def __init__(self, symbol):
self.symbol = "%s" % symbol
d = _pt_data[symbol]
# Store key variables for quick access
self.Z = d["Atomic no"]
self.X = d.get("X", 0)
for a in [
"mendeleev_no", "electrical_resistivity", "velocity_of_sound",
"reflectivity", "refractive_index", "poissons_ratio",
"molar_volume", "electronic_structure", "thermal_conductivity",
"boiling_point", "melting_point", "critical_temperature",
"superconduction_temperature", "liquid_range", "bulk_modulus",
"youngs_modulus", "brinell_hardness", "rigidity_modulus",
"mineral_hardness", "vickers_hardness", "density_of_solid",
"atomic_radius_calculated", "van_der_waals_radius",
"coefficient_of_linear_thermal_expansion"
]:
kstr = a.capitalize().replace("_", " ")
val = d.get(kstr, None)
if str(val).startswith("no data"):
val = None
else:
try:
val = float(val)
except ValueError:
toks_nobracket = re.sub(r'\(.*\)', "", val)
toks = toks_nobracket.replace("about",
"").strip().split(" ", 1)
if len(toks) == 2:
try:
if "10<sup>" in toks[1]:
base_power = re.findall(r'([+-]?\d+)', toks[1])
factor = "e" + base_power[1]
toks[0] += factor
if a == "electrical_resistivity":
unit = "ohm m"
elif a == "coefficient_of_linear_thermal_expansion":
unit = "K^-1"
else:
unit = toks[1]
val = FloatWithUnit(toks[0], unit)
else:
unit = toks[1].replace("<sup>", "^").replace(
"</sup>", "").replace("Ω", "ohm")
units = Unit(unit)
if set(units.keys()).issubset(
SUPPORTED_UNIT_NAMES):
val = FloatWithUnit(toks[0], unit)
except ValueError as ex:
# Ignore error. val will just remain a string.
pass
setattr(self, a, val)
if str(d.get("Atomic radius", "no data")).startswith("no data"):
self.atomic_radius = None
else:
self.atomic_radius = Length(d["Atomic radius"], "ang")
self.atomic_mass = Mass(d["Atomic mass"], "amu")
self._data = d
def __getattr__(self, item):
if item in ["mendeleev_no", "electrical_resistivity",
"velocity_of_sound", "reflectivity",
"refractive_index", "poissons_ratio", "molar_volume",
"electronic_structure", "thermal_conductivity",
"boiling_point", "melting_point",
"critical_temperature", "superconduction_temperature",
"liquid_range", "bulk_modulus", "youngs_modulus",
"brinell_hardness", "rigidity_modulus",
"mineral_hardness", "vickers_hardness",
"density_of_solid", "atomic_radius_calculated",
"van_der_waals_radius", "atomic_orbitals",
"coefficient_of_linear_thermal_expansion"]:
kstr = item.capitalize().replace("_", " ")
val = self._data.get(kstr, None)
if str(val).startswith("no data"):
val = None
elif type(val) == dict:
pass
else:
try:
val = float(val)
except ValueError:
nobracket = re.sub(r'\(.*\)', "", val)
toks = nobracket.replace("about", "").strip().split(" ", 1)
if len(toks) == 2:
try:
if "10<sup>" in toks[1]:
base_power = re.findall(r'([+-]?\d+)', toks[1])
factor = "e" + base_power[1]
if toks[0] in [">", "high"]:
toks[0] = "1" # return the border value
toks[0] += factor
if item == "electrical_resistivity":
unit = "ohm m"
elif (
item ==
"coefficient_of_linear_thermal_expansion"
):
unit = "K^-1"
else:
unit = toks[1]
val = FloatWithUnit(toks[0], unit)
else:
unit = toks[1].replace("<sup>", "^").replace(
"</sup>", "").replace("Ω",
"ohm")
units = Unit(unit)
if set(units.keys()).issubset(
SUPPORTED_UNIT_NAMES):
val = FloatWithUnit(toks[0], unit)
except ValueError as ex:
# Ignore error. val will just remain a string.
pass
return val
raise AttributeError
def average_anionic_radius(self) -> float:
"""
Average anionic radius for element (with units). The average is
taken over all negative oxidation states of the element for which
data is present.
"""
if "Ionic radii" in self._data:
radii = [v for k, v in self._data["Ionic radii"].items() if int(k) < 0]
if radii:
return FloatWithUnit(sum(radii) / len(radii), "ang")
return FloatWithUnit(0.0, "ang")
def __new__(cls, *args):
"""Extends the base class adding type conversion of arguments."""
