def read_all_structures(self):
"""Return the list of structures at the different iteration steps."""
rprimd_list = self.read_value("rprimd")
xred_list = self.read_value("xred")
# Alchemical mixing is not supported.
num_pseudos = self.read_dimvalue("npsp")
ntypat = self.read_dimvalue("ntypat")
if num_pseudos != ntypat:
raise NotImplementedError("Alchemical mixing is not supported, num_pseudos != ntypat")
znucl, typat = self.read_value("znucl"), self.read_value("typat").astype(int)
#print(znucl.dtype, typat)
cart_forces_step = self.read_cart_forces(unit="eV ang^-1")
structures = []
#print("typat", type(typat))
for step in range(self.num_steps):
s = Structure.from_abivars(
xred=xred_list[step],
rprim=rprimd_list[step],
acell=3 * [1.0],
# FIXME ntypat, typat, znucl are missing!
znucl=znucl,
typat=typat,
)
s.add_site_property("cartesian_forces", cart_forces_step[step])
structures.append(s)
return structures
def read_all_structures(self):
"""Return the list of structures at the different iteration steps."""
rprimd_list = self.read_value("rprimd")
xred_list = self.read_value("xred")
# Alchemical mixing is not supported.
num_pseudos = self.read_dimvalue("npsp")
ntypat = self.read_dimvalue("ntypat")
if num_pseudos != ntypat:
raise NotImplementedError(
"Alchemical mixing is not supported, num_pseudos != ntypat")
znucl, typat = self.read_value("znucl"), self.read_value(
"typat").astype(int)
#print(znucl.dtype, typat)
cart_forces_step = self.read_cart_forces(unit="eV ang^-1")
structures = []
#print("typat", type(typat))
for step in range(self.num_steps):
s = Structure.from_abivars(
xred=xred_list[step],
rprim=rprimd_list[step],
acell=3 * [1.0],
# FIXME ntypat, typat, znucl are missing!
znucl=znucl,
typat=typat,
)
s.add_site_property("cartesian_forces", cart_forces_step[step])
structures.append(s)
return structures
def structure(self):
kwargs = {}
if "angdeg" in self:
assert "rprim" not in self
raise NotImplementedError("angdeg")
#kwargs["angdeg"] =
else:
# Handle structure specified with rprim.
kwargs["rprim"] = str2array_bohr(self.get("rprim", "1.0 0 0 0 1 0 0 0 1"))
# Default value for acell
acell = str2array_bohr(self.get("acell", "1.0 1.0 1.0"))
check = {k: 1 for k in ("xred", "xcart", "xangst") if k in self}
if len(check) != 1:
raise ValueError("Atomic positions are not specified correctly:\n%s" % str(check))
if "xred" in self:
kwargs["xred"] = np.fromstring(self["xred"], sep=" ")
elif "xcart" in self:
kwargs["xcart"] = str2array_bohr(self["xcart"])
elif "xangst" in self:
kwargs["xangst"] = np.fromstring(self["xangst"], sep=" ")
return Structure.from_abivars(
acell=acell,
znucl=str2array(self["znucl"]),
typat=str2array(self["typat"]),
**kwargs
)
def structure(self):
structure = Structure.from_abivars(**self.header)
# Add Spacegroup (needed in guessed_ngkpt)
# FIXME: has_timerev is always True
spgid, has_timerev, h = 0, True, self.header
structure.set_spacegroup(SpaceGroup(spgid, h.symrel, h.tnons, h.symafm, has_timerev))
return structure
def structure(self):
# Get lattice.
kwargs = {}
if "angdeg" in self:
if "rprim" in self:
raise ValueError("rprim and angdeg cannot be used together!")
angdeg = str2array(self["angdeg"])
angdeg.shape = (3)
kwargs["angdeg"] = angdeg
else:
# Handle structure specified with rprim.
kwargs["rprim"] = str2array_bohr(self.get("rprim", "1.0 0 0 0 1 0 0 0 1"))
# Default value for acell.
acell = str2array_bohr(self.get("acell", "1.0 1.0 1.0"))
# Get important dimensions.
ntypat = int(self.get("ntypat", 1))
natom = int(self.get("natom", 1))
# znucl(npsp)
znucl = self["znucl"]
if znucl.startswith("*"):
i = znucl.find("*")
znucl_size = natom if "npsp" not in self else int(self["npsp"])
znucl = znucl_size * [float(znucl[i+1:])]
else:
znucl = str2array(self["znucl"])
# v67mbpt/Input/t12.in
typat = self["typat"]
if typat.startswith("*"):
i = typat.find("*")
typat = np.array(natom * [int(typat[i+1:])], dtype=int)
else:
typat = str2array(self["typat"], dtype=int)
# Extract atomic positions.
# Select first natom entries (needed if multidatasets with different natom)
# # v3/Input/t05.in
typat = typat[:natom]
for k in ("xred", "xcart", "xangst"):
toarray = str2array_bohr if k == "xcart" else str2array
if k in self:
arr = np.reshape(toarray(self[k]), (-1, 3))
kwargs[k] = arr[:natom]
break
else:
raise ValueError("xred|xcart|xangst must be given in input")
try:
return Structure.from_abivars(acell=acell, znucl=znucl, typat=typat, **kwargs)
except Exception as exc:
print("Wrong inputs passed to Structure.from_abivars:")
print(" acell", acell)
print(" znucl", znucl)
print(" typat", typat)
print(" kwargs", kwargs)
raise exc
def structure(self):
# Get lattice.
kwargs = {}
if "angdeg" in self:
if "rprim" in self:
raise ValueError("rprim and angdeg cannot be used together!")
