def from_ncreader(cls, r, inord="F"):
"""
Builds the object from a netcdf reader
"""
kptopt = int(r.read_value("kptopt", default=1))
symrel = r.read_value("reduced_symmetry_matrices")
return cls(spgid=r.read_value("space_group"),
symrel=symrel,
tnons=r.read_value("reduced_symmetry_translations"),
symafm=r.read_value("symafm"),
has_timerev=has_timrev_from_kptopt(kptopt),
inord=inord)
def from_file(cls, ncfile, inord="F"):
"""Initialize the object from a Netcdf file."""
r, closeit = as_etsfreader(ncfile)
kptopt = int(r.read_value("kptopt", default=1))
new = cls(spgid=r.read_value("space_group"),
symrel=r.read_value("reduced_symmetry_matrices"),
tnons=r.read_value("reduced_symmetry_translations"),
symafm=r.read_value("symafm"),
has_timerev=has_timrev_from_kptopt(kptopt),
inord=inord)
if closeit:
file.close()
return new
def from_file(cls, ncfile, inord="F"):
"""Initialize the object from a Netcdf file."""
r, closeit = as_etsfreader(ncfile)
kptopt = int(r.read_value("kptopt", default=1))
new = cls(spgid=r.read_value("space_group"),
symrel=r.read_value("reduced_symmetry_matrices"),
tnons=r.read_value("reduced_symmetry_translations"),
symafm=r.read_value("symafm"),
has_timerev=has_timrev_from_kptopt(kptopt),
inord=inord)
if closeit:
file.close()
return new
def test_has_timrev_from_kptopt(self):
"""Testing has_timrev_from_kptopt."""
assert has_timrev_from_kptopt(1)
assert not has_timrev_from_kptopt(4)
assert has_timrev_from_kptopt(-7)
def test_has_timrev_from_kptopt(self):
"""Testing has_timrev_from_kptopt."""
assert has_timrev_from_kptopt(1)
assert not has_timrev_from_kptopt(4)
assert has_timrev_from_kptopt(-7)
def _get_structures(self, what):
if what == "header":
vars_global, vars_dataset = self.initial_vars_global, self.initial_vars_dataset
elif what == "footer":
vars_global, vars_dataset = self.final_vars_global, self.final_vars_dataset
else:
raise ValueError("Invalid value for what: `%s`" % str(what))
#print("global", vars_global["acell"])
from abipy.abio.abivars import is_abiunit
inigeo = {k: vars_global[k] for k in GEOVARS if k in vars_global}
spgvars = ("spgroup", "symrel", "tnons", "symafm")
spgd_global = {k: vars_global[k] for k in spgvars if k in vars_global}
global_kptopt = vars_global.get("kptopt", 1)
structures = []
for i in self.datasets:
# This code breaks down if there are conflicting GEOVARS in globals and dataset.
d = inigeo.copy()
d.update({
k: vars_dataset[i][k]
for k in GEOVARS if k in vars_dataset[i]
})
for key, value in d.items():
# Must handle possible unit.
fact = 1.0
tokens = [t.lower() for t in value.split()]
if is_abiunit(tokens[-1]):
tokens, unit = tokens[:-1], tokens[-1]
if unit in ("angstr", "angstrom", "angstroms"):
fact = 1.0 / bohr_to_ang
elif unit in ("bohr", "bohrs", "au"):
fact = 1.0
else:
raise ValueError("Don't know how to handle unit: %s" %
unit)
s = " ".join(tokens)
dtype = np.float if key not in ("ntypat", "typat",
"natom") else np.int
try:
#print(key, s)
value = np.fromstring(s, sep=" ", dtype=dtype)
#print(key, value)
if fact != 1.0:
value *= fact # Do not change integer arrays e.g typat!
d[key] = value
except ValueError as exc:
print(key, s)
raise exc
if "rprim" not in d and "angdeg" not in d: d["rprim"] = np.eye(3)
if "natom" in d and d["natom"] == 1 and all(
k not in d for k in ("xred", "xcart", "xangst")):
d["xred"] = np.zeros(3)
#print(d)
abistr = Structure.from_abivars(d)