new_args = len(args) * [None]
for i, arg in enumerate(args[:-1]):
converter = float
if i == 0: converter = str
new_args[i] = converter(arg)
v0 = FloatWithUnit(new_args[1], "ang^3")
b0 = FloatWithUnit(new_args[2], "eV ang^-3")
return super(cls, DeltaFactorEntry).__new__(cls,
symbol=new_args[0], v0=v0, b0=b0, b1=new_args[3], xc=args[-1])
def test_compound_operations(self):
g = 10 * Length(1, "m") / (Time(1, "s") ** 2)
e = Mass(1, "kg") * g * Length(1, "m")
self.assertEqual(str(e), "10.0 N m")
form_e = FloatWithUnit(10, unit="kJ mol^-1")
self.assertEqual(str(form_e.to("eV atom^-1")), "0.103642691905 eV atom^-1")
self.assertRaises(UnitError, form_e.to, "m s^-1")
a = FloatWithUnit(1.0, "Ha^3")
self.assertEqual(str(a.to("J^3")), "8.28672661615e-53 J^3")
a = FloatWithUnit(1.0, "Ha bohr^-2")
self.assertEqual(str(a.to("J m^-2")), "1556.89291457 J m^-2")
def nmr_quadrupole_moment(self):
"""
Get a dictionary the nuclear electric quadrupole moment in units of
e*millibarns for various isotopes
"""
return {k: FloatWithUnit(v, "mbarn")
for k, v in self.data.get("NMR Quadrupole Moment", {}).items()}
def test_compound_operations(self):
g = 10 * Length(1, "m") / (Time(1, "s") ** 2)
e = Mass(1, "kg") * g * Length(1, "m")
self.assertEqual(str(e), "10.0 N m")
form_e = FloatWithUnit(10, unit="kJ mol^-1").to("eV atom^-1")
self.assertAlmostEqual(float(form_e), 0.103642691905)
self.assertEqual(str(form_e.unit), "eV atom^-1")
self.assertRaises(UnitError, form_e.to, "m s^-1")
a = FloatWithUnit(1.0, "Ha^3")
b = a.to("J^3")
self.assertAlmostEqual(b, 8.28672661615e-53)
self.assertEqual(str(b.unit), "J^3")
a = FloatWithUnit(1.0, "Ha bohr^-2")
b = a.to("J m^-2")
self.assertAlmostEqual(b, 1556.893078472351)
self.assertEqual(str(b.unit), "J m^-2")
def b0_GPa(self):
"""
Returns the bulk modulus in GPa.
Note: This assumes that the energy and volumes are in eV and Ang^3
respectively
"""
return FloatWithUnit(self.b0, "eV ang^-3").to("GPa")
def coupling_constant(self, specie):
"""
Computes the couplling constant C_q as defined in:
Wasylishen R E, Ashbrook S E, Wimperis S. NMR of quadrupolar nuclei
in solid materials[M]. John Wiley & Sons, 2012. (Chapter 3.2)
C_q for a specific atom type for this electric field tensor:
C_q=e*Q*V_zz/h
h: planck's constant
Q: nuclear electric quadrupole moment in mb (millibarn
e: elementary proton charge
Args:
specie: flexible input to specify the species at this site.
Can take a isotope or element string, Specie object,
or Site object
Return:
the coupling constant as a FloatWithUnit in MHz
"""
planks_constant = FloatWithUnit(6.62607004E-34, "m^2 kg s^-1")
Vzz = FloatWithUnit(self.V_zz, "V ang^-2")
e = FloatWithUnit(-1.60217662E-19, "C")
# Convert from string to Specie object
if isinstance(specie, str):
# isotope was provided in string format
if len(specie.split("-")) > 1:
isotope = str(specie)
specie = Specie(specie.split("-")[0])
Q = specie.get_nmr_quadrupole_moment(isotope)
else:
specie = Specie(specie)
Q = specie.get_nmr_quadrupole_moment()
elif isinstance(specie, Site):
specie = specie.specie
Q = specie.get_nmr_quadrupole_moment()
elif isinstance(specie, Specie):
Q = specie.get_nmr_quadrupole_moment()
else:
raise ValueError(
"Invalid speciie provided for quadrupolar coupling constant calcuations"
)
return (e * Q * Vzz / planks_constant).to("MHz")
def ionic_radii(self) -> Dict[int, float]:
"""
All ionic radii of the element as a dict of
{oxidation state: ionic radii}. Radii are given in ang.
"""
if "Ionic radii" in self._data:
return {int(k): FloatWithUnit(v, "ang") for k, v in self._data["Ionic radii"].items()}
return {}
def average_ionic_radius(self):
"""
Average ionic radius for element (with units). The average is taken
over all oxidation states of the element for which data is present.