angdeg = str2array(self["angdeg"])
angdeg.shape = (3)
kwargs["angdeg"] = angdeg
else:
# Handle structure specified with rprim.
kwargs["rprim"] = str2array_bohr(self.get("rprim", "1.0 0 0 0 1 0 0 0 1"))
# Default value for acell.
acell = str2array_bohr(self.get("acell", "1.0 1.0 1.0"))
# Get important dimensions.
ntypat = int(self.get("ntypat", 1))
natom = int(self.get("natom", 1))
# znucl(npsp)
znucl = self["znucl"]
if znucl.startswith("*"):
i = znucl.find("*")
znucl_size = natom if "npsp" not in self else int(self["npsp"])
znucl = znucl_size * [float(znucl[i+1:])]
else:
znucl = str2array(self["znucl"])
# v67mbpt/Input/t12.in
typat = self["typat"]
if typat.startswith("*"):
i = typat.find("*")
typat = np.array(natom * [int(typat[i+1:])], dtype=int)
else:
typat = str2array(self["typat"], dtype=int)
# Extract atomic positions.
# Select first natom entries (needed if multidatasets with different natom)
# # v3/Input/t05.in
typat = typat[:natom]
for k in ("xred", "xcart", "xangst"):
toarray = str2array_bohr if k == "xcart" else str2array
if k in self:
arr = np.reshape(toarray(self[k]), (-1, 3))
kwargs[k] = arr[:natom]
break
else:
raise ValueError("xred|xcart|xangst must be given in input")
try:
return Structure.from_abivars(acell=acell, znucl=znucl, typat=typat, **kwargs)
except Exception as exc:
print("Wrong inputs passed to Structure.from_abivars:")
print("acell:", acell, "znucl:", znucl, "typat:", typat, "kwargs:", kwargs, sep="\n")
raise exc
def __init__(self, filepath):
super(DdbFile, self).__init__(filepath)
self._header = self._parse_header()
self._structure = Structure.from_abivars(**self.header)
# Add Spacegroup (needed in guessed_ngkpt)
# FIXME: has_timerev is always True
spgid, has_timerev, h = 0, True, self.header
self._structure.set_spacegroup(SpaceGroup(spgid, h.symrel, h.tnons, h.symafm, has_timerev))
frac_coords = self._read_qpoints()
self._qpoints = KpointList(self.structure.reciprocal_lattice, frac_coords, weights=None, names=None)
# Guess q-mesh
self._guessed_ngqpt = self._guess_ngqpt()
def structure(self):
"""Returns the :class:`Structure` associated to this dataset."""
# TODO: Avoid calling Structure.from_abivars, find a way to cache the object and invalidate it.
return Structure.from_abivars(self.allvars)
def structure(self):
"""Returns the :class:`Structure` associated to this dataset."""
# TODO: Avoid calling Structure.from_abivars, find a way to cache the object and invalidate it.
return Structure.from_abivars(self.allvars)
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
def structure(self):
"""
The initial structure associated to the dataset.
"""
# First of all check whether the structure is defined through external file.
if "structure" in self:
s = self["structure"].replace('"', "")
filetype, path = s.split(":")
from abipy import abilab
with abilab.abiopen(path) as abifile:
return abifile.structure
# Get lattice.
kwargs = {}
if "angdeg" in self:
if "rprim" in self:
raise ValueError("rprim and angdeg cannot be used together!")
angdeg = str2array(self["angdeg"])
angdeg.shape = (3)
kwargs["angdeg"] = angdeg
else:
# Handle structure specified with rprim.
kwargs["rprim"] = str2array_bohr(
self.get("rprim", "1.0 0 0 0 1 0 0 0 1"))
# Default value for acell.
acell = str2array_bohr(self.get("acell", "1.0 1.0 1.0"))
# Get important dimensions.
ntypat = int(self.get("ntypat", 1))
natom = int(self.get("natom", 1))
# znucl(npsp)
znucl = self["znucl"]
if znucl.startswith("*"):
i = znucl.find("*")
znucl_size = natom if "npsp" not in self else int(self["npsp"])
znucl = znucl_size * [float(znucl[i + 1:])]
else:
znucl = str2array(self["znucl"])
# v67mbpt/Input/t12.in
typat = self["typat"]
if typat.startswith("*"):
i = typat.find("*")
typat = np.array(natom * [int(typat[i + 1:])], dtype=int)
else:
typat = str2array(self["typat"], dtype=int)
# Extract atomic positions.
# Select first natom entries (needed if multidatasets with different natom)
# # v3/Input/t05.in
typat = typat[:natom]
for k in ("xred", "xcart", "xangst"):
toarray = str2array_bohr if k == "xcart" else str2array
if k in self:
arr = np.reshape(toarray(self[k]), (-1, 3))
kwargs[k] = arr[:natom]
break
else:
raise ValueError("xred|xcart|xangst must be given in input")
try:
return Structure.from_abivars(acell=acell,
znucl=znucl,
typat=typat,
**kwargs)
except Exception as exc:
print("Wrong inputs passed to Structure.from_abivars:")
print("acell:",
acell,
"znucl:",
znucl,
"typat:",
typat,
"kwargs:",
kwargs,
sep="\n")
raise exc