# Extract Abinit spacegroup.
spgd = spgd_global.copy()
spgd.update({
k: vars_dataset[i][k]
for k in spgvars if k in vars_dataset[i]
})
spgid = int(spgd.get("spgroup", 0))
if "symrel" not in spgd:
symrel = np.reshape(np.eye(3, 3, dtype=np.int), (1, 3, 3))
spgd["symrel"] = " ".join((str(i) for i in symrel.flatten()))
else:
symrel = np.reshape(
np.array([int(n) for n in spgd["symrel"].split()],
dtype=np.int), (-1, 3, 3))
nsym = len(symrel)
assert nsym == spgd.get("nsym", nsym) #; print(symrel.shape)
if "tnons" in spgd:
tnons = np.reshape(
np.array([float(t) for t in spgd["tnons"].split()],
dtype=np.float), (nsym, 3))
else:
tnons = np.zeros((nsym, 3))
if "symafm" in spgd:
symafm = np.array([int(n) for n in spgd["symafm"].split()],
dtype=np.int)
symafm.shape = (nsym, )
else:
symafm = np.ones(nsym, dtype=np.int)
try:
has_timerev = has_timrev_from_kptopt(vars_dataset[i].get(
"kptopt", global_kptopt))
abi_spacegroup = AbinitSpaceGroup(spgid,
symrel,
tnons,
symafm,
has_timerev,
inord="C")
abistr.set_abi_spacegroup(abi_spacegroup)
except Exception as exc:
print(
"Cannot build AbinitSpaceGroup from the variables reported in file!\n",
str(exc))
structures.append(abistr)
return structures
def _get_structures(self, what):
if what == "header":
vars_global, vars_dataset = self.initial_vars_global, self.initial_vars_dataset
elif what == "footer":
vars_global, vars_dataset = self.final_vars_global, self.final_vars_dataset
else:
raise ValueError("Invalid value for what: `%s`" % str(what))
#print("global", vars_global["acell"])
from abipy.abio.abivars import is_abiunit
inigeo = {k: vars_global[k] for k in GEOVARS if k in vars_global}
spgvars = ("spgroup", "symrel", "tnons", "symafm")
spgd_global = {k: vars_global[k] for k in spgvars if k in vars_global}
global_kptopt = vars_global.get("kptopt", 1)
structures = []
for i in self.datasets:
# This code breaks down if there are conflicting GEOVARS in globals and dataset.
d = inigeo.copy()
d.update({k: vars_dataset[i][k] for k in GEOVARS if k in vars_dataset[i]})
for key, value in d.items():
# Must handle possible unit.
fact = 1.0
tokens = [t.lower() for t in value.split()]
if is_abiunit(tokens[-1]):
tokens, unit = tokens[:-1], tokens[-1]
if unit in ("angstr", "angstrom", "angstroms"):
fact = 1.0 / bohr_to_ang
elif unit in ("bohr", "bohrs", "au"):
fact = 1.0
else:
raise ValueError("Don't know how to handle unit: %s" % unit)
s = " ".join(tokens)
dtype = np.float if key not in ("ntypat", "typat", "natom") else np.int
try:
#print(key, s)
value = np.fromstring(s, sep=" ", dtype=dtype)
#print(key, value)
if fact != 1.0: value *= fact # Do not change integer arrays e.g typat!
d[key] = value
except ValueError as exc:
print(key, s)
raise exc
if "rprim" not in d and "angdeg" not in d: d["rprim"] = np.eye(3)
if "natom" in d and d["natom"] == 1 and all(k not in d for k in ("xred", "xcart", "xangst")):
d["xred"] = np.zeros(3)
#print(d)
abistr = Structure.from_abivars(d)
# Extract Abinit spacegroup.
spgd = spgd_global.copy()
spgd.update({k: vars_dataset[i][k] for k in spgvars if k in vars_dataset[i]})
spgid = int(spgd.get("spgroup", 0))
if "symrel" not in spgd:
symrel = np.reshape(np.eye(3, 3, dtype=np.int), (1, 3, 3))
spgd["symrel"] = " ".join((str(i) for i in symrel.flatten()))
else:
symrel = np.reshape(np.array([int(n) for n in spgd["symrel"].split()], dtype=np.int), (-1, 3, 3))
nsym = len(symrel)
assert nsym == spgd.get("nsym", nsym) #; print(symrel.shape)
if "tnons" in spgd:
tnons = np.reshape(np.array([float(t) for t in spgd["tnons"].split()], dtype=np.float), (nsym, 3))
else:
tnons = np.zeros((nsym, 3))
if "symafm" in spgd:
symafm = np.array([int(n) for n in spgd["symafm"].split()], dtype=np.int)
symafm.shape = (nsym,)
else:
symafm = np.ones(nsym, dtype=np.int)
try:
has_timerev = has_timrev_from_kptopt(vars_dataset[i].get("kptopt", global_kptopt))
abi_spacegroup = AbinitSpaceGroup(spgid, symrel, tnons, symafm, has_timerev, inord="C")
abistr.set_abi_spacegroup(abi_spacegroup)
except Exception as exc:
print("Cannot build AbinitSpaceGroup from the variables reported in file!\n", str(exc))
structures.append(abistr)
return structures