"""
if "Ionic radii" in self._data:
radii = self._data["Ionic radii"]
radius = sum(radii.values()) / len(radii)
else:
radius = 0.0
return FloatWithUnit(radius, "ang")
def gruneisen_parameter(self, temperature, volume):
"""
Slater-gamma formulation(the default):
gruneisen paramter = - d log(theta)/ d log(V)
= - ( 1/6 + 0.5 d log(B)/ d log(V) )
= - (1/6 + 0.5 V/B dB/dV),
where dB/dV = d^2E/dV^2 + V * d^3E/dV^3
Mie-gruneisen formulation:
Eq(31) in doi.org/10.1016/j.comphy.2003.12.001
Eq(7) in Blanco et. al. Joumal of Molecular Structure (Theochem)
368 (1996) 245-255
Also se J.P. Poirier, Introduction to the Physics of the Earth’s
Interior, 2nd ed. (Cambridge University Press, Cambridge,
2000) Eq(3.53)
Args:
temperature (float): temperature in K
volume (float): in Ang^3
Returns:
float: unitless
"""
if isinstance(self.eos, PolynomialEOS):
p = np.poly1d(self.eos.eos_params) # pylint: disable=E1101
# first derivative of energy at 0K wrt volume evaluated at the
# given volume, in eV/Ang^3
dEdV = np.polyder(p, 1)(volume)
# second derivative of energy at 0K wrt volume evaluated at the
# given volume, in eV/Ang^6
d2EdV2 = np.polyder(p, 2)(volume)
# third derivative of energy at 0K wrt volume evaluated at the
# given volume, in eV/Ang^9
d3EdV3 = np.polyder(p, 3)(volume)
else:
func = self.ev_eos_fit.func
dEdV = derivative(func, volume, dx=1e-3)
d2EdV2 = derivative(func, volume, dx=1e-3, n=2, order=5)
d3EdV3 = derivative(func, volume, dx=1e-3, n=3, order=7)
# Mie-gruneisen formulation
if self.use_mie_gruneisen:
p0 = dEdV
return (
self.gpa_to_ev_ang
* volume
* (self.pressure + p0 / self.gpa_to_ev_ang)
/ self.vibrational_internal_energy(temperature, volume)
)
# Slater-gamma formulation
# first derivative of bulk modulus wrt volume, eV/Ang^6
dBdV = d2EdV2 + d3EdV3 * volume
return -(1.0 / 6.0 + 0.5 * volume * dBdV / FloatWithUnit(self.ev_eos_fit.b0_GPa, "GPa").to("eV ang^-3"))
def __new__(cls, **kwargs):
"""Extends the base class adding type conversion of arguments."""
for k, v in kwargs.items():
if k in ["symbol", "struct_type"]: continue
if v == "-":
# Set missing entries to None
v = None
else:
# Values in GBRV tables are in Angstrom.
v = FloatWithUnit(v, "ang")
kwargs[k] = v
return super(cls, GbrvEntry).__new__(cls, **kwargs)
def test_compound_operations(self):
g = 10 * Length(1, "m") / (Time(1, "s")**2)
e = Mass(1, "kg") * g * Length(1, "m")
self.assertEqual(str(e), "10.0 N m")
form_e = FloatWithUnit(10, unit="kJ mol^-1").to("eV atom^-1")
self.assertAlmostEqual(float(form_e), 0.103642691905)
self.assertEqual(str(form_e.unit), "eV atom^-1")
self.assertRaises(UnitError, form_e.to, "m s^-1")
a = FloatWithUnit(1.0, "Ha^3")
b = a.to("J^3")
self.assertAlmostEqual(b, 8.28672661615e-53)
self.assertEqual(str(b.unit), "J^3")
a = FloatWithUnit(1.0, "Ha bohr^-2")
b = a.to("J m^-2")
self.assertAlmostEqual(b, 1556.893078472351)
self.assertEqual(str(b.unit), "J m^-2")
def read_data_from_filepath(filepath, xc):
"""
Reads (v0, b0, b1) from file filename. b0 is in GPa.
xc is the XcFunc associated to these data.
Returns a dict of `DeltaFactorEntry` objects indexed by element symbol.
"""
data = collections.OrderedDict()
with open(filepath, "r") as fh:
for line in fh:
line = line.strip()
if line.startswith("#") or not line:
continue
tokens = line.split()
symbol = tokens[0]
# Conversion GPa --> eV / A**3 and pass xc info to the Entry.
tokens[2] = FloatWithUnit(tokens[2], "GPa").to("eV ang^-3")
tokens.append(xc)
data[symbol] = DeltaFactorEntry(*tokens)
return data
def test_unitized(self):
@unitized("eV")
def f():
return [1, 2, 3]
self.assertEqual(str(f()[0]), "1.0 eV")
self.assertIsInstance(f(), list)
@unitized("eV")
def g():
return 2, 3, 4
self.assertEqual(str(g()[0]), "2.0 eV")
self.assertIsInstance(g(), tuple)
@unitized("pm")
def h():
d = collections.OrderedDict()
for i in range(3):
d[i] = i * 20
return d
self.assertEqual(str(h()[1]), "20.0 pm")
self.assertIsInstance(h(), collections.OrderedDict)
@unitized("kg")
def i():
return FloatWithUnit(5, "g")
self.assertEqual(i(), FloatWithUnit(0.005, "kg"))
@unitized("kg")
def j():
return ArrayWithUnit([5, 10], "g")
j_out = j()
self.assertEqual(j_out.unit, Unit("kg"))
self.assertEqual(j_out[0], 0.005)
self.assertEqual(j_out[1], 0.01)
def b0_GPa(self):
return FloatWithUnit(self.b0, "eV ang^-3").to("GPa")
def df_compute(v0w, b0w, b1w, v0f, b0f, b1f, b0_GPa=False, v=3, useasymm=False):
"""
Compute the deltafactor. Based on the code of the offical calcDelta.py script.
