def __init__(self, struct_type, formula, pseudos_or_dict, dojo_pptable):
"""
Initialize the record for the chemical formula and the list of
pseudopotentials.
"""
keys = ("basename", "Z_val", "l_max", "md5")
#if isinstance(pseudos_or_dict, (list, tuple)):
if all(hasattr(p, "as_dict") for p in pseudos_or_dict):
def get_info(p):
"""Extract the most important info from the pseudo."""
#symbol = p.symbol
d = p.as_dict()
return {k: d[k] for k in keys}
meta = {p.symbol: get_info(p) for p in pseudos_or_dict}
pseudos = pseudos_or_dict
else:
meta = pseudos_or_dict
for v in meta.values():
assert set(v.keys()) == set(keys)
def pmatch(ps, esymb, d):
return (ps.md5 == d["md5"] and ps.symbol == esymb
and ps.Z_val == d["Z_val"] and ps.l_max == d["l_max"])
pseudos = []
for esymb, d in meta.items():
for p in dojo_pptable.pseudo_with_symbol(esymb,
allow_multi=True):
if pmatch(p, esymb, d):
pseudos.append(p)
break
else:
raise ValueError(
"Cannot find pseudo:\n %s\n in dojo_pptable" % str(d))
super(GbrvRecord, self).__init__(formula=formula,
pseudos_metadata=meta,
normal=None,
high=None)
self.pseudos = DojoTable.as_table(pseudos)
self.dojo_pptable = dojo_pptable
self.struct_type = struct_type
def __init__(self, struct_type, formula, pseudos_or_dict, dojo_pptable):
"""
Initialize the record for the chemical formula and the list of
pseudopotentials.
"""
keys = ("basename", "Z_val", "l_max", "md5")
#if isinstance(pseudos_or_dict, (list, tuple)):
if all(hasattr(p, "as_dict") for p in pseudos_or_dict):
def get_info(p):
"""Extract the most important info from the pseudo."""
#symbol = p.symbol
d = p.as_dict()
return {k: d[k] for k in keys}
meta = {p.symbol: get_info(p) for p in pseudos_or_dict}
pseudos = pseudos_or_dict
else:
meta = pseudos_or_dict
for v in meta.values():
assert set(v.keys()) == set(keys)
def pmatch(ps, esymb, d):
return (ps.md5 == d["md5"] and
ps.symbol == esymb and
ps.Z_val == d["Z_val"] and
ps.l_max == d["l_max"])
pseudos = []
for esymb, d in meta.items():
for p in dojo_pptable.pseudo_with_symbol(esymb, allow_multi=True):
if pmatch(p, esymb, d):
pseudos.append(p)
break
else:
raise ValueError("Cannot find pseudo:\n %s\n in dojo_pptable" % str(d))
super(GbrvRecord, self).__init__(formula=formula, pseudos_metadata=meta,
normal=None, high=None)
self.pseudos = DojoTable.as_table(pseudos)
self.dojo_pptable = dojo_pptable
self.struct_type = struct_type
def relax_and_eos_work(self,
accuracy,
pseudos,
formula,
struct_type,
ecut=None,
pawecutdg=None,
ref="ae",
ngkpt=(8, 8, 8),
fband=2.0):
"""
Returns a :class:`Work` object from the given pseudopotential.
Args:
kwargs: Extra variables passed to Abinit.
.. note::
GBRV tests are done with the following parameteres:
- No spin polarization for structural relaxation
(only for magnetic moments for which spin-unpolarized structures are used)
- All calculations are done on an 8x8x8 k-point density and with 0.002 Ry Fermi-Dirac smearing
"""
pseudos = DojoTable.as_table(pseudos)
if pseudos.allpaw and pawecutdg is None:
raise ValueError(
"pawecutdg must be specified for PAW calculations.")
structure = self.make_ref_structure(formula,
struct_type=struct_type,
ref=ref)
return GbrvCompoundRelaxAndEosWork(structure,
formula,
struct_type,
pseudos,
self.db.xc,
accuracy,
ecut=ecut,
pawecutdg=pawecutdg,
ngkpt=ngkpt,
fband=fband)
def test_db_update(self):
"""Testing DB update"""
dirpath = dojotable_absdir("ONCVPSP-PBE")
# Init an empty object.
outdb = RocksaltOutdb.new_from_dojodir(dirpath)
# No change here
u = outdb.check_update()
print(u)
assert u.nrec_added == 0 and u.nrec_removed == 0
# Now I hack a bit the object to simulate a pseudo that has been removed
new_table = [p for p in outdb.dojo_pptable if p.basename != "Si.psp8"]
outdb.dojo_pptable = DojoTable.as_table(new_table)
# TODO:
u = outdb.check_update()
print(u)
assert u.nrec_added == 0 and u.nrec_removed == 0
def test_db_update(self):
"""Testing DB update"""
return
dirpath = dojotable_absdir("ONCVPSP-PBE")
# Init an empty object.
outdb = RocksaltOutdb.new_from_dojodir(dirpath)
# No change here
u = outdb.check_update()
print(u)
assert u.nrec_added == 0 and u.nrec_removed == 0
# Now I hack a bit the object to simulate a pseudo that has been removed
new_table = [p for p in outdb.dojo_pptable if p.basename != "Si.psp8"]
outdb.dojo_pptable = DojoTable.as_table(new_table)
# TODO:
u = outdb.check_update()
print(u)
assert u.nrec_added == 0 and u.nrec_removed == 0
def relax_and_eos_work(self, accuracy, pseudos, formula, struct_type,
ecut=None, pawecutdg=None, ref="ae", ngkpt=(8, 8, 8), fband=2.0):
"""
Returns a :class:`Work` object from the given pseudopotential.
Args:
kwargs: Extra variables passed to Abinit.
.. note::
GBRV tests are done with the following parameteres:
- No spin polarization for structural relaxation
(only for magnetic moments for which spin-unpolarized structures are used)
- All calculations are done on an 8x8x8 k-point density and with 0.002 Ry Fermi-Dirac smearing
"""
pseudos = DojoTable.as_table(pseudos)
if pseudos.allpaw and pawecutdg is None:
raise ValueError("pawecutdg must be specified for PAW calculations.")
structure = self.make_ref_structure(formula, struct_type=struct_type, ref=ref)
return GbrvCompoundRelaxAndEosWork(structure, formula, struct_type, pseudos, self.db.xc, accuracy,
ecut=ecut, pawecutdg=pawecutdg, ngkpt=ngkpt, fband=fband)
