
# skip this d_muO2 stuff if you do note have oxygen
if Element('O') in en.composition.elements:
d_muO2 = [{
'reaction': str(itr['reaction']),
'chempot': itr['chempot'],
'evolution': itr['evolution']
} for itr in phdi.get_element_profile('O', en.composition)]
else:
d_muO2 = None
en.data['muO2'] = d_muO2
en.data['decomposition_energy'] = phdi.get_e_above_hull(en)
# sort out the sandboxes
# for each sandbox core+sandbox will both contribute entries
all_sbx = [ent.data['sbxn'] for ent in group]
all_sbx = set(chain.from_iterable(all_sbx))
self.logger.debug(f"All sandboxes {', '.join(list(all_sbx))}")
for isbx in all_sbx:
group_sbx = list(
filter(
lambda ent: (isbx in ent.data['sbxn']) or (ent.data[
'sbxn'] == ['core']), group))
# Need more than one level of lithiation to define a electrode material
if len(group_sbx) == 1:
continue
self.logger.debug(
f"Grouped entries in sandbox {isbx} -- {', '.join([en.name for en in group_sbx])}"
)
try:
result = InsertionElectrode(group_sbx,
self.working_ion_entry)
assert (len(result._stable_entries) > 1)
except:
self.logger.warn(
f"Not able to generate a entries in sandbox {isbx} using the following entires-- {', '.join([en.entry_id for en in group_sbx])}"
)
continue
spacegroup = SpacegroupAnalyzer(
result.get_stable_entries(
charge_to_discharge=True)[0].structure)
d = result.as_dict_summary()
ids = [entry.entry_id for entry in result.get_all_entries()]
lowest_id = sorted(ids, key=lambda x: x.split('-')[-1])[0]
d['spacegroup'] = {
k: spacegroup._space_group_data[k]
for k in sg_fields
}
if isbx == 'core':
d['battid'] = lowest_id + '_' + self.working_ion
else:
d['battid'] = lowest_id + '_' + self.working_ion + '_' + isbx
# Only allow one sandbox value for each electrode
d['sbxn'] = [isbx]
docs.append(d)
return docs
def test_get_oxidation(self):
self.assertEqual([-4, 2, 4],
self.data_source.get_oxidation_states(Element("C")))