Args:
v0w, b0w, b1w: Volume, bulk-modulus and pressure derivative of b0w (reference values).
v0f, b0f, b1f: Volume, bulk-modulus and pressure derivative of b0f (computed values).
v: version of delta factor, current version is 3, 1 for symmetrical old version
.. note::
v0 is A**3/natom, by default b0 is in eV/A**3, GPa units are used if b0_GPa is True.
"""
#print(v0w, b0w, b1w, v0f, b0f, b1f)
if v == 1:
# delta factor form version 1
if b0_GPa:
# Conversion GPa --> eV/A**3
b0w = FloatWithUnit(b0w, "GPa").to("eV ang^-3")
b0f = FloatWithUnit(b0f, "GPa").to("eV ang^-3")
Vi = 0.94 * v0w
Vf = 1.06 * v0w
a3f = 9. * v0f**3. * b0f / 16. * (b1f - 4.)
a2f = 9. * v0f**(7./3.) * b0f / 16. * (14. - 3. * b1f)
a1f = 9. * v0f**(5./3.) * b0f / 16. * (3. * b1f - 16.)
a0f = 9. * v0f * b0f / 16. * (6. - b1f)
a3w = 9. * v0w**3. * b0w / 16. * (b1w - 4.)
a2w = 9. * v0w**(7./3.) * b0w / 16. * (14. - 3. * b1w)
a1w = 9. * v0w**(5./3.) * b0w / 16. * (3. * b1w - 16.)
a0w = 9. * v0w * b0w / 16. * (6. - b1w)
x = [0, 0, 0, 0, 0, 0, 0]
x[0] = (a0f - a0w)**2
x[1] = 6. * (a1f - a1w) * (a0f - a0w)
x[2] = -3. * (2. * (a2f - a2w) * (a0f - a0w) + (a1f - a1w)**2.)
x[3] = -2. * (a3f - a3w) * (a0f - a0w) - 2. * (a2f - a2w) * (a1f - a1w)
x[4] = -3./5. * (2. * (a3f - a3w) * (a1f - a1w) + (a2f - a2w)**2.)
x[5] = -6./7. * (a3f - a3w) * (a2f - a2w)
x[6] = -1./3. * (a3f - a3w)**2.
Fi = np.zeros_like(Vi)
Ff = np.zeros_like(Vf)
for n in range(7):
Fi = Fi + x[n] * Vi**(-(2.*n-3.)/3.)
Ff = Ff + x[n] * Vf**(-(2.*n-3.)/3.)
return 1000. * np.sqrt((Ff - Fi) / (0.12 * v0w))
elif v == 3:
# version 3
if b0_GPa:
# Conversion GPa --> eV/A**3
b0w = FloatWithUnit(b0w, "GPa").to("eV ang^-3")
b0f = FloatWithUnit(b0f, "GPa").to("eV ang^-3")
if useasymm:
Vi = 0.94 * v0w
Vf = 1.06 * v0w
else:
Vi = 0.94 * (v0w + v0f) / 2.
Vf = 1.06 * (v0w + v0f) / 2.
a3f = 9. * v0f**3. * b0f / 16. * (b1f - 4.)
a2f = 9. * v0f**(7./3.) * b0f / 16. * (14. - 3. * b1f)
a1f = 9. * v0f**(5./3.) * b0f / 16. * (3. * b1f - 16.)
a0f = 9. * v0f * b0f / 16. * (6. - b1f)
a3w = 9. * v0w**3. * b0w / 16. * (b1w - 4.)
a2w = 9. * v0w**(7./3.) * b0w / 16. * (14. - 3. * b1w)
a1w = 9. * v0w**(5./3.) * b0w / 16. * (3. * b1w - 16.)
a0w = 9. * v0w * b0w / 16. * (6. - b1w)
x = [0, 0, 0, 0, 0, 0, 0]
x[0] = (a0f - a0w)**2
x[1] = 6. * (a1f - a1w) * (a0f - a0w)
x[2] = -3. * (2. * (a2f - a2w) * (a0f - a0w) + (a1f - a1w)**2.)
x[3] = -2. * (a3f - a3w) * (a0f - a0w) - 2. * (a2f - a2w) * (a1f - a1w)
x[4] = -3./5. * (2. * (a3f - a3w) * (a1f - a1w) + (a2f - a2w)**2.)
x[5] = -6./7. * (a3f - a3w) * (a2f - a2w)
x[6] = -1./3. * (a3f - a3w)**2.
y = [0, 0, 0, 0, 0, 0, 0]
y[0] = (a0f + a0w)**2 / 4.
y[1] = 3. * (a1f + a1w) * (a0f + a0w) / 2.
y[2] = -3. * (2. * (a2f + a2w) * (a0f + a0w) + (a1f + a1w)**2.) / 4.
y[3] = -(a3f + a3w) * (a0f + a0w) / 2. - (a2f + a2w) * (a1f + a1w) / 2.
y[4] = -3./20. * (2. * (a3f + a3w) * (a1f + a1w) + (a2f + a2w)**2.)
y[5] = -3./14. * (a3f + a3w) * (a2f + a2w)
y[6] = -1./12. * (a3f + a3w)**2.
Fi = np.zeros_like(Vi)
Ff = np.zeros_like(Vf)
Gi = np.zeros_like(Vi)
Gf = np.zeros_like(Vf)
for n in range(7):
Fi += x[n] * Vi**(-(2.*n-3.)/3.)
Ff += x[n] * Vf**(-(2.*n-3.)/3.)
Gi += y[n] * Vi**(-(2.*n-3.)/3.)
Gf += y[n] * Vf**(-(2.*n-3.)/3.)
Delta = 1000. * np.sqrt((Ff - Fi) / (Vf - Vi))
#Deltarel = 100. * np.sqrt((Ff - Fi) / (Gf - Gi))
#if useasymm:
# Delta1 = 1000. * np.sqrt((Ff - Fi) / (Vf - Vi)) \
# / v0w / b0w * vref * bref
#else:
# Delta1 = 1000. * np.sqrt((Ff - Fi) / (Vf - Vi)) \
# / (v0w + v0f) / (b0w + b0f) * 4. * vref * bref
return Delta
else:
raise ValueError("Wrong version %s" % v)
def _parse_job(self, output):
energy_patt = re.compile(r'Total \w+ energy\s+=\s+([.\-\d]+)')
energy_gas_patt = re.compile(r'gas phase energy\s+=\s+([.\-\d]+)')
energy_sol_patt = re.compile(r'sol phase energy\s+=\s+([.\-\d]+)')
coord_patt = re.compile(r'\d+\s+(\w+)\s+[.\-\d]+\s+([.\-\d]+)\s+'
r'([.\-\d]+)\s+([.\-\d]+)')
lat_vector_patt = re.compile(r'a[123]=<\s+([.\-\d]+)\s+'
r'([.\-\d]+)\s+([.\-\d]+)\s+>')
corrections_patt = re.compile(r'([\w\-]+ correction to \w+)\s+='
r'\s+([.\-\d]+)')
preamble_patt = re.compile(r'(No. of atoms|No. of electrons'
r'|SCF calculation type|Charge|Spin '
r'multiplicity)\s*:\s*(\S+)')
force_patt = re.compile(r'\s+(\d+)\s+(\w+)' + 6 * r'\s+([0-9\.\-]+)')
time_patt = re.compile(
r'\s+ Task \s+ times \s+ cpu: \s+ ([.\d]+)s .+ ', re.VERBOSE)
error_defs = {
"calculations not reaching convergence": "Bad convergence",
"Calculation failed to converge": "Bad convergence",
"geom_binvr: #indep variables incorrect": "autoz error",
"dft optimize failed": "Geometry optimization failed"}
fort2py = lambda x: x.replace("D", "e")
isfloatstring = lambda s: s.find(".") == -1
parse_hess = False
parse_proj_hess = False
hessian = None
projected_hessian = None
parse_force = False
all_forces = []
forces = []
data = {}
energies = []
frequencies = None
normal_frequencies = None
corrections = {}
molecules = []
structures = []
species = []
coords = []
lattice = []
errors = []
basis_set = {}
bset_header = []
parse_geom = False
parse_freq = False
parse_bset = False
parse_projected_freq = False
job_type = ""
parse_time = False
time = 0
for l in output.split("\n"):
for e, v in error_defs.items():
if l.find(e) != -1:
errors.append(v)
if parse_time:
m = time_patt.search(l)
if m:
time = m.group(1)
parse_time = False
if parse_geom:
if l.strip() == "Atomic Mass":
if lattice:
structures.append(Structure(lattice, species, coords,
coords_are_cartesian=True))
else:
molecules.append(Molecule(species, coords))
species = []
coords = []
lattice = []
parse_geom = False
else:
m = coord_patt.search(l)
if m:
species.append(m.group(1).capitalize())
coords.append([float(m.group(2)), float(m.group(3)),
float(m.group(4))])
m = lat_vector_patt.search(l)
if m:
lattice.append([float(m.group(1)), float(m.group(2)),
float(m.group(3))])
if parse_force:
m = force_patt.search(l)
if m:
forces.extend(map(float, m.groups()[5:]))
elif len(forces) > 0:
all_forces.append(forces)
forces = []
parse_force = False
elif parse_freq:
if len(l.strip()) == 0:
if len(normal_frequencies[-1][1]) == 0:
continue
else:
parse_freq = False
else:
vibs = [float(vib) for vib in l.strip().split()[1:]]
num_vibs = len(vibs)
for mode, dis in zip(normal_frequencies[-num_vibs:], vibs):
mode[1].append(dis)
elif parse_projected_freq:
if len(l.strip()) == 0:
if len(frequencies[-1][1]) == 0:
continue
else:
parse_projected_freq = False
else:
vibs = [float(vib) for vib in l.strip().split()[1:]]
num_vibs = len(vibs)
for mode, dis in zip(
frequencies[-num_vibs:], vibs):
mode[1].append(dis)
elif parse_bset:
if l.strip() == "":
parse_bset = False
else:
toks = l.split()
if toks[0] != "Tag" and not re.match(r"-+", toks[0]):
basis_set[toks[0]] = dict(zip(bset_header[1:],
toks[1:]))
elif toks[0] == "Tag":
bset_header = toks
bset_header.pop(4)
bset_header = [h.lower() for h in bset_header]
elif parse_hess:
if l.strip() == "":
continue
if len(hessian) > 0 and l.find("----------") != -1:
parse_hess = False
continue
toks = l.strip().split()
if len(toks) > 1:
try:
row = int(toks[0])
except Exception:
continue
if isfloatstring(toks[1]):
continue
vals = [float(fort2py(x)) for x in toks[1:]]
if len(hessian) < row:
hessian.append(vals)
else:
hessian[row - 1].extend(vals)
elif parse_proj_hess:
if l.strip() == "":
continue
nat3 = len(hessian)
toks = l.strip().split()
if len(toks) > 1:
try:
row = int(toks[0])
except Exception:
continue
if isfloatstring(toks[1]):
continue
vals = [float(fort2py(x)) for x in toks[1:]]
if len(projected_hessian) < row:
projected_hessian.append(vals)
else:
projected_hessian[row - 1].extend(vals)
if len(projected_hessian[-1]) == nat3:
parse_proj_hess = False
else:
m = energy_patt.search(l)
if m:
energies.append(Energy(m.group(1), "Ha").to("eV"))
parse_time = True
continue
m = energy_gas_patt.search(l)
if m:
cosmo_scf_energy = energies[-1]
energies[-1] = dict()
energies[-1].update({"cosmo scf": cosmo_scf_energy})
energies[-1].update({"gas phase":
Energy(m.group(1), "Ha").to("eV")})
m = energy_sol_patt.search(l)
if m:
energies[-1].update(
{"sol phase": Energy(m.group(1), "Ha").to("eV")})
m = preamble_patt.search(l)
if m:
try:
val = int(m.group(2))
except ValueError:
val = m.group(2)
k = m.group(1).replace("No. of ", "n").replace(" ", "_")
data[k.lower()] = val
elif l.find("Geometry \"geometry\"") != -1:
parse_geom = True
elif l.find("Summary of \"ao basis\"") != -1:
parse_bset = True
elif l.find("P.Frequency") != -1:
parse_projected_freq = True
if frequencies is None:
frequencies = []
toks = l.strip().split()[1:]
frequencies.extend([(float(freq), []) for freq in toks])
elif l.find("Frequency") != -1:
toks = l.strip().split()
if len(toks) > 1 and toks[0] == "Frequency":
parse_freq = True
if normal_frequencies is None:
normal_frequencies = []
normal_frequencies.extend([(float(freq), []) for freq
in l.strip().split()[1:]])
elif l.find("MASS-WEIGHTED NUCLEAR HESSIAN") != -1:
parse_hess = True
if not hessian:
hessian = []
elif l.find("MASS-WEIGHTED PROJECTED HESSIAN") != -1:
parse_proj_hess = True
if not projected_hessian:
projected_hessian = []
elif l.find("atom coordinates gradient") != -1:
parse_force = True
elif job_type == "" and l.strip().startswith("NWChem"):
job_type = l.strip()
if job_type == "NWChem DFT Module" and \
"COSMO solvation results" in output:
job_type += " COSMO"
else:
m = corrections_patt.search(l)
if m:
corrections[m.group(1)] = FloatWithUnit(
m.group(2), "kJ mol^-1").to("eV atom^-1")
if frequencies:
for freq, mode in frequencies:
mode[:] = zip(*[iter(mode)]*3)
if normal_frequencies:
for freq, mode in normal_frequencies:
mode[:] = zip(*[iter(mode)]*3)
if hessian:
n = len(hessian)
for i in range(n):
for j in range(i + 1, n):
hessian[i].append(hessian[j][i])
if projected_hessian:
n = len(projected_hessian)
for i in range(n):
for j in range(i + 1, n):
projected_hessian[i].append(projected_hessian[j][i])
data.update({"job_type": job_type, "energies": energies,
"corrections": corrections,
"molecules": molecules,
"structures": structures,
"basis_set": basis_set,
"errors": errors,
"has_error": len(errors) > 0,
"frequencies": frequencies,
"normal_frequencies": normal_frequencies,
"hessian": hessian,
"projected_hessian": projected_hessian,
"forces": all_forces,
"task_time": time})
return data
def test_as_base_units(self):
x = FloatWithUnit(5, "MPa")
self.assertEqual(FloatWithUnit(5000000, "Pa"), x.as_base_units)
def find_theo_redenth(compstr):
"""
Finds theoretical redox enthalpies from the Materials Project from perovskite to brownmillerite
based partially on https://github.com/materialsproject/pymatgen/blob/b3e972e293885c5b3c69fb3e9aa55287869d4d84/
examples/Calculating%20Reaction%20Energies%20with%20the%20Materials%20API.ipynb
:param compstr: composition as a string
:return:
red_enth: redox enthalpy in kJ/mol O
"""
compstr_perovskite = compstr.split("O")[0] + "O3"
comp_spl = split_comp(compstr)
chem_sys = ""
for i in range(len(comp_spl)):
if comp_spl[i] is not None:
chem_sys = chem_sys + comp_spl[i][0] + "-"
chem_sys = chem_sys + "O"
chem_sys = chem_sys.split("-")
all_entries = mpr.get_entries_in_chemsys(chem_sys)
# This method simply gets the lowest energy entry for all entries with the same composition.
def get_most_stable_entry(formula):
relevant_entries = [entry for entry in all_entries if
entry.composition.reduced_formula == Composition(formula).reduced_formula]
relevant_entries = sorted(relevant_entries, key=lambda e: e.energy_per_atom)
return relevant_entries[0]
formula_spl = [''.join(g) for _, g in groupby(str(compstr), str.isalpha)]
perov_formula = []
for k in range(len(formula_spl)):
try:
perov_formula += str(int(float(formula_spl[k]) * 8))
except ValueError:
perov_formula += str(formula_spl[k])
perov_formula = "".join(perov_formula)
perov_formula = str(perov_formula).split("O")[0] + "O24"
perovskite = get_most_stable_entry(perov_formula)
brownm_formula = []
for k in range(len(formula_spl)):
try:
brownm_formula += str(int(float(formula_spl[k]) * 32))
except ValueError:
brownm_formula += str(formula_spl[k])
brownm_formula = "".join(brownm_formula)
brownm_formula = str(brownm_formula).split("O")[0] + "O80"
brownmillerite = get_most_stable_entry(brownm_formula)
# for oxygen: do not use the most stable phase O8 but the most stable O2 phase
def get_oxygen():
relevant_entries = [entry for entry in all_entries if
entry.composition == Composition("O2")]
relevant_entries = sorted(relevant_entries, key=lambda e: e.energy_per_atom)
return relevant_entries[0]
oxygen = get_oxygen()
reaction = ComputedReaction([perovskite], [brownmillerite, oxygen])
energy = FloatWithUnit(reaction.calculated_reaction_energy, "eV atom^-1")
# figure out the stoichiometry of O2 in the reaction equation in order to normalize the energies per mol of O
try:
o_stoich = float(str(str(reaction.as_dict).split(" O2")[0]).split()[-1])
except ValueError:
o_stoich = 1
# energy in J/mol per mol of O2
ener = (float(energy.to("kJ mol^-1")) * 1000) / o_stoich
# per mol of O
ener = ener / 2
return ener
def i():
return FloatWithUnit(5, "g")
def metallic_radius(self):
"""
Metallic radius of the element. Radius is given in ang.
"""
return FloatWithUnit(self._data["Metallic radius"], "ang")
def _parse_job(self, output):
energy_patt = re.compile("Total \w+ energy\s+=\s+([\.\-\d]+)")
#In cosmo solvation results; gas phase energy = -152.5044774212
energy_gas_patt = re.compile("gas phase energy\s+=\s+([\.\-\d]+)")
#In cosmo solvation results; sol phase energy = -152.5044774212
energy_sol_patt = re.compile("sol phase energy\s+=\s+([\.\-\d]+)")
coord_patt = re.compile("\d+\s+(\w+)\s+[\.\-\d]+\s+([\.\-\d]+)\s+"
"([\.\-\d]+)\s+([\.\-\d]+)")
corrections_patt = re.compile("([\w\-]+ correction to \w+)\s+="
"\s+([\.\-\d]+)")
preamble_patt = re.compile("(No. of atoms|No. of electrons"
"|SCF calculation type|Charge|Spin "
"multiplicity)\s*:\s*(\S+)")
error_defs = {
"calculations not reaching convergence": "Bad convergence",
"Calculation failed to converge": "Bad convergence",
"geom_binvr: #indep variables incorrect": "autoz error",
"dft optimize failed": "Geometry optimization failed"
}
data = {}
energies = []
frequencies = None
corrections = {}
molecules = []
species = []
coords = []
errors = []
basis_set = {}
parse_geom = False
parse_freq = False
parse_bset = False
job_type = ""
for l in output.split("\n"):
for e, v in error_defs.items():
if l.find(e) != -1:
errors.append(v)
if parse_geom:
if l.strip() == "Atomic Mass":
molecules.append(Molecule(species, coords))
species = []
coords = []
parse_geom = False
else:
m = coord_patt.search(l)
if m:
species.append(m.group(1).capitalize())
coords.append([
float(m.group(2)),
float(m.group(3)),
float(m.group(4))
])
if parse_freq:
if len(l.strip()) == 0:
if len(frequencies[-1][1]) == 0:
continue
else:
parse_freq = False
else:
vibs = [float(vib) for vib in l.strip().split()[1:]]
num_vibs = len(vibs)
for mode, dis in zip(frequencies[-num_vibs:], vibs):
mode[1].append(dis)
elif parse_bset:
if l.strip() == "":
parse_bset = False
else:
toks = l.split()
if toks[0] != "Tag" and not re.match("\-+", toks[0]):
basis_set[toks[0]] = dict(
zip(bset_header[1:], toks[1:]))
elif toks[0] == "Tag":
bset_header = toks
bset_header.pop(4)
bset_header = [h.lower() for h in bset_header]
else:
m = energy_patt.search(l)
if m:
energies.append(Energy(m.group(1), "Ha").to("eV"))
continue
m = energy_gas_patt.search(l)
if m:
cosmo_scf_energy = energies[-1]
energies[-1] = dict()
energies[-1].update({"cosmo scf": cosmo_scf_energy})
energies[-1].update(
{"gas phase": Energy(m.group(1), "Ha").to("eV")})
m = energy_sol_patt.search(l)
if m:
energies[-1].update(
{"sol phase": Energy(m.group(1), "Ha").to("eV")})
m = preamble_patt.search(l)
if m:
try:
val = int(m.group(2))
except ValueError:
val = m.group(2)
k = m.group(1).replace("No. of ", "n").replace(" ", "_")
data[k.lower()] = val
elif l.find("Geometry \"geometry\"") != -1:
parse_geom = True
elif l.find("Summary of \"ao basis\"") != -1:
parse_bset = True
elif l.find("P.Frequency") != -1:
parse_freq = True
if not frequencies:
frequencies = []
frequencies.extend([(float(freq), [])
for freq in l.strip().split()[1:]])
elif job_type == "" and l.strip().startswith("NWChem"):
job_type = l.strip()
if job_type == "NWChem DFT Module" and \
"COSMO solvation results" in output:
job_type += " COSMO"
else:
m = corrections_patt.search(l)
if m:
corrections[m.group(1)] = FloatWithUnit(
m.group(2), "kJ mol^-1").to("eV atom^-1")
if frequencies:
for freq, mode in frequencies:
mode[:] = zip(*[iter(mode)] * 3)
data.update({
"job_type": job_type,
"energies": energies,
"corrections": corrections,
"molecules": molecules,
"basis_set": basis_set,
"errors": errors,
"has_error": len(errors) > 0,
"frequencies": frequencies
})
return data
def get_most_stable_entry(formula):
relevant_entries = [
entry for entry in all_entries if entry.composition.reduced_formula ==
Composition(formula).reduced_formula
]
relevant_entries = sorted(relevant_entries,
key=lambda e: e.energy_per_atom)
return relevant_entries[0]
CaO = get_most_stable_entry("CaO")
CO2 = get_most_stable_entry("CO2")
CaCO3 = get_most_stable_entry("CaCO3")
reaction = ComputedReaction([CaO, CO2], [CaCO3]) #得到化学反应
energy = FloatWithUnit(reaction.calculated_reaction_energy,
"eV atom^-1") #计算化学反应的能量，并且转换单位
print("Caculated")
print(reaction)
print("Reaction energy = {}".format(energy.to("kJ mol^-1")))
# The following portions demonstrate how to get the experimental values as well.
exp_CaO = a.get_exp_entry("CaO") #获得ExpEntry对象，可用于实验数据分析
exp_CaCO3 = a.get_exp_entry("CaCO3")
#Unfortunately, the Materials Project database does not have gas phase experimental entries. This is the value from NIST. We manually create the entry.
#这是一个气相实验，而且数据库没有关于这个的数据条目，所以我们要自己创建
#NIST是化学信息的标准参考数据库
exp_CO2 = ComputedEntry("CO2", -393.51) #Exp entries should be in kJ/mol.
exp_reaction = ComputedReaction([exp_CaO, exp_CO2], [exp_CaCO3])
def compute(self, input_data):
return FloatWithUnit(input_data, "g")
stable_result = get_most_stable_entry(result)
except IndexError:
error["error"] = "No structure with that formula"
json_dir = output_path + "/" + "output.json"
with open(json_dir, "w") as outfile:
json.dump(error, outfile)
print(error)
exit()
# print stable_result.name, phase.get_form_energy(stable_result)
(compo,
factor) = stable_result.composition.get_reduced_composition_and_factor()
form_energy[stable_result.name] = phase.get_form_energy(stable_result) / factor
reaction = ComputedReaction(stable_formula, [stable_result])
energy = FloatWithUnit(reaction.calculated_reaction_energy, "eV atom^-1")
json_result = dict()
json_result["reaction"] = str(reaction)
value1 = dict()
value1["value"] = energy.to("kJ mol^-1")
value1["unit"] = "kJ mol^-1"
value2 = dict()
value2["value"] = energy.to("eV atom^-1")
value2["unit"] = "eV"
json_result["value1"] = value1
json_result["value2"] = value2
json_result["formationenergy"] = form_energy
def b0_GPa(self):
"""
Returns the bulk modulus in GPa
"""
return FloatWithUnit(self.params[1], "eV ang^-3").to("GPa")